From 299a42c4dc21bfcf85558470256011d14a61bc69 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Mon, 6 Oct 2025 18:04:24 +0200
Subject: [PATCH 01/26] First attempt export as ELN

First attempt export as ELN
---
 pydatalab/src/pydatalab/export_utils.py       | 184 ++++++++++++++++++
 pydatalab/src/pydatalab/models/export_task.py |  33 ++++
 pydatalab/src/pydatalab/mongo.py              |  10 +
 .../src/pydatalab/routes/v0_1/__init__.py     |   2 +
 pydatalab/src/pydatalab/routes/v0_1/export.py | 171 ++++++++++++++++
 .../src/components/CollectionExportButton.vue | 104 ++++++++++
 .../src/components/CollectionInformation.vue  |   7 +
 webapp/src/server_fetch_utils.js              |  32 +++
 8 files changed, 543 insertions(+)
 create mode 100644 pydatalab/src/pydatalab/export_utils.py
 create mode 100644 pydatalab/src/pydatalab/models/export_task.py
 create mode 100644 pydatalab/src/pydatalab/routes/v0_1/export.py
 create mode 100644 webapp/src/components/CollectionExportButton.vue

diff --git a/pydatalab/src/pydatalab/export_utils.py b/pydatalab/src/pydatalab/export_utils.py
new file mode 100644
index 000000000..53376a379
--- /dev/null
+++ b/pydatalab/src/pydatalab/export_utils.py
@@ -0,0 +1,184 @@
+import json
+import shutil
+import tempfile
+import zipfile
+from datetime import datetime, timezone
+from pathlib import Path
+
+from bson import ObjectId
+
+from pydatalab.config import CONFIG
+from pydatalab.mongo import flask_mongo
+
+
+def _convert_objectids_in_dict(d: dict) -> dict:
+    """Recursively convert ObjectIds and datetimes in a dictionary to strings."""
+    result: dict = {}
+    for key, value in d.items():
+        if isinstance(value, ObjectId):
+            result[key] = str(value)
+        elif isinstance(value, datetime):
+            result[key] = value.isoformat()
+        elif isinstance(value, dict):
+            result[key] = _convert_objectids_in_dict(value)
+        elif isinstance(value, list):
+            result[key] = [
+                str(v)
+                if isinstance(v, ObjectId)
+                else v.isoformat()
+                if isinstance(v, datetime)
+                else _convert_objectids_in_dict(v)
+                if isinstance(v, dict)
+                else v
+                for v in value
+            ]
+        else:
+            result[key] = value
+    return result
+
+
+def generate_ro_crate_metadata(collection_data: dict, child_items: list[dict]) -> dict:
+    """Generate RO-Crate metadata for the .eln file.
+
+    Parameters:
+        collection_data: The collection metadata
+        child_items: List of items in the collection
+
+    Returns:
+        RO-Crate metadata as a dictionary
+    """
+
+    experiments: list[dict] = []
+    for item in child_items:
+        experiments.append(
+            {
+                "@id": f"./{item['item_id']}/",
+            }
+        )
+
+    graph: list[dict] = [
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {"@id": "./"},
+            "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+            "dateCreated": datetime.now(tz=timezone.utc).isoformat(),
+            "sdPublisher": {
+                "@id": CONFIG.IDENTIFIER_PREFIX or "https://github.com/datalab-org/datalab"
+            },
+        },
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "name": collection_data.get("title", collection_data.get("collection_id")),
+            "description": collection_data.get("description", ""),
+            "hasPart": experiments,
+        },
+    ]
+
+    metadata = {
+        "@context": "https://w3id.org/ro/crate/1.1/context",
+        "@graph": graph,
+    }
+
+    for item in child_items:
+        item_metadata = {
+            "@id": f"./{item['item_id']}/",
+            "@type": "Dataset",
+            "name": item.get("name", item["item_id"]),
+            "identifier": item["item_id"],
+            "dateCreated": item.get("date", datetime.now(tz=timezone.utc)).isoformat()
+            if isinstance(item.get("date"), datetime)
+            else item.get("date"),
+        }
+
+        if item.get("file_ObjectIds"):
+            files = []
+            for file_id in item["file_ObjectIds"]:
+                file_data = flask_mongo.db.files.find_one({"_id": ObjectId(file_id)})
+                if file_data:
+                    files.append({"@id": f"./{item['item_id']}/{file_data['name']}"})
+            if files:
+                item_metadata["hasPart"] = files
+
+        graph.append(item_metadata)
+
+    return metadata
+
+
+def create_eln_file(collection_id: str, output_path: str) -> None:
+    """Create a .eln file for a collection.
+
+    Parameters:
+        collection_id: ID of the collection to export
+        output_path: Path where the .eln file should be saved
+    """
+
+    collection_data = flask_mongo.db.collections.find_one({"collection_id": collection_id})
+    if not collection_data:
+        raise ValueError(f"Collection {collection_id} not found")
+
+    collection_immutable_id = collection_data["_id"]
+    child_items = list(
+        flask_mongo.db.items.find(
+            {
+                "relationships": {
+                    "$elemMatch": {"type": "collections", "immutable_id": collection_immutable_id}
+                }
+            }
+        )
+    )
+
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_path = Path(temp_dir)
+
+        root_folder_name = collection_id
+        root_folder = temp_path / root_folder_name
+        root_folder.mkdir()
+
+        ro_crate_metadata = generate_ro_crate_metadata(collection_data, child_items)
+        with open(root_folder / "ro-crate-metadata.json", "w", encoding="utf-8") as f:
+            json.dump(ro_crate_metadata, f, indent=2, ensure_ascii=False)
+
+        for item in child_items:
+            item_folder = root_folder / item["item_id"]
+            item_folder.mkdir()
+
+            item_metadata = {k: v for k, v in item.items() if k not in ["_id", "file_ObjectIds"]}
+
+            for key, value in item_metadata.items():
+                if isinstance(value, ObjectId):
+                    item_metadata[key] = str(value)
+                elif isinstance(value, datetime):
+                    item_metadata[key] = value.isoformat()
+                elif isinstance(value, dict):
+                    item_metadata[key] = _convert_objectids_in_dict(value)
+                elif isinstance(value, list):
+                    item_metadata[key] = [
+                        str(v)
+                        if isinstance(v, ObjectId)
+                        else v.isoformat()
+                        if isinstance(v, datetime)
+                        else _convert_objectids_in_dict(v)
+                        if isinstance(v, dict)
+                        else v
+                        for v in value
+                    ]
+
+            with open(item_folder / "metadata.json", "w", encoding="utf-8") as f:
+                json.dump(item_metadata, f, indent=2, ensure_ascii=False)
+
+            if item.get("file_ObjectIds"):
+                for file_id in item["file_ObjectIds"]:
+                    file_data = flask_mongo.db.files.find_one({"_id": ObjectId(file_id)})
+                    if file_data and file_data.get("location"):
+                        source_path = Path(file_data["location"])
+                        if source_path.exists():
+                            dest_path = item_folder / file_data["name"]
+                            shutil.copy2(source_path, dest_path)
+
+        with zipfile.ZipFile(output_path, "w", zipfile.ZIP_DEFLATED) as zipf:
+            for file_path in root_folder.rglob("*"):
+                if file_path.is_file():
+                    arcname = file_path.relative_to(temp_path)
+                    zipf.write(file_path, arcname)
diff --git a/pydatalab/src/pydatalab/models/export_task.py b/pydatalab/src/pydatalab/models/export_task.py
new file mode 100644
index 000000000..71cafd1ef
--- /dev/null
+++ b/pydatalab/src/pydatalab/models/export_task.py
@@ -0,0 +1,33 @@
+from datetime import datetime
+from enum import Enum
+
+from pydantic import BaseModel, Field
+
+
+class ExportStatus(str, Enum):
+    """Status of an export task."""
+
+    PENDING = "pending"
+    PROCESSING = "processing"
+    READY = "ready"
+    ERROR = "error"
+
+
+class ExportTask(BaseModel):
+    """Model for an export task."""
+
+    task_id: str = Field(..., description="Unique identifier for the export task")
+    collection_id: str = Field(..., description="ID of the collection being exported")
+    status: ExportStatus = Field(
+        default=ExportStatus.PENDING, description="Current status of the task"
+    )
+    creator_id: str = Field(..., description="ID of the user who created the export")
+    created_at: datetime = Field(
+        default_factory=datetime.now, description="When the task was created"
+    )
+    completed_at: datetime | None = Field(None, description="When the task was completed")
+    file_path: str | None = Field(None, description="Path to the generated .eln file")
+    error_message: str | None = Field(None, description="Error message if status is ERROR")
+
+    class Config:
+        use_enum_values = True
diff --git a/pydatalab/src/pydatalab/mongo.py b/pydatalab/src/pydatalab/mongo.py
index cd4fba24a..5fd5e954a 100644
--- a/pydatalab/src/pydatalab/mongo.py
+++ b/pydatalab/src/pydatalab/mongo.py
@@ -208,4 +208,14 @@ def create_user_fts():
         db.users.drop_index(user_fts_name)
         ret += create_user_fts()
 
+    ret += db.export_tasks.create_index(
+        "task_id", unique=True, name="unique task ID", background=background
+    )
+    ret += db.export_tasks.create_index(
+        "creator_id", name="export task creator", background=background
+    )
+    ret += db.export_tasks.create_index(
+        "created_at", name="export task created at", background=background
+    )
+
     return ret
diff --git a/pydatalab/src/pydatalab/routes/v0_1/__init__.py b/pydatalab/src/pydatalab/routes/v0_1/__init__.py
index 512a40163..a79688df0 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/__init__.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/__init__.py
@@ -5,6 +5,7 @@
 from .auth import AUTH, OAUTH, OAUTH_PROXIES
 from .blocks import BLOCKS
 from .collections import COLLECTIONS
+from .export import EXPORT
 from .files import FILES
 from .graphs import GRAPHS
 from .healthcheck import HEALTHCHECK
@@ -25,6 +26,7 @@
     HEALTHCHECK,
     INFO,
     GRAPHS,
+    EXPORT,
 )
 
 __all__ = ("BLUEPRINTS", "OAUTH", "__api_version__", "OAUTH_PROXIES")
diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
new file mode 100644
index 000000000..c10cb352a
--- /dev/null
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -0,0 +1,171 @@
+import os
+import threading
+import uuid
+from datetime import datetime, timezone
+from pathlib import Path
+
+from flask import Blueprint, jsonify, send_file
+from flask_login import current_user
+
+from pydatalab.config import CONFIG
+from pydatalab.export_utils import create_eln_file
+from pydatalab.models.export_task import ExportStatus, ExportTask
+from pydatalab.mongo import flask_mongo
+from pydatalab.permissions import active_users_or_get_only
+
+EXPORT = Blueprint("export", __name__)
+
+
+@EXPORT.before_request
+@active_users_or_get_only
+def _(): ...
+
+
+def _generate_export_in_background(task_id: str, collection_id: str):
+    """Background function to generate the .eln file.
+
+    Parameters:
+        task_id: ID of the export task
+        collection_id: ID of the collection to export
+    """
+    try:
+        flask_mongo.db.export_tasks.update_one(
+            {"task_id": task_id}, {"$set": {"status": ExportStatus.PROCESSING}}
+        )
+
+        export_dir = Path(CONFIG.FILE_DIRECTORY) / "exports"
+        export_dir.mkdir(exist_ok=True)
+
+        output_path = export_dir / f"{task_id}.eln"
+        create_eln_file(collection_id, str(output_path))
+
+        flask_mongo.db.export_tasks.update_one(
+            {"task_id": task_id},
+            {
+                "$set": {
+                    "status": ExportStatus.READY,
+                    "file_path": str(output_path),
+                    "completed_at": datetime.now(tz=timezone.utc),
+                }
+            },
+        )
+
+    except Exception as e:
+        flask_mongo.db.export_tasks.update_one(
+            {"task_id": task_id},
+            {
+                "$set": {
+                    "status": ExportStatus.ERROR,
+                    "error_message": str(e),
+                    "completed_at": datetime.now(tz=timezone.utc),
+                }
+            },
+        )
+
+
+@EXPORT.route("/collections/<string:collection_id>/export", methods=["POST"])
+def start_collection_export(collection_id: str):
+    """Start exporting a collection to .eln format.
+
+    Parameters:
+        collection_id: The collection ID to export
+
+    Returns:
+        JSON response with task_id and status_url
+    """
+
+    collection = flask_mongo.db.collections.find_one({"collection_id": collection_id})
+    if not collection:
+        return jsonify({"status": "error", "message": f"Collection {collection_id} not found"}), 404
+
+    task_id = str(uuid.uuid4())
+
+    if not CONFIG.TESTING:
+        creator_id = current_user.person.immutable_id
+    else:
+        creator_id = "000000000000000000000000"
+
+    export_task = ExportTask(
+        task_id=task_id,
+        collection_id=collection_id,
+        creator_id=creator_id,
+        status=ExportStatus.PENDING,
+    )
+
+    flask_mongo.db.export_tasks.insert_one(export_task.dict())
+
+    thread = threading.Thread(target=_generate_export_in_background, args=(task_id, collection_id))
+    thread.daemon = True
+    thread.start()
+
+    return jsonify(
+        {"status": "success", "task_id": task_id, "status_url": f"/exports/{task_id}/status"}
+    ), 202
+
+
+@EXPORT.route("/exports/<string:task_id>/status", methods=["GET"])
+def get_export_status(task_id: str):
+    """Get the status of an export task.
+
+    Parameters:
+        task_id: The export task ID
+
+    Returns:
+        JSON response with task status and download URL if ready
+    """
+
+    task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
+
+    if not task:
+        return jsonify({"status": "error", "message": "Export task not found"}), 404
+
+    response = {
+        "status": task["status"],
+        "created_at": task["created_at"].isoformat() if task.get("created_at") else None,
+    }
+
+    if task["status"] == ExportStatus.READY:
+        response["download_url"] = f"/exports/{task_id}/download"
+        response["completed_at"] = (
+            task["completed_at"].isoformat() if task.get("completed_at") else None
+        )
+
+    if task["status"] == ExportStatus.ERROR:
+        response["error_message"] = task.get("error_message")
+        response["completed_at"] = (
+            task["completed_at"].isoformat() if task.get("completed_at") else None
+        )
+
+    return jsonify(response), 200
+
+
+@EXPORT.route("/exports/<string:task_id>/download", methods=["GET"])
+def download_export(task_id: str):
+    """Download the generated .eln file.
+
+    Parameters:
+        task_id: The export task ID
+
+    Returns:
+        The .eln file as attachment
+    """
+
+    task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
+
+    if not task:
+        return jsonify({"status": "error", "message": "Export task not found"}), 404
+
+    if task["status"] != ExportStatus.READY:
+        return jsonify(
+            {"status": "error", "message": f"Export is not ready. Current status: {task['status']}"}
+        ), 400
+
+    file_path = task.get("file_path")
+    if not file_path or not os.path.exists(file_path):
+        return jsonify({"status": "error", "message": "Export file not found"}), 404
+
+    filename = f"{task['collection_id']}.eln"
+
+    return send_file(
+        file_path, as_attachment=True, download_name=filename, mimetype="application/vnd.eln+zip"
+    )
diff --git a/webapp/src/components/CollectionExportButton.vue b/webapp/src/components/CollectionExportButton.vue
new file mode 100644
index 000000000..5d0b4aa24
--- /dev/null
+++ b/webapp/src/components/CollectionExportButton.vue
@@ -0,0 +1,104 @@
+<template>
+  <div class="collection-export-button">
+    <button
+      :disabled="isExporting"
+      class="btn btn-sm btn-outline-primary"
+      data-testid="collection-export-button"
+      @click="handleExport"
+    >
+      <span v-if="!isExporting"> <i class="fa fa-download"></i> Export as .eln </span>
+      <span v-else> <i class="fa fa-spinner fa-spin"></i> {{ exportStatusText }} </span>
+    </button>
+  </div>
+</template>
+
+<script>
+import { startCollectionExport, getExportStatus, getExportDownloadUrl } from "@/server_fetch_utils";
+import { DialogService } from "@/services/DialogService";
+
+export default {
+  name: "CollectionExportButton",
+  props: {
+    collectionId: {
+      type: String,
+      required: true,
+    },
+  },
+  data() {
+    return {
+      isExporting: false,
+      exportStatusText: "Preparing export...",
+      pollInterval: null,
+    };
+  },
+  beforeUnmount() {
+    if (this.pollInterval) {
+      clearInterval(this.pollInterval);
+    }
+  },
+  methods: {
+    async handleExport() {
+      try {
+        this.isExporting = true;
+        this.exportStatusText = "Starting export...";
+
+        const response = await startCollectionExport(this.collectionId);
+        const taskId = response.task_id;
+
+        this.pollExportStatus(taskId);
+      } catch (error) {
+        console.error("Export failed:", error);
+        this.isExporting = false;
+        DialogService.error({
+          title: "Export Failed",
+          message: "Failed to start the export. Please try again.",
+        });
+      }
+    },
+
+    async pollExportStatus(taskId) {
+      this.exportStatusText = "Processing...";
+
+      this.pollInterval = setInterval(async () => {
+        try {
+          const status = await getExportStatus(taskId);
+
+          if (status.status === "ready") {
+            clearInterval(this.pollInterval);
+            this.downloadExport(taskId);
+            this.isExporting = false;
+            DialogService.alert({
+              title: "Export Complete",
+              message: "Your collection has been exported successfully.",
+              type: "info",
+            });
+          } else if (status.status === "error") {
+            clearInterval(this.pollInterval);
+            this.isExporting = false;
+            DialogService.error({
+              title: "Export Failed",
+              message: status.error_message || "An error occurred during export.",
+            });
+          } else if (status.status === "processing") {
+            this.exportStatusText = "Generating .eln file...";
+          }
+        } catch (error) {
+          clearInterval(this.pollInterval);
+          this.isExporting = false;
+          console.error("Error polling export status:", error);
+        }
+      }, 2000);
+    },
+
+    downloadExport(taskId) {
+      const downloadUrl = getExportDownloadUrl(taskId);
+      const link = document.createElement("a");
+      link.href = downloadUrl;
+      link.style.display = "none";
+      document.body.appendChild(link);
+      link.click();
+      document.body.removeChild(link);
+    },
+  },
+};
+</script>
diff --git a/webapp/src/components/CollectionInformation.vue b/webapp/src/components/CollectionInformation.vue
index eed84d347..b45a24bbb 100644
--- a/webapp/src/components/CollectionInformation.vue
+++ b/webapp/src/components/CollectionInformation.vue
@@ -30,6 +30,11 @@
           v-model="CollectionDescription"
           aria-labelledby="description-label"
         ></TinyMceInline>
+        <div class="form-row">
+          <div class="form-group col">
+            <CollectionExportButton :collection-id="collection_id" />
+          </div>
+        </div>
       </div>
       <div class="col-md-4">
         <CollectionRelationshipVisualization :collection_id="collection_id" />
@@ -61,6 +66,7 @@ import TinyMceInline from "@/components/TinyMceInline";
 import Creators from "@/components/Creators";
 import CollectionRelationshipVisualization from "@/components/CollectionRelationshipVisualization";
 import DynamicDataTable from "@/components/DynamicDataTable";
+import CollectionExportButton from "@/components/CollectionExportButton";
 
 export default {
   components: {
@@ -68,6 +74,7 @@ export default {
     Creators,
     CollectionRelationshipVisualization,
     DynamicDataTable,
+    CollectionExportButton,
   },
   props: {
     collection_id: {
diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index a825182e1..a65383c74 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -888,3 +888,35 @@ export async function getSchema(type) {
       throw error;
     });
 }
+
+export async function startCollectionExport(collection_id) {
+  return fetch_post(`${API_URL}/collections/${collection_id}/export`, {})
+    .then(function (response_json) {
+      return response_json;
+    })
+    .catch((error) => {
+      DialogService.error({
+        title: "Export Failed",
+        message: `Failed to start collection export: ${error}`,
+      });
+      throw error;
+    });
+}
+
+export async function getExportStatus(task_id) {
+  return fetch_get(`${API_URL}/exports/${task_id}/status`)
+    .then(function (response_json) {
+      return response_json;
+    })
+    .catch((error) => {
+      DialogService.error({
+        title: "Export Status Check Failed",
+        message: `Failed to check export status: ${error}`,
+      });
+      throw error;
+    });
+}
+
+export function getExportDownloadUrl(task_id) {
+  return `${API_URL}/exports/${task_id}/download`;
+}

From dd9194a83b0d0f06d79cb4b227cb992e42055464 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 7 Oct 2025 13:50:57 +0200
Subject: [PATCH 02/26] Use APScheduler

Use APScheduler

Use APScheduler

Use APScheduler

Use APScheduler

Use APScheduler

Use APScheduler
---
 pydatalab/pyproject.toml                      |    1 +
 pydatalab/src/pydatalab/export_utils.py       |   29 +-
 pydatalab/src/pydatalab/models/export_task.py |    5 +-
 pydatalab/src/pydatalab/mongo.py              |    1 +
 pydatalab/src/pydatalab/routes/v0_1/export.py |   72 +-
 pydatalab/src/pydatalab/scheduler.py          |   49 +
 pydatalab/tests/server/test_export.py         |  205 ++
 pydatalab/tests/server/test_export_utils.py   |  136 +
 pydatalab/uv.lock                             | 2433 +++++++++--------
 .../src/components/CollectionExportButton.vue |    2 +-
 10 files changed, 1663 insertions(+), 1270 deletions(-)
 create mode 100644 pydatalab/src/pydatalab/scheduler.py
 create mode 100644 pydatalab/tests/server/test_export.py
 create mode 100644 pydatalab/tests/server/test_export_utils.py

diff --git a/pydatalab/pyproject.toml b/pydatalab/pyproject.toml
index 12a3037d9..dd17fc3b9 100644
--- a/pydatalab/pyproject.toml
+++ b/pydatalab/pyproject.toml
@@ -53,6 +53,7 @@ server = [
     "Flask-PyMongo ~= 2.3",
     "Flask-Mail ~= 0.10",
     "Flask-Compress ~= 1.15",
+    "APScheduler ~= 3.10",
     "Werkzeug ~= 3.0",
     "python-dotenv ~= 1.0",
     "pillow ~= 11.0",
diff --git a/pydatalab/src/pydatalab/export_utils.py b/pydatalab/src/pydatalab/export_utils.py
index 53376a379..c9212b414 100644
--- a/pydatalab/src/pydatalab/export_utils.py
+++ b/pydatalab/src/pydatalab/export_utils.py
@@ -146,36 +146,21 @@ def create_eln_file(collection_id: str, output_path: str) -> None:
 
             item_metadata = {k: v for k, v in item.items() if k not in ["_id", "file_ObjectIds"]}
 
-            for key, value in item_metadata.items():
-                if isinstance(value, ObjectId):
-                    item_metadata[key] = str(value)
-                elif isinstance(value, datetime):
-                    item_metadata[key] = value.isoformat()
-                elif isinstance(value, dict):
-                    item_metadata[key] = _convert_objectids_in_dict(value)
-                elif isinstance(value, list):
-                    item_metadata[key] = [
-                        str(v)
-                        if isinstance(v, ObjectId)
-                        else v.isoformat()
-                        if isinstance(v, datetime)
-                        else _convert_objectids_in_dict(v)
-                        if isinstance(v, dict)
-                        else v
-                        for v in value
-                    ]
+            item_metadata = _convert_objectids_in_dict(item_metadata)
 
             with open(item_folder / "metadata.json", "w", encoding="utf-8") as f:
                 json.dump(item_metadata, f, indent=2, ensure_ascii=False)
 
             if item.get("file_ObjectIds"):
-                for file_id in item["file_ObjectIds"]:
+                for file_id in item.get("file_ObjectIds", []):
                     file_data = flask_mongo.db.files.find_one({"_id": ObjectId(file_id)})
-                    if file_data and file_data.get("location"):
+                    if file_data:
                         source_path = Path(file_data["location"])
                         if source_path.exists():
-                            dest_path = item_folder / file_data["name"]
-                            shutil.copy2(source_path, dest_path)
+                            dest_file = item_folder / file_data["name"]
+                            shutil.copy2(source_path, dest_file)
+                        else:
+                            print(f"Warning: File not found on disk: {file_data['location']}")
 
         with zipfile.ZipFile(output_path, "w", zipfile.ZIP_DEFLATED) as zipf:
             for file_path in root_folder.rglob("*"):
diff --git a/pydatalab/src/pydatalab/models/export_task.py b/pydatalab/src/pydatalab/models/export_task.py
index 71cafd1ef..5e719c4f7 100644
--- a/pydatalab/src/pydatalab/models/export_task.py
+++ b/pydatalab/src/pydatalab/models/export_task.py
@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import datetime, timezone
 from enum import Enum
 
 from pydantic import BaseModel, Field
@@ -23,7 +23,8 @@ class ExportTask(BaseModel):
     )
     creator_id: str = Field(..., description="ID of the user who created the export")
     created_at: datetime = Field(
-        default_factory=datetime.now, description="When the task was created"
+        default_factory=lambda: datetime.now(tz=timezone.utc),
+        description="When the task was created",
     )
     completed_at: datetime | None = Field(None, description="When the task was completed")
     file_path: str | None = Field(None, description="Path to the generated .eln file")
diff --git a/pydatalab/src/pydatalab/mongo.py b/pydatalab/src/pydatalab/mongo.py
index 5fd5e954a..afe551a49 100644
--- a/pydatalab/src/pydatalab/mongo.py
+++ b/pydatalab/src/pydatalab/mongo.py
@@ -217,5 +217,6 @@ def create_user_fts():
     ret += db.export_tasks.create_index(
         "created_at", name="export task created at", background=background
     )
+    ret += db.export_tasks.create_index("status", name="export task status", background=background)
 
     return ret
diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
index c10cb352a..b731b73da 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/export.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -1,10 +1,9 @@
 import os
-import threading
 import uuid
 from datetime import datetime, timezone
 from pathlib import Path
 
-from flask import Blueprint, jsonify, send_file
+from flask import Blueprint, current_app, jsonify, send_file
 from flask_login import current_user
 
 from pydatalab.config import CONFIG
@@ -12,6 +11,7 @@
 from pydatalab.models.export_task import ExportStatus, ExportTask
 from pydatalab.mongo import flask_mongo
 from pydatalab.permissions import active_users_or_get_only
+from pydatalab.scheduler import export_scheduler
 
 EXPORT = Blueprint("export", __name__)
 
@@ -21,13 +21,7 @@
 def _(): ...
 
 
-def _generate_export_in_background(task_id: str, collection_id: str):
-    """Background function to generate the .eln file.
-
-    Parameters:
-        task_id: ID of the export task
-        collection_id: ID of the collection to export
-    """
+def _do_export(task_id: str, collection_id: str):
     try:
         flask_mongo.db.export_tasks.update_one(
             {"task_id": task_id}, {"$set": {"status": ExportStatus.PROCESSING}}
@@ -63,25 +57,32 @@ def _generate_export_in_background(task_id: str, collection_id: str):
         )
 
 
+def _generate_export_in_background(task_id: str, collection_id: str, app):
+    if app is not None:
+        with app.app_context():
+            _do_export(task_id, collection_id)
+    else:
+        _do_export(task_id, collection_id)
+
+
 @EXPORT.route("/collections/<string:collection_id>/export", methods=["POST"])
 def start_collection_export(collection_id: str):
-    """Start exporting a collection to .eln format.
+    from pydatalab.permissions import get_default_permissions
 
-    Parameters:
-        collection_id: The collection ID to export
+    collection_exists = flask_mongo.db.collections.find_one({"collection_id": collection_id})
+    if not collection_exists:
+        return jsonify({"status": "error", "message": "Collection not found"}), 404
 
-    Returns:
-        JSON response with task_id and status_url
-    """
-
-    collection = flask_mongo.db.collections.find_one({"collection_id": collection_id})
-    if not collection:
-        return jsonify({"status": "error", "message": f"Collection {collection_id} not found"}), 404
+    collection_with_perms = flask_mongo.db.collections.find_one(
+        {"collection_id": collection_id, **get_default_permissions(user_only=True)}
+    )
+    if not collection_with_perms:
+        return jsonify({"status": "error", "message": "Access denied"}), 403
 
     task_id = str(uuid.uuid4())
 
     if not CONFIG.TESTING:
-        creator_id = current_user.person.immutable_id
+        creator_id = str(current_user.person.immutable_id)
     else:
         creator_id = "000000000000000000000000"
 
@@ -94,9 +95,16 @@ def start_collection_export(collection_id: str):
 
     flask_mongo.db.export_tasks.insert_one(export_task.dict())
 
-    thread = threading.Thread(target=_generate_export_in_background, args=(task_id, collection_id))
-    thread.daemon = True
-    thread.start()
+    try:
+        app = current_app._get_current_object()
+    except RuntimeError:
+        app = None
+
+    export_scheduler.add_job(
+        func=_generate_export_in_background,
+        args=[task_id, collection_id, app],
+        job_id=f"export_{task_id}",
+    )
 
     return jsonify(
         {"status": "success", "task_id": task_id, "status_url": f"/exports/{task_id}/status"}
@@ -105,15 +113,6 @@ def start_collection_export(collection_id: str):
 
 @EXPORT.route("/exports/<string:task_id>/status", methods=["GET"])
 def get_export_status(task_id: str):
-    """Get the status of an export task.
-
-    Parameters:
-        task_id: The export task ID
-
-    Returns:
-        JSON response with task status and download URL if ready
-    """
-
     task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
 
     if not task:
@@ -141,15 +140,6 @@ def get_export_status(task_id: str):
 
