From 76aa3332232cac85ffe2787a894355ccbc4a6928 Mon Sep 17 00:00:00 2001
From: steve-fischer-200 <sfischer@upenn.edu>
Date: Sat, 31 Jan 2026 17:14:42 -0500
Subject: [PATCH 1/2] add new metadata tables

---
 .../wdk/model/records/userDatasetRecord.xml   | 57 +++++++++++++++
 .../records/userDatasetRecordQueries.xml      | 70 ++++++++++++++++++-
 2 files changed, 126 insertions(+), 1 deletion(-)

diff --git a/Model/lib/wdk/model/records/userDatasetRecord.xml b/Model/lib/wdk/model/records/userDatasetRecord.xml
index 29d176a4..75179a04 100644
--- a/Model/lib/wdk/model/records/userDatasetRecord.xml
+++ b/Model/lib/wdk/model/records/userDatasetRecord.xml
@@ -276,6 +276,63 @@
         <columnAttribute name="identifier_value" displayName="Identifier"/>
       </table>
 
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <!-- Dependencies -->
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+<!-- not needed in UI
+      <table name="Dependencies"
+             displayName="Dependencies"
+             queryRef="UserDatasetTables.Dependencies">
+        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
+        <columnAttribute name="identifier" displayName="Identifier"/>
+        <columnAttribute name="display_name" displayName="Name"/>
+        <columnAttribute name="version" displayName="Version"/>
+      </table>
+-->
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <!-- Associated Factors -->
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <table name="AssociatedFactors"
+             displayName="Associated Factors"
+             queryRef="UserDatasetTables.AssociatedFactors">
+        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
+        <columnAttribute name="factor" displayName="Factor"/>
+      </table>
+
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <!-- Sample Types -->
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <table name="SampleTypes"
+             displayName="Sample Types"
+             queryRef="UserDatasetTables.SampleTypes">
+        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
+        <columnAttribute name="type" displayName="Sample Type"/>
+      </table>
+
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <!-- Dataset Links -->
+      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+      <table name="DatasetLinks"
+             displayName="Dataset Links"
+             queryRef="UserDatasetTables.DatasetLinks">
+        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
+        <columnAttribute name="dataset_uri" displayName="URI" internal="true"/>
+        <columnAttribute name="shares_records" displayName="Shares Records"/>
+
+        <linkAttribute name="dataset_link" displayName="Link">
+          <displayText>
+            <![CDATA[
+              $$dataset_uri$$
+            ]]>
+          </displayText>
+          <url>
+            <![CDATA[
+              $$dataset_uri$$
+            ]]>
+          </url>
+        </linkAttribute>
+      </table>
+
     </recordClass>
 
   </recordClassSet>
diff --git a/Model/lib/wdk/model/records/userDatasetRecordQueries.xml b/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
index 501eccf9..65531b76 100644
--- a/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
+++ b/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
@@ -302,11 +302,13 @@
     <sqlQuery name="Projects" isCacheable='false'>
       <column name="dataset_id"/>
       <column name="project_id"/>
+      <column name="project_display_name"/>
       <sql>
         <![CDATA[
           SELECT
             dataset_id,
-            project_id
+            project_id,
+            project_display_name
           FROM  @VDI_CONTROL_SCHEMA@.dataset_project
           ORDER BY project_id
         ]]>
@@ -332,6 +334,72 @@
       </sql>
     </sqlQuery>
 
