use donor_code in MAb learn details page (#662)

new combined ETL
LabKey · Oct 3, 2024 · 48ad7f6 · 48ad7f6
1 parent ecb7dc7
commit 48ad7f6
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diff --git a/resources/etls/CDSImportAndLoad.xml b/resources/etls/CDSImportAndLoad.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>Import Dataspace Archive and Load Application</name>
+    <description>Combines the import archive and load application tables ETLs</description>
+    <transforms>
+        <transform id="import" type="TaskrefTransformStep">
+            <taskref ref="org.labkey.di.steps.QueueJobTask">
+                <settings>
+                    <setting name="transformId" value="{CDS}/CDSImport"/>
+                </settings>
+            </taskref>
+        </transform>
+        <transform id="load application" type="TaskrefTransformStep">
+            <taskref ref="org.labkey.di.steps.QueueJobTask">
+                <settings>
+                    <setting name="transformId" value="{CDS}/LoadApplication"/>
+                </settings>
+            </taskref>
+        </transform>
+    </transforms>
+</etl>
diff --git a/resources/queries/cds/MAbMixMAbMeta.sql b/resources/queries/cds/MAbMixMAbMeta.sql
@@ -32,7 +32,8 @@ SELECT
   mabmeta.donor_id AS mab_donorid,
 -- donor meta
   donormeta.donor_species AS mab_donor_species,
-  donormeta.donor_clade AS mab_donor_clade
+  donormeta.donor_clade AS mab_donor_clade,
+  donormeta.donor_code AS mab_donor_code
 
 FROM MAbMix mix
 

diff --git a/test/sampledata/dataspace/cdsimport/donor_metadata.txt b/test/sampledata/dataspace/cdsimport/donor_metadata.txt
@@ -1,26 +1,26 @@
-donor_id	donor_species	donor_clade
-Donor 36	human	CRF02_AG
-Donor 31	human	
-Donor b	human	
-3065	human	
-N70	human	
-Donor 24	human	A1
-Donor 17	human	A
-Donor 39	human	C
-Donor 84	human	C
-Donor L1	llama	
-NIH45	human	B
-L9	human	
-donor_uncoded_1	human	B
-Donor M1	mouse	
-Patient 1	human	B
-Patient 3	human	B
-Donor CH505	human	C
-Donor N152	human	B
-44	human	B
-CAP256	human	C
-Donore N152	human	B
-347759	human	
-CH0457	human	C
-CH0219	human	A
-CH0210	human	C
+donor_id	donor_species	donor_clade	donor_code
+Donor 36	human	CRF02_AG	3053
+Donor 31	human		3054
+Donor b	human		3055
+3065	human		
+N70	human		
+Donor 24	human	A1	M1214
+Donor 17	human	A	M1215
+Donor 39	human	C	M1216
+Donor 84	human	C	M1217
+Donor L1	llama		M1218
+NIH45	human	B	M1219
+L9	human		M1210
+donor_uncoded_1	human	B	
+Donor M1	mouse		
+Patient 1	human	B	
+Patient 3	human	B	
+Donor CH505	human	C	
+Donor N152	human	B	
+44	human	B	
+CAP256	human	C	
+Donore N152	human	B	
+347759	human		
+CH0457	human	C	
+CH0219	human	A	
+CH0210	human	C	
diff --git a/test/src/org/labkey/test/tests/cds/CDSTestLearnAbout.java b/test/src/org/labkey/test/tests/cds/CDSTestLearnAbout.java
@@ -445,7 +445,7 @@ public void verifyLearnAboutMabDetails()
         final String labelHXB2 = "HXB2 Location";
         final String labelBindingType = "Antibody binding type";
         final String labelSpecies = "Species";
-        final String labelDonorId = "Donor ID";
+        final String labelDonorCode = "Donor code";
         final String labelDonarClade = "Donor clade";
 
         LearnGrid learnGrid = cds.viewLearnAboutPage(LearnTab.MABS);
@@ -497,13 +497,13 @@ public void verifyLearnAboutMabDetails()
 
         log("Verify mAb detail field labels");
         verifyDetailFieldLabels(labelStandardname, labelAntibodyType, labelOthernames, labelIsotype,
-                labelHXB2, labelBindingType, labelLanlid, labelSpecies, labelDonorId, labelDonarClade);
+                labelHXB2, labelBindingType, labelLanlid, labelSpecies, labelDonorCode, labelDonarClade);
 
         log("Verify mab detail field values");
         verifyDetailFieldValues(mAbName, "Bispecific mAb mixture", "PGT128/3BNC117 + PGDM1400 (other)",
-                "IgG", "gp160", "gp120 CD4BS", "2586", "human", "Patient 3", "B",
-                "Env", "gp120 V2", "3201", "Donor 84", "C",
-                "IgG1", "gp120 V3", "2642", "Donor 36", "CRF02_AG");
+                "IgG", "gp160", "gp120 CD4BS", "2586", "human", "M1217", "B",
+                "Env", "gp120 V2", "3201", "C",
+                "IgG1", "gp120 V3", "2642", "3053", "CRF02_AG");
     }
 
     private void verifySectionHeaders(String... headers)

diff --git a/webapp/Connector/src/app/store/MAb.js b/webapp/Connector/src/app/store/MAb.js
@@ -124,7 +124,8 @@ Ext.define('Connector.app.store.MAb', {
                         bindingType: mix.mab_ab_binding_type,
                         donorSpecies: donorSpecies,
                         donorId: mix.mab_donorid,
-                        donorClade: mix.mab_donor_clade
+                        donorClade: mix.mab_donor_clade,
+                        donorCode: mix.mab_donor_code
                     };
                 }, this);
 

diff --git a/webapp/Connector/src/app/view/module/MabDetails.js b/webapp/Connector/src/app/view/module/MabDetails.js
@@ -42,7 +42,7 @@ Ext.define('Connector.view.module.MabDetails', {
                 '<div class="reportmodulecontainer">',
                 '<h3>{mabName:htmlEncode} details</h3>',
 
-                '<tpl if="isotype || hxb2Loc || bindingType || mab_lanlid || donorSpecies || donorId || donorClade">',
+                '<tpl if="isotype || hxb2Loc || bindingType || mab_lanlid || donorSpecies || donorCode || donorClade">',
                     '<table class="learn-study-info">',
                     '<tpl if="isotype">',
                     '<tr>',
@@ -67,16 +67,16 @@ Ext.define('Connector.view.module.MabDetails', {
                     '</tr>',
                     '</tpl>',
 
-                    '<tpl if="donorSpecies || donorId || donorClade">',
+                    '<tpl if="donorSpecies || donorCode || donorClade">',
                     '<tr><td class="item-label">Donor</td><td></td></tr>',
                     '<tpl if="donorSpecies">',
                     '<tr>',
                     '<td class="item-label sub-label">Species:</td><td class="item-value">{donorSpecies:htmlEncode}</td>',
                     '</tr>',
                     '</tpl>',
-                    '<tpl if="donorId">',
+                    '<tpl if="donorCode">',
                     '<tr>',
-                    '<td class="item-label sub-label">Donor ID:</td><td class="item-value">{donorId:htmlEncode}</td>',
+                    '<td class="item-label sub-label">Donor code:</td><td class="item-value">{donorCode:htmlEncode}</td>',
                     '</tr>',
                     '</tpl>',
                     '<tpl if="donorClade">',