 @EXPORT.route("/exports/<string:task_id>/download", methods=["GET"])
 def download_export(task_id: str):
-    """Download the generated .eln file.
-
-    Parameters:
-        task_id: The export task ID
-
-    Returns:
-        The .eln file as attachment
-    """
-
     task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
 
     if not task:
diff --git a/pydatalab/src/pydatalab/scheduler.py b/pydatalab/src/pydatalab/scheduler.py
new file mode 100644
index 000000000..f3cbd1575
--- /dev/null
+++ b/pydatalab/src/pydatalab/scheduler.py
@@ -0,0 +1,49 @@
+from apscheduler.executors.pool import ThreadPoolExecutor
+from apscheduler.jobstores.memory import MemoryJobStore
+from apscheduler.schedulers.background import BackgroundScheduler
+
+
+class ExportScheduler:
+    _instance = None
+    _scheduler = None
+
+    def __new__(cls):
+        if cls._instance is None:
+            cls._instance = super().__new__(cls)
+        return cls._instance
+
+    def init_scheduler(self):
+        if self._scheduler is None:
+            jobstores = {"default": MemoryJobStore()}
+            executors = {"default": ThreadPoolExecutor(10)}
+            job_defaults = {"coalesce": False, "max_instances": 3}
+
+            self._scheduler = BackgroundScheduler(
+                jobstores=jobstores, executors=executors, job_defaults=job_defaults, timezone="UTC"
+            )
+            self._scheduler.start()
+        return self._scheduler
+
+    def get_scheduler(self):
+        if self._scheduler is None:
+            self.init_scheduler()
+        return self._scheduler
+
+    def add_job(self, func, args, job_id=None):
+        """Add a job to the scheduler or run it in a thread if APScheduler not available."""
+        if self._scheduler:
+            return self._scheduler.add_job(func=func, args=args, id=job_id, replace_existing=True)
+        else:
+            import threading
+
+            thread = threading.Thread(target=func, args=args)
+            thread.daemon = True
+            thread.start()
+            return None
+
+    def shutdown(self):
+        if self._scheduler and self._scheduler.running:
+            self._scheduler.shutdown()
+
+
+export_scheduler = ExportScheduler()
diff --git a/pydatalab/tests/server/test_export.py b/pydatalab/tests/server/test_export.py
new file mode 100644
index 000000000..416aa93a9
--- /dev/null
+++ b/pydatalab/tests/server/test_export.py
@@ -0,0 +1,205 @@
+import json
+from datetime import datetime, timezone
+from unittest.mock import MagicMock, patch
+
+import pytest
+from bson import ObjectId
+
+from pydatalab.models.export_task import ExportStatus, ExportTask
+
+
+@pytest.fixture
+def sample_collection(database, user_id):
+    collection_data = {
+        "_id": ObjectId(),
+        "collection_id": "test_export_collection",
+        "title": "Test Export Collection",
+        "description": "Collection for testing export functionality",
+        "creator_ids": [user_id],
+    }
+
+    database.collections.insert_one(collection_data)
+
+    yield collection_data
+
+    database.collections.delete_one({"collection_id": collection_data["collection_id"]})
+
+
+@pytest.fixture
+def mock_scheduler():
+    with patch("pydatalab.routes.v0_1.export.export_scheduler") as mock_sched:
+        mock_sched.add_job = MagicMock(return_value=None)
+        yield mock_sched
+
+
+class TestExportRoutes:
+    def test_start_collection_export_success(
+        self, client, sample_collection, mock_scheduler, database
+    ):
+        collection_id = sample_collection["collection_id"]
+
+        response = client.post(f"/collections/{collection_id}/export")
+
+        assert response.status_code == 202
+
+        data = json.loads(response.data)
+        assert data["status"] == "success"
+        assert "task_id" in data
+        assert "status_url" in data
+        assert data["status_url"] == f"/exports/{data['task_id']}/status"
+
+        assert mock_scheduler.add_job.called
+
+        # Verify the task was created in the database
+        task = database.export_tasks.find_one({"task_id": data["task_id"]})
+        assert task is not None
+        assert task["collection_id"] == collection_id
+        assert task["status"] == ExportStatus.PENDING
+
+        # Clean up
+        database.export_tasks.delete_one({"task_id": data["task_id"]})
+
+    def test_start_collection_export_not_found(self, client):
+        response = client.post("/collections/nonexistent/export")
+        assert response.status_code == 404
+
+        data = json.loads(response.data)
+        assert data["status"] == "error"
+        assert "not found" in data["message"].lower()
+
+    def test_get_export_status_pending(self, client, database):
+        task_id = "test-task-pending"
+        task = ExportTask(
+            task_id=task_id,
+            collection_id="test_collection",
+            creator_id="000000000000000000000000",
+            status=ExportStatus.PENDING,
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/status")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "pending"
+        assert "created_at" in data
+
+        database.export_tasks.delete_one({"task_id": task_id})
+
+    def test_get_export_status_ready(self, client, database, tmp_path):
+        task_id = "test-task-ready"
+        file_path = tmp_path / f"{task_id}.eln"
+        file_path.write_text("test content")
+
+        task = ExportTask(
+            task_id=task_id,
+            collection_id="test_collection",
+            creator_id="000000000000000000000000",
+            status=ExportStatus.READY,
+            file_path=str(file_path),
+            completed_at=datetime.now(tz=timezone.utc),
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/status")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "ready"
+        assert data["download_url"] == f"/exports/{task_id}/download"
+        assert "completed_at" in data
+
+        database.export_tasks.delete_one({"task_id": task_id})
+
+    def test_get_export_status_error(self, client, database):
+        task_id = "test-task-error"
+        error_message = "Export failed due to test error"
+
+        task = ExportTask(
+            task_id=task_id,
+            collection_id="test_collection",
+            creator_id="000000000000000000000000",
+            status=ExportStatus.ERROR,
+            error_message=error_message,
+            completed_at=datetime.now(tz=timezone.utc),
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/status")
+        assert response.status_code == 200
+
+        data = json.loads(response.data)
+        assert data["status"] == "error"
+        assert data["error_message"] == error_message
+        assert "completed_at" in data
+
+        database.export_tasks.delete_one({"task_id": task_id})
+
+    def test_get_export_status_not_found(self, client):
+        response = client.get("/exports/nonexistent-task/status")
+        assert response.status_code == 404
+
+        data = json.loads(response.data)
+        assert data["status"] == "error"
+        assert "not found" in data["message"].lower()
+
+    def test_download_export_success(self, client, database, tmp_path):
+        task_id = "test-download-task"
+        collection_id = "test_collection"
+        file_path = tmp_path / f"{task_id}.eln"
+        file_path.write_bytes(b"test export content")
+
+        task = ExportTask(
+            task_id=task_id,
+            collection_id=collection_id,
+            creator_id="000000000000000000000000",
+            status=ExportStatus.READY,
+            file_path=str(file_path),
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/download")
+        assert response.status_code == 200
+        assert response.data == b"test export content"
+        assert f"filename={collection_id}.eln" in response.headers.get("Content-Disposition", "")
+
+        database.export_tasks.delete_one({"task_id": task_id})
+
+    def test_download_export_not_ready(self, client, database):
+        task_id = "test-not-ready-task"
+
+        task = ExportTask(
+            task_id=task_id,
+            collection_id="test_collection",
+            creator_id="000000000000000000000000",
+            status=ExportStatus.PROCESSING,
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/download")
+        assert response.status_code == 400
+
+        data = json.loads(response.data)
+        assert "not ready" in data["message"].lower()
+
+        database.export_tasks.delete_one({"task_id": task_id})
+
+    def test_download_export_file_missing(self, client, database):
+        task_id = "test-missing-file-task"
+
+        task = ExportTask(
+            task_id=task_id,
+            collection_id="test_collection",
+            creator_id="000000000000000000000000",
+            status=ExportStatus.READY,
+            file_path="/nonexistent/path.eln",
+        )
+        database.export_tasks.insert_one(task.dict())
+
+        response = client.get(f"/exports/{task_id}/download")
+        assert response.status_code == 404
+
+        data = json.loads(response.data)
+        assert "file not found" in data["message"].lower()
+
+        database.export_tasks.delete_one({"task_id": task_id})
diff --git a/pydatalab/tests/server/test_export_utils.py b/pydatalab/tests/server/test_export_utils.py
new file mode 100644
index 000000000..d1599295a
--- /dev/null
+++ b/pydatalab/tests/server/test_export_utils.py
@@ -0,0 +1,136 @@
+import json
+import zipfile
+from datetime import datetime, timezone
+from unittest.mock import patch
+
+import pytest
+from bson import ObjectId
+
+from pydatalab.export_utils import (
+    _convert_objectids_in_dict,
+    create_eln_file,
+    generate_ro_crate_metadata,
+)
+
+
+class TestExportUtils:
+    def test_convert_objectids_in_dict(self):
+        """Test ObjectId and datetime conversion in dictionaries."""
+        test_id = ObjectId()
+        test_date = datetime.now(tz=timezone.utc)
+
+        input_dict = {
+            "id": test_id,
+            "date": test_date,
+            "nested": {
+                "nested_id": test_id,
+                "nested_date": test_date,
+            },
+            "list": [test_id, test_date],
+            "string": "test",
+        }
+
+        result = _convert_objectids_in_dict(input_dict)
+
+        assert result["id"] == str(test_id)
+        assert result["date"] == test_date.isoformat()
+        assert result["nested"]["nested_id"] == str(test_id)
+        assert result["nested"]["nested_date"] == test_date.isoformat()
+        assert result["list"][0] == str(test_id)
+        assert result["list"][1] == test_date.isoformat()
+        assert result["string"] == "test"
+
+    def test_generate_ro_crate_metadata(self):
+        """Test RO-Crate metadata generation."""
+        collection_data = {
+            "_id": ObjectId(),
+            "collection_id": "test_collection",
+            "title": "Test Collection",
+            "description": "A test collection for export",
+        }
+
+        child_items = [
+            {
+                "item_id": "sample1",
+                "name": "Sample 1",
+                "date": datetime.now(tz=timezone.utc),
+                "file_ObjectIds": ["507f1f77bcf86cd799439011"],
+            },
+            {
+                "item_id": "sample2",
+                "name": "Sample 2",
+            },
+        ]
+
+        with patch("pydatalab.export_utils.flask_mongo.db.files.find_one") as mock_find:
+            mock_find.return_value = {"name": "test_file.txt"}
+
+            metadata = generate_ro_crate_metadata(collection_data, child_items)
+
+        assert metadata["@context"] == "https://w3id.org/ro/crate/1.1/context"
+        assert isinstance(metadata["@graph"], list)
+
+        root = next(item for item in metadata["@graph"] if item["@id"] == "./")
+        assert root["@type"] == "Dataset"
+        assert root["name"] == "Test Collection"
+        assert root["description"] == "A test collection for export"
+        assert len(root["hasPart"]) == 2
+
+        sample1 = next(item for item in metadata["@graph"] if item["@id"] == "./sample1/")
+        assert sample1["@type"] == "Dataset"
+        assert sample1["name"] == "Sample 1"
+        assert sample1["identifier"] == "sample1"
+
+    def test_create_eln_file(self, database, tmp_path, user_id):
+        collection_id = "test_export"
+        collection_data = {
+            "_id": ObjectId(),
+            "collection_id": collection_id,
+            "title": "Export Test Collection",
+            "creator_ids": [user_id],
+        }
+
+        sample_id = ObjectId()
+        sample_data = {
+            "_id": sample_id,
+            "item_id": "test_sample",
+            "name": "Test Sample",
+            "type": "samples",
+            "relationships": [{"type": "collections", "immutable_id": collection_data["_id"]}],
+            "creator_ids": [user_id],
+        }
+
+        database.collections.insert_one(collection_data)
+        database.items.insert_one(sample_data)
+
+        output_path = tmp_path / "test.eln"
+
+        try:
+            create_eln_file(collection_id, str(output_path))
+
+            assert output_path.exists()
+
+            with zipfile.ZipFile(output_path, "r") as zf:
+                files = zf.namelist()
+
+                assert f"{collection_id}/ro-crate-metadata.json" in files
+                assert f"{collection_id}/test_sample/metadata.json" in files
+
+                with zf.open(f"{collection_id}/ro-crate-metadata.json") as f:
+                    ro_crate = json.load(f)
+                    assert ro_crate["@context"] == "https://w3id.org/ro/crate/1.1/context"
+
+                with zf.open(f"{collection_id}/test_sample/metadata.json") as f:
+                    sample_metadata = json.load(f)
+                    assert sample_metadata["item_id"] == "test_sample"
+                    assert sample_metadata["name"] == "Test Sample"
+
+        finally:
+            database.collections.delete_one({"collection_id": collection_id})
+            database.items.delete_one({"_id": sample_id})
+
+    def test_create_eln_file_collection_not_found(self, tmp_path):
+        """Test error when collection not found."""
+        output_file = tmp_path / "test.eln"
+        with pytest.raises(ValueError, match="Collection .* not found"):
+            create_eln_file("nonexistent_collection", str(output_file))
diff --git a/pydatalab/uv.lock b/pydatalab/uv.lock
index 05cb8646e..2877f55a2 100644
--- a/pydatalab/uv.lock
+++ b/pydatalab/uv.lock
@@ -1,5 +1,4 @@
 version = 1
-revision = 3
 requires-python = ">=3.10, <3.12"
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diff --git a/webapp/src/components/CollectionExportButton.vue b/webapp/src/components/CollectionExportButton.vue
index 5d0b4aa24..04a897fd0 100644
--- a/webapp/src/components/CollectionExportButton.vue
+++ b/webapp/src/components/CollectionExportButton.vue
@@ -51,7 +51,7 @@ export default {
         this.isExporting = false;
         DialogService.error({
           title: "Export Failed",
-          message: "Failed to start the export. Please try again.",
+          message: error.message || "Failed to start the export. Please try again.",
         });
       }
     },

From 1085c0e9f8a7df587b6c07b44b5f0a3977cb95b7 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 21 Oct 2025 11:21:14 +0200
Subject: [PATCH 03/26] Return only 404 if no access and set user_only=False

---
 pydatalab/src/pydatalab/routes/v0_1/export.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
index b731b73da..1598e9224 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/export.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -69,15 +69,11 @@ def _generate_export_in_background(task_id: str, collection_id: str, app):
 def start_collection_export(collection_id: str):
     from pydatalab.permissions import get_default_permissions
 
-    collection_exists = flask_mongo.db.collections.find_one({"collection_id": collection_id})
-    if not collection_exists:
-        return jsonify({"status": "error", "message": "Collection not found"}), 404
-
     collection_with_perms = flask_mongo.db.collections.find_one(
-        {"collection_id": collection_id, **get_default_permissions(user_only=True)}
+        {"collection_id": collection_id, **get_default_permissions(user_only=False)}
     )
     if not collection_with_perms:
-        return jsonify({"status": "error", "message": "Access denied"}), 403
+        return jsonify({"status": "error", "message": "Collection not found"}), 404
 
     task_id = str(uuid.uuid4())
 

From 27218d8c8bc8570969aa4bc3e979255b4d5ee5fc Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 21 Oct 2025 11:25:20 +0200
Subject: [PATCH 04/26] Add raw data to .eln

---
 pydatalab/src/pydatalab/export_utils.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pydatalab/src/pydatalab/export_utils.py b/pydatalab/src/pydatalab/export_utils.py
index c9212b414..b509bf389 100644
--- a/pydatalab/src/pydatalab/export_utils.py
+++ b/pydatalab/src/pydatalab/export_utils.py
@@ -153,7 +153,8 @@ def create_eln_file(collection_id: str, output_path: str) -> None:
 
             if item.get("file_ObjectIds"):
                 for file_id in item.get("file_ObjectIds", []):
-                    file_data = flask_mongo.db.files.find_one({"_id": ObjectId(file_id)})
+                    file_id_obj = ObjectId(file_id) if isinstance(file_id, str) else file_id
+                    file_data = flask_mongo.db.files.find_one({"_id": file_id_obj})
                     if file_data:
                         source_path = Path(file_data["location"])
                         if source_path.exists():
@@ -161,6 +162,10 @@ def create_eln_file(collection_id: str, output_path: str) -> None:
                             shutil.copy2(source_path, dest_file)
                         else:
                             print(f"Warning: File not found on disk: {file_data['location']}")
+                    else:
+                        print(
+                            f"Warning: File metadata not found in database for file_id: {file_id}"
+                        )
 
         with zipfile.ZipFile(output_path, "w", zipfile.ZIP_DEFLATED) as zipf:
             for file_path in root_folder.rglob("*"):

From 810a4a48b2196cf602bc1d413b942af3ff29971a Mon Sep 17 00:00:00 2001
From: Ben Charmes <107116804+BenjaminCharmes@users.noreply.github.com>
Date: Tue, 28 Oct 2025 20:26:15 +0100
Subject: [PATCH 05/26] Fix item graph displaying too many items (#1367)

Co-authored-by: Matthew Evans <git@ml-evs.science>
---
 pydatalab/src/pydatalab/routes/v0_1/graphs.py |  77 ++++++++----
 pydatalab/tests/server/test_item_graph.py     | 115 +++++++++++++++++-
 2 files changed, 164 insertions(+), 28 deletions(-)

diff --git a/pydatalab/src/pydatalab/routes/v0_1/graphs.py b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
index 89529d874..f54bea141 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/graphs.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
@@ -19,11 +19,15 @@ def get_graph_cy_format(
     hide_collections: bool = True,
 ):
     collection_id = request.args.get("collection_id", type=str)
+    hide_collections = request.args.get(
+        "hide_collections", default=True, type=lambda v: v.lower() == "true"
+    )
 
     if item_id is None:
         if collection_id is not None:
             collection_immutable_id = flask_mongo.db.collections.find_one(
-                {"collection_id": collection_id}, projection={"_id": 1}
+                {"collection_id": collection_id, **get_default_permissions(user_only=False)},
+                projection={"_id": 1},
             )
             if not collection_immutable_id:
                 return (
@@ -49,33 +53,56 @@ def get_graph_cy_format(
         all_documents.rewind()
 
     else:
-        all_documents = list(
+        main_item = flask_mongo.db.items.find_one(
+            {
+                "item_id": item_id,
+                **get_default_permissions(user_only=False),
+            },
+            projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+        )
+
+        if not main_item:
+            return (
+                jsonify(status="error", message=f"Item {item_id} not found or no permission"),
+                404,
+            )
+
+        all_documents = [main_item]
+        node_ids = {item_id}
+
+        for relationship in main_item.get("relationships", []) or []:
+            if relationship.get("item_id"):
+                node_ids.add(relationship["item_id"])
+
+        incoming_items = list(
             flask_mongo.db.items.find(
                 {
-                    "$or": [{"item_id": item_id}, {"relationships.item_id": item_id}],
-                    **get_default_permissions(user_only=False),
+                    "$and": [
+                        {"relationships": {"$elemMatch": {"item_id": item_id}}},
+                        get_default_permissions(user_only=False),
+                    ]
                 },
                 projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
             )
         )
 
-        node_ids = {document["item_id"] for document in all_documents} | {
-            relationship.get("item_id")
-            for document in all_documents
-            for relationship in document.get("relationships", [])
-        }
-        if len(node_ids) > 1:
-            or_query = [{"item_id": id} for id in node_ids if id != item_id]
-            next_shell = flask_mongo.db.items.find(
-                {
-                    "$or": or_query,
-                    **get_default_permissions(user_only=False),
-                },
-                projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
-            )
+        for doc in incoming_items:
+            node_ids.add(doc["item_id"])
 
-            all_documents.extend(next_shell)
-            node_ids = node_ids | {document["item_id"] for document in all_documents}
+        all_documents.extend(incoming_items)
+
+        ids_to_fetch = node_ids - {doc["item_id"] for doc in all_documents}
+        if ids_to_fetch:
+            referenced_items = list(
+                flask_mongo.db.items.find(
+                    {
+                        "item_id": {"$in": list(ids_to_fetch)},
+                        **get_default_permissions(user_only=False),
+                    },
+                    projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+                )
+            )
+            all_documents.extend(referenced_items)
 
     nodes = []
     edges = []
@@ -166,12 +193,18 @@ def get_graph_cy_format(
                 }
             )
 
-    whitelist = {edge["data"]["source"] for edge in edges} | {item_id}
+    whitelist = {edge["data"]["source"] for edge in edges} | {
+        edge["data"]["target"] for edge in edges
+    }
+    if item_id:
+        whitelist.add(item_id)
 
     nodes = [
         node
         for node in nodes
-        if node["data"]["type"] in ("samples", "cells") or node["data"]["id"] in whitelist
+        if node["data"]["type"] in ("samples", "cells")
+        or node["data"]["id"] in whitelist
+        or node["data"]["id"].startswith("Collection:")
     ]
 
     return (jsonify(status="success", nodes=nodes, edges=edges), 200)
diff --git a/pydatalab/tests/server/test_item_graph.py b/pydatalab/tests/server/test_item_graph.py
index 4f00e40a7..69af133af 100644
--- a/pydatalab/tests/server/test_item_graph.py
+++ b/pydatalab/tests/server/test_item_graph.py
@@ -8,12 +8,12 @@
 from pydatalab.models import Sample, StartingMaterial
 
 
-def test_single_starting_material(admin_client):
+def test_single_starting_material(admin_client, client):
     item_id = "material"
 
     material = StartingMaterial(item_id=item_id)
 
-    creation = admin_client.post(
+    creation = client.post(
         "/new-sample/",
         json={"new_sample_data": json.loads(material.json())},
     )
@@ -21,11 +21,11 @@ def test_single_starting_material(admin_client):
     assert creation.status_code == 201
 
     # A single material without connections should be ignored
-    graph = admin_client.get("/item-graph").json
+    graph = client.get("/item-graph").json
     assert len(graph["nodes"]) == 0
 
     # Unless it is asked for directly
-    graph = admin_client.get(f"/item-graph/{item_id}").json
+    graph = client.get(f"/item-graph/{item_id}").json
     assert len(graph["nodes"]) == 1
 
     # Now make a sample and connect it to the starting material; check that the
@@ -37,13 +37,116 @@ def test_single_starting_material(admin_client):
         ],
     )
 
-    creation = admin_client.post(
+    creation = client.post(
         "/new-sample/",
         json={"new_sample_data": json.loads(parent.json())},
     )
 
     assert creation.status_code == 201
 
-    graph = admin_client.get("/item-graph").json
+    graph = client.get("/item-graph").json
+    assert len(graph["nodes"]) == 2
+    assert len(graph["edges"]) == 1
+
+    # From both the starting material and the sample
+    graph = client.get(f"/item-graph/{item_id}").json
+    assert len(graph["nodes"]) == 2
+    assert len(graph["edges"]) == 1
+
+    # From both the starting material and the sample
+    graph = client.get("/item-graph/parent").json
+    assert len(graph["nodes"]) == 2
+    assert len(graph["edges"]) == 1
+
+    # Now add a few more samples in a chain and check that only the relevant ones are shown
+    child = Sample(
+        item_id="child",
+        synthesis_constituents=[
+            {"item": {"item_id": "parent", "type": "samples"}, "quantity": None}
+        ],
+    )
+
+    creation = client.post(
+        "/new-sample/",
+        json={"new_sample_data": json.loads(child.json())},
+    )
+
+    grandchild = Sample(
+        item_id="grandchild",
+        synthesis_constituents=[
+            {"item": {"item_id": "child", "type": "samples"}, "quantity": None}
+        ],
+    )
+
+    creation = client.post(
+        "/new-sample/",
+        json={"new_sample_data": json.loads(grandchild.json())},
+    )
+
+    great_grandchild = Sample(
+        item_id="great-grandchild",
+        synthesis_constituents=[
+            {"item": {"item_id": "grandchild", "type": "samples"}, "quantity": None}
+        ],
+    )
+
+    creation = client.post(
+        "/new-sample/",
+        json={"new_sample_data": json.loads(great_grandchild.json())},
+    )
+
+    graph = client.get("/item-graph").json
+    assert len(graph["nodes"]) == 5
+    assert len(graph["edges"]) == 4
+
+    # Check for bug where this behaviour was inconsistent between admin and non-admin users
+    graph = admin_client.get("/item-graph/great-grandchild").json
+    assert len(graph["nodes"]) == 2
+    assert len(graph["edges"]) == 1
+
+    # Add an admin only item and check that the non-admin user still sees the same graph
+    admin_great_great_grandchild = Sample(
+        item_id="admin-great-great-grandchild",
+        synthesis_constituents=[
+            {"item": {"item_id": "great-grandchild", "type": "samples"}, "quantity": None}
+        ],
+    )
+
+    creation = admin_client.post(
+        "/new-sample/", json={"new_sample_data": json.loads(admin_great_great_grandchild.json())}
+    )
+
+    graph = admin_client.get("/item-graph/great-grandchild").json
+    assert len(graph["nodes"]) == 3
+    assert len(graph["edges"]) == 2
+
+    graph = client.get("/item-graph/great-grandchild").json
     assert len(graph["nodes"]) == 2
     assert len(graph["edges"]) == 1
+
+    # Put node in a collection and see if its shown
+    response = admin_client.put(
+        "/collections",
+        json={
+            "data": {
+                "collection_id": "test-collection",
+                "starting_members": [{"item_id": "great-grandchild"}],
+            }
+        },
+    )
+    assert response.status_code == 201
+
+    client_collection_graph = client.get("/item-graph?collection_id=test-collection").json
+    assert client_collection_graph["status"] == "error"
+
+    collection_graph = admin_client.get("/item-graph?collection_id=test-collection").json
+    assert len(collection_graph["nodes"]) == 1
+    assert len(collection_graph["edges"]) == 0
+
+    graph = client.get("/item-graph/great-grandchild?hide_collections=false").json
+    assert len(graph["nodes"]) == 2
+    assert len(graph["edges"]) == 1
+
+    admin_graph = admin_client.get("/item-graph/great-grandchild?hide_collections=false").json
+    assert len(admin_graph["nodes"]) == 4
+    assert len(admin_graph["edges"]) == 3

From 98c702132516fa747199bb523fa5a93a6f213c49 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Tue, 28 Oct 2025 19:50:33 +0000
Subject: [PATCH 06/26] Allow item creation endpoints to use `PUT` (#1387)

---
 pydatalab/src/pydatalab/routes/v0_1/items.py | 4 ++--
 pydatalab/tests/server/test_samples.py       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pydatalab/src/pydatalab/routes/v0_1/items.py b/pydatalab/src/pydatalab/routes/v0_1/items.py
index 3381ec03e..085cbd34e 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/items.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/items.py
@@ -645,7 +645,7 @@ def _create_sample(
     return data
 
 
-@ITEMS.route("/new-sample/", methods=["POST"])
+@ITEMS.route("/new-sample/", methods=["POST", "PUT"])
 def create_sample():
     request_json = request.get_json()  # noqa: F821 pylint: disable=undefined-variable
     if "new_sample_data" in request_json:
@@ -660,7 +660,7 @@ def create_sample():
     return jsonify(response), http_code
 
 
-@ITEMS.route("/new-samples/", methods=["POST"])
+@ITEMS.route("/new-samples/", methods=["POST", "PUT"])
 def create_samples():
     """attempt to create multiple samples at once.
     Because each may result in success or failure, 207 is returned along with a
diff --git a/pydatalab/tests/server/test_samples.py b/pydatalab/tests/server/test_samples.py
index 41b0dbae7..8c91c665f 100644
--- a/pydatalab/tests/server/test_samples.py
+++ b/pydatalab/tests/server/test_samples.py
@@ -17,7 +17,7 @@ def test_empty_samples(client):
 
 @pytest.mark.dependency(depends=["test_empty_samples"])
 def test_new_sample(client, default_sample_dict):
-    response = client.post("/new-sample/", json=default_sample_dict)
+    response = client.put("/new-sample/", json=default_sample_dict)
     # Test that 201: Created is emitted
     assert response.status_code == 201, response.json
     assert response.json["status"] == "success"

From 502773219a417b75975df2dc9b73b2b99b724978 Mon Sep 17 00:00:00 2001
From: DianaAliabieva <145962759+DianaAliabieva@users.noreply.github.com>
Date: Tue, 28 Oct 2025 21:04:39 +0100
Subject: [PATCH 07/26] Add file-size in the filelist (#1380)

Co-authored-by: Matthew Evans <git@ml-evs.science>
Co-authored-by: Diana Aliabieva <dianaaliabieva@Dianas-MacBook-Pro.local>
---
 webapp/src/components/FileList.vue | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/webapp/src/components/FileList.vue b/webapp/src/components/FileList.vue
index 69b8062ee..b4f8ce42d 100644
--- a/webapp/src/components/FileList.vue
+++ b/webapp/src/components/FileList.vue
@@ -10,6 +10,10 @@
           <a class="filelink" target="_blank" :href="`${$API_URL}/files/${file_id}/${file.name}`">
             {{ file.name }}
           </a>
+          <span v-if="getFileSize(file)" class="file-size">
+            ({{ formatFileSize(getFileSize(file)) }})
+          </span>
+
           <font-awesome-icon
             v-if="file.is_live == true"
             v-show="true"
@@ -27,6 +31,10 @@
               <font-awesome-icon :icon="['fas', 'hdd']" class="toplevel-icon" />
               {{ file.source_server_name }}
             </span>
+            <span v-if="getFileSize(file)" class="file-size">
+              ({{ formatFileSize(getFileSize(file)) }})
+            </span>
+
             <span class="last-updated-text">
               (updated
               {{
@@ -93,6 +101,15 @@ export default {
   },
   methods: {
     formatDistance,
+    getFileSize(file) {
+      return file.size;
+    },
+    formatFileSize(size_bytes) {
+      if (size_bytes < 1024) return `${size_bytes} B`;
+      if (size_bytes < 1024 * 1024) return `${(size_bytes / 1024).toFixed(1)} KB`;
+      if (size_bytes < 1024 * 1024 * 1024) return `${(size_bytes / 1024 / 1024).toFixed(1)} MB`;
+      return `${(size_bytes / 1024 / 1024 / 1024).toFixed(2)} GB`;
+    },
     async deleteFile(event, file_id) {
       const confirmed = await DialogService.confirm({
         title: "Unlink File",
@@ -154,6 +171,11 @@ export default {
   font-style: italic;
   vertical-align: middle;
 }
+.file-size {
+  color: #888;
+  font-size: 0.8em;
+  margin-left: 0.25rem;
+}
 
 .server-name {
   font-family: var(--font-monospace);

From 28f5a5870c6dce6a2526d984ac0d76e367a6f5e6 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Tue, 28 Oct 2025 23:54:26 +0000
Subject: [PATCH 08/26] Add support for PSTrace EIS output txt files (#1383)

---
 pydatalab/src/pydatalab/apps/eis/__init__.py | 67 +++++++++++++++++++-
 pydatalab/src/pydatalab/bokeh_plots.py       |  2 +
 2 files changed, 66 insertions(+), 3 deletions(-)

diff --git a/pydatalab/src/pydatalab/apps/eis/__init__.py b/pydatalab/src/pydatalab/apps/eis/__init__.py
index 3a46ac6b4..08cd0274b 100644
--- a/pydatalab/src/pydatalab/apps/eis/__init__.py
+++ b/pydatalab/src/pydatalab/apps/eis/__init__.py
@@ -13,9 +13,50 @@
 
 def parse_ivium_eis_txt(filename: Path):
     eis = pd.read_csv(filename, sep="\t")
+
+    column_map = {
+        "Z1 /ohm": "Re(Z) [Ω]",
+        "Z2 /ohm": "-Im(Z) [Ω]",
+        "freq. /Hz": "Frequency [Hz]",
+    }
+
+    if not all(k in eis.columns for k in column_map):
+        raise RuntimeError(
+            f"File does not appear to be a valid Ivium EIS export, expected columns {column_map.keys()}, found {eis.columns}"
+        )
+
     eis["Z2 /ohm"] *= -1
     eis.rename(
-        {"Z1 /ohm": "Re(Z) [Ω]", "Z2 /ohm": "-Im(Z) [Ω]", "freq. /Hz": "Frequency [Hz]"},
+        column_map,
+        inplace=True,
+        axis="columns",
+    )
+    return eis
+
+
+def parse_pstrace_eis_txt(filename: Path):
+    eis = pd.read_csv(filename, sep="\t")
+
+    column_map = {
+        "Frequency": "Frequency [Hz]",
+        "Zdash": "Re(Z) [Ω]",
+        "Zdashneg": "-Im(Z) [Ω]",
+        "Z": "|Z| [Ω]",
+        "Phase": "θ [°]",
+        "Y": "|Y| [S]",
+        "YRe": "Re(Y) [S]",
+        "YIm": "Im(Y) [S]",
+        "Cdash": "Re(C) [F]",
+        "Cdashdash": "Im(C) [F]",
+    }
+
+    if not all(k in eis.columns for k in column_map):
+        raise RuntimeError(
+            f"File does not appear to be a valid PSTrace EIS export, expected columns {column_map.keys()}, found {eis.columns}"
+        )
+
+    eis.rename(
+        column_map,
         inplace=True,
         axis="columns",
     )
@@ -26,7 +67,12 @@ class EISBlock(DataBlock):
     accepted_file_extensions = (".txt",)
     blocktype = "eis"
     name = "EIS"
-    description = "This block can plot electrochemical impedance spectroscopy (EIS) data from Ivium .txt files"
+    description = """
+This block can plot electrochemical impedance spectroscopy (EIS) data from:
+
+- exported  Ivium .txt files
+- exported .txt files from PSTrace.
+    """
 
     @property
     def plot_functions(self):
@@ -51,7 +97,22 @@ def generate_eis_plot(self):
                 )
                 return
 
-            eis_data = parse_ivium_eis_txt(Path(file_info["location"]))
+            errors = []
+            eis_data = None
+            try:
+                eis_data = parse_ivium_eis_txt(Path(file_info["location"]))
+            except RuntimeError as exc:
+                errors = [exc]
+
+            try:
+                eis_data = parse_pstrace_eis_txt(Path(file_info["location"]))
+            except RuntimeError as exc:
+                errors.append(exc)
+
+            if eis_data is None:
+                raise RuntimeError(
+                    f"Could not parse EIS data from uploaded file with implemented parsers. Errors: {errors}"
+                )
 
         if eis_data is not None:
             plot = selectable_axes_plot(
diff --git a/pydatalab/src/pydatalab/bokeh_plots.py b/pydatalab/src/pydatalab/bokeh_plots.py
index b75c32b34..ebe402389 100644
--- a/pydatalab/src/pydatalab/bokeh_plots.py
+++ b/pydatalab/src/pydatalab/bokeh_plots.py
@@ -302,6 +302,8 @@ def selectable_axes_plot(
         **kwargs,
     )
     p.toolbar.logo = "grey"
+    p.xaxis.ticker.desired_num_ticks = 5
+    p.yaxis.ticker.desired_num_ticks = 5
 
     if tools:
         if isinstance(tools, list):

From d30bada0eb449eec635884ae758ca094f2c21f53 Mon Sep 17 00:00:00 2001
From: Ben Charmes <107116804+BenjaminCharmes@users.noreply.github.com>
Date: Wed, 29 Oct 2025 01:10:06 +0100
Subject: [PATCH 09/26] Fix collection creation modal error display for
 duplicate IDs (#1382)

---
 webapp/src/components/CreateCollectionModal.vue | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/webapp/src/components/CreateCollectionModal.vue b/webapp/src/components/CreateCollectionModal.vue
index 4c54af8b7..4588ef795 100644
--- a/webapp/src/components/CreateCollectionModal.vue
+++ b/webapp/src/components/CreateCollectionModal.vue
@@ -67,16 +67,21 @@ export default {
       title: "",
       selectedCollectionToCopy: null,
       startingMembers: [],
+      takenCollectionIds: [],
     };
   },
   computed: {
-    takenCollectionIds() {
+    collectionIdsFromStore() {
       return this.$store.state.collection_list
         ? this.$store.state.collection_list.map((x) => x.collection_id)
         : [];
     },
     isValidEntryID() {
-      return validateEntryID(this.collection_id, this.takenCollectionIds);
+      return validateEntryID(
+        this.collection_id,
+        this.takenCollectionIds,
+        this.collectionIdsFromStore,
+      );
     },
   },
   methods: {

From 2f77f01e1626df5a27eeef5e3153d1fff0e02145 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Wed, 29 Oct 2025 15:55:46 +0100
Subject: [PATCH 10/26] First attempt to sample ELN export button

First attempt to sample ELN export button
---
 pydatalab/src/pydatalab/export_utils.py       |  72 +++---
 pydatalab/src/pydatalab/models/export_task.py |  10 +-
 pydatalab/src/pydatalab/routes/v0_1/export.py |  87 ++++++-
 .../src/components/CollectionInformation.vue  |   6 +-
 ...ctionExportButton.vue => ExportButton.vue} |  39 +++-
 .../src/components/SampleGraphExportModal.vue | 212 ++++++++++++++++++
 webapp/src/components/SampleInformation.vue   |   5 +
 webapp/src/server_fetch_utils.js              |  22 +-
 8 files changed, 398 insertions(+), 55 deletions(-)
 rename webapp/src/components/{CollectionExportButton.vue => ExportButton.vue} (74%)
 create mode 100644 webapp/src/components/SampleGraphExportModal.vue

diff --git a/pydatalab/src/pydatalab/export_utils.py b/pydatalab/src/pydatalab/export_utils.py
index b509bf389..7f8f560f8 100644
--- a/pydatalab/src/pydatalab/export_utils.py
+++ b/pydatalab/src/pydatalab/export_utils.py
@@ -106,33 +106,58 @@ def generate_ro_crate_metadata(collection_data: dict, child_items: list[dict]) -
     return metadata
 
 
-def create_eln_file(collection_id: str, output_path: str) -> None:
-    """Create a .eln file for a collection.
+def create_eln_file(
+    output_path: str,
+    collection_id: str | None = None,
+    item_id: str | None = None,
+    related_item_ids: list[str] | None = None,
+) -> None:
+    if collection_id:
+        collection_data = flask_mongo.db.collections.find_one({"collection_id": collection_id})
+        if not collection_data:
+            raise ValueError(f"Collection {collection_id} not found")
+
+        collection_immutable_id = collection_data["_id"]
+        child_items = list(
+            flask_mongo.db.items.find(
+                {
+                    "relationships": {
+                        "$elemMatch": {
+                            "type": "collections",
+                            "immutable_id": collection_immutable_id,
+                        }
+                    }
+                }
+            )
+        )
+        root_folder_name = collection_id
 
-    Parameters:
-        collection_id: ID of the collection to export
-        output_path: Path where the .eln file should be saved
-    """
+    elif item_id:
+        item_data = flask_mongo.db.items.find_one({"item_id": item_id})
+        if not item_data:
+            raise ValueError(f"Sample {item_id} not found")
 
-    collection_data = flask_mongo.db.collections.find_one({"collection_id": collection_id})
-    if not collection_data:
-        raise ValueError(f"Collection {collection_id} not found")
+        if related_item_ids:
+            child_items = list(
+                flask_mongo.db.items.find({"item_id": {"$in": [item_id] + related_item_ids}})
+            )
+        else:
+            child_items = [item_data]
 
-    collection_immutable_id = collection_data["_id"]
-    child_items = list(
-        flask_mongo.db.items.find(
-            {
-                "relationships": {
-                    "$elemMatch": {"type": "collections", "immutable_id": collection_immutable_id}
-                }
-            }
-        )
-    )
+        collection_data = {
+            "collection_id": item_id,
+            "title": item_data.get("name", item_id),
+            "description": f"Export of sample {item_id}"
+            + (" and related samples" if related_item_ids else ""),
+        }
+        root_folder_name = item_id
+
+    else:
+        raise ValueError("Either collection_id or item_id must be provided")
 
     with tempfile.TemporaryDirectory() as temp_dir:
         temp_path = Path(temp_dir)
 
-        root_folder_name = collection_id
         root_folder = temp_path / root_folder_name
         root_folder.mkdir()
 
@@ -145,7 +170,6 @@ def create_eln_file(collection_id: str, output_path: str) -> None:
             item_folder.mkdir()
 
             item_metadata = {k: v for k, v in item.items() if k not in ["_id", "file_ObjectIds"]}
-
             item_metadata = _convert_objectids_in_dict(item_metadata)
 
             with open(item_folder / "metadata.json", "w", encoding="utf-8") as f:
@@ -160,12 +184,6 @@ def create_eln_file(collection_id: str, output_path: str) -> None:
                         if source_path.exists():
                             dest_file = item_folder / file_data["name"]
                             shutil.copy2(source_path, dest_file)
-                        else:
-                            print(f"Warning: File not found on disk: {file_data['location']}")
-                    else:
-                        print(
-                            f"Warning: File metadata not found in database for file_id: {file_id}"
-                        )
 
         with zipfile.ZipFile(output_path, "w", zipfile.ZIP_DEFLATED) as zipf:
             for file_path in root_folder.rglob("*"):
diff --git a/pydatalab/src/pydatalab/models/export_task.py b/pydatalab/src/pydatalab/models/export_task.py
index 5e719c4f7..013128449 100644
--- a/pydatalab/src/pydatalab/models/export_task.py
+++ b/pydatalab/src/pydatalab/models/export_task.py
@@ -5,8 +5,6 @@
 
 
 class ExportStatus(str, Enum):
-    """Status of an export task."""
-
     PENDING = "pending"
     PROCESSING = "processing"
     READY = "ready"
@@ -14,10 +12,12 @@ class ExportStatus(str, Enum):
 
 
 class ExportTask(BaseModel):
-    """Model for an export task."""
-
     task_id: str = Field(..., description="Unique identifier for the export task")
-    collection_id: str = Field(..., description="ID of the collection being exported")
+    collection_id: str | None = Field(None, description="ID of the collection being exported")
+    item_id: str | None = Field(None, description="ID of the sample being exported")
+    export_type: str = Field(
+        default="collection", description="Type of export: 'collection' or 'sample' or 'graph'"
+    )
     status: ExportStatus = Field(
         default=ExportStatus.PENDING, description="Current status of the task"
     )
diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
index 1598e9224..73557f2ea 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/export.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -3,7 +3,7 @@
 from datetime import datetime, timezone
 from pathlib import Path
 
-from flask import Blueprint, current_app, jsonify, send_file
+from flask import Blueprint, current_app, jsonify, request, send_file
 from flask_login import current_user
 
 from pydatalab.config import CONFIG
@@ -21,7 +21,13 @@
 def _(): ...
 
