From 31c66167f51635dec7e5c039fcebd7db2fb1780e Mon Sep 17 00:00:00 2001
From: steve-fischer-200 <sfischer@upenn.edu>
Date: Wed, 23 Apr 2025 20:56:26 -0400
Subject: [PATCH 1/3] update ud meta data

---
 .../lib/wdk/model/records/datasetRecords.xml  | 228 +++++++++++-------
 1 file changed, 145 insertions(+), 83 deletions(-)

diff --git a/Model/lib/wdk/model/records/datasetRecords.xml b/Model/lib/wdk/model/records/datasetRecords.xml
index 4157bfb0..f8b4f0d9 100644
--- a/Model/lib/wdk/model/records/datasetRecords.xml
+++ b/Model/lib/wdk/model/records/datasetRecords.xml
@@ -179,7 +179,12 @@
         </linkAttribute>
       </attributeQueryRef>
 -->
-      <attributeQueryRef ref="DatasetAttributes.ClinepiStudyAttributes" includeProjects="MicrobiomeDB,ClinEpiDB">
+      <attributeQueryRef ref="DatasetAttributes.UserDatasetAccessibility" includeProjects="MicrobiomeDB,ClinEpiDB">
+        <columnAttribute name="accessibility"/>
+	<columnAttribute name="days_for_approval"/>
+      </attributeQueryRef>
+
+	<attributeQueryRef ref="DatasetAttributes.ClinepiStudyAttributes" includeProjects="MicrobiomeDB,ClinEpiDB">
         <columnAttribute name="project_availability" internal="true"/>
         <columnAttribute name="is_public" internal="true"/>
          <columnAttribute name="is_prerelease" type="number"/>
@@ -999,11 +1004,13 @@ Based on evolutionarily informed expectations of gene content of near-universal
               coalesce(dsp.display_category, dsp.category) as newcategory
           FROM ApidbTuning.DatasetPresenter dsp
           WHERE project_id = '@PROJECT_ID@'
-          -- UNION
-          -- SELECT DISTINCT
-          --   CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
-          --   null as newcategory
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT DISTINCT
+            CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
+            null as newcategory
+            FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
+
         ]]>
       </sql>
          <sql includeProjects="UniDB">
@@ -1016,7 +1023,8 @@ Based on evolutionarily informed expectations of gene content of near-universal
           SELECT DISTINCT
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             null as newcategory
-          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+            FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
          <sql includeProjects="EuPathDB">
@@ -1042,9 +1050,11 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           select DISTINCT
             null as dataset_sha1_digest,
-                    CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
+            CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             d.name as dataset_display_name
-          from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+            from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
+
         ]]>
       </sql>
       <sql includeProjects="MicrobiomeDB,VectorBase">
@@ -1060,6 +1070,37 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             d.name as dataset_display_name
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
+        ]]>
+      </sql>
+    </sqlQuery>
+
+     <sqlQuery name="UserDatasetAccessibility"  isCacheable="false" includeProjects="MicrobiomeDB,ClinEpiDB">
+      <column name="accessibility" columnType="string"/>
+      <column name="days_for_approval"/>
+      <sql>
+        <![CDATA[
+          SELECT DISTINCT
+            CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
+            d.accessibility, d.days_for_approval
+            FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
+        ]]>
+      </sql>
+    </sqlQuery>
+	
+     <sqlQuery name="UserDatasetProperties"  isCacheable="false">
+      <column name="key" columnType="string"/>
+      <column name="value" columnType="string"/>
+      <sql>
+        <![CDATA[
+          SELECT DISTINCT
+            CONCAT('EDAUD_', dc.dataset_id) as dataset_id,
+            key,
+	    value
+            FROM @VDI_CONTROL_SCHEMA@.dataset_property dp, @VDI_CONTROL_SCHEMA@.AvailableUserDatasets aud
+	    where dp.dataset_id = aud.user_dataset_id
+	    and aud.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1190,6 +1231,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
                   , null as custom_download_tab
                   , null as custom_download_ack
               FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	      	    where accessibility != 'private'
             ]]>
           </sql>
       </sqlQuery>
@@ -1220,6 +1262,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             null as study_categories
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1298,6 +1341,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
                  , null
                  , null
           from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
       ]]>
       </sql>
     </sqlQuery>
