From e6592d6ece08f1c7a4882d5fe2bcef646f6fb09b Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 10 Jun 2025 13:20:15 +0200 Subject: [PATCH 01/12] Dataverse Deposit Plugin & init Integration --- poetry.lock | 1598 ++++++++++------- pyproject.toml | 24 +- src/hermes/commands/deposit/dataverse.py | 158 ++ src/hermes/commands/deposit/invenio.py | 15 - src/hermes/commands/init/base.py | 150 +- .../commands/init/util/connect_zenodo.py | 17 +- src/hermes/commands/init/util/slim_click.py | 2 +- 7 files changed, 1258 insertions(+), 706 deletions(-) create mode 100644 src/hermes/commands/deposit/dataverse.py diff --git a/poetry.lock b/poetry.lock index 131af6ca..a2fd6abe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. 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"Makes working with XML feel like you are working with JSON" +optional = false +python-versions = ">=3.4" +groups = ["main"] +files = [ + {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, + {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"}, ] [metadata] lock-version = "2.1" python-versions = ">=3.10, <4.0.0" -content-hash = "58304fd33d6ec1ce3400b43ecffb16b3f48a5621e513c3e8057f9e3e050835e8" +content-hash = "b982fd34b27ceca07579cac6f4e7fd58dcd4e0ace6ee022ee9ea2e1d4bc7d501" diff --git a/pyproject.toml b/pyproject.toml index 4ef373c3..01b4fd15 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,6 +39,7 @@ dependencies = [ "pydantic-settings>=2.1.0, <3.0.0", "requests-oauthlib>=2.0.0, <3.0.0", "pynacl>=1.5.0, <2.0.0", + "easydataverse>=0.4.4, <0.5.0", ] requires-python = ">=3.10, <4.0.0" @@ -48,12 +49,10 @@ documentation = "https://hermes.software-metadata.pub" repository = "https://github.com/softwarepub/hermes.git" issues = "https://github.com/softwarepub/hermes/issues" - [project.scripts] hermes = "hermes.commands.cli:main" hermes-marketplace = "hermes.commands.marketplace:main" - [project.entry-points."hermes.harvest"] cff = "hermes.commands.harvest.cff:CffHarvestPlugin" codemeta = "hermes.commands.harvest.codemeta:CodeMetaHarvestPlugin" @@ -69,7 +68,6 @@ config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id config_invenio_rdm_record_id = "hermes.commands.postprocess.invenio_rdm:config_record_id" cff_doi = "hermes.commands.postprocess.invenio:cff_doi" - [tool.poetry.group.dev.dependencies] pytest = "^7.1.1" pytest-cov = "^3.0.0" @@ -99,6 +97,24 @@ sphinx-togglebutton="^0.3.2" reuse = "^1.1.2" sphinxcontrib-datatemplates = "^0.11.0" +[tool.poetry.plugins.console_scripts] +hermes = "hermes.commands.cli:main" +hermes-marketplace = "hermes.commands.marketplace:main" + +[tool.poetry.plugins."hermes.harvest"] +cff = "hermes.commands.harvest.cff:CffHarvestPlugin" +codemeta = "hermes.commands.harvest.codemeta:CodeMetaHarvestPlugin" + +[tool.poetry.plugins."hermes.deposit"] +file = "hermes.commands.deposit.file:FileDepositPlugin" +invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" +invenio_rdm = "hermes.commands.deposit.invenio_rdm:IvenioRDMDepositPlugin" +rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" + +[tool.poetry.plugins."hermes.postprocess"] +config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id" +config_invenio_rdm_record_id = "hermes.commands.postprocess.invenio_rdm:config_record_id" +cff_doi = "hermes.commands.postprocess.invenio:cff_doi" [tool.taskipy.tasks] docs-build = "poetry run sphinx-build -M html docs/source docs/build -W" @@ -106,7 +122,6 @@ docs-clean = "poetry run sphinx-build -M clean docs/source docs/build" docs-live = "poetry run sphinx-autobuild docs/source docs/build" flake8 = "poetry run flake8 ./test/ ./src/ --count --select=E9,F63,F7,F82 --statistics" - [tool.pytest.ini_options] norecursedirs = "docs/*" testpaths = [ @@ -114,7 +129,6 @@ testpaths = [ ] addopts = "--cov=hermes --cov-report term" - [build-system] requires = [ "poetry-core>=2.1.3, <3.0.0" diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py new file mode 100644 index 00000000..11a3ac40 --- /dev/null +++ b/src/hermes/commands/deposit/dataverse.py @@ -0,0 +1,158 @@ +# SPDX-FileCopyrightText: 2025 Forschungszentrum Jülich GmbH +# SPDX-License-Identifier: Apache-2.0 +# SPDX-FileContributor: Nitai Heeb + +import json +import logging +import requests +from pathlib import Path + +from hermes.commands.deposit.base import BaseDepositPlugin +from hermes.commands.deposit.error import DepositionUnauthorizedError +from hermes.model.path import ContextPath +from pydantic import BaseModel +from easyDataverse import Dataverse, License, Dataset +from hermes.utils import hermes_doi + + +_log = logging.getLogger("cli.deposit.dataverse") + + +class DataverseDepositSettings(BaseModel): + """Settings required to deposit into Dataverse.""" + site_url: str = "" + host_dataverse: str = "" + auth_token: str = "" + dataset_pid: str = None + files: list[Path] = [] + + +class DataverseDepositPlugin(BaseDepositPlugin): + platform_name = "dataverse" + settings_class = DataverseDepositSettings + + def __init__(self, command, ctx) -> None: + super().__init__(command, ctx) + self.config = getattr(self.command.settings, self.platform_name) + auth_token = self.config.auth_token + if not auth_token: + raise DepositionUnauthorizedError("No valid auth token given for deposition platform") + self.client = Dataverse(server_url=self.config.site_url, api_token=self.config.auth_token) + self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") + + def map_metadata(self) -> None: + """ + Saves the given codemeta-metadata, so it's ready to be used. + Since we add the metadata with easyDataverse there is no mapping needed at this point. + """ + metadata = self.ctx["codemeta"] + self.ctx.update(self.ctx_path["depositionMetadata"], metadata) + with open(self.ctx.get_cache("deposit", self.platform_name, create=True), 'w') as f: + json.dump(metadata, f, indent=2) + + def is_initial_publication(self) -> bool: + return self.config.dataset_pid is None + + def update_metadata_on_dataset(self, dataset: Dataset): + """ + Sets metadata on an easyDataverse.Dataset using the depositionMetadata + """ + metadata = self.ctx[self.ctx_path["depositionMetadata"]] + dataset.citation.title = metadata.get("name", "") + dataset.citation.subject = ["Other"] + dataset.citation.add_ds_description(value=metadata.get("description", "")) + + authors = metadata.get("author", []) + for i, author in enumerate(authors): + full_name = f"{author.get('familyName')}, {author.get('givenName')}" \ + if author.get("familyName") and author.get("givenName") \ + else author.get("name") + affiliation_name = "" + if affiliation_dict := author.get("affiliation"): + affiliation_name = affiliation_dict.get("legalName", "") + dataset.citation.add_author(name=full_name, affiliation=affiliation_name) + if i == 0: + dataset.citation.add_dataset_contact(name=full_name, email=author.get("email")) + + if date_published := metadata.get("datePublished"): + dataset.citation.date_of_deposit = date_published + # TODO look for "version" or something similar in dataverse + # if version := metadata.get("version"): + # dataset.citation.version = version <- does not exist + if keywords := metadata.get("keywords", []): + if keywords is list: + for keyword in keywords: + dataset.citation.add_keyword(keyword) + if deposition_license := metadata.get("license"): + try: + dataverse_license = License.fetch_by_name(deposition_license, server_url=self.client.server_url) + dataset.citation.license = dataverse_license + except Exception as e: + _log.warning(f"Could not match license '{deposition_license}' to Dataverse vocabulary: {e}") + dataset.citation.other_references = [f"Compiled by HERMES ({hermes_doi})"] + + def create_initial_version(self) -> None: + """ + Creates an initial version of a publication. + The original DepositPlugin flow with first creating the initial version