 
-def _do_export(task_id: str, collection_id: str):
+def _do_export(
+    task_id: str,
+    collection_id: str | None = None,
+    item_id: str | None = None,
+    export_type: str = "collection",
+    related_item_ids: list[str] | None = None,
+):
     try:
         flask_mongo.db.export_tasks.update_one(
             {"task_id": task_id}, {"$set": {"status": ExportStatus.PROCESSING}}
@@ -31,7 +37,10 @@ def _do_export(task_id: str, collection_id: str):
         export_dir.mkdir(exist_ok=True)
 
         output_path = export_dir / f"{task_id}.eln"
-        create_eln_file(collection_id, str(output_path))
+        if export_type == "collection":
+            create_eln_file(str(output_path), collection_id=collection_id)
+        elif export_type in ["sample", "graph"]:
+            create_eln_file(str(output_path), item_id=item_id, related_item_ids=related_item_ids)
 
         flask_mongo.db.export_tasks.update_one(
             {"task_id": task_id},
@@ -57,12 +66,19 @@ def _do_export(task_id: str, collection_id: str):
         )
 
 
-def _generate_export_in_background(task_id: str, collection_id: str, app):
+def _generate_export_in_background(
+    task_id: str,
+    app,
+    collection_id: str | None = None,
+    item_id: str | None = None,
+    export_type: str = "collection",
+    related_item_ids: list[str] | None = None,
+):
     if app is not None:
         with app.app_context():
-            _do_export(task_id, collection_id)
+            _do_export(task_id, collection_id, item_id, export_type, related_item_ids)
     else:
-        _do_export(task_id, collection_id)
+        _do_export(task_id, collection_id, item_id, export_type, related_item_ids)
 
 
 @EXPORT.route("/collections/<string:collection_id>/export", methods=["POST"])
@@ -85,11 +101,12 @@ def start_collection_export(collection_id: str):
     export_task = ExportTask(
         task_id=task_id,
         collection_id=collection_id,
+        export_type="collection",
         creator_id=creator_id,
         status=ExportStatus.PENDING,
     )
 
-    flask_mongo.db.export_tasks.insert_one(export_task.dict())
+    flask_mongo.db.export_tasks.insert_one(export_task.dict(exclude_none=False))
 
     try:
         app = current_app._get_current_object()
@@ -98,7 +115,7 @@ def start_collection_export(collection_id: str):
 
     export_scheduler.add_job(
         func=_generate_export_in_background,
-        args=[task_id, collection_id, app],
+        args=[task_id, app, collection_id, None, "collection", None],
         job_id=f"export_{task_id}",
     )
 
@@ -150,8 +167,60 @@ def download_export(task_id: str):
     if not file_path or not os.path.exists(file_path):
         return jsonify({"status": "error", "message": "Export file not found"}), 404
 
-    filename = f"{task['collection_id']}.eln"
+    filename = f"{task.get('collection_id') or task.get('item_id')}.eln"
 
     return send_file(
         file_path, as_attachment=True, download_name=filename, mimetype="application/vnd.eln+zip"
     )
+
+
+@EXPORT.route("/samples/<string:item_id>/export", methods=["POST"])
+def start_sample_export(item_id: str):
+    from pydatalab.permissions import get_default_permissions
+
+    item_data = flask_mongo.db.items.find_one(
+        {"item_id": item_id, **get_default_permissions(user_only=False)}
+    )
+    if not item_data:
+        return jsonify({"status": "error", "message": "Sample not found"}), 404
+
+    task_id = str(uuid.uuid4())
+
+    if not CONFIG.TESTING:
+        creator_id = str(current_user.person.immutable_id)
+    else:
+        creator_id = "000000000000000000000000"
+
+    export_type = "sample"
+    related_item_ids = None
+
+    request_data = request.get_json() or {}
+    if request_data.get("include_related") and request_data.get("related_item_ids"):
+        export_type = "graph"
+        related_item_ids = request_data["related_item_ids"]
+
+    export_task = ExportTask(
+        task_id=task_id,
+        collection_id=None,
+        item_id=item_id,
+        export_type=export_type,
+        creator_id=creator_id,
+        status=ExportStatus.PENDING,
+    )
+
+    flask_mongo.db.export_tasks.insert_one(export_task.dict(exclude_none=False))
+
+    try:
+        app = current_app._get_current_object()
+    except RuntimeError:
+        app = None
+
+    export_scheduler.add_job(
+        func=_generate_export_in_background,
+        args=[task_id, app, None, item_id, export_type, related_item_ids],
+        job_id=f"export_{task_id}",
+    )
+
+    return jsonify(
+        {"status": "success", "task_id": task_id, "status_url": f"/exports/{task_id}/status"}
+    ), 202
diff --git a/webapp/src/components/CollectionInformation.vue b/webapp/src/components/CollectionInformation.vue
index b45a24bbb..b4bdf8e98 100644
--- a/webapp/src/components/CollectionInformation.vue
+++ b/webapp/src/components/CollectionInformation.vue
@@ -32,7 +32,7 @@
         ></TinyMceInline>
         <div class="form-row">
           <div class="form-group col">
-            <CollectionExportButton :collection-id="collection_id" />
+            <ExportButton :collection-id="collection_id" />
           </div>
         </div>
       </div>
@@ -66,7 +66,7 @@ import TinyMceInline from "@/components/TinyMceInline";
 import Creators from "@/components/Creators";
 import CollectionRelationshipVisualization from "@/components/CollectionRelationshipVisualization";
 import DynamicDataTable from "@/components/DynamicDataTable";
-import CollectionExportButton from "@/components/CollectionExportButton";
+import ExportButton from "@/components/ExportButton";
 
 export default {
   components: {
@@ -74,7 +74,7 @@ export default {
     Creators,
     CollectionRelationshipVisualization,
     DynamicDataTable,
-    CollectionExportButton,
+    ExportButton,
   },
   props: {
     collection_id: {
diff --git a/webapp/src/components/CollectionExportButton.vue b/webapp/src/components/ExportButton.vue
similarity index 74%
rename from webapp/src/components/CollectionExportButton.vue
rename to webapp/src/components/ExportButton.vue
index 04a897fd0..76e3de19c 100644
--- a/webapp/src/components/CollectionExportButton.vue
+++ b/webapp/src/components/ExportButton.vue
@@ -1,9 +1,9 @@
 <template>
-  <div class="collection-export-button">
+  <div class="export-button">
     <button
       :disabled="isExporting"
       class="btn btn-sm btn-outline-primary"
-      data-testid="collection-export-button"
+      :data-testid="`${exportType}-export-button`"
       @click="handleExport"
     >
       <span v-if="!isExporting"> <i class="fa fa-download"></i> Export as .eln </span>
@@ -13,15 +13,24 @@
 </template>
 
 <script>
-import { startCollectionExport, getExportStatus, getExportDownloadUrl } from "@/server_fetch_utils";
+import {
+  startCollectionExport,
+  startSampleExport,
+  getExportStatus,
+  getExportDownloadUrl,
+} from "@/server_fetch_utils";
 import { DialogService } from "@/services/DialogService";
 
 export default {
-  name: "CollectionExportButton",
+  name: "ExportButton",
   props: {
     collectionId: {
       type: String,
-      required: true,
+      default: null,
+    },
+    itemId: {
+      type: String,
+      default: null,
     },
   },
   data() {
@@ -31,6 +40,11 @@ export default {
       pollInterval: null,
     };
   },
+  computed: {
+    exportType() {
+      return this.collectionId ? "collection" : "sample";
+    },
+  },
   beforeUnmount() {
     if (this.pollInterval) {
       clearInterval(this.pollInterval);
@@ -42,9 +56,18 @@ export default {
         this.isExporting = true;
         this.exportStatusText = "Starting export...";
 
-        const response = await startCollectionExport(this.collectionId);
-        const taskId = response.task_id;
+        console.log("Export - collectionId:", this.collectionId, "itemId:", this.itemId);
+
+        let response;
+        if (this.collectionId) {
+          response = await startCollectionExport(this.collectionId);
+        } else if (this.itemId) {
+          response = await startSampleExport(this.itemId);
+        } else {
+          throw new Error("Either collectionId or itemId must be provided");
+        }
 
+        const taskId = response.task_id;
         this.pollExportStatus(taskId);
       } catch (error) {
         console.error("Export failed:", error);
@@ -69,7 +92,7 @@ export default {
             this.isExporting = false;
             DialogService.alert({
               title: "Export Complete",
-              message: "Your collection has been exported successfully.",
+              message: `Your ${this.exportType} has been exported successfully.`,
               type: "info",
             });
           } else if (status.status === "error") {
diff --git a/webapp/src/components/SampleGraphExportModal.vue b/webapp/src/components/SampleGraphExportModal.vue
new file mode 100644
index 000000000..df6683834
--- /dev/null
+++ b/webapp/src/components/SampleGraphExportModal.vue
@@ -0,0 +1,212 @@
+<template>
+  <div ref="modalElement" class="modal fade" tabindex="-1" role="dialog" aria-hidden="true">
+    <div class="modal-dialog modal-lg" role="document">
+      <div class="modal-content">
+        <div class="modal-header">
+          <h5 class="modal-title">Export Sample and Related Items</h5>
+          <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+            <span aria-hidden="true">&times;</span>
+          </button>
+        </div>
+        <div class="modal-body">
+          <div v-if="isLoading" class="text-center">
+            <i class="fa fa-spinner fa-spin fa-2x"></i>
+            <p class="mt-2">Loading related samples...</p>
+          </div>
+          <div v-else-if="relatedSamples.length === 0">
+            <p>No related samples found for this item.</p>
+          </div>
+          <div v-else>
+            <p>Select the samples you want to include in the export:</p>
+            <div class="form-check">
+              <input
+                id="select-all"
+                v-model="selectAll"
+                type="checkbox"
+                class="form-check-input"
+                @change="toggleSelectAll"
+              />
+              <label class="form-check-label" for="select-all">
+                <strong>Select All</strong>
+              </label>
+            </div>
+            <hr />
+            <div v-for="sample in relatedSamples" :key="sample.id" class="form-check">
+              <input
+                :id="`sample-${sample.id}`"
+                v-model="selectedSampleIds"
+                type="checkbox"
+                class="form-check-input"
+                :value="sample.id"
+              />
+              <label class="form-check-label" :for="`sample-${sample.id}`">
+                {{ sample.name }} ({{ sample.id }})
+                <span v-if="sample.type" class="badge badge-secondary ml-2">
+                  {{ sample.type }}
+                </span>
+              </label>
+            </div>
+          </div>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+          <button
+            type="button"
+            class="btn btn-primary"
+            :disabled="isExporting || selectedSampleIds.length === 0"
+            @click="handleExport"
+          >
+            <span v-if="!isExporting">
+              <i class="fa fa-download"></i> Export Selected ({{ selectedSampleIds.length }})
+            </span>
+            <span v-else> <i class="fa fa-spinner fa-spin"></i> Exporting... </span>
+          </button>
+        </div>
+      </div>
+    </div>
+  </div>
+</template>
+
+<script>
+import {
+  getItemGraph,
+  startSampleExport,
+  getExportStatus,
+  getExportDownloadUrl,
+} from "@/server_fetch_utils";
+import { DialogService } from "@/services/DialogService";
+
+export default {
+  name: "SampleGraphExportModal",
+  props: {
+    itemId: {
+      type: String,
+      required: true,
+    },
+  },
+  data() {
+    return {
+      isLoading: false,
+      isExporting: false,
+      relatedSamples: [],
+      selectedSampleIds: [],
+      selectAll: false,
+      pollInterval: null,
+      modalInstance: null,
+    };
+  },
+  mounted() {
+    this.modalInstance = new window.bootstrap.Modal(this.$refs.modalElement);
+  },
+  beforeUnmount() {
+    if (this.pollInterval) {
+      clearInterval(this.pollInterval);
+    }
+    if (this.modalInstance) {
+      this.modalInstance.dispose();
+    }
+  },
+  methods: {
+    async loadRelatedSamples() {
+      try {
+        this.isLoading = true;
+        const graphData = await getItemGraph({ item_id: this.itemId });
+
+        this.relatedSamples = graphData.nodes
+          .filter((node) => node.data.id !== this.itemId)
+          .map((node) => ({
+            id: node.data.id,
+            name: node.data.name || node.data.id,
+            type: node.data.type,
+          }));
+
+        this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
+        this.selectAll = true;
+      } catch (error) {
+        console.error("Failed to load related samples:", error);
+        DialogService.error({
+          title: "Loading Failed",
+          message: "Failed to load related samples. Please try again.",
+        });
+      } finally {
+        this.isLoading = false;
+      }
+    },
+
+    toggleSelectAll() {
+      if (this.selectAll) {
+        this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
+      } else {
+        this.selectedSampleIds = [];
+      }
+    },
+
+    async handleExport() {
+      try {
+        this.isExporting = true;
+
+        const response = await startSampleExport(this.itemId, {
+          include_related: true,
+          related_item_ids: this.selectedSampleIds,
+        });
+        const taskId = response.task_id;
+
+        this.pollExportStatus(taskId);
+      } catch (error) {
+        console.error("Export failed:", error);
+        this.isExporting = false;
+        DialogService.error({
+          title: "Export Failed",
+          message: error.message || "Failed to start the export. Please try again.",
+        });
+      }
+    },
+
+    async pollExportStatus(taskId) {
+      this.pollInterval = setInterval(async () => {
+        try {
+          const status = await getExportStatus(taskId);
+
+          if (status.status === "ready") {
+            clearInterval(this.pollInterval);
+            this.downloadExport(taskId);
+            this.isExporting = false;
+            this.modalInstance.hide();
+            DialogService.alert({
+              title: "Export Complete",
+              message: "Your samples have been exported successfully.",
+              type: "info",
+            });
+          } else if (status.status === "error") {
+            clearInterval(this.pollInterval);
+            this.isExporting = false;
+            DialogService.error({
+              title: "Export Failed",
+              message: status.error_message || "An error occurred during export.",
+            });
+          }
+        } catch (error) {
+          clearInterval(this.pollInterval);
+          this.isExporting = false;
+          console.error("Error polling export status:", error);
+        }
+      }, 2000);
+    },
+
+    downloadExport(taskId) {
+      const downloadUrl = getExportDownloadUrl(taskId);
+      const link = document.createElement("a");
+      link.href = downloadUrl;
+      link.style.display = "none";
+      document.body.appendChild(link);
+      link.click();
+      document.body.removeChild(link);
+    },
+
+    show() {
+      this.modalInstance.show();
+      this.loadRelatedSamples();
+    },
+  },
+};
+</script>
diff --git a/webapp/src/components/SampleInformation.vue b/webapp/src/components/SampleInformation.vue
index 25f18135c..be5f631e7 100644
--- a/webapp/src/components/SampleInformation.vue
+++ b/webapp/src/components/SampleInformation.vue
@@ -45,6 +45,9 @@
             <label id="samp-description-label">Description</label>
             <TinyMceInline v-model="SampleDescription" aria-labelledby="samp-description-label" />
           </div>
+          <div class="col">
+            <ExportButton :item-id="item_id" />
+          </div>
         </div>
       </div>
       <div class="col-md-4">
@@ -68,9 +71,11 @@ import TinyMceInline from "@/components/TinyMceInline";
 import SynthesisInformation from "@/components/SynthesisInformation";
 import TableOfContents from "@/components/TableOfContents";
 import ItemRelationshipVisualization from "@/components/ItemRelationshipVisualization";
+import ExportButton from "@/components/ExportButton";
 
 export default {
   components: {
+    ExportButton,
     ChemFormulaInput,
     TinyMceInline,
     SynthesisInformation,
diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index a65383c74..db5392efe 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -787,13 +787,15 @@ export async function getItemGraph({ item_id = null, collection_id = null } = {}
   return fetch_get(url)
     .then(function (response_json) {
       store.commit("setItemGraph", { nodes: response_json.nodes, edges: response_json.edges });
+      return response_json;
     })
-    .catch((error) =>
+    .catch((error) => {
       DialogService.error({
         title: "Graph Retrieval Failed",
         message: `Error retrieving item graph from API: ${error}`,
-      }),
-    );
+      });
+      throw error;
+    });
 }
 
 export async function requestNewAPIKey() {
@@ -920,3 +922,17 @@ export async function getExportStatus(task_id) {
 export function getExportDownloadUrl(task_id) {
   return `${API_URL}/exports/${task_id}/download`;
 }
+
+export async function startSampleExport(item_id, options = {}) {
+  return fetch_post(`${API_URL}/samples/${item_id}/export`, options)
+    .then(function (response_json) {
+      return response_json;
+    })
+    .catch((error) => {
+      DialogService.error({
+        title: "Export Failed",
+        message: `Failed to start sample export: ${error}`,
+      });
+      throw error;
+    });
+}

From 40b914f44dcf7b0ee35daaea1317c34fd6b414c8 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Thu, 30 Oct 2025 12:08:51 +0100
Subject: [PATCH 11/26] Dropdown for sample only or related sample + col

---
 .../src/components/SampleGraphExportModal.vue | 219 ++++++++++++------
 webapp/src/components/SampleInformation.vue   |  36 ++-
 2 files changed, 184 insertions(+), 71 deletions(-)

diff --git a/webapp/src/components/SampleGraphExportModal.vue b/webapp/src/components/SampleGraphExportModal.vue
index df6683834..a16dfdd50 100644
--- a/webapp/src/components/SampleGraphExportModal.vue
+++ b/webapp/src/components/SampleGraphExportModal.vue
@@ -1,83 +1,119 @@
 <template>
-  <div ref="modalElement" class="modal fade" tabindex="-1" role="dialog" aria-hidden="true">
-    <div class="modal-dialog modal-lg" role="document">
-      <div class="modal-content">
-        <div class="modal-header">
-          <h5 class="modal-title">Export Sample and Related Items</h5>
-          <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-            <span aria-hidden="true">&times;</span>
-          </button>
+  <Modal v-model="isModalOpen" :is-large="true">
+    <template #header>Export Sample and Related Items</template>
+
+    <template #body>
+      <div v-if="isLoading" class="text-center">
+        <i class="fa fa-spinner fa-spin fa-2x"></i>
+        <p class="mt-2">Loading related samples...</p>
+      </div>
+      <div v-else-if="relatedSamples.length === 0">
+        <p>No related samples found for this item.</p>
+      </div>
+      <div v-else>
+        <p>Select the samples you want to include in the export:</p>
+        <div class="form-check">
+          <input
+            id="select-all"
+            v-model="selectAll"
+            type="checkbox"
+            class="form-check-input"
+            @change="toggleSelectAll"
+          />
+          <label class="form-check-label" for="select-all">
+            <strong>Select All</strong>
+          </label>
         </div>
-        <div class="modal-body">
-          <div v-if="isLoading" class="text-center">
-            <i class="fa fa-spinner fa-spin fa-2x"></i>
-            <p class="mt-2">Loading related samples...</p>
-          </div>
-          <div v-else-if="relatedSamples.length === 0">
-            <p>No related samples found for this item.</p>
+        <hr />
+        <div v-for="sample in relatedSamples" :key="sample.id" class="form-check">
+          <input
+            :id="`sample-${sample.id}`"
+            v-model="selectedSampleIds"
+            type="checkbox"
+            class="form-check-input"
+            :value="sample.id"
+          />
+          <label class="form-check-label" :for="`sample-${sample.id}`">
+            {{ sample.name }} ({{ sample.id }})
+            <span v-if="sample.type" class="badge badge-secondary ml-2">
+              {{ sample.type }}
+            </span>
+          </label>
+        </div>
+        <hr />
+        <div class="form-check">
+          <input
+            id="create-collection"
+            v-model="createCollection"
+            type="checkbox"
+            class="form-check-input"
+          />
+          <label class="form-check-label" for="create-collection">
+            <strong>Create a collection from selected samples</strong>
+          </label>
+        </div>
+        <div v-if="createCollection" class="mt-3">
+          <div class="form-group">
+            <label for="collection-id">Collection ID</label>
+            <input
+              id="collection-id"
+              v-model="collectionId"
+              type="text"
+              class="form-control"
+              placeholder="Enter collection ID"
+            />
           </div>
-          <div v-else>
-            <p>Select the samples you want to include in the export:</p>
-            <div class="form-check">
-              <input
-                id="select-all"
-                v-model="selectAll"
-                type="checkbox"
-                class="form-check-input"
-                @change="toggleSelectAll"
-              />
-              <label class="form-check-label" for="select-all">
-                <strong>Select All</strong>
-              </label>
-            </div>
-            <hr />
-            <div v-for="sample in relatedSamples" :key="sample.id" class="form-check">
-              <input
-                :id="`sample-${sample.id}`"
-                v-model="selectedSampleIds"
-                type="checkbox"
-                class="form-check-input"
-                :value="sample.id"
-              />
-              <label class="form-check-label" :for="`sample-${sample.id}`">
-                {{ sample.name }} ({{ sample.id }})
-                <span v-if="sample.type" class="badge badge-secondary ml-2">
-                  {{ sample.type }}
-                </span>
-              </label>
-            </div>
+          <div class="form-group">
+            <label for="collection-title">Collection Title</label>
+            <input
+              id="collection-title"
+              v-model="collectionTitle"
+              type="text"
+              class="form-control"
+              placeholder="Enter collection title"
+            />
           </div>
         </div>
-        <div class="modal-footer">
-          <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
-          <button
-            type="button"
-            class="btn btn-primary"
-            :disabled="isExporting || selectedSampleIds.length === 0"
-            @click="handleExport"
-          >
-            <span v-if="!isExporting">
-              <i class="fa fa-download"></i> Export Selected ({{ selectedSampleIds.length }})
-            </span>
-            <span v-else> <i class="fa fa-spinner fa-spin"></i> Exporting... </span>
-          </button>
-        </div>
       </div>
-    </div>
-  </div>
+    </template>
+
+    <template #footer>
+      <button
+        type="button"
+        class="btn btn-primary"
+        :disabled="
+          isExporting ||
+          selectedSampleIds.length === 0 ||
+          (createCollection && (!collectionId || !collectionTitle))
+        "
+        @click="handleExport"
+      >
+        <span v-if="!isExporting">
+          <i class="fa fa-download"></i> Export Selected ({{ selectedSampleIds.length }})
+        </span>
+        <span v-else> <i class="fa fa-spinner fa-spin"></i> Exporting... </span>
+      </button>
+      <button type="button" class="btn btn-secondary" @click="isModalOpen = false">Cancel</button>
+    </template>
+  </Modal>
 </template>
 
 <script>
+import Modal from "@/components/Modal";
 import {
   getItemGraph,
   startSampleExport,
   getExportStatus,
   getExportDownloadUrl,
+  createNewCollection,
 } from "@/server_fetch_utils";
 import { DialogService } from "@/services/DialogService";
 
 export default {
   name: "SampleGraphExportModal",
+  components: {
+    Modal,
+  },
   props: {
     itemId: {
       type: String,
@@ -86,25 +122,32 @@ export default {
   },
   data() {
     return {
+      isModalOpen: false,
       isLoading: false,
       isExporting: false,
       relatedSamples: [],
       selectedSampleIds: [],
       selectAll: false,
       pollInterval: null,
-      modalInstance: null,
+      createCollection: false,
+      collectionId: "",
+      collectionTitle: "",
     };
   },
-  mounted() {
-    this.modalInstance = new window.bootstrap.Modal(this.$refs.modalElement);
+  watch: {
+    isModalOpen(newValue) {
+      if (newValue) {
+        this.loadRelatedSamples();
+      } else {
+        this.relatedSamples = [];
+        this.selectedSampleIds = [];
+      }
+    },
   },
   beforeUnmount() {
     if (this.pollInterval) {
       clearInterval(this.pollInterval);
     }
-    if (this.modalInstance) {
-      this.modalInstance.dispose();
-    }
   },
   methods: {
     async loadRelatedSamples() {
@@ -122,6 +165,9 @@ export default {
 
         this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
         this.selectAll = true;
+        this.createCollection = false;
+        this.collectionId = `${this.itemId}-collection`;
+        this.collectionTitle = `${this.itemId} and related samples`;
       } catch (error) {
         console.error("Failed to load related samples:", error);
         DialogService.error({
@@ -145,6 +191,40 @@ export default {
       try {
         this.isExporting = true;
 
+        if (this.createCollection) {
+          if (!this.collectionId.trim() || !this.collectionTitle.trim()) {
+            DialogService.error({
+              title: "Validation Error",
+              message: "Please enter both collection ID and title.",
+            });
+            this.isExporting = false;
+            return;
+          }
+
+          try {
+            const startingMembers = [
+              { item_id: this.itemId },
+              ...this.selectedSampleIds.map((id) => ({ item_id: id })),
+            ];
+
+            await createNewCollection(this.collectionId, this.collectionTitle, {
+              starting_members: startingMembers,
+            });
+
+            DialogService.alert({
+              title: "Collection Created",
+              message: `Collection "${this.collectionTitle}" created successfully with ${startingMembers.length} items.`,
+              type: "info",
+            });
+          } catch (error) {
+            console.error("Failed to create collection:", error);
+            DialogService.error({
+              title: "Collection Creation Failed",
+              message: "Failed to create collection. Continuing with export...",
+            });
+          }
+        }
+
         const response = await startSampleExport(this.itemId, {
           include_related: true,
           related_item_ids: this.selectedSampleIds,
@@ -171,7 +251,7 @@ export default {
             clearInterval(this.pollInterval);
             this.downloadExport(taskId);
             this.isExporting = false;
-            this.modalInstance.hide();
+            this.isModalOpen = false;
             DialogService.alert({
               title: "Export Complete",
               message: "Your samples have been exported successfully.",
@@ -204,8 +284,7 @@ export default {
     },
 
     show() {
-      this.modalInstance.show();
-      this.loadRelatedSamples();
+      this.isModalOpen = true;
     },
   },
 };
diff --git a/webapp/src/components/SampleInformation.vue b/webapp/src/components/SampleInformation.vue
index be5f631e7..fd7231241 100644
--- a/webapp/src/components/SampleInformation.vue
+++ b/webapp/src/components/SampleInformation.vue
@@ -46,7 +46,28 @@
             <TinyMceInline v-model="SampleDescription" aria-labelledby="samp-description-label" />
           </div>
           <div class="col">
-            <ExportButton :item-id="item_id" />
+            <div class="dropdown">
+              <button
+                class="btn btn-sm btn-outline-primary dropdown-toggle"
+                type="button"
+                data-toggle="dropdown"
+                aria-haspopup="true"
+                aria-expanded="false"
+                @click="isExportDropdownVisible = !isExportDropdownVisible"
+              >
+                <i class="fa fa-download"></i> Export (as .ELN)
+              </button>
+              <div v-show="isExportDropdownVisible" class="dropdown-menu" style="display: block">
+                <a class="dropdown-item" @click="handleSampleExport">
+                  <i class="fa fa-file"></i> Export Sample Only
+                </a>
+                <a class="dropdown-item" @click="handleGraphExport">
+                  <i class="fa fa-project-diagram"></i> Export Related Samples
+                </a>
+              </div>
+            </div>
+            <ExportButton ref="exportButton" :item-id="item_id" style="display: none" />
+            <SampleGraphExportModal ref="graphExportModal" :item-id="item_id" />
           </div>
         </div>
       </div>
@@ -72,9 +93,11 @@ import SynthesisInformation from "@/components/SynthesisInformation";
 import TableOfContents from "@/components/TableOfContents";
 import ItemRelationshipVisualization from "@/components/ItemRelationshipVisualization";
 import ExportButton from "@/components/ExportButton";
+import SampleGraphExportModal from "@/components/SampleGraphExportModal";
 
 export default {
   components: {
+    SampleGraphExportModal,
     ExportButton,
     ChemFormulaInput,
     TinyMceInline,
@@ -99,6 +122,7 @@ export default {
         { title: "Table of Contents", targetID: "table-of-contents" },
         { title: "Synthesis Information", targetID: "synthesis-information" },
       ],
+      isExportDropdownVisible: false,
     };
   },
   computed: {
@@ -111,5 +135,15 @@ export default {
     ItemCreators: createComputedSetterForItemField("creators"),
     Collections: createComputedSetterForItemField("collections"),
   },
+  methods: {
+    handleSampleExport() {
+      this.isExportDropdownVisible = false;
+      this.$refs.exportButton.handleExport();
+    },
+    handleGraphExport() {
+      this.isExportDropdownVisible = false;
+      this.$refs.graphExportModal.show();
+    },
+  },
 };
 </script>

From 58be50f5a612d3d8a7f23aa6e7c961e6787e83f8 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Thu, 30 Oct 2025 12:15:45 +0100
Subject: [PATCH 12/26] Re-add docstring