@@ -1455,6 +1499,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null
                , null
             from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1471,6 +1516,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT DISTINCT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, d.name as display_name
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
          <sql includeProjects="EuPathDB">
@@ -1496,9 +1542,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
             LEFT JOIN apidbtuning.organismattributes oa ON dsp.name = oa.internal_abbrev || '_primary_genome_RSRC'
           WHERE dsp.project_id = '@PROJECT_ID@'
           AND dsp.category != 'Link outs'
-          -- UNION
-          -- SELECT DISTINCT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, d.name as display_name
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT DISTINCT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, d.name as display_name
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1527,9 +1574,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
           FROM apidbtuning.datasetpresenter dsp
             LEFT JOIN apidbtuning.organismattributes oa ON dsp.name = oa.internal_abbrev || '_primary_genome_RSRC'
           WHERE dsp.project_id = '@PROJECT_ID@'
-          -- UNION
-          -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as megabase_pairs, null as genecount
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as megabase_pairs, null as genecount
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1583,10 +1631,11 @@ Based on evolutionarily informed expectations of gene content of near-universal
                   GROUP BY dataset_presenter_id
               ) dp ON dsp.dataset_presenter_id = dp.dataset_presenter_id
             WHERE dsp.project_id = '@PROJECT_ID@'
-            -- UNION
-            -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
-            --   CASE WHEN is_public = 1 THEN 'yes' ELSE 'no' END as is_public
-            -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+            UNION
+            SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
+              CASE WHEN is_public = 1 THEN 'yes' ELSE 'no' END as is_public
+            FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
           ]]>
         </sql>
       </sqlQuery>
@@ -1651,9 +1700,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
           FROM apidbtuning.datasetpresenter dsp
             LEFT JOIN all_versions_filtered av ON dsp.dataset_presenter_id = av.dataset_presenter_id
           WHERE dsp.project_id = '@PROJECT_ID@'
-          -- UNION
-          -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as genome_version, null as annotation_version, null as functional_annotation_version
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as genome_version, null as annotation_version, null as functional_annotation_version
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1730,24 +1780,24 @@ Based on evolutionarily informed expectations of gene content of near-universal
               FROM apidbTuning.EupathBuildDates
               WHERE project = '@PROJECT_ID@'
             ) introduced ON dsp.build_number_introduced = introduced.build_number::numeric
-          -- TODO:  add this back
-          --  UNION ALL
-          -- SELECT CONCAT('EDAUD_', d.dataset_id) as dataset_id
-          --      , null as dataset_name
-          --     , null as dataset_name_pattern
-          --     , null as version
-          --     , d.name as short_display_name
-          --     , d.description
-          --     , d.summary::TEXT as summary
-          --     , null as protocol
-          --     , null as usage
-          --     , null as type
-          --     , null as is_species_scope
-          --     , null as build_number_introduced
-          --     , null as eupath_release
-          --     , null as pmids
-          --     , null as pmids_download
-          --FROM @VDI_CONTROL_SCHEMA@.dataset_meta d -- NOTE: We're reaching into VDI control and selecting from dataset_meta here. This is because availabledatasets has duplicate rows and cannot be selected "distinct"ly since we're selecting clobs.
+            UNION ALL
+            SELECT CONCAT('EDAUD_', d.dataset_id) as dataset_id
+               , null as dataset_name
+               , null as dataset_name_pattern
+               , null as version
+               , d.name as short_display_name
+               , d.description
+               , d.summary::TEXT as summary
+               , null as protocol
+               , null as usage
+               , null as type
+               , null as is_species_scope
+               , null as build_number_introduced
+               , to_char(d.release_date, 'YYYY-MON-DD') as eupath_release
+               , null as pmids
+               , null as pmids_download
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
 