and then adding metadata doesn't + fit well with easyDataverse module since it requires certain metadata field to create the initial version. + As solution, we use update_metadata_on_dataset(dataset) both in this method and in update_metadata(). + """ + if not self.command.args.initial: + raise RuntimeError("Please use `--initial` to make an initial deposition.") + dataset = self.client.create_dataset() + self.update_metadata_on_dataset(dataset) + persistent_id = dataset.upload(dataverse_name=self.config.host_dataverse) + self.ctx.update(self.ctx_path["persistentId"], persistent_id) + + def create_new_version(self) -> None: + """ + Creates a new version of an existing publication. + TODO implement this + """ + persistent_id = self.ctx[self.ctx_path["persistentId"]] + if not persistent_id: + raise RuntimeError("No persistent ID found in context. Cannot create new version.") + dataset = self.client.load_dataset(persistent_id) + if not dataset: + raise RuntimeError(f"Could not load dataset for persistent ID {persistent_id}") + _log.warning("Creating a new version of a dataset is not implemented right now.") + + def update_metadata(self) -> None: + """ + Updates the dataset's metadata if the dataset is not newly created. + If it is newly created, update_metadata_on_dataset was already called in create_initial_version. + """ + if not self.command.args.initial: + persistent_id = self.ctx[self.ctx_path["persistentId"]] + dataset = self.client.load_dataset(persistent_id) + self.update_metadata_on_dataset(dataset) + res = dataset.update() + if not res.ok: + raise RuntimeError(f"Failed to update metadata: {res.status_code}: {res.text}") + + def upload_artifacts(self) -> None: + """ + Uploads new artifacts to the current dataverse-dataset. + """ + persistent_id = self.ctx[self.ctx_path["persistentId"]] + dataset = self.client.load_dataset(persistent_id) + files = *self.config.files, *[f[0] for f in self.command.args.file] + for path_string in files: + path_string = str(path_string) + dataset.add_file(path_string) + dataset.update() + + def publish(self) -> None: + """ + Publishes the newly created dataset / publication. + Unfortunately easyDataverse module does not support publishing. So we do that with requests. + """ + persistent_id = self.ctx[self.ctx_path["persistentId"]] + url = f"{self.config.site_url}/api/datasets/:persistentId/actions/:publish" + params = {"type": "major"} + headers = {"X-Dataverse-key": self.config.auth_token} + res = requests.post(url, headers=headers, params=params, data={"persistentId": persistent_id}) + if not res.ok: + raise RuntimeError(f"Publish failed: {res.status_code}: {res.text}") + diff --git a/src/hermes/commands/deposit/invenio.py b/src/hermes/commands/deposit/invenio.py index e88066c6..b6bd4c60 100644 --- a/src/hermes/commands/deposit/invenio.py +++ b/src/hermes/commands/deposit/invenio.py @@ -267,21 +267,6 @@ def __init__(self, command: HermesDepositCommand, ctx: CodeMetaContext, client=N if client is None: auth_token = self.config.auth_token - - # TODO reactivate this code again, once we use Zenodo OAuth again (once the refresh token works) - # If auth_token is a refresh-token, get the auth-token from that. - # if str(auth_token).startswith("REFRESH_TOKEN:"): - # _log.debug(f"Getting token from refresh_token {auth_token}") - # # TODO How do we know if this targets sandbox or not? - # # Now we assume it's sandbox - # connect_zenodo.setup(True) - # tokens = connect_zenodo.oauth_process() \ - # .get_tokens_from_refresh_token(auth_token.split("REFRESH_TOKEN:")[1]) - # _log.debug(f"Tokens: {str(tokens)}") - # auth_token = tokens.get("access_token", "") - # _log.debug(f"Auth Token: {auth_token}") - # # TODO Update the secret (github/lab token is needed) - if not auth_token: raise DepositionUnauthorizedError("No valid auth token given for deposition platform") self.client = self.invenio_client_class(self.config, diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index 5937eded..8d59fefb 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -35,22 +35,44 @@ class GitHoster(Enum): GitLab = auto() -class DepositPlatform(Enum): +class DepositId(Enum): + """ + Enum as additional identifier for DepositPlatforms so we have something persistent to code with. + """ Empty = auto() Zenodo = auto() ZenodoSandbox = auto() + JuelichData = auto() + DemoDataverse = auto() -DepositPlatformNames: dict[DepositPlatform, str] = { - DepositPlatform.ZenodoSandbox: "Zenodo (Sandbox)", - DepositPlatform.Zenodo: "Zenodo", - } - - -DepositPlatformUrls: dict[DepositPlatform, str] = { - DepositPlatform.Zenodo: "https://zenodo.org/", - DepositPlatform.ZenodoSandbox: "https://sandbox.zenodo.org/" - } +@dataclass +class DepositPlatform: + """ + This dataclass contains all relevant data to set up hermes for a given platform. + """ + def __init__(self, name: str = "", url: str = "", plugin_name: str = "", deposit_id: DepositId = DepositId.Empty): + self.name: str = name + self.url: str = url + """Base url of the deposit platform""" + self.plugin_name: str = plugin_name + """Internal name of our related hermes deposit plugin""" + self.id: DepositId = deposit_id + """Non changing enum-based ID to keep the consistency""" + self.internal_name: str = deposit_id.name + self.token: str = "" + """This is the access token which will get filled in connect_deposit_platform""" + self.token_name: str = re.sub(r'(? None: self.mark_as_new_path(ci_file_path) # Creating folder & ci file ci_file_folder.mkdir(parents=True, exist_ok=True) + sc.debug_info(f"Downloading github template from {template_url}") download_file_from_url(template_url, ci_file_path) self.configure_ci_template(ci_file_path) sc.echo(f"GitHub CI: File was created at {ci_file_path}", formatting=sc.Formats.OKGREEN) @@ -470,24 +491,24 @@ def configure_ci_template(self, ci_file_path) -> None: with open(ci_file_path, 'r') as file: content = file.read() parameters = list(set(re.findall(r'{%(.*?)%}', content))) + sc.debug_info(f"Replacing template params {parameters} with {self.ci_parameters}") for parameter in parameters: if parameter in self.ci_parameters: value = str(self.ci_parameters[parameter]) content = content.replace(f'{{%{parameter}%}}', value) else: - sc.debug_info(f"CI File Parameter {{%{parameter}%}} was not set.", formatting=sc.Formats.WARNING) + sc.debug_info(f"CI File Parameter {{%{parameter}%}} was not set.") content = content.replace(f'{{%{parameter}%}}', '') with open(ci_file_path, 'w') as file: file.write(content) def create_zenodo_token(self) -> None: - """Makes the user create a zenodo token and saves it in self.tokens.""" - self.tokens[self.deposit_platform] = "" + """Makes the user create a zenodo token and saves it in self.deposit_platform.token.""" # Deactivated Zenodo OAuth as long as the refresh token bug is not fixed. if self.setup_method == "a": sc.echo("Doing OAuth with Zenodo is currently not available.") - if self.setup_method == "m" or self.tokens[self.deposit_platform] == '': - zenodo_token_url = urljoin(DepositPlatformUrls[self.deposit_platform], + if self.setup_method == "m" or self.deposit_platform.token == '': + zenodo_token_url = urljoin(self.deposit_platform.url, "account/settings/applications/tokens/new/") sc.echo("{} and create an access token.".format( sc.create_console_hyperlink(zenodo_token_url, "Open this link") @@ -497,18 +518,30 @@ def create_zenodo_token(self) -> None: sc.press_enter_to_continue() else: while True: - self.tokens[self.deposit_platform] = sc.answer("Enter the token here: ") - valid = connect_zenodo.test_if_token_is_valid(self.tokens[self.deposit_platform]) + self.deposit_platform.token = sc.answer("Enter the token here: ") + valid = connect_zenodo.test_if_token_is_valid(self.deposit_platform.token) if valid: - sc.echo(f"The token was validated by {connect_zenodo.name}.", + sc.echo(f"The token was validated by {self.deposit_platform.name}.", formatting=sc.Formats.OKGREEN) break else: - sc.echo(f"The token could not be validated by {connect_zenodo.name}. " + sc.echo(f"The token could not be validated by {self.deposit_platform.name}. " "Make sure to enter the complete token.