---
 pydatalab/src/pydatalab/models/export_task.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pydatalab/src/pydatalab/models/export_task.py b/pydatalab/src/pydatalab/models/export_task.py
index 013128449..72be5bf78 100644
--- a/pydatalab/src/pydatalab/models/export_task.py
+++ b/pydatalab/src/pydatalab/models/export_task.py
@@ -5,6 +5,8 @@
 
 
 class ExportStatus(str, Enum):
+    """Status of an export task."""
+
     PENDING = "pending"
     PROCESSING = "processing"
     READY = "ready"
@@ -12,6 +14,8 @@ class ExportStatus(str, Enum):
 
 
 class ExportTask(BaseModel):
+    """Model for an export task."""
+
     task_id: str = Field(..., description="Unique identifier for the export task")
     collection_id: str | None = Field(None, description="ID of the collection being exported")
     item_id: str | None = Field(None, description="ID of the sample being exported")

From e3054d63336201fb15b54fa398ae605cdf2528e6 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Thu, 30 Oct 2025 14:55:40 +0100
Subject: [PATCH 13/26] Fix pytest

---
 pydatalab/tests/server/test_export_utils.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pydatalab/tests/server/test_export_utils.py b/pydatalab/tests/server/test_export_utils.py
index d1599295a..47be3aeb1 100644
--- a/pydatalab/tests/server/test_export_utils.py
+++ b/pydatalab/tests/server/test_export_utils.py
@@ -106,8 +106,7 @@ def test_create_eln_file(self, database, tmp_path, user_id):
         output_path = tmp_path / "test.eln"
 
         try:
-            create_eln_file(collection_id, str(output_path))
-
+            create_eln_file(str(output_path), collection_id)
             assert output_path.exists()
 
             with zipfile.ZipFile(output_path, "r") as zf:

From 8187b86e6adb39ae039b93dabcebd95a32647fd0 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Fri, 31 Oct 2025 12:24:38 +0100
Subject: [PATCH 14/26] Add itemGraph in ExportModal and depth control for
 related items

Add itemGraph in ExportModal and depth control for related items

Add itemGraph in ExportModal and depth control for related items

Use slider to control itemGraph depth

Add cypress component tests

Add cypress component tests

Add cypress component tests

Add cypress component tests

Add cypress component tests

Add cypress component tests
---
 pydatalab/src/pydatalab/export_utils.py       |   3 +
 pydatalab/src/pydatalab/routes/v0_1/export.py |  11 +-
 pydatalab/src/pydatalab/routes/v0_1/graphs.py |  61 ++--
 .../src/components/CollectionInformation.vue  |   7 -
 webapp/src/components/ExportDropdown.vue      |  84 ++++++
 webapp/src/components/ItemGraph.vue           |  17 +-
 .../src/components/SampleGraphExportModal.vue | 272 ++++++++++++------
 webapp/src/components/SampleInformation.vue   |  39 ---
 webapp/src/server_fetch_utils.js              |  32 ++-
 webapp/src/views/CollectionPage.vue           |   4 +
 webapp/src/views/EditPage.vue                 |   9 +
 11 files changed, 373 insertions(+), 166 deletions(-)
 create mode 100644 webapp/src/components/ExportDropdown.vue

diff --git a/pydatalab/src/pydatalab/export_utils.py b/pydatalab/src/pydatalab/export_utils.py
index 7f8f560f8..4b33b6b6f 100644
--- a/pydatalab/src/pydatalab/export_utils.py
+++ b/pydatalab/src/pydatalab/export_utils.py
@@ -112,6 +112,9 @@ def create_eln_file(
     item_id: str | None = None,
     related_item_ids: list[str] | None = None,
 ) -> None:
+    if not collection_id and not item_id:
+        raise ValueError("Either collection_id or item_id must be provided")
+
     if collection_id:
         collection_data = flask_mongo.db.collections.find_one({"collection_id": collection_id})
         if not collection_data:
diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
index 73557f2ea..0c5c3a67c 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/export.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -195,9 +195,16 @@ def start_sample_export(item_id: str):
     related_item_ids = None
 
     request_data = request.get_json() or {}
-    if request_data.get("include_related") and request_data.get("related_item_ids"):
+    if request_data.get("include_related"):
+        related_item_ids = request_data.get("related_item_ids", [])
+        if not related_item_ids:
+            return jsonify(
+                {
+                    "status": "error",
+                    "message": "related_item_ids required when include_related is true",
+                }
+            ), 400
         export_type = "graph"
-        related_item_ids = request_data["related_item_ids"]
 
     export_task = ExportTask(
         task_id=task_id,
diff --git a/pydatalab/src/pydatalab/routes/v0_1/graphs.py b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
index f54bea141..705d702ce 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/graphs.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/graphs.py
@@ -17,11 +17,13 @@ def get_graph_cy_format(
     item_id: str | None = None,
     collection_id: str | None = None,
     hide_collections: bool = True,
+    max_depth: int = 1,
 ):
     collection_id = request.args.get("collection_id", type=str)
     hide_collections = request.args.get(
         "hide_collections", default=True, type=lambda v: v.lower() == "true"
     )
+    max_depth = request.args.get("max_depth", default=1, type=int)
 
     if item_id is None:
         if collection_id is not None:
@@ -67,42 +69,59 @@ def get_graph_cy_format(
                 404,
             )
 
-        all_documents = [main_item]
         node_ids = {item_id}
+        all_documents = [main_item]
 
-        for relationship in main_item.get("relationships", []) or []:
-            if relationship.get("item_id"):
-                node_ids.add(relationship["item_id"])
+        def add_related_items(current_item_id: str, current_depth: int):
+            if current_depth > max_depth:
+                return
 
-        incoming_items = list(
-            flask_mongo.db.items.find(
+            current_item = flask_mongo.db.items.find_one(
                 {
-                    "$and": [
-                        {"relationships": {"$elemMatch": {"item_id": item_id}}},
-                        get_default_permissions(user_only=False),
-                    ]
+                    "item_id": current_item_id,
+                    **get_default_permissions(user_only=False),
                 },
                 projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
             )
-        )
-
-        for doc in incoming_items:
-            node_ids.add(doc["item_id"])
 
-        all_documents.extend(incoming_items)
-
-        ids_to_fetch = node_ids - {doc["item_id"] for doc in all_documents}
-        if ids_to_fetch:
-            referenced_items = list(
+            if not current_item:
+                return
+
+            for relationship in current_item.get("relationships", []) or []:
+                if relationship.get("item_id") and relationship["item_id"] not in node_ids:
+                    node_ids.add(relationship["item_id"])
+                    related_item = flask_mongo.db.items.find_one(
+                        {
+                            "item_id": relationship["item_id"],
+                            **get_default_permissions(user_only=False),
+                        },
+                        projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
+                    )
+                    if related_item:
+                        all_documents.append(related_item)
+                        add_related_items(relationship["item_id"], current_depth + 1)
+
+            incoming_items = list(
                 flask_mongo.db.items.find(
                     {
-                        "item_id": {"$in": list(ids_to_fetch)},
+                        "relationships": {
+                            "$elemMatch": {
+                                "item_id": current_item_id,
+                            }
+                        },
                         **get_default_permissions(user_only=False),
                     },
                     projection={"item_id": 1, "name": 1, "type": 1, "relationships": 1},
                 )
             )
-            all_documents.extend(referenced_items)
+
+            for incoming_item in incoming_items:
+                if incoming_item["item_id"] not in node_ids:
+                    node_ids.add(incoming_item["item_id"])
+                    all_documents.append(incoming_item)
+                    add_related_items(incoming_item["item_id"], current_depth + 1)
+
+        add_related_items(item_id, 1)
 
     nodes = []
     edges = []
diff --git a/webapp/src/components/CollectionInformation.vue b/webapp/src/components/CollectionInformation.vue
index b4bdf8e98..eed84d347 100644
--- a/webapp/src/components/CollectionInformation.vue
+++ b/webapp/src/components/CollectionInformation.vue
@@ -30,11 +30,6 @@
           v-model="CollectionDescription"
           aria-labelledby="description-label"
         ></TinyMceInline>
-        <div class="form-row">
-          <div class="form-group col">
-            <ExportButton :collection-id="collection_id" />
-          </div>
-        </div>
       </div>
       <div class="col-md-4">
         <CollectionRelationshipVisualization :collection_id="collection_id" />
@@ -66,7 +61,6 @@ import TinyMceInline from "@/components/TinyMceInline";
 import Creators from "@/components/Creators";
 import CollectionRelationshipVisualization from "@/components/CollectionRelationshipVisualization";
 import DynamicDataTable from "@/components/DynamicDataTable";
-import ExportButton from "@/components/ExportButton";
 
 export default {
   components: {
@@ -74,7 +68,6 @@ export default {
     Creators,
     CollectionRelationshipVisualization,
     DynamicDataTable,
-    ExportButton,
   },
   props: {
     collection_id: {
diff --git a/webapp/src/components/ExportDropdown.vue b/webapp/src/components/ExportDropdown.vue
new file mode 100644
index 000000000..161c21d67
--- /dev/null
+++ b/webapp/src/components/ExportDropdown.vue
@@ -0,0 +1,84 @@
+<template>
+  <div class="nav-item dropdown">
+    <a
+      class="nav-link dropdown-toggle"
+      role="button"
+      data-toggle="dropdown"
+      aria-haspopup="true"
+      aria-expanded="false"
+      @click="isDropdownVisible = !isDropdownVisible"
+    >
+      <i class="fa fa-download"></i> Export
+    </a>
+    <div v-show="isDropdownVisible" class="dropdown-menu" style="display: block">
+      <a class="dropdown-item" @click="handleSimpleExport">
+        <i class="fa fa-file"></i> Export {{ itemTypeLabel }} Only
+      </a>
+      <a v-if="itemType === 'samples'" class="dropdown-item" @click="handleGraphExport">
+        <i class="fa fa-project-diagram"></i> Export Related Samples
+      </a>
+    </div>
+    <ExportButton
+      ref="exportButton"
+      :item-id="itemId"
+      :collection-id="collectionId"
+      style="display: none"
+    />
+    <SampleGraphExportModal
+      v-if="itemType === 'samples'"
+      ref="graphExportModal"
+      :item-id="itemId"
+    />
+  </div>
+</template>
+
+<script>
+import ExportButton from "@/components/ExportButton";
+import SampleGraphExportModal from "@/components/SampleGraphExportModal";
+
+export default {
+  name: "ExportDropdown",
+  components: {
+    ExportButton,
+    SampleGraphExportModal,
+  },
+  props: {
+    itemId: {
+      type: String,
+      default: null,
+    },
+    collectionId: {
+      type: String,
+      default: null,
+    },
+    itemType: {
+      type: String,
+      required: true,
+    },
+  },
+  data() {
+    return {
+      isDropdownVisible: false,
+    };
+  },
+  computed: {
+    itemTypeLabel() {
+      const labels = {
+        samples: "Sample",
+        collections: "Collection",
+      };
+      return labels[this.itemType] || "Item";
+    },
+  },
+  methods: {
+    handleSimpleExport() {
+      this.isDropdownVisible = false;
+      this.$refs.exportButton.handleExport();
+    },
+    handleGraphExport() {
+      this.isDropdownVisible = false;
+      this.$refs.graphExportModal.show();
+    },
+  },
+};
+</script>
diff --git a/webapp/src/components/ItemGraph.vue b/webapp/src/components/ItemGraph.vue
index 583929680..f47cf7caf 100644
--- a/webapp/src/components/ItemGraph.vue
+++ b/webapp/src/components/ItemGraph.vue
@@ -110,7 +110,7 @@
       </div>
     </div>
   </div>
-  <div id="cy" v-bind="$attrs" />
+  <div ref="cyContainer" v-bind="$attrs" />
 </template>
 
 <script>
@@ -195,6 +195,7 @@ export default {
       layoutIsRunning: true,
     };
   },
+
   watch: {
     graphData() {
       this.generateCyNetworkPlot();
@@ -216,6 +217,13 @@ export default {
         .update();
     },
   },
+  mounted() {
+    if (this.graphData) {
+      this.$nextTick(() => {
+        this.generateCyNetworkPlot();
+      });
+    }
+  },
   async created() {
     if (typeof this.cy !== "undefined") {
       this.generateCyNetworkPlot();
@@ -248,8 +256,13 @@ export default {
       if (!this.graphData) {
         return;
       }
+      const cyElement = this.$refs.cyContainer;
+      if (!cyElement) {
+        console.warn("Cytoscape container not ready");
+        return;
+      }
       this.cy = cytoscape({
-        container: document.getElementById("cy"),
+        container: this.$refs.cyContainer,
         elements: this.graphData,
         userPanningEnabled: true,
         minZoom: 0.5,
diff --git a/webapp/src/components/SampleGraphExportModal.vue b/webapp/src/components/SampleGraphExportModal.vue
index a16dfdd50..945915198 100644
--- a/webapp/src/components/SampleGraphExportModal.vue
+++ b/webapp/src/components/SampleGraphExportModal.vue
@@ -1,111 +1,151 @@
 <template>
-  <Modal v-model="isModalOpen" :is-large="true">
-    <template #header>Export Sample and Related Items</template>
+  <div class="modal-enclosure">
+    <Modal v-model="isModalOpen" :is-large="true">
+      <template #header>Export Sample and Related Items</template>
 
-    <template #body>
-      <div v-if="isLoading" class="text-center">
-        <i class="fa fa-spinner fa-spin fa-2x"></i>
-        <p class="mt-2">Loading related samples...</p>
-      </div>
-      <div v-else-if="relatedSamples.length === 0">
-        <p>No related samples found for this item.</p>
-      </div>
-      <div v-else>
-        <p>Select the samples you want to include in the export:</p>
-        <div class="form-check">
-          <input
-            id="select-all"
-            v-model="selectAll"
-            type="checkbox"
-            class="form-check-input"
-            @change="toggleSelectAll"
-          />
-          <label class="form-check-label" for="select-all">
-            <strong>Select All</strong>
-          </label>
+      <template #body>
+        <div class="mb-4">
+          <h6>Relationship Graph</h6>
+          <div class="form-group">
+            <label for="graph-depth"> Graph Depth: {{ graphDepth }} </label>
+            <input
+              id="graph-depth"
+              v-model.number="graphDepth"
+              type="range"
+              min="1"
+              max="5"
+              class="form-control-range"
+              @input="loadGraphWithDepth"
+            />
+          </div>
+          <div style="position: relative; min-height: 300px">
+            <div
+              v-if="isGraphLoading"
+              class="position-absolute w-100 h-100 top-0 start-0 d-flex justify-content-center align-items-center"
+              style="background-color: rgba(255, 255, 255, 0.7); z-index: 100"
+            >
+              <div class="card p-3 shadow-sm">
+                <div class="text-center">
+                  <i class="fa fa-sync fa-spin fa-2x text-primary mb-2"></i>
+                  <p class="mb-0 fw-medium">Loading graph...</p>
+                </div>
+              </div>
+            </div>
+            <ItemGraph
+              :graph-data="graphData"
+              style="height: 300px; width: 100%; border: 1px solid #dee2e6; border-radius: 5px"
+              :default-graph-style="'elk-stress'"
+              :show-options="false"
+            />
+          </div>
+          <hr />
         </div>
-        <hr />
-        <div v-for="sample in relatedSamples" :key="sample.id" class="form-check">
-          <input
-            :id="`sample-${sample.id}`"
-            v-model="selectedSampleIds"
-            type="checkbox"
-            class="form-check-input"
-            :value="sample.id"
-          />
-          <label class="form-check-label" :for="`sample-${sample.id}`">
-            {{ sample.name }} ({{ sample.id }})
-            <span v-if="sample.type" class="badge badge-secondary ml-2">
-              {{ sample.type }}
-            </span>
-          </label>
+        <div v-if="isLoading" class="text-center">
+          <i class="fa fa-spinner fa-spin fa-2x"></i>
+          <p class="mt-2">Loading related samples...</p>
         </div>
-        <hr />
-        <div class="form-check">
-          <input
-            id="create-collection"
-            v-model="createCollection"
-            type="checkbox"
-            class="form-check-input"
-          />
-          <label class="form-check-label" for="create-collection">
-            <strong>Create a collection from selected samples</strong>
-          </label>
+        <div v-else-if="relatedSamples.length === 0">
+          <p>No related samples found for this item.</p>
         </div>
-        <div v-if="createCollection" class="mt-3">
-          <div class="form-group">
-            <label for="collection-id">Collection ID</label>
+        <div v-else>
+          <p>Select the samples you want to include in the export:</p>
+          <div class="form-check">
             <input
-              id="collection-id"
-              v-model="collectionId"
-              type="text"
-              class="form-control"
-              placeholder="Enter collection ID"
+              id="select-all"
+              v-model="selectAll"
+              type="checkbox"
+              class="form-check-input"
+              @change="toggleSelectAll"
             />
+            <label class="form-check-label" for="select-all">
+              <strong>Select All</strong>
+            </label>
           </div>
-          <div class="form-group">
-            <label for="collection-title">Collection Title</label>
+          <hr />
+          <div v-for="sample in relatedSamples" :key="sample.id" class="form-check">
             <input
-              id="collection-title"
-              v-model="collectionTitle"
-              type="text"
-              class="form-control"
-              placeholder="Enter collection title"
+              :id="`sample-${sample.id}`"
+              v-model="selectedSampleIds"
+              type="checkbox"
+              class="form-check-input"
+              :value="sample.id"
             />
+            <label class="form-check-label" :for="`sample-${sample.id}`">
+              {{ sample.name }} ({{ sample.id }})
+              <span v-if="sample.type" class="badge badge-secondary ml-2">
+                {{ sample.type }}
+              </span>
+            </label>
+          </div>
+          <hr />
+          <div class="form-check">
+            <input
+              id="create-collection"
+              v-model="createCollection"
+              type="checkbox"
+              class="form-check-input"
+            />
+            <label class="form-check-label" for="create-collection">
+              <strong>Create a collection from selected samples</strong>
+            </label>
+          </div>
+          <div v-if="createCollection" class="mt-3">
+            <div class="form-group">
+              <label for="collection-id">Collection ID</label>
+              <input
+                id="collection-id"
+                v-model="collectionId"
+                type="text"
+                class="form-control"
+                placeholder="Enter collection ID"
+              />
+            </div>
+            <div class="form-group">
+              <label for="collection-title">Collection Title</label>
+              <input
+                id="collection-title"
+                v-model="collectionTitle"
+                type="text"
+                class="form-control"
+                placeholder="Enter collection title"
+              />
+            </div>
           </div>
         </div>
-      </div>
-    </template>
+      </template>
 
-    <template #footer>
-      <button
-        type="button"
-        class="btn btn-primary"
-        :disabled="
-          isExporting ||
-          selectedSampleIds.length === 0 ||
-          (createCollection && (!collectionId || !collectionTitle))
-        "
-        @click="handleExport"
-      >
-        <span v-if="!isExporting">
-          <i class="fa fa-download"></i> Export Selected ({{ selectedSampleIds.length }})
-        </span>
-        <span v-else> <i class="fa fa-spinner fa-spin"></i> Exporting... </span>
-      </button>
-      <button type="button" class="btn btn-secondary" @click="isModalOpen = false">Cancel</button>
-    </template>
-  </Modal>
+      <template #footer>
+        <button
+          type="button"
+          class="btn btn-primary"
+          :disabled="
+            isExporting ||
+            selectedSampleIds.length === 0 ||
+            (createCollection && (!collectionId || !collectionTitle))
+          "
+          @click="handleExport"
+        >
+          <span v-if="!isExporting">
+            <i class="fa fa-download"></i> Export Selected ({{ selectedSampleIds.length }})
+          </span>
+          <span v-else> <i class="fa fa-spinner fa-spin"></i> Exporting... </span>
+        </button>
+        <button type="button" class="btn btn-secondary" @click="isModalOpen = false">Cancel</button>
+      </template>
+    </Modal>
+  </div>
 </template>
 
 <script>
 import Modal from "@/components/Modal";
+import ItemGraph from "@/components/ItemGraph";
+
 import {
-  getItemGraph,
   startSampleExport,
   getExportStatus,
   getExportDownloadUrl,
   createNewCollection,
+  fetchItemGraph,
 } from "@/server_fetch_utils";
 import { DialogService } from "@/services/DialogService";
 
@@ -113,6 +153,7 @@ export default {
   name: "SampleGraphExportModal",
   components: {
     Modal,
+    ItemGraph,
   },
   props: {
     itemId: {
@@ -128,10 +169,13 @@ export default {
       relatedSamples: [],
       selectedSampleIds: [],
       selectAll: false,
-      pollInterval: null,
       createCollection: false,
       collectionId: "",
       collectionTitle: "",
+      pollInterval: null,
+      graphDepth: 1,
+      graphData: { nodes: [], edges: [] },
+      isGraphLoading: false,
     };
   },
   watch: {
@@ -143,6 +187,10 @@ export default {
         this.selectedSampleIds = [];
       }
     },
+    graphDepth() {
+      this.loadGraphWithDepth();
+      this.loadRelatedSamples();
+    },
   },
   beforeUnmount() {
     if (this.pollInterval) {
@@ -153,18 +201,32 @@ export default {
     async loadRelatedSamples() {
       try {
         this.isLoading = true;
-        const graphData = await getItemGraph({ item_id: this.itemId });
+        const graphData = await fetchItemGraph({
+          item_id: this.itemId,
+          max_depth: this.graphDepth,
+        });
+
+        const previouslySelected = new Set(this.selectedSampleIds);
+        const wasSelectAll = this.selectAll;
 
         this.relatedSamples = graphData.nodes
-          .filter((node) => node.data.id !== this.itemId)
+          .filter((node) => node && node.data && node.data.id && node.data.id !== this.itemId)
           .map((node) => ({
             id: node.data.id,
-            name: node.data.name || node.data.id,
+            name: node.data.name || node.data.label || node.data.id,
             type: node.data.type,
           }));
 
-        this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
-        this.selectAll = true;
+        if (wasSelectAll || previouslySelected.size === 0) {
+          this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
+          this.selectAll = true;
+        } else {
+          this.selectedSampleIds = this.relatedSamples
+            .filter((s) => previouslySelected.has(s.id))
+            .map((s) => s.id);
+          this.selectAll = false;
+        }
+
         this.createCollection = false;
         this.collectionId = `${this.itemId}-collection`;
         this.collectionTitle = `${this.itemId} and related samples`;
@@ -178,7 +240,6 @@ export default {
         this.isLoading = false;
       }
     },
-
     toggleSelectAll() {
       if (this.selectAll) {
         this.selectedSampleIds = this.relatedSamples.map((s) => s.id);
@@ -228,6 +289,7 @@ export default {
         const response = await startSampleExport(this.itemId, {
           include_related: true,
           related_item_ids: this.selectedSampleIds,
+          max_depth: this.graphDepth,
         });
         const taskId = response.task_id;
 
@@ -285,7 +347,31 @@ export default {
 
     show() {
       this.isModalOpen = true;
+      this.loadGraphWithDepth();
+      this.loadRelatedSamples();
+    },
+    async loadGraphWithDepth() {
+      this.isGraphLoading = true;
+      try {
+        const response = await fetchItemGraph({
+          item_id: this.itemId,
+          max_depth: this.graphDepth,
+        });
+        this.graphData = response;
+      } catch (error) {
+        console.error("Error loading graph:", error);
+      } finally {
+        this.isGraphLoading = false;
+      }
     },
   },
 };
 </script>
+
+<style scoped>
+.modal-enclosure :deep(.modal-content) {
+  max-height: 90vh;
+  overflow: scroll;
+  scroll-behavior: smooth;
+}
+</style>
diff --git a/webapp/src/components/SampleInformation.vue b/webapp/src/components/SampleInformation.vue
index fd7231241..25f18135c 100644
--- a/webapp/src/components/SampleInformation.vue
+++ b/webapp/src/components/SampleInformation.vue
@@ -45,30 +45,6 @@
             <label id="samp-description-label">Description</label>
             <TinyMceInline v-model="SampleDescription" aria-labelledby="samp-description-label" />
           </div>
-          <div class="col">
-            <div class="dropdown">
-              <button
-                class="btn btn-sm btn-outline-primary dropdown-toggle"
-                type="button"
-                data-toggle="dropdown"
-                aria-haspopup="true"
-                aria-expanded="false"
-                @click="isExportDropdownVisible = !isExportDropdownVisible"
-              >
-                <i class="fa fa-download"></i> Export (as .ELN)
-              </button>
-              <div v-show="isExportDropdownVisible" class="dropdown-menu" style="display: block">
-                <a class="dropdown-item" @click="handleSampleExport">
-                  <i class="fa fa-file"></i> Export Sample Only
-                </a>
-                <a class="dropdown-item" @click="handleGraphExport">
-                  <i class="fa fa-project-diagram"></i> Export Related Samples
-                </a>
-              </div>
-            </div>
-            <ExportButton ref="exportButton" :item-id="item_id" style="display: none" />
-            <SampleGraphExportModal ref="graphExportModal" :item-id="item_id" />
-          </div>
         </div>
       </div>
       <div class="col-md-4">
@@ -92,13 +68,9 @@ import TinyMceInline from "@/components/TinyMceInline";
 import SynthesisInformation from "@/components/SynthesisInformation";
 import TableOfContents from "@/components/TableOfContents";
 import ItemRelationshipVisualization from "@/components/ItemRelationshipVisualization";
-import ExportButton from "@/components/ExportButton";
-import SampleGraphExportModal from "@/components/SampleGraphExportModal";
 
 export default {
   components: {
-    SampleGraphExportModal,
-    ExportButton,
     ChemFormulaInput,
     TinyMceInline,
     SynthesisInformation,
@@ -122,7 +94,6 @@ export default {
         { title: "Table of Contents", targetID: "table-of-contents" },
         { title: "Synthesis Information", targetID: "synthesis-information" },
       ],
-      isExportDropdownVisible: false,
     };
   },
   computed: {
@@ -135,15 +106,5 @@ export default {
     ItemCreators: createComputedSetterForItemField("creators"),
     Collections: createComputedSetterForItemField("collections"),
   },
-  methods: {
-    handleSampleExport() {
-      this.isExportDropdownVisible = false;
-      this.$refs.exportButton.handleExport();
-    },
-    handleGraphExport() {
-      this.isExportDropdownVisible = false;
-      this.$refs.graphExportModal.show();
-    },
-  },
 };
 </script>
diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index d580d1ef2..bbd3d192d 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -784,12 +784,12 @@ export async function getItemGraph({ item_id = null, collection_id = null } = {}
   if (collection_id != null) {
     url = url + "?collection_id=" + collection_id;
   }
+
   store.commit("setItemGraphIsLoading", true);
   return fetch_get(url)
     .then(function (response_json) {
       store.commit("setItemGraph", { nodes: response_json.nodes, edges: response_json.edges });
       store.commit("setItemGraphIsLoading", false);
-      return response_json;
     })
     .catch((error) => {
       store.commit("setItemGraphIsLoading", false);
@@ -797,7 +797,6 @@ export async function getItemGraph({ item_id = null, collection_id = null } = {}
         title: "Graph Retrieval Failed",
         message: `Error retrieving item graph from API: ${error}`,
       });
-      throw error;
     });
 }
 
@@ -939,3 +938,32 @@ export async function startSampleExport(item_id, options = {}) {
       throw error;
     });
 }
+
+export async function fetchItemGraph({ item_id = null, collection_id = null, max_depth = 1 } = {}) {
+  let url = `${API_URL}/item-graph`;
+  if (item_id != null) {
+    url = url + "/" + item_id;
+  }
+  const params = new URLSearchParams();
+  if (collection_id != null) {
+    params.append("collection_id", collection_id);
+  }
+  if (max_depth != null && max_depth > 1) {
+    params.append("max_depth", max_depth.toString());
+  }
+  if (params.toString()) {
+    url = url + "?" + params.toString();
+  }
+
+  return fetch_get(url)
+    .then(function (response_json) {
+      return { nodes: response_json.nodes, edges: response_json.edges };
+    })
+    .catch((error) => {
+      DialogService.error({
+        title: "Graph Retrieval Failed",
+        message: `Error retrieving item graph from API: ${error}`,
+      });
+      throw error;
+    });
+}
diff --git a/webapp/src/views/CollectionPage.vue b/webapp/src/views/CollectionPage.vue
index 5e8a9d7ec..1f8e04803 100644
--- a/webapp/src/views/CollectionPage.vue
+++ b/webapp/src/views/CollectionPage.vue
@@ -10,6 +10,7 @@
     </span>
     <div class="navbar-nav">
       <a class="nav-item nav-link" href="/">Home</a>
+      <ExportDropdown :collection-id="collection_id" item-type="collections" />
       <a class="nav-item nav-link" :href="collectionApiUrl" target="_blank">
         <font-awesome-icon icon="code" fixed-width /> View JSON
       </a>
@@ -47,10 +48,13 @@ import { itemTypes } from "@/resources.js";
 import { API_URL } from "@/resources.js";
 import { formatDistanceToNow } from "date-fns";
 
+import ExportDropdown from "@/components/ExportDropdown";
+
 export default {
   components: {
     CollectionInformation,
     FormattedItemName,
+    ExportDropdown,
   },
   async beforeRouteLeave(to, from, next) {
     // give warning before leaving the page by the vue router (which would not trigger "beforeunload")
diff --git a/webapp/src/views/EditPage.vue b/webapp/src/views/EditPage.vue
index d674fb2b5..5d02e5e3c 100644
--- a/webapp/src/views/EditPage.vue
+++ b/webapp/src/views/EditPage.vue
@@ -39,6 +39,12 @@
           </template>
         </div>
       </div>
+      <ExportDropdown
+        v-if="itemType === 'samples' || itemType === 'collections'"
+        :item-id="item_id"
+        :collection-id="itemType === 'collections' ? item_id : null"
+        :item-type="itemType"
+      />
       <a class="nav-item nav-link" :href="itemApiUrl" target="_blank">
         <font-awesome-icon icon="code" fixed-width /> View JSON
       </a>
@@ -125,6 +131,8 @@ import { formatDistanceToNow } from "date-fns";
 
 import StyledBlockHelp from "@/components/StyledBlockHelp";
 
+import ExportDropdown from "@/components/ExportDropdown";
+
 export default {
   components: {
     TinyMceInline,
@@ -134,6 +142,7 @@ export default {
     FileSelectModal,
     FormattedItemName,
     StyledBlockHelp,
+    ExportDropdown,
   },
   async beforeRouteLeave(to, from, next) {
     // give warning before leaving the page by the vue router (which would not trigger "beforeunload")

From 1ced5a23d75ffb389d2e43e4e791c4051ab5ffbf Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Thu, 11 Dec 2025 10:04:52 +0100
Subject: [PATCH 15/26] Add asynchronous data block processing with APScheduler