@@ -1888,7 +1938,8 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null as eupath_release
                , null as pmids
                , null as pmids_download
-          FROM @VDI_CONTROL_SCHEMA@.dataset_meta d -- NOTE: We're reaching into VDI control and selecting from dataset_meta here. This is because availabledatasets has duplicate rows and cannot be selected "distinct"ly since we're selecting clobs.
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1896,13 +1947,13 @@ Based on evolutionarily informed expectations of gene content of near-universal
      <sqlQuery name="OwnerVisibility"  isCacheable="false">
          <column name="dataset_id"/>
          <column name="owner"/>
-         <column name="community"/>
+         <column name="accessibility"/>
 
          <sql includeProjects="EuPathDB">
             <![CDATA[
             select dsp.dataset_presenter_id as dataset_id,
                    null as owner,
-                   null as community
+                   null as accessibility
             from apidbTuning.DatasetPresenter dsp
             ]]>
          </sql>
@@ -1913,11 +1964,11 @@ Based on evolutionarily informed expectations of gene content of near-universal
                    null as owner,
                    null as community
             from apidbTuning.DatasetPresenter dsp
-            -- UNION
-            -- SELECT CONCAT('EDAUD_', dataset_id) as dataset_id,
-            --        owner,
-            --        is_public as community
-            --     from @VDI_CONTROL_SCHEMA@.dataset
+            UNION
+            SELECT CONCAT('EDAUD_', dataset_id) as dataset_id,
+                    owner,
+                    is_public as community
+                 from @VDI_CONTROL_SCHEMA@.dataset
             ]]>
          </sql>
       </sqlQuery>
@@ -1935,12 +1986,13 @@ Based on evolutionarily informed expectations of gene content of near-universal
                    dsp.release_policy
             from apidbTuning.DatasetPresenter dsp
             where dsp.project_id = '@PROJECT_ID@'
-            -- UNION
-            -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
-            --    , null as caveat
-            --    , null as acknowledgement
-            --   , null as release_policy
-            -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+            UNION
+            SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
+               , null as caveat
+               , null as acknowledgement
+               , null as release_policy
+            FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
             ]]>
          </sql>
          <sql includeProjects="EuPathDB">
@@ -1978,20 +2030,15 @@ Based on evolutionarily informed expectations of gene content of near-universal
               AND dsc.is_primary_contact = true
               AND dsp.project_id = '@PROJECT_ID@'
           UNION
---          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
---               , dc.name as contact
---               , affiliation as institution
---               , email
---               , short_attribution
---               from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
---	       where dc.is_primary = 1
---	       and dc.dataset_id = d.user_dataset_id
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
-               , null as contact
-               , null as institution
-               , null as email
-               , null as short_attribution
-          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+               , dc.name as contact
+               , affiliation as institution
+               , email
+               , short_attribution
+               from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
+	       where dc.is_primary = 1
+	       and dc.dataset_id = d.user_dataset_id
+	       and d.accessibility != 'private'
         ]]>
       </sql>
 
@@ -2027,13 +2074,16 @@ Based on evolutionarily informed expectations of gene content of near-universal
             LEFT JOIN ApidbTuning.DatasetContact dsc ON dsp.dataset_presenter_id = dsc.dataset_presenter_id
           WHERE dsc.is_primary_contact = true
           AND dsp.project_id = '@PROJECT_ID@'
-          -- UNION
-          -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
-          --      , null as contact
-          --      , null as institution
-          --      , null as email
-          --      , null as short_attribution
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
+               , dc.name as contact
+               , affiliation as institution
+               , email
+               , short_attribution
+               from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
+	       where dc.is_primary = 1
+	       and dc.dataset_id = d.user_dataset_id
+	       and d.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2056,9 +2106,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
           FROM apidbtuning.datasetPresenter dsp
             LEFT JOIN apollo_dataset ad ON dsp.dataset_presenter_id = ad.dataset_presenter_id
           WHERE dsp.project_id = '@PROJECT_ID@'
-          -- UNION
-          -- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, 'N/A' as in_apollo
-          -- FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, 'N/A' as in_apollo
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2083,6 +2134,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, project_id as project
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2125,9 +2177,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
               LEFT JOIN apidbtuning.organismattributes tn ON dsnt.taxon_id = tn.component_taxon_id
           ) t
           GROUP BY dataset_id
-          --UNION
-          --SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as organism_prefix
-          --FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+          UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as organism_prefix
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
 