\n" "(If this error persists, you should try switching to the manual setup mode.)", formatting=sc.Formats.WARNING) + def create_dataverse_token(self): + # TODO Try dataverse oauth + token_url = urljoin(self.deposit_platform.url, "dataverseuser.xhtml?selectTab=apiTokenTab") + sc.echo("{} and create an access token.".format( + sc.create_console_hyperlink(token_url, "Open this link") + )) + if self.setup_method == "m": + sc.press_enter_to_continue() + else: + # TODO try to validate the token + self.deposit_platform.token = sc.answer("Enter the token here: ") + def configure_git_project(self) -> None: """Adds the token to the git secrets & changes action workflow settings.""" match self.git_hoster: @@ -524,8 +557,8 @@ def configure_github(self) -> None: if self.tokens[GitHoster.GitHub]: sc.echo("OAuth at GitHub was successful.", formatting=sc.Formats.OKGREEN) sc.debug_info(github_token=self.tokens[GitHoster.GitHub]) - connect_github.create_secret(self.git_remote_url, "ZENODO_SANDBOX", - secret_value=self.tokens[self.deposit_platform], + connect_github.create_secret(self.git_remote_url, self.deposit_platform.token_name, + secret_value=self.deposit_platform.token, token=self.tokens[GitHoster.GitHub]) connect_github.allow_actions(self.git_remote_url, token=self.tokens[GitHoster.GitHub]) @@ -534,13 +567,14 @@ def configure_github(self) -> None: sc.echo("Something went wrong while doing OAuth. You'll have to do it manually instead.", formatting=sc.Formats.WARNING) if not oauth_success: - sc.echo("Add the {} token{} to your {} under the name ZENODO_SANDBOX.".format( + sc.echo("Add the {} token{} to your {} under the name {}.".format( self.deposit_platform.name, - f" ({self.tokens[self.deposit_platform]})" if self.tokens[self.deposit_platform] else "", + f" ({self.deposit_platform.token})" if self.deposit_platform.token else "", sc.create_console_hyperlink( self.git_remote_url + "/settings/secrets/actions", "project's GitHub secrets" - ) + ), + self.deposit_platform.token_name )) sc.press_enter_to_continue() sc.echo("Next open your {} and check the checkbox which reads:".format( @@ -569,7 +603,7 @@ def configure_gitlab(self) -> None: token = sc.answer("Then paste the token here: ") if gl.authorize(token): vars_created = gl.create_variable( - "ZENODO_TOKEN", self.tokens[self.deposit_platform], + self.deposit_platform.token_name, self.deposit_platform.token, f"This token is used by Hermes to publish on {self.deposit_platform.name}." ) if vars_created: @@ -601,30 +635,40 @@ def configure_gitlab(self) -> None: sc.echo("Then, add that token as variable with key HERMES_PUSH_TOKEN.") sc.echo("(For your safety, you should set the visibility to 'Masked'.)") sc.press_enter_to_continue() - sc.echo("Next, add the {} token{} as variable with key ZENODO_TOKEN.".format( + sc.echo("Next, add the {} token{} as variable with key {}.".format( self.deposit_platform.name, - f" ({self.tokens[self.deposit_platform]})" if self.tokens[self.deposit_platform] else "" + f" ({self.deposit_platform.token})" if self.deposit_platform.token else "", + self.deposit_platform.token_name )) sc.echo("(For your safety, you should set the visibility to 'Masked'.)") sc.press_enter_to_continue() def choose_deposit_platform(self) -> None: """User chooses his desired deposit platform.""" - deposit_platform_list = list(DepositPlatformNames.keys()) deposit_platform_index = sc.choose( - "Where do you want to publish the software?", [DepositPlatformNames[dp] for dp in deposit_platform_list] + "Where do you want to publish the software?", [do.name for do in DepositOptions] ) - self.deposit_platform = deposit_platform_list[deposit_platform_index] + self.deposit_platform = DepositOptions[deposit_platform_index] def integrate_deposit_platform(self) -> None: """Makes changes to the toml data or something else based on the chosen deposit platform.""" - deposit_url = DepositPlatformUrls.get(self.deposit_platform) - self.hermes_toml_data["deposit"]["invenio_rdm"]["site_url"] = deposit_url + deposit_plugin: str = self.deposit_platform.plugin_name + self.hermes_toml_data["deposit"]["target"] = deposit_plugin + self.hermes_toml_data["deposit"][deposit_plugin] = {} + self.hermes_toml_data["deposit"][deposit_plugin]["site_url"] = self.deposit_platform.url + self.ci_parameters["deposit_parameter_token"] = f"-O {deposit_plugin}.auth_token" + self.ci_parameters["deposit_token_name"] = self.deposit_platform.token_name + if deposit_plugin.startswith("invenio"): + self.hermes_toml_data["deposit"][deposit_plugin]["access_right"] = "open" + elif deposit_plugin == "dataverse": + host_dataverse = sc.answer("Enter the name of the dataverse where you want to publish: ") + self.hermes_toml_data["deposit"][deposit_plugin]["host_dataverse"] = host_dataverse + def choose_setup_method(self) -> None: """User chooses his desired setup method: Either preferring automatic (if available) or manual.""" setup_method_index = sc.choose( - f"How do you want to connect {DepositPlatformNames[self.deposit_platform]} " + f"How do you want to connect {self.deposit_platform.name} " f"with your {self.git_hoster.name} CI?", options=[ "Automatically (using OAuth / Device Flow)", @@ -635,14 +679,18 @@ def choose_setup_method(self) -> None: def connect_deposit_platform(self) -> None: """Acquires the access token of the chosen deposit platform.""" - assert self.deposit_platform != DepositPlatform.Empty - match self.deposit_platform: - case DepositPlatform.Zenodo: - connect_zenodo.setup(using_sandbox=False) - self.create_zenodo_token() - case DepositPlatform.ZenodoSandbox: - connect_zenodo.setup(using_sandbox=True) - self.create_zenodo_token() + used_deposit_plugin = self.deposit_platform.plugin_name + deposit_url = self.deposit_platform + deposit_name = self.deposit_platform.name + if used_deposit_plugin == "invenio_rdm": + connect_zenodo.setup(zenodo_url=self.deposit_platform.url, display_name=self.deposit_platform.name) + self.create_zenodo_token() + elif used_deposit_plugin == "dataverse": + self.create_dataverse_token() + else: + sc.echo(f"Unknown deposit plugin: {used_deposit_plugin}", formatting=sc.Formats.WARNING) + sc.echo(f"Getting an access token from {deposit_name} ({deposit_url}) is not supported by hermes init." + "You might have to do it manually instead.", formatting=sc.Formats.WARNING) def choose_plugins(self) -> None: """User chooses the plugins he wants to use.""" @@ -739,7 +787,7 @@ def choose_push_branch(self) -> None: def choose_deposit_files(self) -> None: """User chooses the files that should be included in the deposition.""" - dp_name = DepositPlatformNames[self.deposit_platform] + dp_name = self.deposit_platform.name add_readme = False if self.folder_info.has_readme: if sc.confirm(f"Do you want to append your README.md to the {dp_name} upload?"): diff --git a/src/hermes/commands/init/util/connect_zenodo.py b/src/hermes/commands/init/util/connect_zenodo.py index e9873cb5..e5ae2918 100644 --- a/src/hermes/commands/init/util/connect_zenodo.py +++ b/src/hermes/commands/init/util/connect_zenodo.py @@ -20,10 +20,8 @@ local_port = 8334 sandbox_client_id = 'QJ8Q9GBI78uOdNmVNK1Vd0oAOJHqmYGvxRxiSFxt' sandbox_client_secret = 'nGuOqoDtd2tckP6lmQS3If3cY39lPLKLU8skcv72JeowNupMD2bnLparsGO9' -sandbox_base_url = 'https://sandbox.zenodo.org' real_client_id = 'L0d9HQVW4Ig9PnC6qh6zkOAwgvYy08GcmHJqVVvV' real_client_secret = '0HIvtC2D2aPvpq2W0GtfWdeivwkqvnvrOTGx14nUJA5lDXrEDSaQAnqxHbLH' -real_base_url = 'https://zenodo.org' url_suffix_authorize = '/oauth/authorize' url_suffix_token = '/oauth/token' url_suffix_api_list = '/api/deposit/depositions' @@ -32,7 +30,7 @@ client_id = client_secret = base_url = authorize_url = token_url = api_list_url = name = "" -def setup(using_sandbox: bool = USING_SANDBOX_AS_DEFAULT): +def setup(zenodo_url = "https://sandbox.zenodo.org/", display_name = ""): global client_id global client_secret global base_url @@ -40,13 +38,16 @@ def setup(using_sandbox: bool = USING_SANDBOX_AS_DEFAULT): global token_url global api_list_url global name - client_id = sandbox_client_id if using_sandbox else real_client_id - client_secret = sandbox_client_secret if using_sandbox else real_client_secret - base_url = sandbox_base_url if using_sandbox else real_base_url + base_url = zenodo_url authorize_url = base_url + url_suffix_authorize token_url = base_url + url_suffix_token api_list_url = base_url + url_suffix_api_list - name = "Zenodo (Sandbox)" if using_sandbox else "Zenodo" + using_sandbox = "sandbox" in zenodo_url + client_id = sandbox_client_id if using_sandbox else real_client_id + client_secret = sandbox_client_secret if using_sandbox else real_client_secret + name = display_name + if name == "": + name = "Zenodo Sandbox" if using_sandbox else "Zenodo" setup() @@ -79,7 +80,7 @@ def test_if_token_is_valid(token: str) -> bool: def test_if_refresh_token_authorization_works(): - for version in [True, False]: + for version in ["https://sandbox.zenodo.org/", "https://zenodo.org/"]: setup(version) sc.echo(f"Testing if the {name} refresh token mechanism works...", formatting=sc.Formats.BOLD+sc.Formats.WARNING) diff --git a/src/hermes/commands/init/util/slim_click.py b/src/hermes/commands/init/util/slim_click.py index 2f72626f..161b052d 100644 --- a/src/hermes/commands/init/util/slim_click.py +++ b/src/hermes/commands/init/util/slim_click.py @@ -10,7 +10,7 @@ import logging from enum import Enum -PRINT_DEBUG = False +PRINT_DEBUG = True """If true, echo() will print debug texts.""" AUTO_LOG_ON_ECHO = True From 4478777062876f68a45fc3e476bda03097d88b60 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 10 Jun 2025 14:09:00 +0200 Subject: [PATCH 02/12] DataverseDeposit flake style changes --- src/hermes/commands/deposit/dataverse.py | 1 - src/hermes/commands/init/base.py | 1 - src/hermes/commands/init/util/connect_zenodo.py | 2 +- 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py index 11a3ac40..cd56ed35 100644 --- a/src/hermes/commands/deposit/dataverse.py +++ b/src/hermes/commands/deposit/dataverse.py @@ -155,4 +155,3 @@ def publish(self) -> None: res = requests.post(url, headers=headers, params=params, data={"persistentId": persistent_id}) if not res.ok: raise RuntimeError(f"Publish failed: {res.status_code}: {res.text}") - diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index 8d59fefb..db3ec63a 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -664,7 +664,6 @@ def integrate_deposit_platform(self) -> None: host_dataverse = sc.answer("Enter the name of the dataverse where you want to publish: ") self.hermes_toml_data["deposit"][deposit_plugin]["host_dataverse"] = host_dataverse - def choose_setup_method(self) -> None: """User chooses his desired setup method: Either preferring automatic (if available) or manual.""" setup_method_index = sc.choose( diff --git a/src/hermes/commands/init/util/connect_zenodo.py b/src/hermes/commands/init/util/connect_zenodo.py index e5ae2918..304cbb52 100644 --- a/src/hermes/commands/init/util/connect_zenodo.py +++ b/src/hermes/commands/init/util/connect_zenodo.py @@ -30,7 +30,7 @@ client_id = client_secret = base_url = authorize_url = token_url = api_list_url = name = "" -def setup(zenodo_url = "https://sandbox.zenodo.org/", display_name = ""): +def setup(zenodo_url="https://sandbox.zenodo.org/", display_name=""): global client_id global client_secret global base_url From e2a242cb30a98d7bede699634f4f08c8add85340 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 10 Jun 2025 14:53:39 +0200 Subject: [PATCH 03/12] DataverseDeposit: isort & customizable hermes branch for init --- src/hermes/commands/deposit/dataverse.py | 8 ++++---- src/hermes/commands/init/base.py | 15 ++++++++++++++- src/hermes/commands/init/util/connect_github.py | 4 ++-- src/hermes/commands/init/util/connect_gitlab.py | 6 +++--- src/hermes/commands/init/util/connect_zenodo.py | 3 ++- src/hermes/commands/init/util/git_info.py | 3 +-- src/hermes/commands/init/util/oauth_process.py | 11 ++++++----- src/hermes/commands/init/util/slim_click.py | 2 +- 8 files changed, 33 insertions(+), 19 deletions(-) diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py index cd56ed35..d3996f30 100644 --- a/src/hermes/commands/deposit/dataverse.py +++ b/src/hermes/commands/deposit/dataverse.py @@ -4,17 +4,17 @@ import json import logging -import requests from pathlib import Path +import requests +from easyDataverse import Dataset, Dataverse, License +from pydantic import BaseModel + from hermes.commands.deposit.base import BaseDepositPlugin from hermes.commands.deposit.error import DepositionUnauthorizedError from hermes.model.path import ContextPath -from pydantic import BaseModel -from easyDataverse import Dataverse, License, Dataset from hermes.utils import hermes_doi - _log = logging.getLogger("cli.deposit.dataverse") diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index db3ec63a..ae08610e 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -27,6 +27,7 @@ connect_zenodo, git_info) TUTORIAL_URL = "https://hermes.software-metadata.pub/en/latest/tutorials/automated-publication-with-ci.html" +REPOSITORY_URL = "https://github.com/softwarepub/hermes" class GitHoster(Enum): @@ -130,6 +131,8 @@ def get_git_hoster_from_url(url: str) -> GitHoster: def download_file_from_url(url, filepath, append: bool = False) -> None: + if not append and os.path.exists(filepath): + os.remove(filepath) try: with requests.get(url, stream=True) as r: r.raise_for_status() @@ -197,6 +200,7 @@ def __init__(self, parser: argparse.ArgumentParser): self.template_repo: str = "softwarepub/ci-templates" self.template_folder: str = "init" self.ci_parameters: dict = { + "pip_install_hermes": "pip install hermes", "deposit_zip_name": "artifact.zip", "deposit_zip_files": "", "deposit_initial": "--initial", @@ -220,6 +224,8 @@ def __init__(self, parser: argparse.ArgumentParser): def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None: command_parser.add_argument('--template-branch', nargs=1, default="", help="Branch or tag of the ci-templates repository.") + command_parser.add_argument('--hermes-branch', nargs=1, default="", + help="Branch of the hermes repository which will be used in the pipeline.") def load_settings(self, args: argparse.Namespace): pass @@ -244,10 +250,17 @@ def __call__(self, args: argparse.Namespace) -> None: # Setup logging self.setup_file_logging() - # Save command parameter (template branch) + # Process command parameters (ci-templates branch & hermes branch) if hasattr(args, "template_branch"): if args.template_branch != "": self.template_branch = args.template_branch + if hasattr(args, "hermes_branch"): + if args.hermes_branch: + branch_name = args.hermes_branch[0] + if branch_name != "": + sc.echo(f"Using Hermes branch: {branch_name}") + self.ci_parameters["pip_install_hermes"] = \ + f"pip install git+{REPOSITORY_URL}.git@{branch_name}" try: # Test if init is valid in current folder diff --git a/src/hermes/commands/init/util/connect_github.py b/src/hermes/commands/init/util/connect_github.py index fdb2961e..9cbfff69 100644 --- a/src/hermes/commands/init/util/connect_github.py +++ b/src/hermes/commands/init/util/connect_github.py @@ -2,14 +2,14 @@ # SPDX-License-Identifier: Apache-2.0 # SPDX-FileContributor: Nitai Heeb -import requests from base64 import b64encode + +import requests from