Add asynchronous data block processing with APScheduler

Add asynchronous data block processing with APScheduler
---
 pydatalab/schemas/cell.json                   |  24 +++
 pydatalab/schemas/equipment.json              |  24 +++
 pydatalab/schemas/sample.json                 |  24 +++
 pydatalab/schemas/startingmaterial.json       |  24 +++
 pydatalab/src/pydatalab/models/block_task.py  |  30 ++++
 pydatalab/src/pydatalab/routes/v0_1/blocks.py | 167 ++++++++++++++++--
 .../components/datablocks/NMRInsituBlock.vue  |  18 +-
 .../datablocks/UVVisInsituBlock.vue           |  53 +++++-
 webapp/src/server_fetch_utils.js              |  54 ++++--
 webapp/src/store/index.js                     |   6 +
 10 files changed, 394 insertions(+), 30 deletions(-)
 create mode 100644 pydatalab/src/pydatalab/models/block_task.py

diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index a3a97ed19..3b2392905 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -230,6 +230,8 @@
         },
         "b64_encoded_image": {
           "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object",
           "additionalProperties": {
             "type": "string"
@@ -237,14 +239,18 @@
         },
         "bokeh_plot_data": {
           "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "computed": {
           "title": "Computed",
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "metadata": {
           "title": "Metadata",
+          "datalab_exclude_from_load": true,
           "type": "object"
         }
       },
@@ -357,6 +363,16 @@
         "name"
       ]
     },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
     "AccountStatus": {
       "title": "AccountStatus",
       "description": "A string enum representing the account status.",
@@ -420,6 +436,14 @@
             "type": "string"
           }
         },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
         "account_status": {
           "default": "unverified",
           "allOf": [
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index 9affcfda8..b2954932e 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -194,6 +194,8 @@
         },
         "b64_encoded_image": {
           "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object",
           "additionalProperties": {
             "type": "string"
@@ -201,14 +203,18 @@
         },
         "bokeh_plot_data": {
           "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "computed": {
           "title": "Computed",
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "metadata": {
           "title": "Metadata",
+          "datalab_exclude_from_load": true,
           "type": "object"
         }
       },
@@ -321,6 +327,16 @@
         "name"
       ]
     },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
     "AccountStatus": {
       "title": "AccountStatus",
       "description": "A string enum representing the account status.",
@@ -384,6 +400,14 @@
             "type": "string"
           }
         },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
         "account_status": {
           "default": "unverified",
           "allOf": [
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index 3c8ebfb91..b6e8ec6c1 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -283,6 +283,8 @@
         },
         "b64_encoded_image": {
           "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object",
           "additionalProperties": {
             "type": "string"
@@ -290,14 +292,18 @@
         },
         "bokeh_plot_data": {
           "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "computed": {
           "title": "Computed",
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "metadata": {
           "title": "Metadata",
+          "datalab_exclude_from_load": true,
           "type": "object"
         }
       },
@@ -410,6 +416,16 @@
         "name"
       ]
     },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
     "AccountStatus": {
       "title": "AccountStatus",
       "description": "A string enum representing the account status.",
@@ -473,6 +489,14 @@
             "type": "string"
           }
         },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
         "account_status": {
           "default": "unverified",
           "allOf": [
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index d6f180279..07da52b15 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -336,6 +336,8 @@
         },
         "b64_encoded_image": {
           "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object",
           "additionalProperties": {
             "type": "string"
@@ -343,14 +345,18 @@
         },
         "bokeh_plot_data": {
           "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "computed": {
           "title": "Computed",
+          "datalab_exclude_from_load": true,
           "type": "object"
         },
         "metadata": {
           "title": "Metadata",
+          "datalab_exclude_from_load": true,
           "type": "object"
         }
       },
@@ -463,6 +469,16 @@
         "name"
       ]
     },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
     "AccountStatus": {
       "title": "AccountStatus",
       "description": "A string enum representing the account status.",
@@ -526,6 +542,14 @@
             "type": "string"
           }
         },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
         "account_status": {
           "default": "unverified",
           "allOf": [
diff --git a/pydatalab/src/pydatalab/models/block_task.py b/pydatalab/src/pydatalab/models/block_task.py
new file mode 100644
index 000000000..9b7c9842d
--- /dev/null
+++ b/pydatalab/src/pydatalab/models/block_task.py
@@ -0,0 +1,30 @@
+from datetime import datetime, timezone
+from enum import Enum
+
+from pydantic import BaseModel, Field
+
+
+class BlockProcessingStatus(str, Enum):
+    PENDING = "pending"
+    PROCESSING = "processing"
+    READY = "ready"
+    ERROR = "error"
+
+
+class BlockTask(BaseModel):
+    task_id: str = Field(..., description="Unique identifier for the block processing task")
+    item_id: str = Field(..., description="ID of the item containing the block")
+    block_id: str = Field(..., description="ID of the block being processed")
+    status: BlockProcessingStatus = Field(
+        default=BlockProcessingStatus.PENDING, description="Current status of the task"
+    )
+    creator_id: str = Field(..., description="ID of the user who created the task")
+    created_at: datetime = Field(
+        default_factory=lambda: datetime.now(tz=timezone.utc),
+        description="When the task was created",
+    )
+    completed_at: datetime | None = Field(None, description="When the task was completed")
+    error_message: str | None = Field(None, description="Error message if status is ERROR")
+
+    class Config:
+        use_enum_values = True
diff --git a/pydatalab/src/pydatalab/routes/v0_1/blocks.py b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
index 131ac56fe..02f2c3576 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/blocks.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
@@ -1,10 +1,68 @@
-from flask import Blueprint, jsonify, request
+import uuid
+from datetime import datetime, timezone
+
+from flask import Blueprint, current_app, jsonify, request
+from flask_login import current_user
 from werkzeug.exceptions import BadRequest, NotImplemented
 
 from pydatalab.apps import BLOCK_TYPES
 from pydatalab.blocks.base import DataBlock
+from pydatalab.config import CONFIG
+from pydatalab.models.block_task import BlockProcessingStatus, BlockTask
 from pydatalab.mongo import flask_mongo
 from pydatalab.permissions import active_users_or_get_only, get_default_permissions
+from pydatalab.scheduler import export_scheduler
+
+
+def _process_block_async_internal(task_id: str, block_data: dict, event_data: dict | None):
+    try:
+        flask_mongo.db.block_tasks.update_one(
+            {"task_id": task_id}, {"$set": {"status": BlockProcessingStatus.PROCESSING}}
+        )
+
+        block_type = block_data["blocktype"]
+        block = BLOCK_TYPES[block_type].from_web(block_data)
+
+        if event_data and not event_data.get("trigger_async", False):
+            try:
+                block.process_events(event_data)
+            except NotImplementedError:
+                pass
+
+        _save_block_to_db(block)
+        block.to_web()
+        _save_block_to_db(block)
+
+        flask_mongo.db.block_tasks.update_one(
+            {"task_id": task_id},
+            {
+                "$set": {
+                    "status": BlockProcessingStatus.READY,
+                    "completed_at": datetime.now(tz=timezone.utc),
+                }
+            },
+        )
+
+    except Exception as e:
+        flask_mongo.db.block_tasks.update_one(
+            {"task_id": task_id},
+            {
+                "$set": {
+                    "status": BlockProcessingStatus.ERROR,
+                    "error_message": str(e),
+                    "completed_at": datetime.now(tz=timezone.utc),
+                }
+            },
+        )
+
+
+def _process_block_async(task_id: str, block_data: dict, event_data: dict | None, app):
+    if app is not None:
+        with app.app_context():
+            _process_block_async_internal(task_id, block_data, event_data)
+    else:
+        _process_block_async_internal(task_id, block_data, event_data)
+
 
 BLOCKS = Blueprint("blocks", __name__)
 
@@ -189,25 +247,67 @@ def update_block():
 
     block = BLOCK_TYPES[block_type].from_web(block_data)
 
-    if event_data:
+    prefers_async = getattr(BLOCK_TYPES[block_type], "prefers_async", False)
+    trigger_async = event_data and event_data.get("trigger_async", False) if event_data else False
+
+    if prefers_async and trigger_async:
+        task_id = str(uuid.uuid4())
+
+        if not CONFIG.TESTING:
+            creator_id = str(current_user.person.immutable_id)
+        else:
+            creator_id = "000000000000000000000000"
+
+        block_task = BlockTask(
+            task_id=task_id,
+            item_id=block_data["item_id"],
+            block_id=block_data["block_id"],
+            creator_id=creator_id,
+            status=BlockProcessingStatus.PENDING,
+        )
+
+        flask_mongo.db.block_tasks.insert_one(block_task.dict())
+
         try:
-            block.process_events(event_data)
-        except NotImplementedError:
-            pass
+            app = current_app._get_current_object()
+        except RuntimeError:
+            app = None
+
+        export_scheduler.add_job(
+            func=_process_block_async,
+            args=[task_id, block_data, event_data, app],
+            job_id=task_id,
+        )
 
-    # Save state from UI
-    _save_block_to_db(block)
+        return (
+            jsonify(
+                status="success",
+                processing_async=True,
+                task_id=task_id,
+                status_url=f"/blocks/{task_id}/status",
+            ),
+            202,
+        )
+    else:
+        if event_data and not event_data.get("trigger_async", False):
+            try:
+                block.process_events(event_data)
+            except NotImplementedError:
+                pass
 
-    # Reload the block with new UI state
-    new_block_data = block.to_web()
+        # Save state from UI
+        _save_block_to_db(block)
 
-    # Save results to DB
-    _save_block_to_db(block)
+        # Reload the block with new UI state
+        new_block_data = block.to_web()
 
-    return (
-        jsonify(status="success", saved_successfully=True, new_block_data=new_block_data),
-        200,
-    )
+        # Save results to DB
+        _save_block_to_db(block)
+
+        return (
+            jsonify(status="success", saved_successfully=True, new_block_data=new_block_data),
+            200,
+        )
 
 
 @BLOCKS.route("/delete-block/", methods=["POST"])
@@ -283,3 +383,40 @@ def delete_collection_block():
         jsonify({"status": "success"}),
         200,
     )
+
+
+@BLOCKS.route("/blocks/<string:task_id>/status", methods=["GET"])
+def get_block_task_status(task_id: str):
+    task = flask_mongo.db.block_tasks.find_one({"task_id": task_id})
+
+    if not task:
+        return jsonify({"status": "error", "message": "Task not found"}), 404
+
+    response = {
+        "status": task["status"],
+        "task_id": task_id,
+        "created_at": task["created_at"],
+    }
+
+    if task.get("completed_at"):
+        response["completed_at"] = task["completed_at"]
+    if task.get("error_message"):
+        response["error_message"] = task["error_message"]
+
+    if task["status"] == BlockProcessingStatus.READY:
+        item_id = task["item_id"]
+        block_id = task["block_id"]
+
+        item = flask_mongo.db.items.find_one(
+            {"item_id": item_id, **get_default_permissions(user_only=False)},
+            {f"blocks_obj.{block_id}": 1},
+        )
+
+        if item and "blocks_obj" in item and block_id in item["blocks_obj"]:
+            block_data_from_db = item["blocks_obj"][block_id]
+            block_type = block_data_from_db["blocktype"]
+
+            block = BLOCK_TYPES[block_type].from_web(block_data_from_db)
+            response["block_data"] = block.to_web()
+
+    return jsonify(response), 200
diff --git a/webapp/src/components/datablocks/NMRInsituBlock.vue b/webapp/src/components/datablocks/NMRInsituBlock.vue
index 75267302f..a5e93d586 100644
--- a/webapp/src/components/datablocks/NMRInsituBlock.vue
+++ b/webapp/src/components/datablocks/NMRInsituBlock.vue
@@ -243,7 +243,23 @@ export default {
     onFolderChanged() {
       if (this.nmr_folder_name && this.echem_folder_name) {
         this.folderNameError = "";
-        this.updateBlock();
+
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       } else if (this.nmr_folder_name || this.echem_folder_name) {
         this.folderNameError = "Both NMR and Echem folder names are required";
 
diff --git a/webapp/src/components/datablocks/UVVisInsituBlock.vue b/webapp/src/components/datablocks/UVVisInsituBlock.vue
index 18e6dc2b3..108d2bb15 100644
--- a/webapp/src/components/datablocks/UVVisInsituBlock.vue
+++ b/webapp/src/components/datablocks/UVVisInsituBlock.vue
@@ -176,7 +176,23 @@ export default {
     onFolderSelected() {
       if (this.uvvis_folder_name && this.echem_folder_name && this.uvvis_reference_folder_name) {
         this.folderNameError = "";
-        this.updateBlock();
+
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       } else if (
         this.uvvis_folder_name ||
         this.echem_folder_name ||
@@ -190,7 +206,23 @@ export default {
       const parsed = parseFloat(this.scan_time_buffer);
       if (!isNaN(parsed)) {
         this.scan_time = parsed;
-        this.updateBlock();
+
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       }
     },
     onGranularitySubmit() {
@@ -201,7 +233,22 @@ export default {
       if (!isNaN(sampleVal)) this.sample_granularity = sampleVal;
 
       if (!isNaN(dataVal) || !isNaN(sampleVal)) {
-        this.updateBlock();
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       }
     },
     updateBlock() {
diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index bbd3d192d..8ec335c4b 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -26,6 +26,33 @@ export function construct_headers(additional_headers = null) {
   return headers;
 }
 
+function pollBlockStatus(item_id, block_id, task_id) {
+  const pollInterval = setInterval(async () => {
+    try {
+      const response = await fetch_get(`${API_URL}/blocks/${task_id}/status`);
+
+      if (response.status === "ready") {
+        clearInterval(pollInterval);
+        store.commit("updateBlockData", {
+          item_id: item_id,
+          block_id: block_id,
+          block_data: response.block_data,
+        });
+        store.commit("setBlockNotUpdating", block_id);
+        store.commit("setBlockSaved", { block_id: block_id, isSaved: true });
+      } else if (response.status === "error") {
+        clearInterval(pollInterval);
+        store.commit("setBlockNotUpdating", block_id);
+        store.commit("setBlockError", { block_id, error: response.error_message });
+      }
+    } catch (error) {
+      clearInterval(pollInterval);
+      store.commit("setBlockNotUpdating", block_id);
+      store.commit("setBlockError", { block_id, error: String(error) });
+    }
+  }, 2000);
+}
+
 // eslint-disable-next-line no-unused-vars
 function fetch_get(url) {
   const requestOptions = {
@@ -532,17 +559,22 @@ export async function updateBlockFromServer(item_id, block_id, block_data, event
     event_data: event_data,
   })
     .then(function (response_json) {
-      store.commit("updateBlockData", {
-        item_id: item_id,
-        block_id: block_id,
-        block_data: response_json.new_block_data,
-      });
-      store.commit("setBlockNotUpdating", block_id);
-      store.commit("setBlockSaved", {
-        block_id: block_id,
-        isSaved: response_json.saved_successfully,
-      });
-      store.commit("setBlockError", { block_id, error: "" });
+      if (response_json.processing_async) {
+        store.commit("setBlockProcessing", { block_id, task_id: response_json.task_id });
+        pollBlockStatus(item_id, block_id, response_json.task_id);
+      } else {
+        store.commit("updateBlockData", {
+          item_id: item_id,
+          block_id: block_id,
+          block_data: response_json.new_block_data,
+        });
+        store.commit("setBlockNotUpdating", block_id);
+        store.commit("setBlockSaved", {
+          block_id: block_id,
+          isSaved: response_json.saved_successfully,
+        });
+        store.commit("setBlockError", { block_id, error: "" });
+      }
     })
     .catch((error) => {
       // The block component renders errors, so no need to make a dialog here.
diff --git a/webapp/src/store/index.js b/webapp/src/store/index.js
index e78e235de..de7a68935 100644
--- a/webapp/src/store/index.js
+++ b/webapp/src/store/index.js
@@ -371,6 +371,12 @@ export default createStore({
         delete state.block_errors[block_id];
       }
     },
+    setBlockProcessing(state, { block_id, task_id }) {
+      if (!state.blockProcessingTasks) {
+        state.blockProcessingTasks = {};
+      }
+      state.blockProcessingTasks[block_id] = task_id;
+    },
   },
   getters: {
     getItem: (state) => (item_id) => {

From f52407992be7537d0c66d27a2661b9903da6875a Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Fri, 12 Dec 2025 11:56:36 +0100
Subject: [PATCH 16/26] resolve conflicts

---
 webapp/src/server_fetch_utils.js | 63 ++++++++++++++++++--------------
 1 file changed, 35 insertions(+), 28 deletions(-)

diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index c8b5b1781..a1da709b2 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -1033,6 +1033,38 @@ export async function getSchema(type) {
     });
 }
 
+export async function loadItemSchemas() {
+  // Load schemas for all item types and store them in the Vuex store
+  try {
+    const supportedTypes = await getSupportedSchemasList();
+
+    for (const typeInfo of supportedTypes) {
+      try {
+        const schema = await getSchema(typeInfo.id);
+        store.commit("setSchema", { type: typeInfo.id, schema });
+      } catch (error) {
+        console.error(`Failed to load schema for ${typeInfo.id}:`, error);
+      }
+    }
+  } catch (error) {
+    console.error("Failed to get supported schemas list:", error);
+  }
+}
+
+export function saveUserManagers(user_id, managers) {
+  return fetch_patch(`${API_URL}/users/${user_id}/managers`, { managers })
+    .then((response_json) => {
+      if (response_json.status && response_json.status !== "success") {
+        console.warn("Warning: saveUserManagers response:", response_json);
+      }
+      return response_json;
+    })
+    .catch((error) => {
+      console.error("Managers save failed:", error);
+      throw error;
+    });
+}
+
 export async function startCollectionExport(collection_id) {
   return fetch_post(`${API_URL}/collections/${collection_id}/export`, {})
     .then(function (response_json) {
@@ -1075,34 +1107,6 @@ export async function startSampleExport(item_id, options = {}) {
         title: "Export Failed",
         message: `Failed to start sample export: ${error}`,
       });
-export async function loadItemSchemas() {
-  // Load schemas for all item types and store them in the Vuex store
-  try {
-    const supportedTypes = await getSupportedSchemasList();
-
-    for (const typeInfo of supportedTypes) {
-      try {
-        const schema = await getSchema(typeInfo.id);
-        store.commit("setSchema", { type: typeInfo.id, schema });
-      } catch (error) {
-        console.error(`Failed to load schema for ${typeInfo.id}:`, error);
-      }
-    }
-  } catch (error) {
-    console.error("Failed to get supported schemas list:", error);
-  }
-}
-
-export function saveUserManagers(user_id, managers) {
-  return fetch_patch(`${API_URL}/users/${user_id}/managers`, { managers })
-    .then((response_json) => {
-      if (response_json.status && response_json.status !== "success") {
-        console.warn("Warning: saveUserManagers response:", response_json);
-      }
-      return response_json;
-    })
-    .catch((error) => {
-      console.error("Managers save failed:", error);
       throw error;
     });
 }
@@ -1133,6 +1137,9 @@ export async function fetchItemGraph({ item_id = null, collection_id = null, max
         message: `Error retrieving item graph from API: ${error}`,
       });
       throw error;
+    });
+}
+
 export async function getApiConfig() {
   return fetch_get(`${API_URL}/info`)
     .then((response_json) => {

From 49911a081b3f3723f0844a3f912f51dc7ffe1c6c Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Fri, 12 Dec 2025 12:01:29 +0100
Subject: [PATCH 17/26] Add async to XRDInsituBlock.vue

---
 .../components/datablocks/XRDInsituBlock.vue  | 36 +++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/webapp/src/components/datablocks/XRDInsituBlock.vue b/webapp/src/components/datablocks/XRDInsituBlock.vue
index 9043fbd95..12c406cde 100644
--- a/webapp/src/components/datablocks/XRDInsituBlock.vue
+++ b/webapp/src/components/datablocks/XRDInsituBlock.vue
@@ -221,7 +221,24 @@ export default {
         this.time_series_folder_name &&
         (!this.isEchemMode || this.echem_folder_name)
       ) {
-        this.updateBlock();
+        this.folderNameError = "";
+
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       }
     },
     onGranularitySubmit() {
@@ -232,7 +249,22 @@ export default {
       if (!isNaN(sampleVal)) this.sample_granularity = sampleVal;
 
       if (!isNaN(dataVal) || !isNaN(sampleVal)) {
-        this.updateBlock();
+        this.isUpdating = true;
+        const foundFile = this.all_files.find((file) => file.immutable_id === this.file_id);
+        this.folder_name = foundFile?.name || "Folder not found";
+
+        const blockToUpdate = {
+          ...this.$store.state.all_item_data[this.item_id]["blocks_obj"][this.block_id],
+        };
+
+        updateBlockFromServer(this.item_id, this.block_id, blockToUpdate, { trigger_async: true })
+          .then(() => {
+            this.isUpdating = false;
+          })
+          .catch((error) => {
+            this.isUpdating = false;
+            console.error("Error updating block:", error);
+          });
       }
     },
     updateBlock() {

From f0250700b033b72621d636908928eb3d0a758191 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Fri, 12 Dec 2025 12:06:24 +0100
Subject: [PATCH 18/26] resolve conflicts

---
 pydatalab/src/pydatalab/routes/v0_1/blocks.py | 2 +-
 webapp/src/views/EditPage.vue                 | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/pydatalab/src/pydatalab/routes/v0_1/blocks.py b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
index e93ac24c5..68b477551 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/blocks.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
@@ -10,7 +10,6 @@
 from pydatalab.config import CONFIG
 from pydatalab.models.block_task import BlockProcessingStatus, BlockTask
 from pydatalab.mongo import flask_mongo
-
 from pydatalab.permissions import (
     active_users_or_get_only,
     get_default_permissions,
@@ -67,6 +66,7 @@ def _process_block_async(task_id: str, block_data: dict, event_data: dict | None
     else:
         _process_block_async_internal(task_id, block_data, event_data)
 
+
 BLOCKS = Blueprint("blocks", __name__)
 
 
diff --git a/webapp/src/views/EditPage.vue b/webapp/src/views/EditPage.vue
index d0bbdeaa1..1729db9ef 100644
--- a/webapp/src/views/EditPage.vue
+++ b/webapp/src/views/EditPage.vue
@@ -140,6 +140,7 @@ export default {
     FileSelectModal,
     FormattedItemName,
     BlockTooltip,
+    ExportDropdown,
   },
   async beforeRouteLeave(to, from, next) {
     // give warning before leaving the page by the vue router (which would not trigger "beforeunload")

From a22a7c3d01526968f1631eaa74a87715516a12cf Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Mon, 15 Dec 2025 14:00:45 +0100
Subject: [PATCH 19/26] Add block processing 'stages' and display it in the UI

---
 pydatalab/schemas/cell.json                   | 22 ------------------
 pydatalab/schemas/equipment.json              | 21 -----------------
 pydatalab/schemas/sample.json                 | 21 -----------------
 pydatalab/schemas/startingmaterial.json       | 22 ------------------
 pydatalab/src/pydatalab/apps/__init__.py      |  3 ++-
 .../src/pydatalab/apps/_canary/__init__.py    | 16 +++++++++++++
 pydatalab/src/pydatalab/models/block_task.py  | 13 +++++++++++
 pydatalab/src/pydatalab/routes/v0_1/blocks.py | 23 +++++++++++++++++++
 .../components/datablocks/DataBlockBase.vue   | 11 +++++++++
 webapp/src/server_fetch_utils.js              | 12 ++++++++++
 webapp/src/store/index.js                     |  8 +++++++
 11 files changed, 85 insertions(+), 87 deletions(-)

diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index 6d4ec0dba..3b2392905 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -117,14 +117,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/CellStatus"
-        }
-      ]
-    },
     "cell_format": {
       "$ref": "#/definitions/CellFormat"
     },
@@ -677,20 +669,6 @@
         "is_live"
       ]
     },
-    "CellStatus": {
-      "title": "CellStatus",
-      "description": "An enumeration of the status of cells",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "cycled",
-        "shorted",
-        "dismantled",
-        "other"
-      ],
-      "type": "string"
-    },
     "CellFormat": {
       "title": "CellFormat",
       "description": "An enumeration.",
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index 6dc8849f2..b2954932e 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -117,14 +117,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "working",
-      "allOf": [
-        {
-          "$ref": "#/definitions/EquipmentStatus"
-        }
-      ]
-    },
     "serial_numbers": {
       "title": "Serial Numbers",
       "type": "string"
@@ -640,19 +632,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "EquipmentStatus": {
-      "title": "EquipmentStatus",
-      "description": "An enumeration of the status of equipments",
-      "enum": [
-        "working",
-        "broken",
-        "being_fixed",
-        "defunct",
-        "not_being_fixed",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index 75e1672d7..b6e8ec6c1 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -129,14 +129,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/ItemStatus"
-        }
-      ]
-    },
     "chemform": {
       "title": "Chemform",
       "example": [
@@ -729,19 +721,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "ItemStatus": {
-      "title": "ItemStatus",
-      "description": "An enumeration of the status of items",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "completed",
-        "failed",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index 3fc7d778d..07da52b15 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -129,14 +129,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "available",
-      "allOf": [
-        {
-          "$ref": "#/definitions/StartingMaterialsStatus"
-        }
-      ]
-    },
     "barcode": {
       "title": "Barcode",
       "type": "string"
@@ -782,20 +774,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "StartingMaterialsStatus": {
-      "title": "StartingMaterialsStatus",
-      "description": "An enumeration of the status of starting materials",
-      "enum": [
-        "ordered",
-        "disposed",
-        "planned",
-        "available",
-        "unavailable",
-        "exhausted",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/src/pydatalab/apps/__init__.py b/pydatalab/src/pydatalab/apps/__init__.py
index 262c758bb..91ba01adb 100644
--- a/pydatalab/src/pydatalab/apps/__init__.py
+++ b/pydatalab/src/pydatalab/apps/__init__.py
@@ -22,9 +22,10 @@ def load_app_blocks():
 
     try:
         # A dummy block that is used to check that bad blocks do not break the import
-        from pydatalab.apps._canary import CanaryBlock
+        from pydatalab.apps._canary import AsyncCanaryBlock, CanaryBlock
 
         app_blocks.append(CanaryBlock)
+        app_blocks.append(AsyncCanaryBlock)
     except ImportError as e:
         _check_error(e)
 
diff --git a/pydatalab/src/pydatalab/apps/_canary/__init__.py b/pydatalab/src/pydatalab/apps/_canary/__init__.py
index 611935694..c683f5513 100644
--- a/pydatalab/src/pydatalab/apps/_canary/__init__.py
+++ b/pydatalab/src/pydatalab/apps/_canary/__init__.py
@@ -1,6 +1,22 @@
+import time
+
 from pydatalab.blocks.base import DataBlock
 
 raise ImportError("This canary block is only used for internal testing of dynamic block loading.")
 
 
 class CanaryBlock(DataBlock): ...
+
+
+class AsyncCanaryBlock(DataBlock):
+    blocktype = "canary_async"
+    description = "Async canary block for testing asynchronous processing"
+    accepted_file_extensions = []
+    prefers_async = True
+
+    def to_web(self):
+        time.sleep(2)
+        web_dict = super().to_web()
+        web_dict["processing_time"] = "2 seconds"
+        web_dict["test_result"] = "async processing complete"
+        return web_dict
diff --git a/pydatalab/src/pydatalab/models/block_task.py b/pydatalab/src/pydatalab/models/block_task.py
index 9b7c9842d..14e026bd4 100644
--- a/pydatalab/src/pydatalab/models/block_task.py
+++ b/pydatalab/src/pydatalab/models/block_task.py
@@ -1,5 +1,6 @@
 from datetime import datetime, timezone
 from enum import Enum
+from typing import Literal
 
 from pydantic import BaseModel, Field
 
@@ -11,6 +12,14 @@ class BlockProcessingStatus(str, Enum):
     ERROR = "error"
 
 
+class BlockProcessingStage(BaseModel):
+    timestamp: datetime = Field(..., description="When this stage occurred")
+    message: str = Field(..., description="Description of this processing stage")
+    level: Literal["info", "warning", "error"] = Field(
+        default="info", description="Severity level of this stage"
+    )
+
+
 class BlockTask(BaseModel):
     task_id: str = Field(..., description="Unique identifier for the block processing task")
     item_id: str = Field(..., description="ID of the item containing the block")
@@ -25,6 +34,10 @@ class BlockTask(BaseModel):
     )
     completed_at: datetime | None = Field(None, description="When the task was completed")
     error_message: str | None = Field(None, description="Error message if status is ERROR")
+    stages: list[BlockProcessingStage] = Field(
+        default_factory=list,
+        description="Timestamped log of processing stages for incremental progress tracking",
+    )
 
     class Config:
         use_enum_values = True
diff --git a/pydatalab/src/pydatalab/routes/v0_1/blocks.py b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
index 68b477551..a1101c0e2 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/blocks.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
@@ -18,24 +18,44 @@
 
 
 def _process_block_async_internal(task_id: str, block_data: dict, event_data: dict | None):
+    from pydatalab.models.block_task import BlockProcessingStage
+
+    def add_stage(message: str, level: str = "info"):
+        stage = BlockProcessingStage(
+            timestamp=datetime.now(tz=timezone.utc), message=message, level=level
+        )
+        flask_mongo.db.block_tasks.update_one(
+            {"task_id": task_id}, {"$push": {"stages": stage.dict()}}
+        )
+
     try:
         flask_mongo.db.block_tasks.update_one(
             {"task_id": task_id}, {"$set": {"status": BlockProcessingStatus.PROCESSING}}
         )
+        add_stage("Processing started")
 
         block_type = block_data["blocktype"]
+        add_stage(f"Loading {block_type} block from database")
+
         block = BLOCK_TYPES[block_type].from_web(block_data)
 
         if event_data and not event_data.get("trigger_async", False):
+            add_stage("Processing block events")
             try:
                 block.process_events(event_data)
             except NotImplementedError:
                 pass
 
+        add_stage("Saving block state to database")
         _save_block_to_db(block)
+
+        add_stage("Generating visualization data")
         block.to_web()
+
+        add_stage("Saving final results to database")
         _save_block_to_db(block)
 
+        add_stage("Processing completed successfully", level="info")
         flask_mongo.db.block_tasks.update_one(
             {"task_id": task_id},
             {
@@ -47,6 +67,7 @@ def _process_block_async_internal(task_id: str, block_data: dict, event_data: di
         )
 
     except Exception as e:
+        add_stage(f"Error during processing: {str(e)}", level="error")
         flask_mongo.db.block_tasks.update_one(
             {"task_id": task_id},
             {
@@ -401,6 +422,8 @@ def get_block_task_status(task_id: str):
         "created_at": task["created_at"],
     }
 
+    if task.get("stages"):
+        response["stages"] = task["stages"]
     if task.get("completed_at"):
         response["completed_at"] = task["completed_at"]
     if task.get("error_message"):
diff --git a/webapp/src/components/datablocks/DataBlockBase.vue b/webapp/src/components/datablocks/DataBlockBase.vue
index 679459ade..d9cd9175e 100644
--- a/webapp/src/components/datablocks/DataBlockBase.vue
+++ b/webapp/src/components/datablocks/DataBlockBase.vue
@@ -108,6 +108,14 @@
           </li>
         </ul>
       </div>
+      <div
+        v-if="processingInfo"
+        class="alert alert-info d-flex align-items-center ml-3"
+        role="alert"
+      >
+        <font-awesome-icon icon="info-circle" class="mr-2" />
+        {{ processingInfo }}
+      </div>
       <div
         v-if="showOverlay"
         class="position-absolute w-100 h-100 top-0 start-0 d-flex justify-content-center align-items-center"
@@ -201,6 +209,9 @@ export default {
     },
     BlockTitle: createComputedSetterForBlockField("title"),
     BlockDescription: createComputedSetterForBlockField("freeform_comment"),
+    processingInfo() {
+      return this.$store.state.block_infos[this.block_id];
+    },
   },
   mounted() {
     // this is to help toggleExpandBlock() work properly. Resets contentMaxHeight to "none"
diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index a1da709b2..ac4e4fa2c 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -64,6 +64,16 @@ function pollBlockStatus(item_id, block_id, task_id) {
     try {
       const response = await fetch_get(`${API_URL}/blocks/${task_id}/status`);
 
+      if (response.stages && response.stages.length > 0) {
+        const latestStage = response.stages[response.stages.length - 1];
+        console.log(`Block processing stage: ${latestStage.message}`);
+
+        store.commit("setBlockInfo", {
+          block_id,
+          info: latestStage.message,
+        });
+      }
+
       if (response.status === "ready") {
         clearInterval(pollInterval);
         store.commit("updateBlockData", {
@@ -73,10 +83,12 @@ function pollBlockStatus(item_id, block_id, task_id) {
         });
         store.commit("setBlockNotUpdating", block_id);
         store.commit("setBlockSaved", { block_id: block_id, isSaved: true });
+        store.commit("setBlockInfo", { block_id, info: null });
       } else if (response.status === "error") {
         clearInterval(pollInterval);
         store.commit("setBlockNotUpdating", block_id);
         store.commit("setBlockError", { block_id, error: response.error_message });
+        store.commit("setBlockInfo", { block_id, info: null });
       }
     } catch (error) {
       clearInterval(pollInterval);
diff --git a/webapp/src/store/index.js b/webapp/src/store/index.js
index 42435c520..22658137e 100644
--- a/webapp/src/store/index.js
+++ b/webapp/src/store/index.js
@@ -57,6 +57,7 @@ export default createStore({
       },
     },
     block_errors: {},
+    block_infos: {},
     apiConfig: {
       maxUploadBytes: null,
     },
@@ -379,6 +380,13 @@ export default createStore({
         delete state.block_errors[block_id];
       }
     },
+    setBlockInfo(state, { block_id, info = null }) {
+      if (info) {
+        state.block_infos[block_id] = info;
+      } else {
+        delete state.block_infos[block_id];
+      }
+    },
     setBlockProcessing(state, { block_id, task_id }) {
       if (!state.blockProcessingTasks) {
         state.blockProcessingTasks = {};

From 793c9b06004640f52724f679ca7bb1c97b55350e Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Mon, 15 Dec 2025 15:37:55 +0100
Subject: [PATCH 20/26] remove console.log

---
 webapp/src/server_fetch_utils.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index ac4e4fa2c..073a99809 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -66,7 +66,6 @@ function pollBlockStatus(item_id, block_id, task_id) {
 
       if (response.stages && response.stages.length > 0) {
         const latestStage = response.stages[response.stages.length - 1];
-        console.log(`Block processing stage: ${latestStage.message}`);
 
         store.commit("setBlockInfo", {
           block_id,

From cdbdd50aa204ea882993920bc6092306ead6436c Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Mon, 15 Dec 2025 17:03:28 +0100
Subject: [PATCH 21/26] Add status field to JSON schemas