@@ -2159,9 +2212,10 @@ Based on evolutionarily informed expectations of gene content of near-universal
        --       lower(substr(ENCODE(DIGEST(replace(name, '_ebi_', '_'), 'SHA1'),'hex'), 0, 10))
        --       as old_dataset_id
        --   FROM apidbtuning.datasetpresenter where name like '%_ebi_%'
-      --    UNION
-      --    SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, CONCAT('EDAUD_', d.user_dataset_id) as old_dataset_id
-      --    FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+        UNION
+          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, CONCAT('EDAUD_', d.user_dataset_id) as old_dataset_id
+          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
 
@@ -2173,6 +2227,7 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, CONCAT('EDAUD_', d.user_dataset_id) as old_dataset_id
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
+	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2354,6 +2409,13 @@ Based on evolutionarily informed expectations of gene content of near-universal
           FROM ApidbTuning.DatasetPresenter dsp, ApidbTuning.DatasetContact dsc
           WHERE dsp.dataset_presenter_id = dsc.dataset_presenter_id
           ORDER BY dsc.is_primary_contact desc, dsc.dataset_contact_id asc
+          UNION
+          SELECT d.name as dataset_name, CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
+               , dc.name as contact_name
+               , affiliation
+               from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
+	       where dc.dataset_id = d.user_dataset_id
+	       and d.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>

From f0f86ae8fae9038444ada12cda7292d793fef49d Mon Sep 17 00:00:00 2001
From: steve-fischer-200 <sfischer@upenn.edu>
Date: Mon, 28 Apr 2025 12:30:46 -0400
Subject: [PATCH 2/3] add JSON fields

---
 .../lib/wdk/model/records/datasetRecords.xml  | 104 +++++++++---------
 1 file changed, 55 insertions(+), 49 deletions(-)

diff --git a/Model/lib/wdk/model/records/datasetRecords.xml b/Model/lib/wdk/model/records/datasetRecords.xml
index f8b4f0d9..28cc837d 100644
--- a/Model/lib/wdk/model/records/datasetRecords.xml
+++ b/Model/lib/wdk/model/records/datasetRecords.xml
@@ -423,7 +423,22 @@
         <columnAttribute name="affiliation" displayName="Affiliation"/>
       </table>
 
+        <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+        <!-- User Dataset Properties Table -->
+        <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
 
+        <table name="UserDatasetPropertiesTable" includeProjects="ClinEpiDB"
+               displayName="Study Properties"
+               queryRef="DatasetTables.UserDatasetProperties">
+            <columnAttribute name="dataset_id"  inReportMaker="false" internal="true"/>
+<!--            <columnAttribute name="dataset_name"  inReportMaker="false" internal="true"/> -->
+            <columnAttribute name="study_design" displayName="Study design" sortable="false"/>
+            <columnAttribute name="disease" displayName="Disease" sortable="false"/>
+            <columnAttribute name="country" displayName="Country" sortable="false"/>
+            <columnAttribute name="years" displayName="Years" sortable="false"/>
+            <columnAttribute name="ages" displayName="Ages" sortable="false"/>
+            <columnAttribute name="sample_type" displayName="Sample type" sortable="false"/>
+        </table>
 