+    <!-- Dependencies table -->
+    <sqlQuery name="Dependencies" isCacheable='false'>
+      <column name="dataset_id"/>
+      <column name="identifier"/>
+      <column name="display_name"/>
+      <column name="version"/>
+      <sql>
+        <![CDATA[
+          SELECT
+            dataset_id,
+            identifier,
+            display_name,
+            version
+          FROM  @VDI_CONTROL_SCHEMA@.dataset_dependency
+          ORDER BY display_name, identifier
+        ]]>
+      </sql>
+    </sqlQuery>
+
+    <!-- Associated Factors table -->
+    <sqlQuery name="AssociatedFactors" isCacheable='false'>
+      <column name="dataset_id"/>
+      <column name="factor"/>
+      <sql>
+        <![CDATA[
+          SELECT
+            dataset_id,
+            factor
+          FROM  @VDI_CONTROL_SCHEMA@.dataset_associated_factor
+          ORDER BY factor
+        ]]>
+      </sql>
+    </sqlQuery>
+
+    <!-- Sample Types table -->
+    <sqlQuery name="SampleTypes" isCacheable='false'>
+      <column name="dataset_id"/>
+      <column name="type"/>
+      <sql>
+        <![CDATA[
+          SELECT
+            dataset_id,
+            type
+          FROM  @VDI_CONTROL_SCHEMA@.dataset_sample_type
+          ORDER BY type
+        ]]>
+      </sql>
+    </sqlQuery>
+
+    <!-- Dataset Links table -->
+    <sqlQuery name="DatasetLinks" isCacheable='false'>
+      <column name="dataset_id"/>
+      <column name="dataset_uri"/>
+      <column name="shares_records"/>
+      <sql>
+        <![CDATA[
+          SELECT
+            dataset_id,
+            dataset_uri,
+            CASE WHEN shares_records THEN 'Yes' ELSE 'No' END as shares_records
+          FROM  @VDI_CONTROL_SCHEMA@.dataset_link
+          ORDER BY dataset_uri
+        ]]>
+      </sql>
+    </sqlQuery>
+
   </querySet>
 
 </wdkModel>

From 7b38a9c7a9c2e9bccada6c06e57fad46b57e9ed5 Mon Sep 17 00:00:00 2001
From: steve-fischer-200 <sfischer@upenn.edu>
Date: Fri, 13 Feb 2026 17:14:03 -0500
Subject: [PATCH 2/2] Species -> Outcome

---
 Model/lib/wdk/model/records/userDatasetRecord.xml    | 10 +++++-----
 .../wdk/model/records/userDatasetRecordQueries.xml   | 12 ++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Model/lib/wdk/model/records/userDatasetRecord.xml b/Model/lib/wdk/model/records/userDatasetRecord.xml
index 75179a04..6a8a4e1f 100644
--- a/Model/lib/wdk/model/records/userDatasetRecord.xml
+++ b/Model/lib/wdk/model/records/userDatasetRecord.xml
@@ -222,13 +222,13 @@
       </table>
 
       <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-      <!-- Species -->
+      <!-- Outcome -->
       <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-      <table name="Species"
-             displayName="Species"
-             queryRef="UserDatasetTables.Species">
+      <table name="Outcome"
+             displayName="Outcome"
+             queryRef="UserDatasetTables.Outcome">
         <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
-        <columnAttribute name="species" displayName="Species"/>
+        <columnAttribute name="outcome" displayName="Outcome"/>
       </table>
 
       <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
diff --git a/Model/lib/wdk/model/records/userDatasetRecordQueries.xml b/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
index 65531b76..245cf117 100644
--- a/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
+++ b/Model/lib/wdk/model/records/userDatasetRecordQueries.xml
@@ -246,17 +246,17 @@
       </sql>
     </sqlQuery>
 
-    <!-- Species table -->
-    <sqlQuery name="Species" isCacheable='false'>
+    <!-- Outcome table -->
+    <sqlQuery name="Outcome" isCacheable='false'>
       <column name="dataset_id"/>
-      <column name="species"/>
+      <column name="outcome"/>
       <sql>
         <![CDATA[
           SELECT
             dataset_id,
-            species
-          FROM  @VDI_CONTROL_SCHEMA@.dataset_species
-          ORDER BY species
+            outcome
+          FROM  @VDI_CONTROL_SCHEMA@.dataset_outcome
+          ORDER BY outcome
         ]]>
       </sql>
     </sqlQuery>