Merge 25.11 to develop

mcc/resources/etls/mcc.xml

@@ -33,6 +33,7 @@
                     <column>usage_future</column>
                     <column>date_of_observations</column>
                     <column>colony</column>
+                    <column>source</column>
                     <column>dam</column>
                     <column>sire</column>
                     <column>objectid</column>

mcc/resources/queries/study/demographicsLittermates.sql

@@ -3,8 +3,8 @@ SELECT
     d1.Id,
     d1.litterId,
 
-    (SELECT GROUP_CONCAT(distinct d2.Id, ',') as litterMates FROM study.Demographics d2 WHERE d2.qcstate.publicdata = true AND d1.litterId = d2.litterId AND d1.id != d2.id) as litterMates
+    (SELECT GROUP_CONCAT(distinct d2.Id, ',') as litterMates FROM study.Demographics d2 WHERE d2.qcstate.publicdata = true AND d2.litterId IS NOT NULL AND d1.litterId = d2.litterId AND d1.id != d2.id) as litterMates
 
 FROM study.Demographics d1
 
-WHERE d1.qcstate.publicdata = true
+WHERE d1.qcstate.publicdata = true AND d1.litterId IS NOT NULL

mcc/resources/queries/study/demographicsMccTransfer.query.xml

@@ -0,0 +1,29 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsMccTransfer" tableDbType="NOT_IN_DB">
+                <tableTitle>MCC Transfers</tableTitle>
+                <description>Summary of MCC Transfers</description>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="mccRequestId">
+                        <columnTitle>MCC Request ID</columnTitle>
+                    </column>
+                    <column columnName="piLastName">
+                        <columnTitle>PI Last Name</columnTitle>
+                    </column>
+                    <column columnName="piFirstName">
+                        <columnTitle>PI First Name</columnTitle>
+                    </column>
+                    <column columnName="piInstitution">
+                        <columnTitle>PI Institution</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>mccRequestId</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

mcc/resources/queries/study/demographicsMccTransfer.sql

@@ -0,0 +1,9 @@
+SELECT
+    d.Id,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.rowId, ', ') as mccRequestId,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.lastName, char(10)) as piLastName,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.firstName, char(10)) as piFirstName,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.institutionname, char(10)) as piInstitution
+FROM study.departure d
+WHERE d.qcstate.publicdata = true AND d.mccRequestId IS NOT NULL
+GROUP BY d.Id

mcc/src/org/labkey/mcc/etl/ProjectAssignmentTransform.java

@@ -28,6 +28,7 @@ public class ProjectAssignmentTransform extends ColumnTransform
     private static final String U24_BREEDER = "U24 breeder";
     private static final String U24_OFFSPRING = "U24 offspring";
     private static final String U24_OTHER = "Other";
+    private static final String U24_INACTIVE = "U24 marmoset breeding- INACTIVE -";
 
     @Override
     protected Object doTransform(Object inputValue)
@@ -42,6 +43,10 @@ protected Object doTransform(Object inputValue)
         {
             return getOrCreateFlag(U24_TITLE);
         }
+        else if (U24_INACTIVE.equalsIgnoreCase(String.valueOf(inputValue)))
+        {
+            return getOrCreateFlag(U24_INACTIVE);
+        }
         // SNPRC:
         else if (U24_BREEDER.equalsIgnoreCase(String.valueOf(inputValue)))
         {
@@ -51,8 +56,11 @@ else if (U24_OFFSPRING.equalsIgnoreCase(String.valueOf(inputValue)))
         {
             return getOrCreateFlag(U24_OFFSPRING);
         }
-
-        return inputValue;
+        else
+        {
+            _log.error("Unknown flag value: " + inputValue + ", in folder: " + getContainerUser().getContainer().getPath());
+            return null;
+        }
     }
 
     private String getOrCreateFlag(String type)

mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java

@@ -16,10 +16,11 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.LookupForeignKey;
 import org.labkey.api.query.QueryForeignKey;
-import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
+import org.labkey.api.security.User;
 import org.labkey.mcc.MccManager;
 import org.labkey.mcc.MccSchema;
+import org.labkey.mcc.security.MccRequestAdminPermission;
 