nacl import encoding, public from . import slim_click as sc from .oauth_process import OauthProcess - local_port = 8333 client_id = 'Ov23linvdC7WzHnOO2WK' client_secret = 'empty-as-not-needed-for-public-device-flow' diff --git a/src/hermes/commands/init/util/connect_gitlab.py b/src/hermes/commands/init/util/connect_gitlab.py index 32b115a8..69f27223 100644 --- a/src/hermes/commands/init/util/connect_gitlab.py +++ b/src/hermes/commands/init/util/connect_gitlab.py @@ -2,14 +2,14 @@ # SPDX-License-Identifier: Apache-2.0 # SPDX-FileContributor: Nitai Heeb -import requests -from urllib.parse import urlparse, urljoin, quote from datetime import datetime, timedelta +from urllib.parse import quote, urljoin, urlparse + +import requests from . import slim_click as sc from .oauth_process import OauthProcess - default_scopes = "api write_repository" device_code_addition = "oauth/authorize_device" token_addition = "oauth/token" diff --git a/src/hermes/commands/init/util/connect_zenodo.py b/src/hermes/commands/init/util/connect_zenodo.py index 304cbb52..530533c5 100644 --- a/src/hermes/commands/init/util/connect_zenodo.py +++ b/src/hermes/commands/init/util/connect_zenodo.py @@ -3,8 +3,9 @@ # SPDX-FileContributor: Nitai Heeb import time -import requests + import oauthlib.oauth2.rfc6749.errors +import requests from . import slim_click as sc from .oauth_process import OauthProcess diff --git a/src/hermes/commands/init/util/git_info.py b/src/hermes/commands/init/util/git_info.py index e26dcf92..8fe12afe 100644 --- a/src/hermes/commands/init/util/git_info.py +++ b/src/hermes/commands/init/util/git_info.py @@ -2,12 +2,11 @@ # SPDX-License-Identifier: Apache-2.0 # SPDX-FileContributor: Nitai Heeb -import re import os +import re import subprocess from pathlib import Path - default_cwd = "" diff --git a/src/hermes/commands/init/util/oauth_process.py b/src/hermes/commands/init/util/oauth_process.py index ba2d88fe..31e354a3 100644 --- a/src/hermes/commands/init/util/oauth_process.py +++ b/src/hermes/commands/init/util/oauth_process.py @@ -4,19 +4,20 @@ # SPDX-FileContributor: David Pape from __future__ import annotations -import logging +import json +import logging import os import threading import time import webbrowser -import requests -import requests_oauthlib -import json -from threading import Event from http.server import BaseHTTPRequestHandler, HTTPServer +from threading import Event from urllib.parse import parse_qs, urlparse +import requests +import requests_oauthlib + from . import slim_click as sc PREFER_DEVICE_FLOW = True diff --git a/src/hermes/commands/init/util/slim_click.py b/src/hermes/commands/init/util/slim_click.py index 161b052d..2f72626f 100644 --- a/src/hermes/commands/init/util/slim_click.py +++ b/src/hermes/commands/init/util/slim_click.py @@ -10,7 +10,7 @@ import logging from enum import Enum -PRINT_DEBUG = True +PRINT_DEBUG = False """If true, echo() will print debug texts.""" AUTO_LOG_ON_ECHO = True From 5b5176d8a07b7a67da43ca390fa14055b54a7b29 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 17 Jun 2025 12:16:00 +0200 Subject: [PATCH 04/12] Added Rodare as DepositOption (not tested) --- src/hermes/commands/init/base.py | 30 +++++++++++++++++++++++++++--- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index ae08610e..baae5339 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -45,6 +45,8 @@ class DepositId(Enum): ZenodoSandbox = auto() JuelichData = auto() DemoDataverse = auto() + Rodare = auto() + RodareTest = auto() @dataclass @@ -73,6 +75,8 @@ def __init__(self, name: str = "", url: str = "", plugin_name: str = "", deposit DepositPlatform("Zenodo", "https://zenodo.org/", "invenio_rdm", DepositId.Zenodo), DepositPlatform("Demo Dataverse", "https://demo.dataverse.org/", "dataverse", DepositId.DemoDataverse), DepositPlatform("Jülich Data", "https://data.fz-juelich.de/", "dataverse", DepositId.JuelichData), + DepositPlatform("Rodare", "https://rodare.hzdr.de/", "rodare", DepositId.Rodare), + DepositPlatform("Rodare Test", "https://rodare-test.hzdr.de/", "rodare", DepositId.RodareTest), ] @@ -555,6 +559,18 @@ def create_dataverse_token(self): # TODO try to validate the token self.deposit_platform.token = sc.answer("Enter the token here: ") + def create_rodare_token(self): + token_url = urljoin(self.deposit_platform.url, "account/settings/applications/tokens/new/") + sc.echo("{} and create an access token.".format( + sc.create_console_hyperlink(token_url, "Open this link") + )) + sc.echo("It needs the scopes \"deposit:actions\" and \"deposit:write\".") + if self.setup_method == "m": + sc.press_enter_to_continue() + else: + # TODO try to validate the token + self.deposit_platform.token = sc.answer("Enter the token here: ") + def configure_git_project(self) -> None: """Adds the token to the git secrets & changes action workflow settings.""" match self.git_hoster: @@ -671,11 +687,17 @@ def integrate_deposit_platform(self) -> None: self.hermes_toml_data["deposit"][deposit_plugin]["site_url"] = self.deposit_platform.url self.ci_parameters["deposit_parameter_token"] = f"-O {deposit_plugin}.auth_token" self.ci_parameters["deposit_token_name"] = self.deposit_platform.token_name + # Invenio needs access_right = "open" (no idea what that does, might be outdated) if deposit_plugin.startswith("invenio"): self.hermes_toml_data["deposit"][deposit_plugin]["access_right"] = "open" - elif deposit_plugin == "dataverse": + # Dataverse needs a host_dataverse name as some sort of directory where the publication will appear + elif deposit_plugin.startswith("dataverse"): host_dataverse = sc.answer("Enter the name of the dataverse where you want to publish: ") self.hermes_toml_data["deposit"][deposit_plugin]["host_dataverse"] = host_dataverse + # Rodare needs the robis_pub_id + elif deposit_plugin.startswith("rodare"): + robis_pub_id = sc.answer("Enter the corresponding Robis Publication ID: ") + self.hermes_toml_data["deposit"][deposit_plugin]["robis_pub_id"] = robis_pub_id def choose_setup_method(self) -> None: """User chooses his desired setup method: Either preferring automatic (if available) or manual.""" @@ -694,11 +716,13 @@ def connect_deposit_platform(self) -> None: used_deposit_plugin = self.deposit_platform.plugin_name deposit_url = self.deposit_platform deposit_name = self.deposit_platform.name - if used_deposit_plugin == "invenio_rdm": + if used_deposit_plugin.startswith("invenio"): connect_zenodo.setup(zenodo_url=self.deposit_platform.url, display_name=self.deposit_platform.name) self.create_zenodo_token() - elif used_deposit_plugin == "dataverse": + elif used_deposit_plugin.startswith("dataverse"): self.create_dataverse_token() + elif used_deposit_plugin.startswith("rodare"): + self.create_rodare_token() else: sc.echo(f"Unknown deposit plugin: {used_deposit_plugin}", formatting=sc.Formats.WARNING) sc.echo(f"Getting an access token from {deposit_name} ({deposit_url}) is not supported by hermes init." From 43bd1b577e3022cffdb0d95b7c5883d89111e872 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 24 Jun 2025 13:45:19 +0200 Subject: [PATCH 05/12] Validate auth token on init with dataverse --- src/hermes/commands/init/base.py | 31 +++++++++++++++++++---- src/hermes/commands/init/util/git_info.py | 14 +++++----- 2 files changed, 33 insertions(+), 12 deletions(-) diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index baae5339..8764feba 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -196,6 +196,7 @@ def __init__(self, parser: argparse.ArgumentParser): self.tokens: dict = {} self.setup_method: str = "" self.deposit_platform: DepositPlatform = DepositPlatform() + self.git_branch: str = "" self.git_remote: str = "" self.git_remote_url = "" self.git_hoster: GitHoster = GitHoster.Empty @@ -344,7 +345,8 @@ def test_initialization(self) -> None: self.no_git_setup() sys.exit() - # Look at git remotes + # Look at git branch & remotes + self.git_branch = git_info.get_current_branch() remotes = git_info.get_remotes() if remotes: self.git_remote = remotes[0] @@ -544,7 +546,7 @@ def create_zenodo_token(self) -> None: else: sc.echo(f"The token could not be validated by {self.deposit_platform.name}. " "Make sure to enter the complete token.