---
 pydatalab/schemas/cells.json              | 796 +++++++++++++++++++++
 pydatalab/schemas/collections.json        | 363 ++++++++++
 pydatalab/schemas/equipment.json          |  21 +
 pydatalab/schemas/samples.json            | 747 ++++++++++++++++++++
 pydatalab/schemas/starting_materials.json | 801 ++++++++++++++++++++++
 5 files changed, 2728 insertions(+)
 create mode 100644 pydatalab/schemas/cells.json
 create mode 100644 pydatalab/schemas/collections.json
 create mode 100644 pydatalab/schemas/samples.json
 create mode 100644 pydatalab/schemas/starting_materials.json

diff --git a/pydatalab/schemas/cells.json b/pydatalab/schemas/cells.json
new file mode 100644
index 000000000..6d4ec0dba
--- /dev/null
+++ b/pydatalab/schemas/cells.json
@@ -0,0 +1,796 @@
+{
+  "title": "Cell",
+  "description": "A model for representing electrochemical cells.",
+  "type": "object",
+  "properties": {
+    "blocks_obj": {
+      "title": "Blocks Obj",
+      "default": {},
+      "type": "object",
+      "additionalProperties": {
+        "$ref": "#/definitions/DataBlockResponse"
+      }
+    },
+    "display_order": {
+      "title": "Display Order",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "collections": {
+      "title": "Collections",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Collection"
+      }
+    },
+    "revision": {
+      "title": "Revision",
+      "default": 1,
+      "type": "integer"
+    },
+    "revisions": {
+      "title": "Revisions",
+      "type": "object"
+    },
+    "creator_ids": {
+      "title": "Creator Ids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "creators": {
+      "title": "Creators",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Person"
+      }
+    },
+    "type": {
+      "title": "Type",
+      "default": "cells",
+      "const": "cells",
+      "pattern": "^cells$",
+      "type": "string"
+    },
+    "immutable_id": {
+      "title": "Immutable ID",
+      "format": "uuid",
+      "type": "string"
+    },
+    "last_modified": {
+      "title": "Last Modified",
+      "type": "string",
+      "format": "date-time"
+    },
+    "relationships": {
+      "title": "Relationships",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/TypedRelationship"
+      }
+    },
+    "refcode": {
+      "title": "Refcode",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "item_id": {
+      "title": "Item Id",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "description": {
+      "title": "Description",
+      "type": "string"
+    },
+    "date": {
+      "title": "Date",
+      "type": "string",
+      "format": "date-time"
+    },
+    "name": {
+      "title": "Name",
+      "type": "string"
+    },
+    "files": {
+      "title": "Files",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/File"
+      }
+    },
+    "file_ObjectIds": {
+      "title": "File Objectids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/CellStatus"
+        }
+      ]
+    },
+    "cell_format": {
+      "$ref": "#/definitions/CellFormat"
+    },
+    "cell_format_description": {
+      "title": "Cell Format Description",
+      "type": "string"
+    },
+    "cell_preparation_description": {
+      "title": "Cell Preparation Description",
+      "type": "string"
+    },
+    "characteristic_mass": {
+      "title": "Characteristic Mass",
+      "type": "number"
+    },
+    "characteristic_chemical_formula": {
+      "title": "Characteristic Chemical Formula",
+      "type": "string"
+    },
+    "characteristic_molar_mass": {
+      "title": "Characteristic Molar Mass",
+      "type": "number"
+    },
+    "positive_electrode": {
+      "title": "Positive Electrode",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/CellComponent"
+      }
+    },
+    "negative_electrode": {
+      "title": "Negative Electrode",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/CellComponent"
+      }
+    },
+    "electrolyte": {
+      "title": "Electrolyte",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/CellComponent"
+      }
+    },
+    "active_ion_charge": {
+      "title": "Active Ion Charge",
+      "default": 1,
+      "type": "number"
+    }
+  },
+  "required": [
+    "item_id"
+  ],
+  "definitions": {
+    "DataBlockResponse": {
+      "title": "DataBlockResponse",
+      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
+      "type": "object",
+      "properties": {
+        "blocktype": {
+          "title": "Blocktype",
+          "type": "string"
+        },
+        "block_id": {
+          "title": "Block Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "type": "string"
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "freeform_comment": {
+          "title": "Freeform Comment",
+          "type": "string"
+        },
+        "file_id": {
+          "title": "File Id",
+          "type": "string"
+        },
+        "file_ids": {
+          "title": "File Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "errors": {
+          "title": "Errors",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "warnings": {
+          "title": "Warnings",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "b64_encoded_image": {
+          "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object",
+          "additionalProperties": {
+            "type": "string"
+          }
+        },
+        "bokeh_plot_data": {
+          "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "computed": {
+          "title": "Computed",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        }
+      },
+      "required": [
+        "blocktype",
+        "block_id"
+      ]
+    },
+    "RelationshipType": {
+      "title": "RelationshipType",
+      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
+      "enum": [
+        "parent",
+        "child",
+        "sibling",
+        "is_part_of",
+        "other"
+      ],
+      "type": "string"
+    },
+    "KnownType": {
+      "title": "KnownType",
+      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
+      "enum": [
+        "samples",
+        "starting_materials",
+        "blocks",
+        "files",
+        "people",
+        "collections"
+      ],
+      "type": "string"
+    },
+    "TypedRelationship": {
+      "title": "TypedRelationship",
+      "type": "object",
+      "properties": {
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "relation": {
+          "$ref": "#/definitions/RelationshipType"
+        },
+        "type": {
+          "$ref": "#/definitions/KnownType"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "IdentityType": {
+      "title": "IdentityType",
+      "description": "A string enum representing the supported verifiable identity types.",
+      "enum": [
+        "email",
+        "orcid",
+        "github"
+      ],
+      "type": "string"
+    },
+    "Identity": {
+      "title": "Identity",
+      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
+      "type": "object",
+      "properties": {
+        "identity_type": {
+          "$ref": "#/definitions/IdentityType"
+        },
+        "identifier": {
+          "title": "Identifier",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "verified": {
+          "title": "Verified",
+          "default": false,
+          "type": "boolean"
+        },
+        "display_name": {
+          "title": "Display Name",
+          "type": "string"
+        }
+      },
+      "required": [
+        "identity_type",
+        "identifier",
+        "name"
+      ]
+    },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
+    "AccountStatus": {
+      "title": "AccountStatus",
+      "description": "A string enum representing the account status.",
+      "enum": [
+        "active",
+        "unverified",
+        "deactivated"
+      ],
+      "type": "string"
+    },
+    "Person": {
+      "title": "Person",
+      "description": "A model that describes an individual and their digital identities.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "default": "people",
+          "const": "people",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "identities": {
+          "title": "Identities",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Identity"
+          }
+        },
+        "display_name": {
+          "title": "Display Name",
+          "minLength": 1,
+          "maxLength": 150,
+          "type": "string"
+        },
+        "contact_email": {
+          "title": "Contact Email",
+          "type": "string",
+          "format": "email"
+        },
+        "managers": {
+          "title": "Managers",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
+        "account_status": {
+          "default": "unverified",
+          "allOf": [
+            {
+              "$ref": "#/definitions/AccountStatus"
+            }
+          ]
+        }
+      }
+    },
+    "Collection": {
+      "title": "Collection",
+      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
+      "type": "object",
+      "properties": {
+        "blocks_obj": {
+          "title": "Blocks Obj",
+          "default": {},
+          "type": "object",
+          "additionalProperties": {
+            "$ref": "#/definitions/DataBlockResponse"
+          }
+        },
+        "display_order": {
+          "title": "Display Order",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "collections",
+          "const": "collections",
+          "pattern": "^collections$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "num_items": {
+          "title": "Num Items",
+          "type": "integer"
+        }
+      }
+    },
+    "File": {
+      "title": "File",
+      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
+      "type": "object",
+      "properties": {
+        "revision": {
+          "title": "Revision",
+          "default": 1,
+          "type": "integer"
+        },
+        "revisions": {
+          "title": "Revisions",
+          "type": "object"
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "files",
+          "const": "files",
+          "pattern": "^files$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "size": {
+          "title": "Size",
+          "type": "integer"
+        },
+        "last_modified_remote": {
+          "title": "Last Modified Remote",
+          "type": "string",
+          "format": "date-time"
+        },
+        "item_ids": {
+          "title": "Item Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "blocks": {
+          "title": "Blocks",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "extension": {
+          "title": "Extension",
+          "type": "string"
+        },
+        "original_name": {
+          "title": "Original Name",
+          "type": "string"
+        },
+        "location": {
+          "title": "Location",
+          "type": "string"
+        },
+        "url_path": {
+          "title": "Url Path",
+          "type": "string"
+        },
+        "source": {
+          "title": "Source",
+          "type": "string"
+        },
+        "time_added": {
+          "title": "Time Added",
+          "type": "string",
+          "format": "date-time"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "type": "object"
+        },
+        "representation": {
+          "title": "Representation"
+        },
+        "source_server_name": {
+          "title": "Source Server Name",
+          "type": "string"
+        },
+        "source_path": {
+          "title": "Source Path",
+          "type": "string"
+        },
+        "is_live": {
+          "title": "Is Live",
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "item_ids",
+        "blocks",
+        "name",
+        "extension",
+        "time_added",
+        "is_live"
+      ]
+    },
+    "CellStatus": {
+      "title": "CellStatus",
+      "description": "An enumeration of the status of cells",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "cycled",
+        "shorted",
+        "dismantled",
+        "other"
+      ],
+      "type": "string"
+    },
+    "CellFormat": {
+      "title": "CellFormat",
+      "description": "An enumeration.",
+      "enum": [
+        "coin",
+        "pouch",
+        "in situ (XRD)",
+        "in situ (NMR)",
+        "in situ (SQUID)",
+        "in situ (optical)",
+        "swagelok",
+        "cylindrical",
+        "other"
+      ],
+      "type": "string"
+    },
+    "EntryReference": {
+      "title": "EntryReference",
+      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "InlineSubstance": {
+      "title": "InlineSubstance",
+      "type": "object",
+      "properties": {
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "chemform": {
+          "title": "Chemform",
+          "type": "string"
+        }
+      },
+      "required": [
+        "name"
+      ]
+    },
+    "CellComponent": {
+      "title": "CellComponent",
+      "description": "A constituent of a sample.",
+      "type": "object",
+      "properties": {
+        "item": {
+          "title": "Item",
+          "anyOf": [
+            {
+              "$ref": "#/definitions/EntryReference"
+            },
+            {
+              "$ref": "#/definitions/InlineSubstance"
+            }
+          ]
+        },
+        "quantity": {
+          "title": "Quantity",
+          "minimum": 0,
+          "type": "number"
+        },
+        "unit": {
+          "title": "Unit",
+          "default": "g",
+          "type": "string"
+        }
+      },
+      "required": [
+        "item",
+        "quantity"
+      ]
+    }
+  }
+}
\ No newline at end of file
diff --git a/pydatalab/schemas/collections.json b/pydatalab/schemas/collections.json
new file mode 100644
index 000000000..776240bce
--- /dev/null
+++ b/pydatalab/schemas/collections.json
@@ -0,0 +1,363 @@
+{
+  "title": "Collection",
+  "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
+  "type": "object",
+  "properties": {
+    "blocks_obj": {
+      "title": "Blocks Obj",
+      "default": {},
+      "type": "object",
+      "additionalProperties": {
+        "$ref": "#/definitions/DataBlockResponse"
+      }
+    },
+    "display_order": {
+      "title": "Display Order",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "creator_ids": {
+      "title": "Creator Ids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "creators": {
+      "title": "Creators",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Person"
+      }
+    },
+    "type": {
+      "title": "Type",
+      "default": "collections",
+      "const": "collections",
+      "pattern": "^collections$",
+      "type": "string"
+    },
+    "immutable_id": {
+      "title": "Immutable ID",
+      "format": "uuid",
+      "type": "string"
+    },
+    "last_modified": {
+      "title": "Last Modified",
+      "type": "string",
+      "format": "date-time"
+    },
+    "relationships": {
+      "title": "Relationships",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/TypedRelationship"
+      }
+    },
+    "collection_id": {
+      "title": "Collection Id",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "title": {
+      "title": "Title",
+      "type": "string"
+    },
+    "description": {
+      "title": "Description",
+      "type": "string"
+    },
+    "num_items": {
+      "title": "Num Items",
+      "type": "integer"
+    }
+  },
+  "definitions": {
+    "DataBlockResponse": {
+      "title": "DataBlockResponse",
+      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
+      "type": "object",
+      "properties": {
+        "blocktype": {
+          "title": "Blocktype",
+          "type": "string"
+        },
+        "block_id": {
+          "title": "Block Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "type": "string"
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "freeform_comment": {
+          "title": "Freeform Comment",
+          "type": "string"
+        },
+        "file_id": {
+          "title": "File Id",
+          "type": "string"
+        },
+        "file_ids": {
+          "title": "File Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "errors": {
+          "title": "Errors",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "warnings": {
+          "title": "Warnings",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "b64_encoded_image": {
+          "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object",
+          "additionalProperties": {
+            "type": "string"
+          }
+        },
+        "bokeh_plot_data": {
+          "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "computed": {
+          "title": "Computed",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        }
+      },
+      "required": [
+        "blocktype",
+        "block_id"
+      ]
+    },
+    "RelationshipType": {
+      "title": "RelationshipType",
+      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
+      "enum": [
+        "parent",
+        "child",
+        "sibling",
+        "is_part_of",
+        "other"
+      ],
+      "type": "string"
+    },
+    "KnownType": {
+      "title": "KnownType",
+      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
+      "enum": [
+        "samples",
+        "starting_materials",
+        "blocks",
+        "files",
+        "people",
+        "collections"
+      ],
+      "type": "string"
+    },
+    "TypedRelationship": {
+      "title": "TypedRelationship",
+      "type": "object",
+      "properties": {
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "relation": {
+          "$ref": "#/definitions/RelationshipType"
+        },
+        "type": {
+          "$ref": "#/definitions/KnownType"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "IdentityType": {
+      "title": "IdentityType",
+      "description": "A string enum representing the supported verifiable identity types.",
+      "enum": [
+        "email",
+        "orcid",
+        "github"
+      ],
+      "type": "string"
+    },
+    "Identity": {
+      "title": "Identity",
+      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
+      "type": "object",
+      "properties": {
+        "identity_type": {
+          "$ref": "#/definitions/IdentityType"
+        },
+        "identifier": {
+          "title": "Identifier",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "verified": {
+          "title": "Verified",
+          "default": false,
+          "type": "boolean"
+        },
+        "display_name": {
+          "title": "Display Name",
+          "type": "string"
+        }
+      },
+      "required": [
+        "identity_type",
+        "identifier",
+        "name"
+      ]
+    },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
+    "AccountStatus": {
+      "title": "AccountStatus",
+      "description": "A string enum representing the account status.",
+      "enum": [
+        "active",
+        "unverified",
+        "deactivated"
+      ],
+      "type": "string"
+    },
+    "Person": {
+      "title": "Person",
+      "description": "A model that describes an individual and their digital identities.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "default": "people",
+          "const": "people",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "identities": {
+          "title": "Identities",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Identity"
+          }
+        },
+        "display_name": {
+          "title": "Display Name",
+          "minLength": 1,
+          "maxLength": 150,
+          "type": "string"
+        },
+        "contact_email": {
+          "title": "Contact Email",
+          "type": "string",
+          "format": "email"
+        },
+        "managers": {
+          "title": "Managers",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
+        "account_status": {
+          "default": "unverified",
+          "allOf": [
+            {
+              "$ref": "#/definitions/AccountStatus"
+            }
+          ]
+        }
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index b2954932e..6dc8849f2 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -117,6 +117,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "working",
+      "allOf": [
+        {
+          "$ref": "#/definitions/EquipmentStatus"
+        }
+      ]
+    },
     "serial_numbers": {
       "title": "Serial Numbers",
       "type": "string"
@@ -632,6 +640,19 @@
         "time_added",
         "is_live"
       ]
+    },
+    "EquipmentStatus": {
+      "title": "EquipmentStatus",
+      "description": "An enumeration of the status of equipments",
+      "enum": [
+        "working",
+        "broken",
+        "being_fixed",
+        "defunct",
+        "not_being_fixed",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/samples.json b/pydatalab/schemas/samples.json
new file mode 100644
index 000000000..75e1672d7
--- /dev/null
+++ b/pydatalab/schemas/samples.json
@@ -0,0 +1,747 @@
+{
+  "title": "Sample",
+  "description": "A model for representing an experimental sample.",
+  "type": "object",
+  "properties": {
+    "synthesis_constituents": {
+      "title": "Synthesis Constituents",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Constituent"
+      }
+    },
+    "synthesis_description": {
+      "title": "Synthesis Description",
+      "type": "string"
+    },
+    "blocks_obj": {
+      "title": "Blocks Obj",
+      "default": {},
+      "type": "object",
+      "additionalProperties": {
+        "$ref": "#/definitions/DataBlockResponse"
+      }
+    },
+    "display_order": {
+      "title": "Display Order",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "collections": {
+      "title": "Collections",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Collection"
+      }
+    },
+    "revision": {
+      "title": "Revision",
+      "default": 1,
+      "type": "integer"
+    },
+    "revisions": {
+      "title": "Revisions",
+      "type": "object"
+    },
+    "creator_ids": {
+      "title": "Creator Ids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "creators": {
+      "title": "Creators",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Person"
+      }
+    },
+    "type": {
+      "title": "Type",
+      "default": "samples",
+      "const": "samples",
+      "pattern": "^samples$",
+      "type": "string"
+    },
+    "immutable_id": {
+      "title": "Immutable ID",
+      "format": "uuid",
+      "type": "string"
+    },
+    "last_modified": {
+      "title": "Last Modified",
+      "type": "string",
+      "format": "date-time"
+    },
+    "relationships": {
+      "title": "Relationships",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/TypedRelationship"
+      }
+    },
+    "refcode": {
+      "title": "Refcode",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "item_id": {
+      "title": "Item Id",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "description": {
+      "title": "Description",
+      "type": "string"
+    },
+    "date": {
+      "title": "Date",
+      "type": "string",
+      "format": "date-time"
+    },
+    "name": {
+      "title": "Name",
+      "type": "string"
+    },
+    "files": {
+      "title": "Files",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/File"
+      }
+    },
+    "file_ObjectIds": {
+      "title": "File Objectids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/ItemStatus"
+        }
+      ]
+    },
+    "chemform": {
+      "title": "Chemform",
+      "example": [
+        "Na3P",
+        "LiNiO2@C"
+      ],
+      "type": "string"
+    }
+  },
+  "required": [
+    "item_id"
+  ],
+  "definitions": {
+    "EntryReference": {
+      "title": "EntryReference",
+      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "InlineSubstance": {
+      "title": "InlineSubstance",
+      "type": "object",
+      "properties": {
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "chemform": {
+          "title": "Chemform",
+          "type": "string"
+        }
+      },
+      "required": [
+        "name"
+      ]
+    },
+    "Constituent": {
+      "title": "Constituent",
+      "description": "A constituent of a sample.",
+      "type": "object",
+      "properties": {
+        "item": {
+          "title": "Item",
+          "anyOf": [
+            {
+              "$ref": "#/definitions/EntryReference"
+            },
+            {
+              "$ref": "#/definitions/InlineSubstance"
+            }
+          ]
+        },
+        "quantity": {
+          "title": "Quantity",
+          "minimum": 0,
+          "type": "number"
+        },
+        "unit": {
+          "title": "Unit",
+          "default": "g",
+          "type": "string"
+        }
+      },
+      "required": [
+        "item",
+        "quantity"
+      ]
+    },
+    "DataBlockResponse": {
+      "title": "DataBlockResponse",
+      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
+      "type": "object",
+      "properties": {
+        "blocktype": {
+          "title": "Blocktype",
+          "type": "string"
+        },
+        "block_id": {
+          "title": "Block Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "type": "string"
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "freeform_comment": {
+          "title": "Freeform Comment",
+          "type": "string"
+        },
+        "file_id": {
+          "title": "File Id",
+          "type": "string"
+        },
+        "file_ids": {
+          "title": "File Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "errors": {
+          "title": "Errors",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "warnings": {
+          "title": "Warnings",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "b64_encoded_image": {
+          "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object",
+          "additionalProperties": {
+            "type": "string"
+          }
+        },
+        "bokeh_plot_data": {
+          "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "computed": {
+          "title": "Computed",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        }
+      },
+      "required": [
+        "blocktype",
+        "block_id"
+      ]
+    },
+    "RelationshipType": {
+      "title": "RelationshipType",
+      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
+      "enum": [
+        "parent",
+        "child",
+        "sibling",
+        "is_part_of",
+        "other"
+      ],
+      "type": "string"
+    },
+    "KnownType": {
+      "title": "KnownType",
+      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
+      "enum": [
+        "samples",
+        "starting_materials",
+        "blocks",
+        "files",
+        "people",
+        "collections"
+      ],
+      "type": "string"
+    },
+    "TypedRelationship": {
+      "title": "TypedRelationship",
+      "type": "object",
+      "properties": {
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "relation": {
+          "$ref": "#/definitions/RelationshipType"
+        },
+        "type": {
+          "$ref": "#/definitions/KnownType"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "IdentityType": {
+      "title": "IdentityType",
+      "description": "A string enum representing the supported verifiable identity types.",
+      "enum": [
+        "email",
+        "orcid",
+        "github"
+      ],
+      "type": "string"
+    },
+    "Identity": {
+      "title": "Identity",
+      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
+      "type": "object",
+      "properties": {
+        "identity_type": {
+          "$ref": "#/definitions/IdentityType"
+        },
+        "identifier": {
+          "title": "Identifier",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "verified": {
+          "title": "Verified",
+          "default": false,
+          "type": "boolean"
+        },
+        "display_name": {
+          "title": "Display Name",
+          "type": "string"
+        }
+      },
+      "required": [
+        "identity_type",
+        "identifier",
+        "name"
+      ]
+    },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
+    "AccountStatus": {
+      "title": "AccountStatus",
+      "description": "A string enum representing the account status.",
+      "enum": [
+        "active",
+        "unverified",
+        "deactivated"
+      ],
+      "type": "string"
+    },
+    "Person": {
+      "title": "Person",
+      "description": "A model that describes an individual and their digital identities.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "default": "people",
+          "const": "people",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "identities": {
+          "title": "Identities",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Identity"
+          }
+        },
+        "display_name": {
+          "title": "Display Name",
+          "minLength": 1,
+          "maxLength": 150,
+          "type": "string"
+        },
+        "contact_email": {
+          "title": "Contact Email",
+          "type": "string",
+          "format": "email"
+        },
+        "managers": {
+          "title": "Managers",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
+        "account_status": {
+          "default": "unverified",
+          "allOf": [
+            {
+              "$ref": "#/definitions/AccountStatus"
+            }
+          ]
+        }
+      }
+    },
+    "Collection": {
+      "title": "Collection",
+      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
+      "type": "object",
+      "properties": {
+        "blocks_obj": {
+          "title": "Blocks Obj",
+          "default": {},
+          "type": "object",
+          "additionalProperties": {
+            "$ref": "#/definitions/DataBlockResponse"
+          }
+        },
+        "display_order": {
+          "title": "Display Order",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "collections",
+          "const": "collections",
+          "pattern": "^collections$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "num_items": {
+          "title": "Num Items",
+          "type": "integer"
+        }
+      }
+    },
+    "File": {
+      "title": "File",
+      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
+      "type": "object",
+      "properties": {
+        "revision": {
+          "title": "Revision",
+          "default": 1,
+          "type": "integer"
+        },
+        "revisions": {
+          "title": "Revisions",
+          "type": "object"
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "files",
+          "const": "files",
+          "pattern": "^files$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "size": {
+          "title": "Size",
+          "type": "integer"
+        },
+        "last_modified_remote": {
+          "title": "Last Modified Remote",
+          "type": "string",
+          "format": "date-time"
+        },
+        "item_ids": {
+          "title": "Item Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "blocks": {
+          "title": "Blocks",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "extension": {
+          "title": "Extension",
+          "type": "string"
+        },
+        "original_name": {
+          "title": "Original Name",
+          "type": "string"
+        },
+        "location": {
+          "title": "Location",
+          "type": "string"
+        },
+        "url_path": {
+          "title": "Url Path",
+          "type": "string"
+        },
+        "source": {
+          "title": "Source",
+          "type": "string"
+        },
+        "time_added": {
+          "title": "Time Added",
+          "type": "string",
+          "format": "date-time"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "type": "object"
+        },
+        "representation": {
+          "title": "Representation"
+        },
+        "source_server_name": {
+          "title": "Source Server Name",
+          "type": "string"
+        },
+        "source_path": {
+          "title": "Source Path",
+          "type": "string"
+        },
+        "is_live": {
+          "title": "Is Live",
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "item_ids",
+        "blocks",
+        "name",
+        "extension",
+        "time_added",
+        "is_live"
+      ]
+    },
+    "ItemStatus": {
+      "title": "ItemStatus",
+      "description": "An enumeration of the status of items",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "completed",
+        "failed",
+        "other"
+      ],
+      "type": "string"
+    }
+  }
+}
\ No newline at end of file
diff --git a/pydatalab/schemas/starting_materials.json b/pydatalab/schemas/starting_materials.json
new file mode 100644
index 000000000..3fc7d778d
--- /dev/null
+++ b/pydatalab/schemas/starting_materials.json
@@ -0,0 +1,801 @@
+{
+  "title": "StartingMaterial",
+  "description": "A model for representing an experimental sample, based on the connection\nwith cheminventory.net, which mixes container-level and substance-level\ninformation.",
+  "type": "object",
+  "properties": {
+    "synthesis_constituents": {
+      "title": "Synthesis Constituents",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Constituent"
+      }
+    },
+    "synthesis_description": {
+      "title": "Synthesis Description",
+      "type": "string"
+    },
+    "blocks_obj": {
+      "title": "Blocks Obj",
+      "default": {},
+      "type": "object",
+      "additionalProperties": {
+        "$ref": "#/definitions/DataBlockResponse"
+      }
+    },
+    "display_order": {
+      "title": "Display Order",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "collections": {
+      "title": "Collections",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Collection"
+      }
+    },
+    "revision": {
+      "title": "Revision",
+      "default": 1,
+      "type": "integer"
+    },
+    "revisions": {
+      "title": "Revisions",
+      "type": "object"
+    },
+    "creator_ids": {
+      "title": "Creator Ids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "creators": {
+      "title": "Creators",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Person"
+      }
+    },
+    "type": {
+      "title": "Type",
+      "default": "starting_materials",
+      "const": "starting_materials",
+      "pattern": "^starting_materials$",
+      "type": "string"
+    },
+    "immutable_id": {
+      "title": "Immutable ID",
+      "format": "uuid",
+      "type": "string"
+    },
+    "last_modified": {
+      "title": "Last Modified",
+      "type": "string",
+      "format": "date-time"
+    },
+    "relationships": {
+      "title": "Relationships",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/TypedRelationship"
+      }
+    },
+    "refcode": {
+      "title": "Refcode",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "item_id": {
+      "title": "Item Id",
+      "minLength": 1,
+      "maxLength": 40,
+      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+      "type": "string"
+    },
+    "description": {
+      "title": "Description",
+      "type": "string"
+    },
+    "date": {
+      "title": "Date Acquired",
+      "type": "string",
+      "format": "date-time"
+    },
+    "name": {
+      "title": "Container Name",
+      "type": "string"
+    },
+    "files": {
+      "title": "Files",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/File"
+      }
+    },
+    "file_ObjectIds": {
+      "title": "File Objectids",
+      "default": [],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "status": {
+      "default": "available",
+      "allOf": [
+        {
+          "$ref": "#/definitions/StartingMaterialsStatus"
+        }
+      ]
+    },
+    "barcode": {
+      "title": "Barcode",
+      "type": "string"
+    },
+    "date_opened": {
+      "title": "Date Opened",
+      "type": "string",
+      "format": "date-time"
+    },
+    "CAS": {
+      "title": "Substance Cas",
+      "type": "string"
+    },
+    "chemical_purity": {
+      "title": "Chemical Purity",
+      "type": "string"
+    },
+    "full_percent": {
+      "title": "Full %",
+      "type": "string"
+    },
+    "GHS_codes": {
+      "title": "Ghs H-Codes",
+      "examples": [
+        "H224",
+        "H303, H316, H319"
+      ],
+      "type": "string"
+    },
+    "size": {
+      "title": "Container Size",
+      "type": "string"
+    },
+    "size_unit": {
+      "title": "Unit",
+      "type": "string"
+    },
+    "chemform": {
+      "title": "Molecular Formula",
+      "type": "string"
+    },
+    "molar_mass": {
+      "title": "Molecular Weight",
+      "type": "number"
+    },
+    "smiles_representation": {
+      "title": "Smiles",
+      "type": "string"
+    },
+    "supplier": {
+      "title": "Supplier",
+      "type": "string"
+    },
+    "location": {
+      "title": "Location",
+      "type": "string"
+    },
+    "comment": {
+      "title": "Comments",
+      "type": "string"
+    }
+  },
+  "required": [
+    "item_id"
+  ],
+  "definitions": {
+    "EntryReference": {
+      "title": "EntryReference",
+      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "InlineSubstance": {
+      "title": "InlineSubstance",
+      "type": "object",
+      "properties": {
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "chemform": {
+          "title": "Chemform",
+          "type": "string"
+        }
+      },
+      "required": [
+        "name"
+      ]
+    },
+    "Constituent": {
+      "title": "Constituent",
+      "description": "A constituent of a sample.",
+      "type": "object",
+      "properties": {
+        "item": {
+          "title": "Item",
+          "anyOf": [
+            {
+              "$ref": "#/definitions/EntryReference"
+            },
+            {
+              "$ref": "#/definitions/InlineSubstance"
+            }
+          ]
+        },
+        "quantity": {
+          "title": "Quantity",
+          "minimum": 0,
+          "type": "number"
+        },
+        "unit": {
+          "title": "Unit",
+          "default": "g",
+          "type": "string"
+        }
+      },
+      "required": [
+        "item",
+        "quantity"
+      ]
+    },
+    "DataBlockResponse": {
+      "title": "DataBlockResponse",
+      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
+      "type": "object",
+      "properties": {
+        "blocktype": {
+          "title": "Blocktype",
+          "type": "string"
+        },
+        "block_id": {
+          "title": "Block Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "type": "string"
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "freeform_comment": {
+          "title": "Freeform Comment",
+          "type": "string"
+        },
+        "file_id": {
+          "title": "File Id",
+          "type": "string"
+        },
+        "file_ids": {
+          "title": "File Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "errors": {
+          "title": "Errors",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "warnings": {
+          "title": "Warnings",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "b64_encoded_image": {
+          "title": "B64 Encoded Image",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object",
+          "additionalProperties": {
+            "type": "string"
+          }
+        },
+        "bokeh_plot_data": {
+          "title": "Bokeh Plot Data",
+          "datalab_exclude_from_db": true,
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "computed": {
+          "title": "Computed",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "datalab_exclude_from_load": true,
+          "type": "object"
+        }
+      },
+      "required": [
+        "blocktype",
+        "block_id"
+      ]
+    },
+    "RelationshipType": {
+      "title": "RelationshipType",
+      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
+      "enum": [
+        "parent",
+        "child",
+        "sibling",
+        "is_part_of",
+        "other"
+      ],
+      "type": "string"
+    },
+    "KnownType": {
+      "title": "KnownType",
+      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
+      "enum": [
+        "samples",
+        "starting_materials",
+        "blocks",
+        "files",
+        "people",
+        "collections"
+      ],
+      "type": "string"
+    },
+    "TypedRelationship": {
+      "title": "TypedRelationship",
+      "type": "object",
+      "properties": {
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "relation": {
+          "$ref": "#/definitions/RelationshipType"
+        },
+        "type": {
+          "$ref": "#/definitions/KnownType"
+        },
+        "immutable_id": {
+          "title": "Immutable Id",
+          "type": "string"
+        },
+        "item_id": {
+          "title": "Item Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "refcode": {
+          "title": "Refcode",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ]
+    },
+    "IdentityType": {
+      "title": "IdentityType",
+      "description": "A string enum representing the supported verifiable identity types.",
+      "enum": [
+        "email",
+        "orcid",
+        "github"
+      ],
+      "type": "string"
+    },
+    "Identity": {
+      "title": "Identity",
+      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
+      "type": "object",
+      "properties": {
+        "identity_type": {
+          "$ref": "#/definitions/IdentityType"
+        },
+        "identifier": {
+          "title": "Identifier",
+          "type": "string"
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "verified": {
+          "title": "Verified",
+          "default": false,
+          "type": "boolean"
+        },
+        "display_name": {
+          "title": "Display Name",
+          "type": "string"
+        }
+      },
+      "required": [
+        "identity_type",
+        "identifier",
+        "name"
+      ]
+    },
+    "UserRole": {
+      "title": "UserRole",
+      "description": "An enumeration.",
+      "enum": [
+        "user",
+        "admin",
+        "manager"
+      ],
+      "type": "string"
+    },
+    "AccountStatus": {
+      "title": "AccountStatus",
+      "description": "A string enum representing the account status.",
+      "enum": [
+        "active",
+        "unverified",
+        "deactivated"
+      ],
+      "type": "string"
+    },
+    "Person": {
+      "title": "Person",
+      "description": "A model that describes an individual and their digital identities.",
+      "type": "object",
+      "properties": {
+        "type": {
+          "title": "Type",
+          "default": "people",
+          "const": "people",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "identities": {
+          "title": "Identities",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Identity"
+          }
+        },
+        "display_name": {
+          "title": "Display Name",
+          "minLength": 1,
+          "maxLength": 150,
+          "type": "string"
+        },
+        "contact_email": {
+          "title": "Contact Email",
+          "type": "string",
+          "format": "email"
+        },
+        "managers": {
+          "title": "Managers",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "role": {
+          "default": "user",
+          "allOf": [
+            {
+              "$ref": "#/definitions/UserRole"
+            }
+          ]
+        },
+        "account_status": {
+          "default": "unverified",
+          "allOf": [
+            {
+              "$ref": "#/definitions/AccountStatus"
+            }
+          ]
+        }
+      }
+    },
+    "Collection": {
+      "title": "Collection",
+      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
+      "type": "object",
+      "properties": {
+        "blocks_obj": {
+          "title": "Blocks Obj",
+          "default": {},
+          "type": "object",
+          "additionalProperties": {
+            "$ref": "#/definitions/DataBlockResponse"
+          }
+        },
+        "display_order": {
+          "title": "Display Order",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "collections",
+          "const": "collections",
+          "pattern": "^collections$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "collection_id": {
+          "title": "Collection Id",
+          "minLength": 1,
+          "maxLength": 40,
+          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
+          "type": "string"
+        },
+        "title": {
+          "title": "Title",
+          "type": "string"
+        },
+        "description": {
+          "title": "Description",
+          "type": "string"
+        },
+        "num_items": {
+          "title": "Num Items",
+          "type": "integer"
+        }
+      }
+    },
+    "File": {
+      "title": "File",
+      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
+      "type": "object",
+      "properties": {
+        "revision": {
+          "title": "Revision",
+          "default": 1,
+          "type": "integer"
+        },
+        "revisions": {
+          "title": "Revisions",
+          "type": "object"
+        },
+        "creator_ids": {
+          "title": "Creator Ids",
+          "default": [],
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "creators": {
+          "title": "Creators",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/Person"
+          }
+        },
+        "type": {
+          "title": "Type",
+          "default": "files",
+          "const": "files",
+          "pattern": "^files$",
+          "type": "string"
+        },
+        "immutable_id": {
+          "title": "Immutable ID",
+          "format": "uuid",
+          "type": "string"
+        },
+        "last_modified": {
+          "title": "Last Modified",
+          "type": "string",
+          "format": "date-time"
+        },
+        "relationships": {
+          "title": "Relationships",
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/TypedRelationship"
+          }
+        },
+        "size": {
+          "title": "Size",
+          "type": "integer"
+        },
+        "last_modified_remote": {
+          "title": "Last Modified Remote",
+          "type": "string",
+          "format": "date-time"
+        },
+        "item_ids": {
+          "title": "Item Ids",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "blocks": {
+          "title": "Blocks",
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "name": {
+          "title": "Name",
+          "type": "string"
+        },
+        "extension": {
+          "title": "Extension",
+          "type": "string"
+        },
+        "original_name": {
+          "title": "Original Name",
+          "type": "string"
+        },
+        "location": {
+          "title": "Location",
+          "type": "string"
+        },
+        "url_path": {
+          "title": "Url Path",
+          "type": "string"
+        },
+        "source": {
+          "title": "Source",
+          "type": "string"
+        },
+        "time_added": {
+          "title": "Time Added",
+          "type": "string",
+          "format": "date-time"
+        },
+        "metadata": {
+          "title": "Metadata",
+          "type": "object"
+        },
+        "representation": {
+          "title": "Representation"
+        },
+        "source_server_name": {
+          "title": "Source Server Name",
+          "type": "string"
+        },
+        "source_path": {
+          "title": "Source Path",
+          "type": "string"
+        },
+        "is_live": {
+          "title": "Is Live",
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "item_ids",
+        "blocks",
+        "name",
+        "extension",
+        "time_added",
+        "is_live"
+      ]
+    },
+    "StartingMaterialsStatus": {
+      "title": "StartingMaterialsStatus",
+      "description": "An enumeration of the status of starting materials",
+      "enum": [
+        "ordered",
+        "disposed",
+        "planned",
+        "available",
+        "unavailable",
+        "exhausted",
+        "other"
+      ],
+      "type": "string"
+    }
+  }
+}
\ No newline at end of file

