Add validation to mGAP release steps

Author: bbimber

mGAP/resources/etls/prime-seq.xml

@@ -131,6 +131,7 @@
                 </columnTransforms>
             </destination>
         </transform>
+
         <transform id="step5" type="RemoteQueryTransformStep">
             <description>Copy to local table</description>
             <source schemaName="mGAP" queryName="variantList" remoteSource="PRIMESEQ" sourceTimeout="0">

mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java

@@ -75,8 +75,9 @@ public static class Provider extends AbstractVariantProcessingStepProvider<Gener
         public Provider()
         {
             super("GenerateMgapTracksStep", "Generate mGAP Tracks", "GenerateMgapTracksStep", "This will use the set of sample IDs from the table mgap.releaseTrackSubsets to subset the input VCF and produce one VCF per track. It will perform basic validation and also update mgap.releaseTracks.", Arrays.asList(
-                    ToolParameterDescriptor.create("releaseVersion", "mGAP Version", "This is the string that was used to annotate novel variants.", "textfield", new JSONObject(){{
+                    ToolParameterDescriptor.create("releaseVersion", "mGAP Version", "This is the string that was used to annotate novel variants.", "ldk-numberfield", new JSONObject(){{
                         put("allowBlank", false);
+                        put("decimalPrecision", 1);
                         put("doNotIncludeInTemplates", true);
                     }}, null)
             ), null, null);
@@ -174,17 +175,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         }
 
         // Also create the Novel Sites track:
-        String releaseVersion = getProvider().getParameterByName("releaseVersion").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
-        if (releaseVersion.toLowerCase().startsWith("v"))
-        {
-            releaseVersion = releaseVersion.substring(1);
-        }
-
-        if (!NumberUtils.isCreatable(releaseVersion))
-        {
-            throw new IllegalArgumentException("Expected the release version to be numeric: " + releaseVersion);
-        }
-
+        Double releaseVersion = getProvider().getParameterByName("releaseVersion").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Double.class);
         File novelSitesOutput = new File(outputDirectory, "mGAP_v" + releaseVersion + "_NovelSites.vcf.gz");
         if (new File(novelSitesOutput.getPath() + ".tbi").exists())
         {

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java

@@ -99,8 +99,10 @@ 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("releaseVersion", "Version", "This string will be used as the version when published.", "textfield", new JSONObject(){{
+                ToolParameterDescriptor.create("releaseVersion", "Version", "This value will be used as the version when published.", "ldk-numberfield", new JSONObject(){{
                     put("allowBlank", false);
+                    put("decimalPrecision", 1);
+                    put("doNotIncludeInTemplates", true);
                 }}, null),
                 ToolParameterDescriptor.createExpDataParam("gtfFile", "GTF File", "The gene file used to create these annotations.", "sequenceanalysis-genomefileselectorfield", new JSONObject()
                 {{