 public class MccEhrCustomizer extends AbstractTableCustomizer
 {
@@ -141,6 +142,39 @@ private void customizeAnimalTable(AbstractTableInfo ti)
             col.setDescription("Summary of genomic data");
             ti.addColumn(col);
         }
+
+        // Only allow this for authorized users:
+        possiblyAddRequestSummary(ti);
+    }
+
+    private void possiblyAddRequestSummary(AbstractTableInfo ti)
+    {
+        if (ti.getColumn("mccTransfers") != null)
+        {
+            return;
+        }
+
+        Container animalDataContainer = MccManager.get().getMCCContainer(ti.getUserSchema().getContainer());
+        if (animalDataContainer == null)
+        {
+            return;
+        }
+
+        if (!animalDataContainer.equals(ti.getUserSchema().getContainer()))
+        {
+            return;
+        }
+
+        User u = ti.getUserSchema().getUser();
+        if (!animalDataContainer.hasPermission(u, MccRequestAdminPermission.class))
+        {
+            return;
+        }
+
+        var col = getWrappedIdCol(ti.getUserSchema(), ti, "mccTransfers", "demographicsMccTransfer");
+        col.setLabel("MCC Transfers");
+        col.setDescription("Summarizes MCC Transfer Information");
+        ti.addColumn(col);
     }
 
     private BaseColumnInfo getWrappedIdCol(UserSchema us, AbstractTableInfo ds, String name, String queryName)

tcrdb/build.gradle

@@ -5,38 +5,12 @@ repositories {
    mavenCentral()
 }
 
-configurations.all {
-    resolutionStrategy {
-        // Related to: https://nvd.nist.gov/vuln/detail/CVE-2025-12183
-        dependencySubstitution {
-            substitute module('org.lz4:lz4-java') using module("at.yawk.lz4:lz4-java:${lz4Version}")
-        }
-    }
-}
-
 dependencies {
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:singlecell", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "assay"), depProjectConfig: "apiJarFile")
-   BuildUtils.addExternalDependency(
-           project,
-           new ExternalDependency(
-                   "io.repseq:repseqio:${repseqVersion}",
-                   "repseqio",
-                   "repseqio",
-                   "https://github.com/repseqio/repseqio",
-                   ExternalDependency.APACHE_2_LICENSE_NAME,
-                   ExternalDependency.APACHE_2_LICENSE_URL,
-                   "TCR Analysis"
-           ),
-           {
-              // exclude logback to prevent excessive logging
-              exclude group: "ch.qos.logback", module :"logback-classic"
-              exclude group: "ch.qos.logback", module :"logback-core"
-           }
-   )
    implementation "com.github.samtools:htsjdk:${htsjdkVersion}"
    implementation "net.sf.opencsv:opencsv:${opencsvVersion}"
 

tcrdb/gradle.properties

@@ -1,2 +0,0 @@
-lz4Version=1.10.1
-repseqVersion=1.7.0

tcrdb/resources/assay/TCRdb/queries/Data.query.xml

@@ -142,9 +142,6 @@
                         <item text="View Alignments">
                             <onClick>TCRdb.window.ExportDataWindow.viewAlignmentHandler(dataRegionName, arguments[0] ? arguments[0].ownerCt : null);</onClick>
                         </item>
-                        <item text="Download Clone Materials">
-                            <onClick>TCRdb.window.DownloadCloneWindow.buttonHandler(dataRegionName);</onClick>
-                        </item>
                         <item text="Download Clone Sequence">
                             <onClick>TCRdb.window.DownloadCloneWindow.downloadSequenceHandler(dataRegionName);</onClick>
                         </item>

tcrdb/resources/web/tcrdb/window/DownloadCloneWindow.js

@@ -2,10 +2,6 @@ Ext4.define('TCRdb.window.DownloadCloneWindow', {
     extend: 'Ext.window.Window',
 
     statics: {
-        buttonHandler: function(dataRegionName) {
-            TCRdb.window.DownloadCloneWindow.showWindow(dataRegionName, 'downloadCloneMaterials', 'The goal of this is to download a ZIP with any extracted clone/read data for the selected sample(s), along with the reference sequence for the segments used.  These files can be imported into Geneious or a similar program to de novo assemble to construct the FL clone.  Note: per sample, it will export all reads overlapping any TCR segments.  This at minimum will tend to include both chains (i.e. 2 different CDR3s), and might include reads that either match a defunct TCR or other noise.');
-        },
-
         downloadSequenceHandler: function(dataRegionName){
             TCRdb.window.DownloadCloneWindow.showWindow(dataRegionName, 'downloadSequence', 'This will download the full sequence (if available) for the selected rows, along with the reference segments.');
         },