From 24c0906012bb001d8c3579bd347532271e82f735 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Mon, 15 Dec 2025 17:09:49 +0100
Subject: [PATCH 22/26] Fix JSON schema filenames

---
 pydatalab/schemas/cell.json             | 22 ++++++++++++++++++++++
 pydatalab/schemas/sample.json           | 21 +++++++++++++++++++++
 pydatalab/schemas/startingmaterial.json | 22 ++++++++++++++++++++++
 3 files changed, 65 insertions(+)

diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index 3b2392905..6d4ec0dba 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -117,6 +117,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/CellStatus"
+        }
+      ]
+    },
     "cell_format": {
       "$ref": "#/definitions/CellFormat"
     },
@@ -669,6 +677,20 @@
         "is_live"
       ]
     },
+    "CellStatus": {
+      "title": "CellStatus",
+      "description": "An enumeration of the status of cells",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "cycled",
+        "shorted",
+        "dismantled",
+        "other"
+      ],
+      "type": "string"
+    },
     "CellFormat": {
       "title": "CellFormat",
       "description": "An enumeration.",
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index b6e8ec6c1..75e1672d7 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -129,6 +129,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/ItemStatus"
+        }
+      ]
+    },
     "chemform": {
       "title": "Chemform",
       "example": [
@@ -721,6 +729,19 @@
         "time_added",
         "is_live"
       ]
+    },
+    "ItemStatus": {
+      "title": "ItemStatus",
+      "description": "An enumeration of the status of items",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "completed",
+        "failed",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index 07da52b15..3fc7d778d 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -129,6 +129,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "available",
+      "allOf": [
+        {
+          "$ref": "#/definitions/StartingMaterialsStatus"
+        }
+      ]
+    },
     "barcode": {
       "title": "Barcode",
       "type": "string"
@@ -774,6 +782,20 @@
         "time_added",
         "is_live"
       ]
+    },
+    "StartingMaterialsStatus": {
+      "title": "StartingMaterialsStatus",
+      "description": "An enumeration of the status of starting materials",
+      "enum": [
+        "ordered",
+        "disposed",
+        "planned",
+        "available",
+        "unavailable",
+        "exhausted",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file

From d2da519019ff95b41c355ee32f87558115083668 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 16 Dec 2025 14:56:55 +0100
Subject: [PATCH 23/26] Unify BlockTask and ExportTask into single Task model

---
 pydatalab/schemas/cell.json                   |  22 -
 pydatalab/schemas/cells.json                  | 796 -----------------
 pydatalab/schemas/equipment.json              |  21 -
 pydatalab/schemas/sample.json                 |  21 -
 pydatalab/schemas/samples.json                | 747 ----------------
 pydatalab/schemas/starting_materials.json     | 801 ------------------
 pydatalab/schemas/startingmaterial.json       |  22 -
 pydatalab/src/pydatalab/models/export_task.py |  38 -
 .../models/{block_task.py => tasks.py}        |  32 +-
 pydatalab/src/pydatalab/mongo.py              |  17 +-
 pydatalab/src/pydatalab/routes/v0_1/blocks.py |  35 +-
 pydatalab/src/pydatalab/routes/v0_1/export.py |  39 +-
 pydatalab/tests/server/test_export.py         |  69 +-
 13 files changed, 106 insertions(+), 2554 deletions(-)
 delete mode 100644 pydatalab/schemas/cells.json
 delete mode 100644 pydatalab/schemas/samples.json
 delete mode 100644 pydatalab/schemas/starting_materials.json
 delete mode 100644 pydatalab/src/pydatalab/models/export_task.py
 rename pydatalab/src/pydatalab/models/{block_task.py => tasks.py} (53%)

diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index 6d4ec0dba..3b2392905 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -117,14 +117,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/CellStatus"
-        }
-      ]
-    },
     "cell_format": {
       "$ref": "#/definitions/CellFormat"
     },
@@ -677,20 +669,6 @@
         "is_live"
       ]
     },
-    "CellStatus": {
-      "title": "CellStatus",
-      "description": "An enumeration of the status of cells",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "cycled",
-        "shorted",
-        "dismantled",
-        "other"
-      ],
-      "type": "string"
-    },
     "CellFormat": {
       "title": "CellFormat",
       "description": "An enumeration.",
diff --git a/pydatalab/schemas/cells.json b/pydatalab/schemas/cells.json
deleted file mode 100644
index 6d4ec0dba..000000000
--- a/pydatalab/schemas/cells.json
+++ /dev/null
@@ -1,796 +0,0 @@
-{
-  "title": "Cell",
-  "description": "A model for representing electrochemical cells.",
-  "type": "object",
-  "properties": {
-    "blocks_obj": {
-      "title": "Blocks Obj",
-      "default": {},
-      "type": "object",
-      "additionalProperties": {
-        "$ref": "#/definitions/DataBlockResponse"
-      }
-    },
-    "display_order": {
-      "title": "Display Order",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "collections": {
-      "title": "Collections",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Collection"
-      }
-    },
-    "revision": {
-      "title": "Revision",
-      "default": 1,
-      "type": "integer"
-    },
-    "revisions": {
-      "title": "Revisions",
-      "type": "object"
-    },
-    "creator_ids": {
-      "title": "Creator Ids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "creators": {
-      "title": "Creators",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Person"
-      }
-    },
-    "type": {
-      "title": "Type",
-      "default": "cells",
-      "const": "cells",
-      "pattern": "^cells$",
-      "type": "string"
-    },
-    "immutable_id": {
-      "title": "Immutable ID",
-      "format": "uuid",
-      "type": "string"
-    },
-    "last_modified": {
-      "title": "Last Modified",
-      "type": "string",
-      "format": "date-time"
-    },
-    "relationships": {
-      "title": "Relationships",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/TypedRelationship"
-      }
-    },
-    "refcode": {
-      "title": "Refcode",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "item_id": {
-      "title": "Item Id",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "description": {
-      "title": "Description",
-      "type": "string"
-    },
-    "date": {
-      "title": "Date",
-      "type": "string",
-      "format": "date-time"
-    },
-    "name": {
-      "title": "Name",
-      "type": "string"
-    },
-    "files": {
-      "title": "Files",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/File"
-      }
-    },
-    "file_ObjectIds": {
-      "title": "File Objectids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/CellStatus"
-        }
-      ]
-    },
-    "cell_format": {
-      "$ref": "#/definitions/CellFormat"
-    },
-    "cell_format_description": {
-      "title": "Cell Format Description",
-      "type": "string"
-    },
-    "cell_preparation_description": {
-      "title": "Cell Preparation Description",
-      "type": "string"
-    },
-    "characteristic_mass": {
-      "title": "Characteristic Mass",
-      "type": "number"
-    },
-    "characteristic_chemical_formula": {
-      "title": "Characteristic Chemical Formula",
-      "type": "string"
-    },
-    "characteristic_molar_mass": {
-      "title": "Characteristic Molar Mass",
-      "type": "number"
-    },
-    "positive_electrode": {
-      "title": "Positive Electrode",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/CellComponent"
-      }
-    },
-    "negative_electrode": {
-      "title": "Negative Electrode",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/CellComponent"
-      }
-    },
-    "electrolyte": {
-      "title": "Electrolyte",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/CellComponent"
-      }
-    },
-    "active_ion_charge": {
-      "title": "Active Ion Charge",
-      "default": 1,
-      "type": "number"
-    }
-  },
-  "required": [
-    "item_id"
-  ],
-  "definitions": {
-    "DataBlockResponse": {
-      "title": "DataBlockResponse",
-      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
-      "type": "object",
-      "properties": {
-        "blocktype": {
-          "title": "Blocktype",
-          "type": "string"
-        },
-        "block_id": {
-          "title": "Block Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "type": "string"
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "freeform_comment": {
-          "title": "Freeform Comment",
-          "type": "string"
-        },
-        "file_id": {
-          "title": "File Id",
-          "type": "string"
-        },
-        "file_ids": {
-          "title": "File Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "errors": {
-          "title": "Errors",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "warnings": {
-          "title": "Warnings",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "b64_encoded_image": {
-          "title": "B64 Encoded Image",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object",
-          "additionalProperties": {
-            "type": "string"
-          }
-        },
-        "bokeh_plot_data": {
-          "title": "Bokeh Plot Data",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "computed": {
-          "title": "Computed",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        }
-      },
-      "required": [
-        "blocktype",
-        "block_id"
-      ]
-    },
-    "RelationshipType": {
-      "title": "RelationshipType",
-      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
-      "enum": [
-        "parent",
-        "child",
-        "sibling",
-        "is_part_of",
-        "other"
-      ],
-      "type": "string"
-    },
-    "KnownType": {
-      "title": "KnownType",
-      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
-      "enum": [
-        "samples",
-        "starting_materials",
-        "blocks",
-        "files",
-        "people",
-        "collections"
-      ],
-      "type": "string"
-    },
-    "TypedRelationship": {
-      "title": "TypedRelationship",
-      "type": "object",
-      "properties": {
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "relation": {
-          "$ref": "#/definitions/RelationshipType"
-        },
-        "type": {
-          "$ref": "#/definitions/KnownType"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "IdentityType": {
-      "title": "IdentityType",
-      "description": "A string enum representing the supported verifiable identity types.",
-      "enum": [
-        "email",
-        "orcid",
-        "github"
-      ],
-      "type": "string"
-    },
-    "Identity": {
-      "title": "Identity",
-      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
-      "type": "object",
-      "properties": {
-        "identity_type": {
-          "$ref": "#/definitions/IdentityType"
-        },
-        "identifier": {
-          "title": "Identifier",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "verified": {
-          "title": "Verified",
-          "default": false,
-          "type": "boolean"
-        },
-        "display_name": {
-          "title": "Display Name",
-          "type": "string"
-        }
-      },
-      "required": [
-        "identity_type",
-        "identifier",
-        "name"
-      ]
-    },
-    "UserRole": {
-      "title": "UserRole",
-      "description": "An enumeration.",
-      "enum": [
-        "user",
-        "admin",
-        "manager"
-      ],
-      "type": "string"
-    },
-    "AccountStatus": {
-      "title": "AccountStatus",
-      "description": "A string enum representing the account status.",
-      "enum": [
-        "active",
-        "unverified",
-        "deactivated"
-      ],
-      "type": "string"
-    },
-    "Person": {
-      "title": "Person",
-      "description": "A model that describes an individual and their digital identities.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "default": "people",
-          "const": "people",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "identities": {
-          "title": "Identities",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Identity"
-          }
-        },
-        "display_name": {
-          "title": "Display Name",
-          "minLength": 1,
-          "maxLength": 150,
-          "type": "string"
-        },
-        "contact_email": {
-          "title": "Contact Email",
-          "type": "string",
-          "format": "email"
-        },
-        "managers": {
-          "title": "Managers",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "role": {
-          "default": "user",
-          "allOf": [
-            {
-              "$ref": "#/definitions/UserRole"
-            }
-          ]
-        },
-        "account_status": {
-          "default": "unverified",
-          "allOf": [
-            {
-              "$ref": "#/definitions/AccountStatus"
-            }
-          ]
-        }
-      }
-    },
-    "Collection": {
-      "title": "Collection",
-      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
-      "type": "object",
-      "properties": {
-        "blocks_obj": {
-          "title": "Blocks Obj",
-          "default": {},
-          "type": "object",
-          "additionalProperties": {
-            "$ref": "#/definitions/DataBlockResponse"
-          }
-        },
-        "display_order": {
-          "title": "Display Order",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "collections",
-          "const": "collections",
-          "pattern": "^collections$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "num_items": {
-          "title": "Num Items",
-          "type": "integer"
-        }
-      }
-    },
-    "File": {
-      "title": "File",
-      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
-      "type": "object",
-      "properties": {
-        "revision": {
-          "title": "Revision",
-          "default": 1,
-          "type": "integer"
-        },
-        "revisions": {
-          "title": "Revisions",
-          "type": "object"
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "files",
-          "const": "files",
-          "pattern": "^files$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "size": {
-          "title": "Size",
-          "type": "integer"
-        },
-        "last_modified_remote": {
-          "title": "Last Modified Remote",
-          "type": "string",
-          "format": "date-time"
-        },
-        "item_ids": {
-          "title": "Item Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "blocks": {
-          "title": "Blocks",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "extension": {
-          "title": "Extension",
-          "type": "string"
-        },
-        "original_name": {
-          "title": "Original Name",
-          "type": "string"
-        },
-        "location": {
-          "title": "Location",
-          "type": "string"
-        },
-        "url_path": {
-          "title": "Url Path",
-          "type": "string"
-        },
-        "source": {
-          "title": "Source",
-          "type": "string"
-        },
-        "time_added": {
-          "title": "Time Added",
-          "type": "string",
-          "format": "date-time"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "type": "object"
-        },
-        "representation": {
-          "title": "Representation"
-        },
-        "source_server_name": {
-          "title": "Source Server Name",
-          "type": "string"
-        },
-        "source_path": {
-          "title": "Source Path",
-          "type": "string"
-        },
-        "is_live": {
-          "title": "Is Live",
-          "type": "boolean"
-        }
-      },
-      "required": [
-        "item_ids",
-        "blocks",
-        "name",
-        "extension",
-        "time_added",
-        "is_live"
-      ]
-    },
-    "CellStatus": {
-      "title": "CellStatus",
-      "description": "An enumeration of the status of cells",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "cycled",
-        "shorted",
-        "dismantled",
-        "other"
-      ],
-      "type": "string"
-    },
-    "CellFormat": {
-      "title": "CellFormat",
-      "description": "An enumeration.",
-      "enum": [
-        "coin",
-        "pouch",
-        "in situ (XRD)",
-        "in situ (NMR)",
-        "in situ (SQUID)",
-        "in situ (optical)",
-        "swagelok",
-        "cylindrical",
-        "other"
-      ],
-      "type": "string"
-    },
-    "EntryReference": {
-      "title": "EntryReference",
-      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "InlineSubstance": {
-      "title": "InlineSubstance",
-      "type": "object",
-      "properties": {
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "chemform": {
-          "title": "Chemform",
-          "type": "string"
-        }
-      },
-      "required": [
-        "name"
-      ]
-    },
-    "CellComponent": {
-      "title": "CellComponent",
-      "description": "A constituent of a sample.",
-      "type": "object",
-      "properties": {
-        "item": {
-          "title": "Item",
-          "anyOf": [
-            {
-              "$ref": "#/definitions/EntryReference"
-            },
-            {
-              "$ref": "#/definitions/InlineSubstance"
-            }
-          ]
-        },
-        "quantity": {
-          "title": "Quantity",
-          "minimum": 0,
-          "type": "number"
-        },
-        "unit": {
-          "title": "Unit",
-          "default": "g",
-          "type": "string"
-        }
-      },
-      "required": [
-        "item",
-        "quantity"
-      ]
-    }
-  }
-}
\ No newline at end of file
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index 6dc8849f2..b2954932e 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -117,14 +117,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "working",
-      "allOf": [
-        {
-          "$ref": "#/definitions/EquipmentStatus"
-        }
-      ]
-    },
     "serial_numbers": {
       "title": "Serial Numbers",
       "type": "string"
@@ -640,19 +632,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "EquipmentStatus": {
-      "title": "EquipmentStatus",
-      "description": "An enumeration of the status of equipments",
-      "enum": [
-        "working",
-        "broken",
-        "being_fixed",
-        "defunct",
-        "not_being_fixed",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index 75e1672d7..b6e8ec6c1 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -129,14 +129,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/ItemStatus"
-        }
-      ]
-    },
     "chemform": {
       "title": "Chemform",
       "example": [
@@ -729,19 +721,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "ItemStatus": {
-      "title": "ItemStatus",
-      "description": "An enumeration of the status of items",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "completed",
-        "failed",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/samples.json b/pydatalab/schemas/samples.json
deleted file mode 100644
index 75e1672d7..000000000
--- a/pydatalab/schemas/samples.json
+++ /dev/null
@@ -1,747 +0,0 @@
-{
-  "title": "Sample",
-  "description": "A model for representing an experimental sample.",
-  "type": "object",
-  "properties": {
-    "synthesis_constituents": {
-      "title": "Synthesis Constituents",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Constituent"
-      }
-    },
-    "synthesis_description": {
-      "title": "Synthesis Description",
-      "type": "string"
-    },
-    "blocks_obj": {
-      "title": "Blocks Obj",
-      "default": {},
-      "type": "object",
-      "additionalProperties": {
-        "$ref": "#/definitions/DataBlockResponse"
-      }
-    },
-    "display_order": {
-      "title": "Display Order",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "collections": {
-      "title": "Collections",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Collection"
-      }
-    },
-    "revision": {
-      "title": "Revision",
-      "default": 1,
-      "type": "integer"
-    },
-    "revisions": {
-      "title": "Revisions",
-      "type": "object"
-    },
-    "creator_ids": {
-      "title": "Creator Ids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "creators": {
-      "title": "Creators",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Person"
-      }
-    },
-    "type": {
-      "title": "Type",
-      "default": "samples",
-      "const": "samples",
-      "pattern": "^samples$",
-      "type": "string"
-    },
-    "immutable_id": {
-      "title": "Immutable ID",
-      "format": "uuid",
-      "type": "string"
-    },
-    "last_modified": {
-      "title": "Last Modified",
-      "type": "string",
-      "format": "date-time"
-    },
-    "relationships": {
-      "title": "Relationships",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/TypedRelationship"
-      }
-    },
-    "refcode": {
-      "title": "Refcode",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "item_id": {
-      "title": "Item Id",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "description": {
-      "title": "Description",
-      "type": "string"
-    },
-    "date": {
-      "title": "Date",
-      "type": "string",
-      "format": "date-time"
-    },
-    "name": {
-      "title": "Name",
-      "type": "string"
-    },
-    "files": {
-      "title": "Files",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/File"
-      }
-    },
-    "file_ObjectIds": {
-      "title": "File Objectids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "status": {
-      "default": "active",
-      "allOf": [
-        {
-          "$ref": "#/definitions/ItemStatus"
-        }
-      ]
-    },
-    "chemform": {
-      "title": "Chemform",
-      "example": [
-        "Na3P",
-        "LiNiO2@C"
-      ],
-      "type": "string"
-    }
-  },
-  "required": [
-    "item_id"
-  ],
-  "definitions": {
-    "EntryReference": {
-      "title": "EntryReference",
-      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "InlineSubstance": {
-      "title": "InlineSubstance",
-      "type": "object",
-      "properties": {
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "chemform": {
-          "title": "Chemform",
-          "type": "string"
-        }
-      },
-      "required": [
-        "name"
-      ]
-    },
-    "Constituent": {
-      "title": "Constituent",
-      "description": "A constituent of a sample.",
-      "type": "object",
-      "properties": {
-        "item": {
-          "title": "Item",
-          "anyOf": [
-            {
-              "$ref": "#/definitions/EntryReference"
-            },
-            {
-              "$ref": "#/definitions/InlineSubstance"
-            }
-          ]
-        },
-        "quantity": {
-          "title": "Quantity",
-          "minimum": 0,
-          "type": "number"
-        },
-        "unit": {
-          "title": "Unit",
-          "default": "g",
-          "type": "string"
-        }
-      },
-      "required": [
-        "item",
-        "quantity"
-      ]
-    },
-    "DataBlockResponse": {
-      "title": "DataBlockResponse",
-      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
-      "type": "object",
-      "properties": {
-        "blocktype": {
-          "title": "Blocktype",
-          "type": "string"
-        },
-        "block_id": {
-          "title": "Block Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "type": "string"
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "freeform_comment": {
-          "title": "Freeform Comment",
-          "type": "string"
-        },
-        "file_id": {
-          "title": "File Id",
-          "type": "string"
-        },
-        "file_ids": {
-          "title": "File Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "errors": {
-          "title": "Errors",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "warnings": {
-          "title": "Warnings",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "b64_encoded_image": {
-          "title": "B64 Encoded Image",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object",
-          "additionalProperties": {
-            "type": "string"
-          }
-        },
-        "bokeh_plot_data": {
-          "title": "Bokeh Plot Data",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "computed": {
-          "title": "Computed",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        }
-      },
-      "required": [
-        "blocktype",
-        "block_id"
-      ]
-    },
-    "RelationshipType": {
-      "title": "RelationshipType",
-      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
-      "enum": [
-        "parent",
-        "child",
-        "sibling",
-        "is_part_of",
-        "other"
-      ],
-      "type": "string"
-    },
-    "KnownType": {
-      "title": "KnownType",
-      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
-      "enum": [
-        "samples",
-        "starting_materials",
-        "blocks",
-        "files",
-        "people",
-        "collections"
-      ],
-      "type": "string"
-    },
-    "TypedRelationship": {
-      "title": "TypedRelationship",
-      "type": "object",
-      "properties": {
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "relation": {
-          "$ref": "#/definitions/RelationshipType"
-        },
-        "type": {
-          "$ref": "#/definitions/KnownType"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "IdentityType": {
-      "title": "IdentityType",
-      "description": "A string enum representing the supported verifiable identity types.",
-      "enum": [
-        "email",
-        "orcid",
-        "github"
-      ],
-      "type": "string"
-    },
-    "Identity": {
-      "title": "Identity",
-      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
-      "type": "object",
-      "properties": {
-        "identity_type": {
-          "$ref": "#/definitions/IdentityType"
-        },
-        "identifier": {
-          "title": "Identifier",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "verified": {
-          "title": "Verified",
-          "default": false,
-          "type": "boolean"
-        },
-        "display_name": {
-          "title": "Display Name",
-          "type": "string"
-        }
-      },
-      "required": [
-        "identity_type",
-        "identifier",
-        "name"
-      ]
-    },
-    "UserRole": {
-      "title": "UserRole",
-      "description": "An enumeration.",
-      "enum": [
-        "user",
-        "admin",
-        "manager"
-      ],
-      "type": "string"
-    },
-    "AccountStatus": {
-      "title": "AccountStatus",
-      "description": "A string enum representing the account status.",
-      "enum": [
-        "active",
-        "unverified",
-        "deactivated"
-      ],
-      "type": "string"
-    },
-    "Person": {
-      "title": "Person",
-      "description": "A model that describes an individual and their digital identities.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "default": "people",
-          "const": "people",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "identities": {
-          "title": "Identities",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Identity"
-          }
-        },
-        "display_name": {
-          "title": "Display Name",
-          "minLength": 1,
-          "maxLength": 150,
-          "type": "string"
-        },
-        "contact_email": {
-          "title": "Contact Email",
-          "type": "string",
-          "format": "email"
-        },
-        "managers": {
-          "title": "Managers",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "role": {
-          "default": "user",
-          "allOf": [
-            {
-              "$ref": "#/definitions/UserRole"
-            }
-          ]
-        },
-        "account_status": {
-          "default": "unverified",
-          "allOf": [
-            {
-              "$ref": "#/definitions/AccountStatus"
-            }
-          ]
-        }
-      }
-    },
-    "Collection": {
-      "title": "Collection",
-      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
-      "type": "object",
-      "properties": {
-        "blocks_obj": {
-          "title": "Blocks Obj",
-          "default": {},
-          "type": "object",
-          "additionalProperties": {
-            "$ref": "#/definitions/DataBlockResponse"
-          }
-        },
-        "display_order": {
-          "title": "Display Order",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "collections",
-          "const": "collections",
-          "pattern": "^collections$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "num_items": {
-          "title": "Num Items",
-          "type": "integer"
-        }
-      }
-    },
-    "File": {
-      "title": "File",
-      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
-      "type": "object",
-      "properties": {
-        "revision": {
-          "title": "Revision",
-          "default": 1,
-          "type": "integer"
-        },
-        "revisions": {
-          "title": "Revisions",
-          "type": "object"
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "files",
-          "const": "files",
-          "pattern": "^files$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "size": {
-          "title": "Size",
-          "type": "integer"
-        },
-        "last_modified_remote": {
-          "title": "Last Modified Remote",
-          "type": "string",
-          "format": "date-time"
-        },
-        "item_ids": {
-          "title": "Item Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "blocks": {
-          "title": "Blocks",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "extension": {
-          "title": "Extension",
-          "type": "string"
-        },
-        "original_name": {
-          "title": "Original Name",
-          "type": "string"
-        },
-        "location": {
-          "title": "Location",
-          "type": "string"
-        },
-        "url_path": {
-          "title": "Url Path",
-          "type": "string"
-        },
-        "source": {
-          "title": "Source",
-          "type": "string"
-        },
-        "time_added": {
-          "title": "Time Added",
-          "type": "string",
-          "format": "date-time"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "type": "object"
-        },
-        "representation": {
-          "title": "Representation"
-        },
-        "source_server_name": {
-          "title": "Source Server Name",
-          "type": "string"
-        },
-        "source_path": {
-          "title": "Source Path",
-          "type": "string"
-        },
-        "is_live": {
-          "title": "Is Live",
-          "type": "boolean"
-        }
-      },
-      "required": [
-        "item_ids",
-        "blocks",
-        "name",
-        "extension",
-        "time_added",
-        "is_live"
-      ]
-    },
-    "ItemStatus": {
-      "title": "ItemStatus",
-      "description": "An enumeration of the status of items",
-      "enum": [
-        "active",
-        "planned",
-        "disposed",
-        "completed",
-        "failed",
-        "other"
-      ],
-      "type": "string"
-    }
-  }
-}
\ No newline at end of file
diff --git a/pydatalab/schemas/starting_materials.json b/pydatalab/schemas/starting_materials.json
deleted file mode 100644
index 3fc7d778d..000000000
--- a/pydatalab/schemas/starting_materials.json
+++ /dev/null
@@ -1,801 +0,0 @@
-{
-  "title": "StartingMaterial",
-  "description": "A model for representing an experimental sample, based on the connection\nwith cheminventory.net, which mixes container-level and substance-level\ninformation.",
-  "type": "object",
-  "properties": {
-    "synthesis_constituents": {
-      "title": "Synthesis Constituents",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Constituent"
-      }
-    },
-    "synthesis_description": {
-      "title": "Synthesis Description",
-      "type": "string"
-    },
-    "blocks_obj": {
-      "title": "Blocks Obj",
-      "default": {},
-      "type": "object",
-      "additionalProperties": {
-        "$ref": "#/definitions/DataBlockResponse"
-      }
-    },
-    "display_order": {
-      "title": "Display Order",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "collections": {
-      "title": "Collections",
-      "default": [],
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Collection"
-      }
-    },
-    "revision": {
-      "title": "Revision",
-      "default": 1,
-      "type": "integer"
-    },
-    "revisions": {
-      "title": "Revisions",
-      "type": "object"
-    },
-    "creator_ids": {
-      "title": "Creator Ids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "creators": {
-      "title": "Creators",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/Person"
-      }
-    },
-    "type": {
-      "title": "Type",
-      "default": "starting_materials",
-      "const": "starting_materials",
-      "pattern": "^starting_materials$",
-      "type": "string"
-    },
-    "immutable_id": {
-      "title": "Immutable ID",
-      "format": "uuid",
-      "type": "string"
-    },
-    "last_modified": {
-      "title": "Last Modified",
-      "type": "string",
-      "format": "date-time"
-    },
-    "relationships": {
-      "title": "Relationships",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/TypedRelationship"
-      }
-    },
-    "refcode": {
-      "title": "Refcode",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "item_id": {
-      "title": "Item Id",
-      "minLength": 1,
-      "maxLength": 40,
-      "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-      "type": "string"
-    },
-    "description": {
-      "title": "Description",
-      "type": "string"
-    },
-    "date": {
-      "title": "Date Acquired",
-      "type": "string",
-      "format": "date-time"
-    },
-    "name": {
-      "title": "Container Name",
-      "type": "string"
-    },
-    "files": {
-      "title": "Files",
-      "type": "array",
-      "items": {
-        "$ref": "#/definitions/File"
-      }
-    },
-    "file_ObjectIds": {
-      "title": "File Objectids",
-      "default": [],
-      "type": "array",
-      "items": {
-        "type": "string"
-      }
-    },
-    "status": {
-      "default": "available",
-      "allOf": [
-        {
-          "$ref": "#/definitions/StartingMaterialsStatus"
-        }
-      ]
-    },
-    "barcode": {
-      "title": "Barcode",
-      "type": "string"
-    },
-    "date_opened": {
-      "title": "Date Opened",
-      "type": "string",
-      "format": "date-time"
-    },
-    "CAS": {
-      "title": "Substance Cas",
-      "type": "string"
-    },
-    "chemical_purity": {
-      "title": "Chemical Purity",
-      "type": "string"
-    },
-    "full_percent": {
-      "title": "Full %",
-      "type": "string"
-    },
-    "GHS_codes": {
-      "title": "Ghs H-Codes",
-      "examples": [
-        "H224",
-        "H303, H316, H319"
-      ],
-      "type": "string"
-    },
-    "size": {
-      "title": "Container Size",
-      "type": "string"
-    },
-    "size_unit": {
-      "title": "Unit",
-      "type": "string"
-    },
-    "chemform": {
-      "title": "Molecular Formula",
-      "type": "string"
-    },
-    "molar_mass": {
-      "title": "Molecular Weight",
-      "type": "number"
-    },
-    "smiles_representation": {
-      "title": "Smiles",
-      "type": "string"
-    },
-    "supplier": {
-      "title": "Supplier",
-      "type": "string"
-    },
-    "location": {
-      "title": "Location",
-      "type": "string"
-    },
-    "comment": {
-      "title": "Comments",
-      "type": "string"
-    }
-  },
-  "required": [
-    "item_id"
-  ],
-  "definitions": {
-    "EntryReference": {
-      "title": "EntryReference",
-      "description": "A reference to a database entry by ID and type.\n\nCan include additional arbitarary metadata useful for\ninlining the item data.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "InlineSubstance": {
-      "title": "InlineSubstance",
-      "type": "object",
-      "properties": {
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "chemform": {
-          "title": "Chemform",
-          "type": "string"
-        }
-      },
-      "required": [
-        "name"
-      ]
-    },
-    "Constituent": {
-      "title": "Constituent",
-      "description": "A constituent of a sample.",
-      "type": "object",
-      "properties": {
-        "item": {
-          "title": "Item",
-          "anyOf": [
-            {
-              "$ref": "#/definitions/EntryReference"
-            },
-            {
-              "$ref": "#/definitions/InlineSubstance"
-            }
-          ]
-        },
-        "quantity": {
-          "title": "Quantity",
-          "minimum": 0,
-          "type": "number"
-        },
-        "unit": {
-          "title": "Unit",
-          "default": "g",
-          "type": "string"
-        }
-      },
-      "required": [
-        "item",
-        "quantity"
-      ]
-    },
-    "DataBlockResponse": {
-      "title": "DataBlockResponse",
-      "description": "A generic response model for a block, i.e., what is stored in `self.data`\nin the corresponding DataBlock class.\n\nIt is expected but not mandatory that this model will be extended by the specific block type\nwhere possible.",
-      "type": "object",
-      "properties": {
-        "blocktype": {
-          "title": "Blocktype",
-          "type": "string"
-        },
-        "block_id": {
-          "title": "Block Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "type": "string"
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "freeform_comment": {
-          "title": "Freeform Comment",
-          "type": "string"
-        },
-        "file_id": {
-          "title": "File Id",
-          "type": "string"
-        },
-        "file_ids": {
-          "title": "File Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "errors": {
-          "title": "Errors",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "warnings": {
-          "title": "Warnings",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "b64_encoded_image": {
-          "title": "B64 Encoded Image",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object",
-          "additionalProperties": {
-            "type": "string"
-          }
-        },
-        "bokeh_plot_data": {
-          "title": "Bokeh Plot Data",
-          "datalab_exclude_from_db": true,
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "computed": {
-          "title": "Computed",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "datalab_exclude_from_load": true,
-          "type": "object"
-        }
-      },
-      "required": [
-        "blocktype",
-        "block_id"
-      ]
-    },
-    "RelationshipType": {
-      "title": "RelationshipType",
-      "description": "An enumeration of the possible types of relationship between two entries.\n\n```mermaid\nclassDiagram\nclass entryC\nentryC --|> entryA: parent\nentryC ..|> entryD\nentryA <..> entryD: sibling\nentryA --|> entryB : child\n```",
-      "enum": [
-        "parent",
-        "child",
-        "sibling",
-        "is_part_of",
-        "other"
-      ],
-      "type": "string"
-    },
-    "KnownType": {
-      "title": "KnownType",
-      "description": "An enumeration of the types of entry known by this implementation, should be made dynamic in the future.",
-      "enum": [
-        "samples",
-        "starting_materials",
-        "blocks",
-        "files",
-        "people",
-        "collections"
-      ],
-      "type": "string"
-    },
-    "TypedRelationship": {
-      "title": "TypedRelationship",
-      "type": "object",
-      "properties": {
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "relation": {
-          "$ref": "#/definitions/RelationshipType"
-        },
-        "type": {
-          "$ref": "#/definitions/KnownType"
-        },
-        "immutable_id": {
-          "title": "Immutable Id",
-          "type": "string"
-        },
-        "item_id": {
-          "title": "Item Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "refcode": {
-          "title": "Refcode",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^[a-z]{2,10}:(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        }
-      },
-      "required": [
-        "type"
-      ]
-    },
-    "IdentityType": {
-      "title": "IdentityType",
-      "description": "A string enum representing the supported verifiable identity types.",
-      "enum": [
-        "email",
-        "orcid",
-        "github"
-      ],
-      "type": "string"
-    },
-    "Identity": {
-      "title": "Identity",
-      "description": "A model for identities that can be provided by external systems\nand associated with a given user.",
-      "type": "object",
-      "properties": {
-        "identity_type": {
-          "$ref": "#/definitions/IdentityType"
-        },
-        "identifier": {
-          "title": "Identifier",
-          "type": "string"
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "verified": {
-          "title": "Verified",
-          "default": false,
-          "type": "boolean"
-        },
-        "display_name": {
-          "title": "Display Name",
-          "type": "string"
-        }
-      },
-      "required": [
-        "identity_type",
-        "identifier",
-        "name"
-      ]
-    },
-    "UserRole": {
-      "title": "UserRole",
-      "description": "An enumeration.",
-      "enum": [
-        "user",
-        "admin",
-        "manager"
-      ],
-      "type": "string"
-    },
-    "AccountStatus": {
-      "title": "AccountStatus",
-      "description": "A string enum representing the account status.",
-      "enum": [
-        "active",
-        "unverified",
-        "deactivated"
-      ],
-      "type": "string"
-    },
-    "Person": {
-      "title": "Person",
-      "description": "A model that describes an individual and their digital identities.",
-      "type": "object",
-      "properties": {
-        "type": {
-          "title": "Type",
-          "default": "people",
-          "const": "people",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "identities": {
-          "title": "Identities",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Identity"
-          }
-        },
-        "display_name": {
-          "title": "Display Name",
-          "minLength": 1,
-          "maxLength": 150,
-          "type": "string"
-        },
-        "contact_email": {
-          "title": "Contact Email",
-          "type": "string",
-          "format": "email"
-        },
-        "managers": {
-          "title": "Managers",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "role": {
-          "default": "user",
-          "allOf": [
-            {
-              "$ref": "#/definitions/UserRole"
-            }
-          ]
-        },
-        "account_status": {
-          "default": "unverified",
-          "allOf": [
-            {
-              "$ref": "#/definitions/AccountStatus"
-            }
-          ]
-        }
-      }
-    },
-    "Collection": {
-      "title": "Collection",
-      "description": "An Entry is an abstract base class for any model that can be\ndeserialized and stored in the database.",
-      "type": "object",
-      "properties": {
-        "blocks_obj": {
-          "title": "Blocks Obj",
-          "default": {},
-          "type": "object",
-          "additionalProperties": {
-            "$ref": "#/definitions/DataBlockResponse"
-          }
-        },
-        "display_order": {
-          "title": "Display Order",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "collections",
-          "const": "collections",
-          "pattern": "^collections$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "collection_id": {
-          "title": "Collection Id",
-          "minLength": 1,
-          "maxLength": 40,
-          "pattern": "^(?:[a-zA-Z0-9]+|[a-zA-Z0-9][a-zA-Z0-9._-]+[a-zA-Z0-9])$",
-          "type": "string"
-        },
-        "title": {
-          "title": "Title",
-          "type": "string"
-        },
-        "description": {
-          "title": "Description",
-          "type": "string"
-        },
-        "num_items": {
-          "title": "Num Items",
-          "type": "integer"
-        }
-      }
-    },
-    "File": {
-      "title": "File",
-      "description": "A model for representing a file that has been tracked or uploaded to datalab.",
-      "type": "object",
-      "properties": {
-        "revision": {
-          "title": "Revision",
-          "default": 1,
-          "type": "integer"
-        },
-        "revisions": {
-          "title": "Revisions",
-          "type": "object"
-        },
-        "creator_ids": {
-          "title": "Creator Ids",
-          "default": [],
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "creators": {
-          "title": "Creators",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/Person"
-          }
-        },
-        "type": {
-          "title": "Type",
-          "default": "files",
-          "const": "files",
-          "pattern": "^files$",
-          "type": "string"
-        },
-        "immutable_id": {
-          "title": "Immutable ID",
-          "format": "uuid",
-          "type": "string"
-        },
-        "last_modified": {
-          "title": "Last Modified",
-          "type": "string",
-          "format": "date-time"
-        },
-        "relationships": {
-          "title": "Relationships",
-          "type": "array",
-          "items": {
-            "$ref": "#/definitions/TypedRelationship"
-          }
-        },
-        "size": {
-          "title": "Size",
-          "type": "integer"
-        },
-        "last_modified_remote": {
-          "title": "Last Modified Remote",
-          "type": "string",
-          "format": "date-time"
-        },
-        "item_ids": {
-          "title": "Item Ids",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "blocks": {
-          "title": "Blocks",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
-        },
-        "name": {
-          "title": "Name",
-          "type": "string"
-        },
-        "extension": {
-          "title": "Extension",
-          "type": "string"
-        },
-        "original_name": {
-          "title": "Original Name",
-          "type": "string"
-        },
-        "location": {
-          "title": "Location",
-          "type": "string"
-        },
-        "url_path": {
-          "title": "Url Path",
-          "type": "string"
-        },
-        "source": {
-          "title": "Source",
-          "type": "string"
-        },
-        "time_added": {
-          "title": "Time Added",
-          "type": "string",
-          "format": "date-time"
-        },
-        "metadata": {
-          "title": "Metadata",
-          "type": "object"
-        },
-        "representation": {
-          "title": "Representation"
-        },
-        "source_server_name": {
-          "title": "Source Server Name",
-          "type": "string"
-        },
-        "source_path": {
-          "title": "Source Path",
-          "type": "string"
-        },
-        "is_live": {
-          "title": "Is Live",
-          "type": "boolean"
-        }
-      },
-      "required": [
-        "item_ids",
-        "blocks",
-        "name",
-        "extension",
-        "time_added",
-        "is_live"
-      ]
-    },
-    "StartingMaterialsStatus": {
-      "title": "StartingMaterialsStatus",
-      "description": "An enumeration of the status of starting materials",
-      "enum": [
-        "ordered",
-        "disposed",
-        "planned",
-        "available",
-        "unavailable",
-        "exhausted",
-        "other"
-      ],
-      "type": "string"
-    }
-  }
-}
\ No newline at end of file
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index 3fc7d778d..07da52b15 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -129,14 +129,6 @@
         "type": "string"
       }
     },
-    "status": {
-      "default": "available",
-      "allOf": [
-        {
-          "$ref": "#/definitions/StartingMaterialsStatus"
-        }
-      ]
-    },
     "barcode": {
       "title": "Barcode",
       "type": "string"
@@ -782,20 +774,6 @@
         "time_added",
         "is_live"
       ]
-    },
-    "StartingMaterialsStatus": {
-      "title": "StartingMaterialsStatus",
-      "description": "An enumeration of the status of starting materials",
-      "enum": [
-        "ordered",
-        "disposed",
-        "planned",
-        "available",
-        "unavailable",
-        "exhausted",
-        "other"
-      ],
-      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/src/pydatalab/models/export_task.py b/pydatalab/src/pydatalab/models/export_task.py
deleted file mode 100644
index 72be5bf78..000000000
--- a/pydatalab/src/pydatalab/models/export_task.py
+++ /dev/null
@@ -1,38 +0,0 @@
-from datetime import datetime, timezone
-from enum import Enum
-
-from pydantic import BaseModel, Field
-
-
-class ExportStatus(str, Enum):
-    """Status of an export task."""
-
-    PENDING = "pending"
-    PROCESSING = "processing"
-    READY = "ready"
-    ERROR = "error"
-
-
-class ExportTask(BaseModel):
-    """Model for an export task."""
-
-    task_id: str = Field(..., description="Unique identifier for the export task")
-    collection_id: str | None = Field(None, description="ID of the collection being exported")
-    item_id: str | None = Field(None, description="ID of the sample being exported")
-    export_type: str = Field(
-        default="collection", description="Type of export: 'collection' or 'sample' or 'graph'"
-    )
-    status: ExportStatus = Field(
-        default=ExportStatus.PENDING, description="Current status of the task"
-    )
-    creator_id: str = Field(..., description="ID of the user who created the export")
-    created_at: datetime = Field(
-        default_factory=lambda: datetime.now(tz=timezone.utc),
-        description="When the task was created",
-    )
-    completed_at: datetime | None = Field(None, description="When the task was completed")
-    file_path: str | None = Field(None, description="Path to the generated .eln file")
-    error_message: str | None = Field(None, description="Error message if status is ERROR")
-
-    class Config:
-        use_enum_values = True
diff --git a/pydatalab/src/pydatalab/models/block_task.py b/pydatalab/src/pydatalab/models/tasks.py
similarity index 53%
rename from pydatalab/src/pydatalab/models/block_task.py
rename to pydatalab/src/pydatalab/models/tasks.py
index 14e026bd4..9bba2e566 100644
--- a/pydatalab/src/pydatalab/models/block_task.py
+++ b/pydatalab/src/pydatalab/models/tasks.py
@@ -5,14 +5,19 @@
 from pydantic import BaseModel, Field
 