       <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
       <!-- Study Characteristic -->
@@ -1009,8 +1024,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             null as newcategory
             FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
-
         ]]>
       </sql>
          <sql includeProjects="UniDB">
@@ -1024,7 +1037,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             null as newcategory
             FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
          <sql includeProjects="EuPathDB">
@@ -1053,8 +1065,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             d.name as dataset_display_name
             from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
-
         ]]>
       </sql>
       <sql includeProjects="MicrobiomeDB,VectorBase">
@@ -1070,7 +1080,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             d.name as dataset_display_name
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1084,23 +1093,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             d.accessibility, d.days_for_approval
             FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
-        ]]>
-      </sql>
-    </sqlQuery>
-	
-     <sqlQuery name="UserDatasetProperties"  isCacheable="false">
-      <column name="key" columnType="string"/>
-      <column name="value" columnType="string"/>
-      <sql>
-        <![CDATA[
-          SELECT DISTINCT
-            CONCAT('EDAUD_', dc.dataset_id) as dataset_id,
-            key,
-	    value
-            FROM @VDI_CONTROL_SCHEMA@.dataset_property dp, @VDI_CONTROL_SCHEMA@.AvailableUserDatasets aud
-	    where dp.dataset_id = aud.user_dataset_id
-	    and aud.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1231,7 +1223,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                   , null as custom_download_tab
                   , null as custom_download_ack
               FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	      	    where accessibility != 'private'
             ]]>
           </sql>
       </sqlQuery>
@@ -1262,7 +1253,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
             CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
             null as study_categories
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1341,7 +1331,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                  , null
                  , null
           from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
       ]]>
       </sql>
     </sqlQuery>
@@ -1499,7 +1488,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null
                , null
             from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1516,7 +1504,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT DISTINCT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, d.name as display_name
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
          <sql includeProjects="EuPathDB">
@@ -1545,7 +1532,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT DISTINCT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, d.name as display_name
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1577,7 +1563,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as megabase_pairs, null as genecount
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1633,9 +1618,8 @@ Based on evolutionarily informed expectations of gene content of near-universal
             WHERE dsp.project_id = '@PROJECT_ID@'
             UNION
             SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
-              CASE WHEN is_public = 1 THEN 'yes' ELSE 'no' END as is_public
+              CASE WHEN accessibility != 'private' THEN 'yes' ELSE 'no' END as is_public
             FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
           ]]>
         </sql>
       </sqlQuery>
@@ -1703,7 +1687,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as genome_version, null as annotation_version, null as functional_annotation_version
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1797,7 +1780,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null as pmids
                , null as pmids_download
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
 
@@ -1939,7 +1921,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null as pmids
                , null as pmids_download
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -1962,12 +1943,12 @@ Based on evolutionarily informed expectations of gene content of near-universal
             <![CDATA[
             select dsp.dataset_presenter_id as dataset_id,
                    null as owner,
-                   null as community
+                   null as accessibility
             from apidbTuning.DatasetPresenter dsp
             UNION
             SELECT CONCAT('EDAUD_', dataset_id) as dataset_id,
                     owner,
-                    is_public as community
+                    accessibility
                  from @VDI_CONTROL_SCHEMA@.dataset
             ]]>
          </sql>
@@ -1992,7 +1973,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , null as acknowledgement
                , null as release_policy
             FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
             ]]>
          </sql>
          <sql includeProjects="EuPathDB">
@@ -2038,7 +2018,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
 	       where dc.is_primary = 1
 	       and dc.dataset_id = d.user_dataset_id
-	       and d.accessibility != 'private'
         ]]>
       </sql>
 
@@ -2083,7 +2062,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
 	       where dc.is_primary = 1
 	       and dc.dataset_id = d.user_dataset_id
-	       and d.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2109,7 +2087,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, 'N/A' as in_apollo
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2134,7 +2111,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, project_id as project
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2171,16 +2147,26 @@ Based on evolutionarily informed expectations of gene content of near-universal
           FROM (
             SELECT DISTINCT dsnt.dataset_presenter_id as dataset_id
               , CASE when tn.organism_name is null then null
-                ELSE REGEXP_REPLACE('Plasmodium vivax P01','^(\w*)\s(\w*)\s(\.*)','<I>\1 \2<\I>')||'</i>'
+                ELSE REGEXP_REPLACE(tn.organism_name,'^(\w*)\s(\w*)\s(\.*)','<I>\1 \2<\I>') || '</i>'
                 END as org
             FROM apidbtuning.datasetnametaxon dsnt
               LEFT JOIN apidbtuning.organismattributes tn ON dsnt.taxon_id = tn.component_taxon_id
           ) t
           GROUP BY dataset_id
           UNION
-          SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as organism_prefix
-          FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
+          SELECT dataset_id,
+            regexp_replace(
+              substr(string_agg(org,'<br>' order by org), 1, 4000) , '<br>[A-Za-z\. <>&]+$', '<br>...') AS organism_prefix
+          FROM (
+            SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
+	    substr(string_agg(oa.organism_name,'<br>' order by org), 1, 4000) , '<br>[A-Za-z\. <>&]+$', '<br>...') AS organism_prefix
+	    FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d,
+	    @VDI_CONTROL_SCHEMA@.dataset_organism do,
+	    apidbtuning.organismattributes oa
+	    where d.user_dataset_id = o.dataset_id
+	    and do.organism_abbrev = oa.internal_abbrev
+          ) t
+          GROUP BY dataset_id
         ]]>
       </sql>
 
