Small bugfixes to mGAP release

bimberlabinternal · Feb 1, 2025 · 1dd37ca · 1dd37ca
1 parent 036af5f
commit 1dd37ca
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Showing 5 changed files with 14 additions and 47 deletions.
diff --git a/mGAP/resources/views/mgapDataDashboard.html b/mGAP/resources/views/mgapDataDashboard.html
@@ -23,9 +23,7 @@
                     header: 'Upcoming Release',
                     items: [{
                         name: 'Release Instructions',
-                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
-                            schemaName: 'wiki',
-                            queryName: 'page',
+                        url: LABKEY.ActionURL.buildURL('wiki', 'page.view', null, {
                             name: 'mgapRelease'
                         })
                     },{

diff --git a/mGAP/resources/web/mGAP/window/ReleaseWindow.js b/mGAP/resources/web/mGAP/window/ReleaseWindow.js
@@ -18,6 +18,7 @@ Ext4.define('mGAP.window.ReleaseWindow', {
                     Ext4.Msg.hide();
                     var outputFiles = [];
                     var distinctGenomesBySpecies = {};
+                    var distinctGenomes = [];
                     Ext4.Array.forEach(results.rows, function(r){
                         if (!r.vcfId) {
                             Ext4.Msg.alert('Error', 'Track lacks VCF ID: ' + r.trackName);
@@ -34,20 +35,29 @@ Ext4.define('mGAP.window.ReleaseWindow', {
                         distinctGenomesBySpecies[r.species] = distinctGenomesBySpecies[r.species] || [];
                         if (r['vcfId/library_id']) {
                             distinctGenomesBySpecies[r.species].push(r['vcfId/library_id']);
+                            distinctGenomes.push(r['vcfId/library_id']);
                         }
                     }, this);
 
+                    distinctGenomes = Ext4.unique(distinctGenomes)
+
                     if (!outputFiles.length){
                         Ext4.Msg.alert('Error', 'None of the tracks have VCF files');
                         return;
                     }
 
-                    for (sn in Ext4.Object.getKeys(distinctGenomesBySpecies)) {
+                    var hadError = false;
+                    Ext4.Array.forEach(Ext4.Object.getKeys(distinctGenomesBySpecies), function(sn) {
                         var genomes = Ext4.Array.unique(distinctGenomesBySpecies[sn]);
                         if (genomes.length !== 1){
                             Ext4.Msg.alert('Error', 'All files must use the same genome.  Genomes found for species ' + sn + ': ' + genomes.length);
-                            return;
+                            hadError = true;
+                            return false;
                         }
+                    }, this);
+
+                    if (hadError) {
+                        return;
                     }
 
                     LABKEY.Ajax.request({

diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
@@ -101,7 +101,7 @@ public class mGapReleaseGenerator extends AbstractParameterizedOutputHandler<Seq
     public mGapReleaseGenerator()
     {
         super(ModuleLoader.getInstance().getModule(mGAPModule.class), "Create mGAP Release", "This will prepare an input VCF for use as an mGAP public release.  This will optionally include: removing excess annotations and program records, limiting to SNVs (optional) and removing genotype data (optional).  If genotypes are retained, the subject names will be checked for mGAP aliases and replaced as needed.", new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js")), Arrays.asList(
-                ToolParameterDescriptor.create("species", "Version", "The species, which is used to filter tracks", "ldk-simplelabkeycombo", new JSONObject(){{
+                ToolParameterDescriptor.create("species", "Species", "The species, which is used to filter tracks", "ldk-simplelabkeycombo", new JSONObject(){{
                     put("allowBlank", false);
                     put("doNotIncludeInTemplates", true);
                     put("width", 400);

diff --git a/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java b/primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java
@@ -39,8 +39,6 @@ public List<ToolParameterDescriptor> getParams()
                     put("minValue", 512);
                 }}, 1028),
                 ToolParameterDescriptor.create("localSSD", "Request Nodes With SSD Scratch", "If selected, -C ssdscratch will be added to the submit script, which limits to node with faster SSD scratch space.  This might be important for I/O intense jobs.", "checkbox", null, null),
-                ToolParameterDescriptor.create("useLustre", "Use Old Lustre Working Space", "If selected, this job will use the older Lustre working space.", "checkbox", null, null),
-                ToolParameterDescriptor.create("requireInfiniband", "Require InfiniBand", "If selected, this job will be flagged as -C IB to force the node to have InfiniBand.", "checkbox", null, null),
                 ToolParameterDescriptor.create("gpus", "GPUs", "The number of GPUs requested for this job. If non-zero, the gpu partition will be used.", "ldk-integerfield", null, null)
         );
     }

diff --git a/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java b/primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java
@@ -310,7 +310,6 @@ public void addExtraSubmitScriptLines(PipelineJob job, RemoteExecutionEngine eng
             possiblyAddSSD(job, engine, lines);
             possiblyAddGpus(job, engine, lines);
             possiblyAddExclusive(job, engine, lines);
-            possiblyAddInfiniband(job, engine, lines);
         }
     }
 
@@ -319,11 +318,6 @@ public void addExtraSubmitScriptLines(PipelineJob job, RemoteExecutionEngine eng
     {
         Map<String, Object> ret = new HashMap<>();
 
-        if (job instanceof HasJobParams && getUseLustreValue((HasJobParams)job))
-        {
-            job.getLogger().info("Requiring using original lustre as working space");
-            ret.put("USE_LUSTRE", "1");
-        }
 
         return ret;
     }
@@ -482,39 +476,6 @@ private void possiblyAddSSD(PipelineJob job, RemoteExecutionEngine engine, List<
         }
     }
 
-    private void possiblyAddInfiniband(PipelineJob job, RemoteExecutionEngine engine, List<String> lines)
-    {
-        Map<String, String> params = ((HasJobParams)job).getJobParams();
-        String val = StringUtils.trimToNull(params.get("resourceSettings.resourceSettings.requireInfiniband"));
-        if (val == null)
-        {
-            return;
-        }
-
-        boolean parsed = Boolean.parseBoolean(val);
-        if (parsed)
-        {
-            job.getLogger().info("Requiring node with infiniband");
-            String line = "#SBATCH -C IB";
-            if (!lines.contains(line))
-            {
-                lines.add(line);
-            }
-        }
-    }
-
-    private boolean getUseLustreValue(HasJobParams job)
-    {
-        Map<String, String> params = (job).getJobParams();
-        String val = StringUtils.trimToNull(params.get("resourceSettings.resourceSettings.useLustre"));
-        if (val == null)
-        {
-            return false;
-        }
-
-        return Boolean.parseBoolean(val);
-    }
-
     private void possiblyAddQOS(PipelineJob job, RemoteExecutionEngine engine, List<String> lines)
     {
         //first remove existing