\n" - "(If this error persists, you should try switching to the manual setup mode.)", + "(If this error persists, you should restart and switch to the manual setup mode.)", formatting=sc.Formats.WARNING) def create_dataverse_token(self): @@ -556,8 +558,20 @@ def create_dataverse_token(self): if self.setup_method == "m": sc.press_enter_to_continue() else: - # TODO try to validate the token - self.deposit_platform.token = sc.answer("Enter the token here: ") + while True: + token = sc.answer("Enter the token here: ") + token_valid_url = f"{self.deposit_platform.url}/api/users/token" + token_valid_response = requests.get(token_valid_url, headers={"X-Dataverse-key": token}) + if token_valid_response.ok: + sc.echo(f"The token was validated by {self.deposit_platform.name}.", + formatting=sc.Formats.OKGREEN) + self.deposit_platform.token = token + break + else: + sc.echo(f"The token could not be validated by {self.deposit_platform.name}. " + "Make sure to enter the complete token.\n" + "(If this error persists, you should restart and switch to the manual setup mode.)", + formatting=sc.Formats.WARNING) def create_rodare_token(self): token_url = urljoin(self.deposit_platform.url, "account/settings/applications/tokens/new/") @@ -807,7 +821,8 @@ def choose_push_branch(self) -> None: push_choice = sc.choose( "When should the automated HERMES process start?", [ - "When I push a branch", + "When I push on custom branch", + f"When I push on current branch ({self.git_branch})", "When I push a specific tag (not implemented)", ] ) @@ -818,6 +833,12 @@ def choose_push_branch(self) -> None: formatting=sc.Formats.OKGREEN) sc.echo() elif push_choice == 1: + self.ci_parameters["push_branch"] = self.git_branch + bold_branch = sc.Formats.BOLD.wrap_around(self.git_branch) + sc.echo(f"The HERMES pipeline will be activated when you push on {bold_branch}", + formatting=sc.Formats.OKGREEN) + sc.echo() + elif push_choice == 2: sc.echo("Setting up triggering by tags is currently not implemented.", formatting=sc.Formats.WARNING) sc.echo(f"You can visit {TUTORIAL_URL} to set it up manually later-on.", formatting=sc.Formats.WARNING) diff --git a/src/hermes/commands/init/util/git_info.py b/src/hermes/commands/init/util/git_info.py index 8fe12afe..f1db3077 100644 --- a/src/hermes/commands/init/util/git_info.py +++ b/src/hermes/commands/init/util/git_info.py @@ -30,7 +30,7 @@ def get_valid_cwd(cwd="") -> str: return str(path) -def run_git_command(command: str, cwd="") -> str: +def run_git_command(command: str, cwd="", throw_exception=False) -> str: """ Runs any git command using subprocess. Raises Exception when returncode != 0. :param command: The command as string with or without the 'git' main command. @@ -44,7 +44,7 @@ def run_git_command(command: str, cwd="") -> str: if command_list[0] != "git": command_list.insert(0, "git") # Run subprocess - result = subprocess.run(command_list, cwd=cwd, capture_output=True, text=True) + result = subprocess.run(command_list, cwd=cwd, capture_output=True, text=True, check=throw_exception) # Return output or error if result.returncode != 0: raise Exception(result.stderr) @@ -87,11 +87,11 @@ def get_current_branch() -> str: """ Returns the name of the current branch. """ - branch_info = run_git_command("branch") - for line in branch_info.splitlines(): - if line.startswith("*"): - return line.split()[1].strip() - raise Exception("Current branch not found.") + try: + branch_name = run_git_command("rev-parse --abbrev-ref HEAD", throw_exception=True) + return branch_name.strip() + except subprocess.CalledProcessError: + return "" def is_git_installed() -> bool: From 0f5814f29e17c2518dd6275e4bdca40d4a443737 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Wed, 25 Jun 2025 11:34:26 +0200 Subject: [PATCH 06/12] Implementation of requested changes (mainly renaming) --- src/hermes/commands/deposit/dataverse.py | 23 ++++++++++++----------- src/hermes/commands/init/base.py | 10 ++++++---- 2 files changed, 18 insertions(+), 15 deletions(-) diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py index d3996f30..ef678f11 100644 --- a/src/hermes/commands/deposit/dataverse.py +++ b/src/hermes/commands/deposit/dataverse.py @@ -21,9 +21,10 @@ class DataverseDepositSettings(BaseModel): """Settings required to deposit into Dataverse.""" site_url: str = "" - host_dataverse: str = "" - auth_token: str = "" - dataset_pid: str = None + target_collection: str = "" + api_token: str = "" + target_pid: str = None + publication_type: str = "software" files: list[Path] = [] @@ -34,10 +35,10 @@ class DataverseDepositPlugin(BaseDepositPlugin): def __init__(self, command, ctx) -> None: super().__init__(command, ctx) self.config = getattr(self.command.settings, self.platform_name) - auth_token = self.config.auth_token - if not auth_token: + api_token = self.config.api_token + if not api_token: raise DepositionUnauthorizedError("No valid auth token given for deposition platform") - self.client = Dataverse(server_url=self.config.site_url, api_token=self.config.auth_token) + self.client = Dataverse(server_url=self.config.site_url, api_token=api_token) self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") def map_metadata(self) -> None: @@ -51,7 +52,7 @@ def map_metadata(self) -> None: json.dump(metadata, f, indent=2) def is_initial_publication(self) -> bool: - return self.config.dataset_pid is None + return self.config.target_pid is None def update_metadata_on_dataset(self, dataset: Dataset): """ @@ -78,7 +79,7 @@ def update_metadata_on_dataset(self, dataset: Dataset): dataset.citation.date_of_deposit = date_published # TODO look for "version" or something similar in dataverse # if version := metadata.get("version"): - # dataset.citation.version = version <- does not exist + # dataset.citation.softwareVersion = version if keywords := metadata.get("keywords", []): if keywords is list: for keyword in keywords: @@ -88,7 +89,7 @@ def update_metadata_on_dataset(self, dataset: Dataset): dataverse_license = License.fetch_by_name(deposition_license, server_url=self.client.server_url) dataset.citation.license = dataverse_license except Exception as e: - _log.warning(f"Could not match license '{deposition_license}' to Dataverse vocabulary: {e}") + _log.warning(f"Could not match license '{deposition_license}' to allowed licenses for deposition: {e}") dataset.citation.other_references = [f"Compiled by HERMES ({hermes_doi})"] def create_initial_version(self) -> None: @@ -102,7 +103,7 @@ def create_initial_version(self) -> None: raise RuntimeError("Please use `--initial` to make an initial deposition.") dataset = self.client.create_dataset() self.update_metadata_on_dataset(dataset) - persistent_id = dataset.upload(dataverse_name=self.config.host_dataverse) + persistent_id = dataset.upload(dataverse_name=self.config.target_collection) self.ctx.update(self.ctx_path["persistentId"], persistent_id) def create_new_version(self) -> None: @@ -151,7 +152,7 @@ def publish(self) -> None: persistent_id = self.ctx[self.ctx_path["persistentId"]] url = f"{self.config.site_url}/api/datasets/:persistentId/actions/:publish" params = {"type": "major"} - headers = {"X-Dataverse-key": self.config.auth_token} + headers = {"X-Dataverse-key": self.config.api_token} res = requests.post(url, headers=headers, params=params, data={"persistentId": persistent_id}) if not res.ok: raise RuntimeError(f"Publish failed: {res.status_code}: {res.text}") diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index 8764feba..05e1b054 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -44,6 +44,7 @@ class DepositId(Enum): Zenodo = auto() ZenodoSandbox = auto() JuelichData = auto() + JuelichDataBeta = auto() DemoDataverse = auto() Rodare = auto() RodareTest = auto() @@ -74,7 +75,8 @@ def __init__(self, name: str = "", url: str = "", plugin_name: str = "", deposit DepositPlatform("Zenodo Sandbox", "https://sandbox.zenodo.org/", "invenio_rdm", DepositId.ZenodoSandbox), DepositPlatform("Zenodo", "https://zenodo.org/", "invenio_rdm", DepositId.Zenodo), DepositPlatform("Demo Dataverse", "https://demo.dataverse.org/", "dataverse", DepositId.DemoDataverse), - DepositPlatform("Jülich Data", "https://data.fz-juelich.de/", "dataverse", DepositId.JuelichData), + DepositPlatform("Jülich DATA", "https://data.fz-juelich.de/", "dataverse", DepositId.JuelichData), + DepositPlatform("Jülich DATA Beta", "https://data-beta.fz-juelich.de/", "dataverse", DepositId.JuelichDataBeta), DepositPlatform("Rodare", "https://rodare.hzdr.de/", "rodare", DepositId.Rodare), DepositPlatform("Rodare Test", "https://rodare-test.hzdr.de/", "rodare", DepositId.RodareTest), ] @@ -704,10 +706,10 @@ def integrate_deposit_platform(self) -> None: # Invenio needs access_right = "open" (no idea what that does, might be outdated) if deposit_plugin.startswith("invenio"): self.hermes_toml_data["deposit"][deposit_plugin]["access_right"] = "open" - # Dataverse needs a host_dataverse name as some sort of directory where the publication will appear + # Dataverse needs a target_collection name as some sort of directory where the publication will appear elif deposit_plugin.startswith("dataverse"): - host_dataverse = sc.answer("Enter the name of the dataverse where you want to publish: ") - self.hermes_toml_data["deposit"][deposit_plugin]["host_dataverse"] = host_dataverse + target_collection = sc.answer("Enter the name of the collection where you want to publish: ") + self.hermes_toml_data["deposit"][deposit_plugin]["target_collection"] = target_collection # Rodare needs the robis_pub_id elif deposit_plugin.startswith("rodare"): robis_pub_id = sc.answer("Enter the corresponding Robis Publication ID: ") From ae1e4921312eb5d4ec88313150b05fbcce8774c9 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 8 Jul 2025 14:36:17 +0200 Subject: [PATCH 07/12] Init choose access_right & dataverse check_if_all_valid --- src/hermes/commands/deposit/dataverse.py | 82 ++++++++++++++++++++++-- src/hermes/commands/init/base.py | 30 +++++++-- 2 files changed, 101 insertions(+), 11 deletions(-) diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py index ef678f11..1b5d315b 100644 --- a/src/hermes/commands/deposit/dataverse.py +++ b/src/hermes/commands/deposit/dataverse.py @@ -33,13 +33,87 @@ class DataverseDepositPlugin(BaseDepositPlugin): settings_class = DataverseDepositSettings def __init__(self, command, ctx) -> None: + """ + Sets up the DataverseDepositPlugin with data from the hermes toml. + Tests if everything is valid and creates an easyDataverse client. + """ super().__init__(command, ctx) self.config = getattr(self.command.settings, self.platform_name) + self.check_if_all_valid() + self.client = Dataverse(server_url=self.config.site_url, api_token=self.config.api_token) + self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") + + def check_if_all_valid(self) -> None: + """ + Tests if all conditions are met before starting the rest of the deposit. + """ + self.check_version() + self.check_api_token() + self.check_target_collection() + self.check_target_pid() + self.check_publication_type() + + def check_version(self) -> None: + """ + Tests if the site_url is reachable as dataverse instance. + Also saves the dataverse version in the context incase we want to use it later on. + """ + url = f"{self.config.site_url}/api/info/version" + res = requests.get(url) + if not res.ok: + raise RuntimeError(f"Dataverse ({self.config.site_url}) not reachable.") + version_info = res.json().get("data", {}).get("version", "") + self.ctx.update(self.ctx_path["dataverse_version"], version_info) + + def check_api_token(self) -> None: api_token = self.config.api_token if not api_token: - raise DepositionUnauthorizedError("No valid auth token given for deposition platform") - self.client = Dataverse(server_url=self.config.site_url, api_token=api_token) - self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") + raise DepositionUnauthorizedError("No api-token given for deposition platform (dataverse).") + token_valid_url = f"{self.config.site_url}/api/users/token" + token_valid_response = requests.get(token_valid_url, headers={"X-Dataverse-key": api_token}) + if not token_valid_response.ok: + raise DepositionUnauthorizedError("Given api-token for deposition platform (dataverse) is not valid.") + + def check_target_collection(self) -> None: + """ + Tests if the target collection exists. + """ + target_collection = self.config.target_collection + url = f"{self.config.site_url}/api/dataverses/{target_collection}" + res = requests.get(url) + if not res.ok: + raise RuntimeError(f"Dataverse collection '{target_collection}' not found.") + + def check_target_pid(self) -> None: + """ + Tests if the given pid is valid. + """ + if not self.config.target_pid: + return + url = f"{self.config.site_url}/api/datasets/:persistentId/?persistentId={self.config.target_pid}" + res = requests.get(url) + if not res.ok: + raise RuntimeError(f"Dataset {self.config.target_pid} not found.") + data = res.json().get("data", {}) + if self.config.target_collection and not data.get("ownerAlias") == self.config.target_collection: + _log.warning("Dataset is not located inside the target collection.") + + def check_publication_type(self) -> None: + """ + Tests if the given publication type (most likely "software") is supported by the target dataverse. + """ + url = f"{self.config.site_url}/api/datasets/datasetTypes" + res = requests.get(url) + if res.ok: + types = res.json().get("data", []) + type_names = [t["name"] for t in types] + if self.config.publication_type not in type_names: + raise RuntimeError( + f"Publication type '{self.config.publication_type}' not supported on target Dataverse.") + else: + # TBD what to do when showing supported datasetTypes does not work? + # This is currently the case for https://data.fz-juelich.de/ & https://data-beta.fz-juelich.de/ + pass def map_metadata(self) -> None: """ @@ -54,7 +128,7 @@ def map_metadata(self) -> None: def is_initial_publication(self) -> bool: return self.config.target_pid is None - def update_metadata_on_dataset(self, dataset: Dataset): + def update_metadata_on_dataset(self, dataset: Dataset) -> None: """ Sets metadata on an easyDataverse.Dataset using the depositionMetadata """ diff --git a/src/hermes/commands/init/base.py b/src/hermes/commands/init/base.py index 05e1b054..49a766a0 100644 --- a/src/hermes/commands/init/base.py +++ b/src/hermes/commands/init/base.py @@ -703,15 +703,31 @@ def integrate_deposit_platform(self) -> None: self.hermes_toml_data["deposit"][deposit_plugin]["site_url"] = self.deposit_platform.url self.ci_parameters["deposit_parameter_token"] = f"-O {deposit_plugin}.auth_token" self.ci_parameters["deposit_token_name"] = self.deposit_platform.token_name - # Invenio needs access_right = "open" (no idea what that does, might be outdated) - if deposit_plugin.startswith("invenio"): - self.hermes_toml_data["deposit"][deposit_plugin]["access_right"] = "open" - # Dataverse needs a target_collection name as some sort of directory where the publication will appear - elif deposit_plugin.startswith("dataverse"): + + if deposit_plugin.startswith("invenio") or deposit_plugin.startswith("rodare"): + # Invenio & rodare need access_right + # For possible