@@ -2215,7 +2201,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
         UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, CONCAT('EDAUD_', d.user_dataset_id) as old_dataset_id
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
 
@@ -2227,7 +2212,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
           UNION
           SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, CONCAT('EDAUD_', d.user_dataset_id) as old_dataset_id
           FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
-	    where accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>
@@ -2239,6 +2223,29 @@ Based on evolutionarily informed expectations of gene content of near-universal
   <querySet name="DatasetTables" queryType="table"
             isCacheable='false'>
 
+     <sqlQuery name="UserDatasetProperties"  isCacheable="false" includeProjects="ClinEpiDB">
+      <column name="study_design" columnType="string"/>
+      <column name="disease" columnType="string"/>
+      <column name="country" columnType="string"/>
+      <column name="years" columnType="string"/>
+      <column name="ages" columnType="string"/>
+      <column name="sample_type" columnType="string"/>
+      <sql>
+        <![CDATA[
+          SELECT DISTINCT
+            CONCAT('EDAUD_', dc.dataset_id) as dataset_id,
+            json->>'studyDesign' AS study_design,
+            json->>'disease' AS disease,
+            json->>'country' AS country,
+            json->>'years' AS years,
+            json->>'ages' AS ages,
+            json->>'sample_type' AS sample_type,
+            FROM @VDI_CONTROL_SCHEMA@.dataset_properties dp, @VDI_CONTROL_SCHEMA@.AvailableUserDatasets aud
+	    where dp.dataset_id = aud.user_dataset_id
+        ]]>
+      </sql>
+    </sqlQuery>
+
     <sqlQuery name="RNASeqSamplesInternal"  isCacheable='false'>
       <column name="dataset_id"/>
       <column name="study_name"/>
@@ -2415,7 +2422,6 @@ Based on evolutionarily informed expectations of gene content of near-universal
                , affiliation
                from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
 	       where dc.dataset_id = d.user_dataset_id
-	       and d.accessibility != 'private'
         ]]>
       </sql>
     </sqlQuery>

From fa0c6e3460684cffc8558eee6de9f10f4912217e Mon Sep 17 00:00:00 2001
From: steve-fischer-200 <sfischer@upenn.edu>
Date: Mon, 28 Apr 2025 13:30:43 -0400
Subject: [PATCH 3/3] accessibility

---
 Model/lib/wdk/model/records/datasetRecords.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Model/lib/wdk/model/records/datasetRecords.xml b/Model/lib/wdk/model/records/datasetRecords.xml
index 28cc837d..65342c8b 100644
--- a/Model/lib/wdk/model/records/datasetRecords.xml
+++ b/Model/lib/wdk/model/records/datasetRecords.xml
@@ -179,10 +179,10 @@
         </linkAttribute>
       </attributeQueryRef>
 -->
-      <attributeQueryRef ref="DatasetAttributes.UserDatasetAccessibility" includeProjects="MicrobiomeDB,ClinEpiDB">
-        <columnAttribute name="accessibility"/>
-	<columnAttribute name="days_for_approval"/>
-      </attributeQueryRef>
+       <attributeQueryRef ref="DatasetAttributes.UserDatasetAccessibility">
+         <columnAttribute name="accessibility" displayName="Accessibility"/>
+         <columnAttribute name="days_for_approval" displayName="Days for approval"/>
+       </attributeQueryRef>
 
 	<attributeQueryRef ref="DatasetAttributes.ClinepiStudyAttributes" includeProjects="MicrobiomeDB,ClinEpiDB">
         <columnAttribute name="project_availability" internal="true"/>