Switch funcotator to use field config from DB

Author: bbimber

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

@@ -10,6 +10,7 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.Results;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.TableSelector;
@@ -43,6 +44,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -148,21 +150,47 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Seque
         Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbook() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer();
         final HashMap<String, List<String>> sourceFieldMap = new HashMap<>();
         final HashMap<String, List<String>> targetFieldMap = new HashMap<>();
-        new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("toolName", "sourceField", "infoKey")).forEachResults(rs -> {
-            if (!sourceFieldMap.containsKey(rs.getString(FieldKey.fromString("toolName"))))
-            {
-                sourceFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
-                targetFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
-            }
+        try (PrintWriter writer = PrintWriters.getPrintWriter(getFieldConfigFile()))
+        {
+            writer.println(StringUtils.join(Arrays.asList("DataSource", "SourceField", "ID", "Number", "Type", "Description"), "\t"));
+
+            new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("toolName", "sourceField", "infoKey")).forEachResults(rs -> {
+                if (!sourceFieldMap.containsKey(rs.getString(FieldKey.fromString("toolName"))))
+                {
+                    sourceFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
+                    targetFieldMap.put(rs.getString(FieldKey.fromString("toolName")), new ArrayList<>());
+                }
 
-            sourceFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("sourceField")));
-            targetFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("infoKey")));
-        });
+                sourceFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("sourceField")));
+                targetFieldMap.get(rs.getString(FieldKey.fromString("toolName"))).add(rs.getString(FieldKey.fromString("infoKey")));
+
+                if ("Funcotator".equals(rs.getString(FieldKey.fromString("toolName"))))
+                {
+                    writer.println(StringUtils.join(Arrays.asList(
+                            getFieldValue(rs, "dataSource"),
+                            getFieldValue(rs, "sourceField"),
+                            getFieldValue(rs, "infoKey"),
+                            getFieldValue(rs, "dataNumber"),
+                            getFieldValue(rs, "dataType"),
+                            getFieldValue(rs, "description")
+                    ), "\t"));
+                }
+            });
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
 
         getPipelineCtx().getSequenceSupport().cacheObject(SOURCE_FIELDS, sourceFieldMap);
         getPipelineCtx().getSequenceSupport().cacheObject(TARGET_FIELDS, targetFieldMap);
     }
 
+    private String getFieldValue(Results rs, String fieldName) throws SQLException
+    {
+        return rs.getObject(FieldKey.fromString(fieldName)) == null ? "" : rs.getString(FieldKey.fromString(fieldName));
+    }
+
     private static final String SOURCE_FIELDS = "sourceFields";
     private static final String TARGET_FIELDS = "targetFields";
 
@@ -452,7 +480,10 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
                     extraArgs.add("-pmf");
                 }
 
-                fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, funcotatorAnnotated, grch37Genome, extraArgs);
+                File configFile = getFieldConfigFile();
+                output.addIntermediateFile(configFile);
+
+                fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, funcotatorAnnotated, grch37Genome, configFile, extraArgs);
             }
             else
             {
@@ -528,6 +559,11 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         return output;
     }
 
+    private File getFieldConfigFile()
+    {
+        return new File(getPipelineCtx().getSourceDirectory(), "funcotatorFields.txt");
+    }
+
     private void addToolFieldNames(String toolName, String argName, List<String> options, File outDir, VariantProcessingStepOutputImpl output, @Nullable List<String> extraFields) throws PipelineJobException
     {
         List<String> fields = getCachedFields(TARGET_FIELDS, toolName);

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

@@ -22,7 +22,7 @@ public FuncotatorWrapper(Logger log)
         super(log);
     }
 
-    public void runFuncotator(File dataDir, File input, File output, ReferenceGenome genome, @Nullable List<String> extraArgs) throws PipelineJobException
+    public void runFuncotator(File dataDir, File input, File output, ReferenceGenome genome, File configFile, @Nullable List<String> extraArgs) throws PipelineJobException
     {
         getLogger().info("Annotating VCF with Funcotator");
 
@@ -41,7 +41,7 @@ public void runFuncotator(File dataDir, File input, File output, ReferenceGenome
         params.add("VCF");
 
         params.add("-cf");
-        params.add(new File(dataDir, "fieldConfig.txt").getPath());
+        params.add(configFile.getPath());
 
         params.add("-V");
         params.add(input.getPath());