Merge pull request #152 from bimberlabinternal/24.3_fb_merge

Merge 23.11 into 24.3
bimberlabinternal · Apr 4, 2024 · cb252fa · cb252fa
2 parents f7ccedf + c2e9f01
commit cb252fa
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Showing 130 changed files with 3,220 additions and 247 deletions.
diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/AlignmentDisplayColumn.java b/GenotypeAssays/src/org/labkey/genotypeassays/AlignmentDisplayColumn.java
diff --git a/LabPurchasing/resources/queries/labpurchasing/purchases.js b/LabPurchasing/resources/queries/labpurchasing/purchases.js
@@ -3,6 +3,30 @@ var console = require("console");
 
 var triggerHelper = new org.labkey.labpurchasing.LabPurchasingTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
 
+function beforeInsert(row, errors){
+    // The purpose of this is to allow the user to provide a string value for
+    // vendorId or vendorName, and attempt to resolve this against known vendors:
+    if (!row.vendorId || isNaN(row.vendorId)) {
+        var vendorName = row.vendorName || row.vendorId;
+        if (vendorName) {
+            LABKEY.Query.selectRows({
+                schemaName: 'labpurchasing',
+                queryName: 'vendors',
+                columns: 'rowid',
+                filterArray: [LABKEY.Filter.create('vendorName', vendorName)],
+                sort: '-rowid',
+                maxRows: 1,
+                scope: this,
+                success: function(results) {
+                    if (results.rows.length) {
+                        row.vendorId = results.rows[0].rowId;
+                    }
+                }
+            })
+        }
+    }
+}
+
 function afterInsert(row, errors){
     afterUpsert(row, null, errors);
 }

diff --git a/LabPurchasing/resources/queries/labpurchasing/referenceItems.js b/LabPurchasing/resources/queries/labpurchasing/referenceItems.js
@@ -19,9 +19,6 @@ function beforeInsert(row, errors){
                     if (results.rows.length) {
                         row.vendorId = results.rows[0].rowId;
                     }
-                    else {
-                        console.error("Unable to resolve vendor: " + vendorName);
-                    }
                 }
             })
         }

diff --git a/MccColony/resources/queries/study/demographics/.qview.xml b/MccColony/resources/queries/study/demographics/.qview.xml
@@ -27,6 +27,46 @@
         <column name="Id/MostRecentWeight/MostRecentWeightDate"/>
         <column name="alternateIds"/>
         <column name="excludeFromCensus"/>
+        <column name="Id/mostRecentObservations/availability::observation">
+            <properties>
+                <property name="columnTitle" value="Availability"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/current_housing_status::observation">
+            <properties>
+                <property name="columnTitle" value="Housing Status"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/infant_history::observation">
+            <properties>
+                <property name="columnTitle" value="Infant History"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/fertility_status::observation">
+            <properties>
+                <property name="columnTitle" value="Fertility Status"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/medical_history::observation">
+            <properties>
+                <property name="columnTitle" value="Medical History"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/usage_current::observation">
+            <properties>
+                <property name="columnTitle" value="Usage (Current)"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/usage_future::observation">
+            <properties>
+                <property name="columnTitle" value="Usage (Future)"/>
+            </properties>
+        </column>
+        <column name="Id/mostRecentObservations/date_of_observations">
+            <properties>
+                <property name="columnTitle" value="Date of Observations"/>
+            </properties>
+        </column>
     </columns>
     <sorts>
         <sort column="Id" descending="false"/>

diff --git a/MccColony/resources/queries/study/kinship/.qview.xml b/MccColony/resources/queries/study/kinship/.qview.xml
@@ -0,0 +1,15 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Flags">
+    <columns>
+        <column name="Id"/>
+        <column name="Id2"/>
+        <column name="kinship"/>
+        <column name="relationship"/>
+        <column name="Id/mccAlias/externalAlias"/>
+        <column name="Id2MccAlias/externalAlias">
+            <properties>
+                <property name="columnTitle" value="Id2 MCC Alias"/>
+            </properties>
+        </column>
+    </columns>
+
+</customView>
diff --git a/PMR/build.gradle b/PMR/build.gradle
@@ -8,6 +8,7 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "published", depExtension: "module")
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "published", depExtension: "module")
     BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:onprcEHRModules:GeneticsCore", depProjectConfig: "published", depExtension: "module")
 
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "apiJarFile")

diff --git a/PMR/resources/etls/KinshipDataStaging.xml b/PMR/resources/etls/KinshipDataStaging.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>KinshipDataStaging</name>
+    <description>Prepare PRIMe-seq Kinship Data for Import into PRIMe</description>
+    <transforms>
+        <transform id="kinship" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.pmr.etl.TriggerRemoteGeneticsImportStep">
+                <settings>
+                    <setting name="remoteSource" value="EHR_ClinicalSource"/>
+                </settings>
+            </taskref>
+        </transform>
+    </transforms>
+</etl>
diff --git a/PMR/resources/folderTypes/PMR.folderType.xml b/PMR/resources/folderTypes/PMR.folderType.xml
@@ -64,6 +64,7 @@
     <modules>
         <moduleName>PMR</moduleName>
         <moduleName>EHR</moduleName>
+        <moduleName>GeneticsCore</moduleName>
     </modules>
     <defaultModule>PMR</defaultModule>
 </folderType>
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,9 +19,6 @@ function beforeInsert(row, errors){ @@
                         if (results.rows.length) {
                             row.vendorId = results.rows[0].rowId;
                         }
-                        else {
-                            console.error("Unable to resolve vendor: " + vendorName);
-                        }
                     }
                 })
             }
@@ Expand Down @@