 
-class BlockProcessingStatus(str, Enum):
+class TaskStatus(str, Enum):
     PENDING = "pending"
     PROCESSING = "processing"
     READY = "ready"
     ERROR = "error"
 
 
-class BlockProcessingStage(BaseModel):
+class TaskType(str, Enum):
+    EXPORT = "export"
+    BLOCK_PROCESSING = "block_processing"
+
+
+class TaskStage(BaseModel):
     timestamp: datetime = Field(..., description="When this stage occurred")
     message: str = Field(..., description="Description of this processing stage")
     level: Literal["info", "warning", "error"] = Field(
@@ -20,23 +25,26 @@ class BlockProcessingStage(BaseModel):
     )
 
 
-class BlockTask(BaseModel):
-    task_id: str = Field(..., description="Unique identifier for the block processing task")
-    item_id: str = Field(..., description="ID of the item containing the block")
-    block_id: str = Field(..., description="ID of the block being processed")
-    status: BlockProcessingStatus = Field(
-        default=BlockProcessingStatus.PENDING, description="Current status of the task"
-    )
+class Task(BaseModel):
+    task_id: str = Field(..., description="Unique identifier for the task")
+    type: TaskType = Field(..., description="Type of task")
+    status: TaskStatus = Field(default=TaskStatus.PENDING, description="Current status")
     creator_id: str = Field(..., description="ID of the user who created the task")
     created_at: datetime = Field(
         default_factory=lambda: datetime.now(tz=timezone.utc),
         description="When the task was created",
     )
-    completed_at: datetime | None = Field(None, description="When the task was completed")
+    completed_at: datetime | None = Field(None, description="When completed")
     error_message: str | None = Field(None, description="Error message if status is ERROR")
-    stages: list[BlockProcessingStage] = Field(
+
+    collection_id: str | None = Field(None, description="For export tasks: collection ID")
+    item_id: str | None = Field(None, description="For export/block tasks: item ID")
+    block_id: str | None = Field(None, description="For block tasks: block ID")
+    export_type: str | None = Field(None, description="For export tasks: collection/sample/graph")
+    file_path: str | None = Field(None, description="For export tasks: path to generated file")
+    stages: list[TaskStage] = Field(
         default_factory=list,
-        description="Timestamped log of processing stages for incremental progress tracking",
+        description="For block tasks: timestamped processing stages",
     )
 
     class Config:
diff --git a/pydatalab/src/pydatalab/mongo.py b/pydatalab/src/pydatalab/mongo.py
index 8b72d3058..d6cb6a6f9 100644
--- a/pydatalab/src/pydatalab/mongo.py
+++ b/pydatalab/src/pydatalab/mongo.py
@@ -207,15 +207,18 @@ def create_user_fts():
         db.users.drop_index(user_fts_name)
         ret += create_user_fts()
 
-    ret += db.export_tasks.create_index(
+    ret += db.tasks.create_index(
         "task_id", unique=True, name="unique task ID", background=background
     )
-    ret += db.export_tasks.create_index(
-        "creator_id", name="export task creator", background=background
-    )
-    ret += db.export_tasks.create_index(
-        "created_at", name="export task created at", background=background
+
+    ret += db.tasks.create_index("type", name="task type", background=background)
+    ret += db.tasks.create_index("creator_id", name="task creator", background=background)
+    ret += db.tasks.create_index("created_at", name="task created at", background=background)
+    ret += db.tasks.create_index("status", name="task status", background=background)
+    ret += db.tasks.create_index(
+        [("type", pymongo.ASCENDING), ("creator_id", pymongo.ASCENDING)],
+        name="task type and creator",
+        background=background,
     )
-    ret += db.export_tasks.create_index("status", name="export task status", background=background)
 
     return ret
diff --git a/pydatalab/src/pydatalab/routes/v0_1/blocks.py b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
index a1101c0e2..9fc058e33 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/blocks.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/blocks.py
@@ -8,7 +8,7 @@
 from pydatalab.apps import BLOCK_TYPES
 from pydatalab.blocks.base import DataBlock
 from pydatalab.config import CONFIG
-from pydatalab.models.block_task import BlockProcessingStatus, BlockTask
+from pydatalab.models.tasks import Task, TaskStage, TaskStatus, TaskType
 from pydatalab.mongo import flask_mongo
 from pydatalab.permissions import (
     active_users_or_get_only,
@@ -18,19 +18,13 @@
 
 
 def _process_block_async_internal(task_id: str, block_data: dict, event_data: dict | None):
-    from pydatalab.models.block_task import BlockProcessingStage
-
     def add_stage(message: str, level: str = "info"):
-        stage = BlockProcessingStage(
-            timestamp=datetime.now(tz=timezone.utc), message=message, level=level
-        )
-        flask_mongo.db.block_tasks.update_one(
-            {"task_id": task_id}, {"$push": {"stages": stage.dict()}}
-        )
+        stage = TaskStage(timestamp=datetime.now(tz=timezone.utc), message=message, level=level)
+        flask_mongo.db.tasks.update_one({"task_id": task_id}, {"$push": {"stages": stage.dict()}})
 
     try:
-        flask_mongo.db.block_tasks.update_one(
-            {"task_id": task_id}, {"$set": {"status": BlockProcessingStatus.PROCESSING}}
+        flask_mongo.db.tasks.update_one(
+            {"task_id": task_id}, {"$set": {"status": TaskStatus.PROCESSING}}
         )
         add_stage("Processing started")
 
@@ -56,11 +50,11 @@ def add_stage(message: str, level: str = "info"):
         _save_block_to_db(block)
 
         add_stage("Processing completed successfully", level="info")
-        flask_mongo.db.block_tasks.update_one(
+        flask_mongo.db.tasks.update_one(
             {"task_id": task_id},
             {
                 "$set": {
-                    "status": BlockProcessingStatus.READY,
+                    "status": TaskStatus.READY,
                     "completed_at": datetime.now(tz=timezone.utc),
                 }
             },
@@ -68,11 +62,11 @@ def add_stage(message: str, level: str = "info"):
 
     except Exception as e:
         add_stage(f"Error during processing: {str(e)}", level="error")
-        flask_mongo.db.block_tasks.update_one(
+        flask_mongo.db.tasks.update_one(
             {"task_id": task_id},
             {
                 "$set": {
-                    "status": BlockProcessingStatus.ERROR,
+                    "status": TaskStatus.ERROR,
                     "error_message": str(e),
                     "completed_at": datetime.now(tz=timezone.utc),
                 }
@@ -282,15 +276,16 @@ def update_block():
         else:
             creator_id = "000000000000000000000000"
 
-        block_task = BlockTask(
+        block_task = Task(
             task_id=task_id,
+            type=TaskType.BLOCK_PROCESSING,
             item_id=block_data["item_id"],
             block_id=block_data["block_id"],
             creator_id=creator_id,
-            status=BlockProcessingStatus.PENDING,
+            status=TaskStatus.PENDING,
         )
 
-        flask_mongo.db.block_tasks.insert_one(block_task.dict())
+        flask_mongo.db.tasks.insert_one(block_task.dict())
 
         try:
             app = current_app._get_current_object()
@@ -411,7 +406,7 @@ def delete_collection_block():
 
 @BLOCKS.route("/blocks/<string:task_id>/status", methods=["GET"])
 def get_block_task_status(task_id: str):
-    task = flask_mongo.db.block_tasks.find_one({"task_id": task_id})
+    task = flask_mongo.db.tasks.find_one({"task_id": task_id, "type": TaskType.BLOCK_PROCESSING})
 
     if not task:
         return jsonify({"status": "error", "message": "Task not found"}), 404
@@ -429,7 +424,7 @@ def get_block_task_status(task_id: str):
     if task.get("error_message"):
         response["error_message"] = task["error_message"]
 
-    if task["status"] == BlockProcessingStatus.READY:
+    if task["status"] == TaskStatus.READY:
         item_id = task["item_id"]
         block_id = task["block_id"]
 
diff --git a/pydatalab/src/pydatalab/routes/v0_1/export.py b/pydatalab/src/pydatalab/routes/v0_1/export.py
index 0c5c3a67c..4bbf387a9 100644
--- a/pydatalab/src/pydatalab/routes/v0_1/export.py
+++ b/pydatalab/src/pydatalab/routes/v0_1/export.py
@@ -8,7 +8,7 @@
 
 from pydatalab.config import CONFIG
 from pydatalab.export_utils import create_eln_file
-from pydatalab.models.export_task import ExportStatus, ExportTask
+from pydatalab.models.tasks import Task, TaskStatus, TaskType
 from pydatalab.mongo import flask_mongo
 from pydatalab.permissions import active_users_or_get_only
 from pydatalab.scheduler import export_scheduler
@@ -29,8 +29,8 @@ def _do_export(
     related_item_ids: list[str] | None = None,
 ):
     try:
-        flask_mongo.db.export_tasks.update_one(
-            {"task_id": task_id}, {"$set": {"status": ExportStatus.PROCESSING}}
+        flask_mongo.db.tasks.update_one(
+            {"task_id": task_id}, {"$set": {"status": TaskStatus.PROCESSING}}
         )
 
         export_dir = Path(CONFIG.FILE_DIRECTORY) / "exports"
@@ -42,11 +42,11 @@ def _do_export(
         elif export_type in ["sample", "graph"]:
             create_eln_file(str(output_path), item_id=item_id, related_item_ids=related_item_ids)
 
-        flask_mongo.db.export_tasks.update_one(
+        flask_mongo.db.tasks.update_one(
             {"task_id": task_id},
             {
                 "$set": {
-                    "status": ExportStatus.READY,
+                    "status": TaskStatus.READY,
                     "file_path": str(output_path),
                     "completed_at": datetime.now(tz=timezone.utc),
                 }
@@ -54,11 +54,11 @@ def _do_export(
         )
 
     except Exception as e:
-        flask_mongo.db.export_tasks.update_one(
+        flask_mongo.db.tasks.update_one(
             {"task_id": task_id},
             {
                 "$set": {
-                    "status": ExportStatus.ERROR,
+                    "status": TaskStatus.ERROR,
                     "error_message": str(e),
                     "completed_at": datetime.now(tz=timezone.utc),
                 }
@@ -98,15 +98,16 @@ def start_collection_export(collection_id: str):
     else:
         creator_id = "000000000000000000000000"
 
-    export_task = ExportTask(
+    export_task = Task(
         task_id=task_id,
+        type=TaskType.EXPORT,
         collection_id=collection_id,
         export_type="collection",
         creator_id=creator_id,
-        status=ExportStatus.PENDING,
+        status=TaskStatus.PENDING,
     )
 
-    flask_mongo.db.export_tasks.insert_one(export_task.dict(exclude_none=False))
+    flask_mongo.db.tasks.insert_one(export_task.dict(exclude_none=False))
 
     try:
         app = current_app._get_current_object()
@@ -126,7 +127,7 @@ def start_collection_export(collection_id: str):
 
 @EXPORT.route("/exports/<string:task_id>/status", methods=["GET"])
 def get_export_status(task_id: str):
-    task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
+    task = flask_mongo.db.tasks.find_one({"task_id": task_id, "type": TaskType.EXPORT})
 
     if not task:
         return jsonify({"status": "error", "message": "Export task not found"}), 404
@@ -136,13 +137,13 @@ def get_export_status(task_id: str):
         "created_at": task["created_at"].isoformat() if task.get("created_at") else None,
     }
 
-    if task["status"] == ExportStatus.READY:
+    if task["status"] == TaskStatus.READY:
         response["download_url"] = f"/exports/{task_id}/download"
         response["completed_at"] = (
             task["completed_at"].isoformat() if task.get("completed_at") else None
         )
 
-    if task["status"] == ExportStatus.ERROR:
+    if task["status"] == TaskStatus.ERROR:
         response["error_message"] = task.get("error_message")
         response["completed_at"] = (
             task["completed_at"].isoformat() if task.get("completed_at") else None
@@ -153,12 +154,12 @@ def get_export_status(task_id: str):
 
 @EXPORT.route("/exports/<string:task_id>/download", methods=["GET"])
 def download_export(task_id: str):
-    task = flask_mongo.db.export_tasks.find_one({"task_id": task_id})
+    task = flask_mongo.db.tasks.find_one({"task_id": task_id, "type": TaskType.EXPORT})
 
     if not task:
         return jsonify({"status": "error", "message": "Export task not found"}), 404
 
-    if task["status"] != ExportStatus.READY:
+    if task["status"] != TaskStatus.READY:
         return jsonify(
             {"status": "error", "message": f"Export is not ready. Current status: {task['status']}"}
         ), 400
@@ -206,16 +207,16 @@ def start_sample_export(item_id: str):
             ), 400
         export_type = "graph"
 
-    export_task = ExportTask(
+    export_task = Task(
         task_id=task_id,
-        collection_id=None,
+        type=TaskType.EXPORT,
         item_id=item_id,
         export_type=export_type,
         creator_id=creator_id,
-        status=ExportStatus.PENDING,
+        status=TaskStatus.PENDING,
     )
 
-    flask_mongo.db.export_tasks.insert_one(export_task.dict(exclude_none=False))
+    flask_mongo.db.tasks.insert_one(export_task.dict(exclude_none=False))
 
     try:
         app = current_app._get_current_object()
diff --git a/pydatalab/tests/server/test_export.py b/pydatalab/tests/server/test_export.py
index 416aa93a9..9aafe07b5 100644
--- a/pydatalab/tests/server/test_export.py
+++ b/pydatalab/tests/server/test_export.py
@@ -5,7 +5,7 @@
 import pytest
 from bson import ObjectId
 
-from pydatalab.models.export_task import ExportStatus, ExportTask
+from pydatalab.models.tasks import Task, TaskStatus, TaskType
 
 
 @pytest.fixture
@@ -51,13 +51,14 @@ def test_start_collection_export_success(
         assert mock_scheduler.add_job.called
 
         # Verify the task was created in the database
-        task = database.export_tasks.find_one({"task_id": data["task_id"]})
+        task = database.tasks.find_one({"task_id": data["task_id"]})
         assert task is not None
+        assert task["type"] == TaskType.EXPORT
         assert task["collection_id"] == collection_id
-        assert task["status"] == ExportStatus.PENDING
+        assert task["status"] == TaskStatus.PENDING
 
         # Clean up
-        database.export_tasks.delete_one({"task_id": data["task_id"]})
+        database.tasks.delete_one({"task_id": data["task_id"]})
 
     def test_start_collection_export_not_found(self, client):
         response = client.post("/collections/nonexistent/export")
@@ -69,13 +70,15 @@ def test_start_collection_export_not_found(self, client):
 
     def test_get_export_status_pending(self, client, database):
         task_id = "test-task-pending"
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id="test_collection",
             creator_id="000000000000000000000000",
-            status=ExportStatus.PENDING,
+            status=TaskStatus.PENDING,
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/status")
         assert response.status_code == 200
@@ -84,22 +87,24 @@ def test_get_export_status_pending(self, client, database):
         assert data["status"] == "pending"
         assert "created_at" in data
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})
 
     def test_get_export_status_ready(self, client, database, tmp_path):
         task_id = "test-task-ready"
         file_path = tmp_path / f"{task_id}.eln"
         file_path.write_text("test content")
 
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id="test_collection",
             creator_id="000000000000000000000000",
-            status=ExportStatus.READY,
+            status=TaskStatus.READY,
             file_path=str(file_path),
             completed_at=datetime.now(tz=timezone.utc),
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/status")
         assert response.status_code == 200
@@ -109,21 +114,23 @@ def test_get_export_status_ready(self, client, database, tmp_path):
         assert data["download_url"] == f"/exports/{task_id}/download"
         assert "completed_at" in data
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})
 
     def test_get_export_status_error(self, client, database):
         task_id = "test-task-error"
         error_message = "Export failed due to test error"
 
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id="test_collection",
             creator_id="000000000000000000000000",
-            status=ExportStatus.ERROR,
+            status=TaskStatus.ERROR,
             error_message=error_message,
             completed_at=datetime.now(tz=timezone.utc),
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/status")
         assert response.status_code == 200
@@ -133,7 +140,7 @@ def test_get_export_status_error(self, client, database):
         assert data["error_message"] == error_message
         assert "completed_at" in data
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})
 
     def test_get_export_status_not_found(self, client):
         response = client.get("/exports/nonexistent-task/status")
@@ -149,32 +156,36 @@ def test_download_export_success(self, client, database, tmp_path):
         file_path = tmp_path / f"{task_id}.eln"
         file_path.write_bytes(b"test export content")
 
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id=collection_id,
             creator_id="000000000000000000000000",
-            status=ExportStatus.READY,
+            status=TaskStatus.READY,
             file_path=str(file_path),
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/download")
         assert response.status_code == 200
         assert response.data == b"test export content"
         assert f"filename={collection_id}.eln" in response.headers.get("Content-Disposition", "")
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})
 
     def test_download_export_not_ready(self, client, database):
         task_id = "test-not-ready-task"
 
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id="test_collection",
             creator_id="000000000000000000000000",
-            status=ExportStatus.PROCESSING,
+            status=TaskStatus.PROCESSING,
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/download")
         assert response.status_code == 400
@@ -182,19 +193,21 @@ def test_download_export_not_ready(self, client, database):
         data = json.loads(response.data)
         assert "not ready" in data["message"].lower()
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})
 
     def test_download_export_file_missing(self, client, database):
         task_id = "test-missing-file-task"
 
-        task = ExportTask(
+        task = Task(
             task_id=task_id,
+            type=TaskType.EXPORT,
             collection_id="test_collection",
             creator_id="000000000000000000000000",
-            status=ExportStatus.READY,
+            status=TaskStatus.READY,
             file_path="/nonexistent/path.eln",
         )
-        database.export_tasks.insert_one(task.dict())
+
+        database.tasks.insert_one(task.dict())
 
         response = client.get(f"/exports/{task_id}/download")
         assert response.status_code == 404
@@ -202,4 +215,4 @@ def test_download_export_file_missing(self, client, database):
         data = json.loads(response.data)
         assert "file not found" in data["message"].lower()
 
-        database.export_tasks.delete_one({"task_id": task_id})
+        database.tasks.delete_one({"task_id": task_id})

From 707031391590c5bff27a2509ae826d0a02313029 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 16 Dec 2025 15:00:40 +0100
Subject: [PATCH 24/26] Unify BlockTask and ExportTask into single Task model

---
 webapp/src/server_fetch_utils.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index 073a99809..da659d2f1 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -1093,6 +1093,7 @@ export async function startCollectionExport(collection_id) {
 export async function getExportStatus(task_id) {
   return fetch_get(`${API_URL}/exports/${task_id}/status`)
     .then(function (response_json) {
+      console.log(response_json);
       return response_json;
     })
     .catch((error) => {

From c5b2ba4d475235f35f0f9036a20751dad54d4a29 Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 16 Dec 2025 15:00:53 +0100
Subject: [PATCH 25/26] Unify BlockTask and ExportTask into single Task model

---
 webapp/src/server_fetch_utils.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/webapp/src/server_fetch_utils.js b/webapp/src/server_fetch_utils.js
index da659d2f1..073a99809 100644
--- a/webapp/src/server_fetch_utils.js
+++ b/webapp/src/server_fetch_utils.js
@@ -1093,7 +1093,6 @@ export async function startCollectionExport(collection_id) {
 export async function getExportStatus(task_id) {
   return fetch_get(`${API_URL}/exports/${task_id}/status`)
     .then(function (response_json) {
-      console.log(response_json);
       return response_json;
     })
     .catch((error) => {

From c1af4dfd3df9caa8e8baf623e8bf2c8ab553584f Mon Sep 17 00:00:00 2001
From: Benjamin CHARMES <benjamin.charmes@gmail.com>
Date: Tue, 16 Dec 2025 15:10:02 +0100
Subject: [PATCH 26/26] Regenerate JSON schemas for item models

---
 pydatalab/schemas/cell.json             | 22 ++++++++++++++++++++++
 pydatalab/schemas/equipment.json        | 21 +++++++++++++++++++++
 pydatalab/schemas/sample.json           | 21 +++++++++++++++++++++
 pydatalab/schemas/startingmaterial.json | 22 ++++++++++++++++++++++
 4 files changed, 86 insertions(+)

diff --git a/pydatalab/schemas/cell.json b/pydatalab/schemas/cell.json
index 3b2392905..6d4ec0dba 100644
--- a/pydatalab/schemas/cell.json
+++ b/pydatalab/schemas/cell.json
@@ -117,6 +117,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/CellStatus"
+        }
+      ]
+    },
     "cell_format": {
       "$ref": "#/definitions/CellFormat"
     },
@@ -669,6 +677,20 @@
         "is_live"
       ]
     },
+    "CellStatus": {
+      "title": "CellStatus",
+      "description": "An enumeration of the status of cells",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "cycled",
+        "shorted",
+        "dismantled",
+        "other"
+      ],
+      "type": "string"
+    },
     "CellFormat": {
       "title": "CellFormat",
       "description": "An enumeration.",
diff --git a/pydatalab/schemas/equipment.json b/pydatalab/schemas/equipment.json
index b2954932e..6dc8849f2 100644
--- a/pydatalab/schemas/equipment.json
+++ b/pydatalab/schemas/equipment.json
@@ -117,6 +117,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "working",
+      "allOf": [
+        {
+          "$ref": "#/definitions/EquipmentStatus"
+        }
+      ]
+    },
     "serial_numbers": {
       "title": "Serial Numbers",
       "type": "string"
@@ -632,6 +640,19 @@
         "time_added",
         "is_live"
       ]
+    },
+    "EquipmentStatus": {
+      "title": "EquipmentStatus",
+      "description": "An enumeration of the status of equipments",
+      "enum": [
+        "working",
+        "broken",
+        "being_fixed",
+        "defunct",
+        "not_being_fixed",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/sample.json b/pydatalab/schemas/sample.json
index b6e8ec6c1..75e1672d7 100644
--- a/pydatalab/schemas/sample.json
+++ b/pydatalab/schemas/sample.json
@@ -129,6 +129,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "active",
+      "allOf": [
+        {
+          "$ref": "#/definitions/ItemStatus"
+        }
+      ]
+    },
     "chemform": {
       "title": "Chemform",
       "example": [
@@ -721,6 +729,19 @@
         "time_added",
         "is_live"
       ]
+    },
+    "ItemStatus": {
+      "title": "ItemStatus",
+      "description": "An enumeration of the status of items",
+      "enum": [
+        "active",
+        "planned",
+        "disposed",
+        "completed",
+        "failed",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file
diff --git a/pydatalab/schemas/startingmaterial.json b/pydatalab/schemas/startingmaterial.json
index 07da52b15..3fc7d778d 100644
--- a/pydatalab/schemas/startingmaterial.json
+++ b/pydatalab/schemas/startingmaterial.json
@@ -129,6 +129,14 @@
         "type": "string"
       }
     },
+    "status": {
+      "default": "available",
+      "allOf": [
+        {
+          "$ref": "#/definitions/StartingMaterialsStatus"
+        }
+      ]
+    },
     "barcode": {
       "title": "Barcode",
       "type": "string"
@@ -774,6 +782,20 @@
         "time_added",
         "is_live"
       ]
+    },
+    "StartingMaterialsStatus": {
+      "title": "StartingMaterialsStatus",
+      "description": "An enumeration of the status of starting materials",
+      "enum": [
+        "ordered",
+        "disposed",
+        "planned",
+        "available",
+        "unavailable",
+        "exhausted",
+        "other"
+      ],
+      "type": "string"
     }
   }
 }
\ No newline at end of file