customization we ask the user here + target_access_right = sc.choose( + text="Select an access right for your publication", + options=["open", "closed", "restricted", "embargoed"] + ) + self.hermes_toml_data["deposit"][deposit_plugin]["access_right"] = target_access_right + if target_access_right == "restricted": + conditions = sc.answer("Enter the access conditions of the restriction: ") + self.hermes_toml_data["deposit"][deposit_plugin]["access_conditions"] = conditions + elif target_access_right == "embargoed": + embargo_date = sc.answer("Enter the embargo date (YYYY-MM-DD): ") + self.hermes_toml_data["deposit"][deposit_plugin]["embargo_date"] = embargo_date + + if deposit_plugin.startswith("dataverse"): + # Dataverse needs a target_collection name as some sort of directory where the publication will appear target_collection = sc.answer("Enter the name of the collection where you want to publish: ") self.hermes_toml_data["deposit"][deposit_plugin]["target_collection"] = target_collection - # Rodare needs the robis_pub_id - elif deposit_plugin.startswith("rodare"): + # To be decided: Should we call it api_token in the other deposit plugins or just in dataverse? + self.ci_parameters["deposit_parameter_token"] = f"-O {deposit_plugin}.api_token" + + if deposit_plugin.startswith("rodare"): + # Rodare needs the robis_pub_id robis_pub_id = sc.answer("Enter the corresponding Robis Publication ID: ") self.hermes_toml_data["deposit"][deposit_plugin]["robis_pub_id"] = robis_pub_id From 42e4ae5fffa4a248019de8b23ead22f6fd7c4077 Mon Sep 17 00:00:00 2001 From: Nitai Heeb Date: Tue, 8 Jul 2025 15:32:45 +0200 Subject: [PATCH 08/12] dataverse small fix --- src/hermes/commands/deposit/dataverse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/hermes/commands/deposit/dataverse.py b/src/hermes/commands/deposit/dataverse.py index 1b5d315b..2f7b7fdc 100644 --- a/src/hermes/commands/deposit/dataverse.py +++ b/src/hermes/commands/deposit/dataverse.py @@ -38,10 +38,10 @@ def __init__(self, command, ctx) -> None: Tests if everything is valid and creates an easyDataverse client. """ super().__init__(command, ctx) + self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") self.config = getattr(self.command.settings, self.platform_name) self.check_if_all_valid() self.client = Dataverse(server_url=self.config.site_url, api_token=self.config.api_token) - self.ctx_path = ContextPath.parse(f"deposit.{self.platform_name}") def check_if_all_valid(self) -> None: """ From a4aefdb0e4dc13d5bb8c329c660dd1cea056b68b Mon Sep 17 00:00:00 2001 From: Oliver Bertuch Date: Fri, 12 Dec 2025 13:44:23 +0100 Subject: [PATCH 09/12] fix: correct Sophie Kernchen's email in pyproject.toml and name order in CITATION.cff --- CITATION.cff | 4 ++-- pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1556b8ff..eee0efb1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -44,8 +44,8 @@ authors: email: d.pape@hzdr.de affiliation: Helmholtz-Zentrum Dresden-Rossendorf (HZDR) orcid: 'https://orcid.org/0000-0002-3145-9880' - - given-names: Kernchen - family-names: Sophie + - given-names: Sophie + family-names: Kernchen email: sophie.kernchen@dlr.de affiliation: German Aerospace Center (DLR) orcid: 'https://orcid.org/0009-0005-4430-6743' diff --git a/pyproject.toml b/pyproject.toml index 6beefcab..3e091e53 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,7 @@ authors = [ { name = "Oliver Bertuch", email = "o.bertuch@fz-juelich.de" }, { name = "Oliver Knodel", email = "o.knodel@hzdr.de" }, { name = "David Pape", email = "d.pape@hzdr.de" }, - { name = "Sophie Kernchen", email = "sohpie.kernchen@dlr.de" }, + { name = "Sophie Kernchen", email = "sophie.kernchen@dlr.de" }, { name = "Nitai Heeb", email = "n.heeb@fz-juelich.de" }, ] maintainers = [ From 09119c71ad74654a0a5fc9680bc2b1ec6618c4d5 Mon Sep 17 00:00:00 2001 From: Oliver Bertuch Date: Fri, 12 Dec 2025 13:44:37 +0100 Subject: [PATCH 10/12] fix: correct typo in class name and entry point for InvenioRDMDepositPlugin --- pyproject.toml | 2 +- src/hermes/commands/deposit/invenio_rdm.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3e091e53..75e130f6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ file_exists = "hermes.commands.harvest.file_exists:FileExistsHarvestPlugin" [project.entry-points."hermes.deposit"] file = "hermes.commands.deposit.file:FileDepositPlugin" invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" -invenio_rdm = "hermes.commands.deposit.invenio_rdm:IvenioRDMDepositPlugin" +invenio_rdm = "hermes.commands.deposit.invenio_rdm:InvenioRDMDepositPlugin" rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" [project.entry-points."hermes.postprocess"] diff --git a/src/hermes/commands/deposit/invenio_rdm.py b/src/hermes/commands/deposit/invenio_rdm.py index a381db90..a90a90f3 100644 --- a/src/hermes/commands/deposit/invenio_rdm.py +++ b/src/hermes/commands/deposit/invenio_rdm.py @@ -84,7 +84,7 @@ def _search_license_info(self, _url: str, valid_licenses: dict) -> t.Optional[di return None -class IvenioRDMDepositPlugin(InvenioDepositPlugin): +class InvenioRDMDepositPlugin(InvenioDepositPlugin): platform_name = "invenio_rdm" invenio_client_class = InvenioRDMClient invenio_resolver_class = InvenioRDMResolver From 0da253b3bd029bf418c823ba465eaa3eac4bd354 Mon Sep 17 00:00:00 2001 From: Oliver Bertuch Date: Fri, 12 Dec 2025 13:45:24 +0100 Subject: [PATCH 11/12] refactor: remove PEP-621 not-supported repository field and poetry based plugin definitions from pyproject.toml --- pyproject.toml | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 75e130f6..27c5d3db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,6 @@ maintainers = [ { name = "Stephan Druskat", email = "stephan.druskat@dlr.de" }, ] readme = "README.md" -repository = "https://github.com/softwarepub/hermes" keywords = ["software", "publication", "metadata", "automation"] dependencies = [ @@ -98,25 +97,6 @@ sphinx-togglebutton="^0.3.2" reuse = "^1.1.2" sphinxcontrib-datatemplates = "^0.11.0" -[tool.poetry.plugins.console_scripts] -hermes = "hermes.commands.cli:main" -hermes-marketplace = "hermes.commands.marketplace:main" - -[tool.poetry.plugins."hermes.harvest"] -cff = "hermes.commands.harvest.cff:CffHarvestPlugin" -codemeta = "hermes.commands.harvest.codemeta:CodeMetaHarvestPlugin" - -[tool.poetry.plugins."hermes.deposit"] -file = "hermes.commands.deposit.file:FileDepositPlugin" -invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" -invenio_rdm = "hermes.commands.deposit.invenio_rdm:IvenioRDMDepositPlugin" -rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" - -[tool.poetry.plugins."hermes.postprocess"] -config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id" -config_invenio_rdm_record_id = "hermes.commands.postprocess.invenio_rdm:config_record_id" -cff_doi = "hermes.commands.postprocess.invenio:cff_doi" - [tool.taskipy.tasks] docs-build = "poetry run sphinx-build -M html docs/source docs/build -W" docs-clean = "poetry run sphinx-build -M clean docs/source docs/build" From 888bf38fcabc53ada9fe03f29dc29ed17ebe9522 Mon Sep 17 00:00:00 2001 From: Oliver Bertuch Date: Fri, 12 Dec 2025 13:46:45 +0100 Subject: [PATCH 12/12] fix: add missing DataverseDepositPlugin entry point to pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 27c5d3db..10dbd191 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,6 +62,7 @@ file = "hermes.commands.deposit.file:FileDepositPlugin" invenio = "hermes.commands.deposit.invenio:InvenioDepositPlugin" invenio_rdm = "hermes.commands.deposit.invenio_rdm:InvenioRDMDepositPlugin" rodare = "hermes.commands.deposit.rodare:RodareDepositPlugin" +dataverse = "hermes.commands.deposit.dataverse:DataverseDepositPlugin" [project.entry-points."hermes.postprocess"] config_invenio_record_id = "hermes.commands.postprocess.invenio:config_record_id"