Refactor LaboratorySerivce to allow registration of DemographicsProvider and perform minor refactors related to generics

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -19,6 +19,7 @@
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.laboratory.DemographicsProvider;
 import org.labkey.api.laboratory.NavItem;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -88,7 +89,7 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public Integer getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
 
-    abstract public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u);
+    abstract public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u, DemographicsProvider d);
 
     abstract public String getVCFLineCount(File vcf, Logger log, boolean passOnly) throws PipelineJobException;
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractAlignmentStepProvider.java

@@ -28,7 +28,7 @@
  * Date: 6/14/2014
  * Time: 2:44 PM
  */
-abstract public class AbstractAlignmentStepProvider<StepType extends AlignmentStep> extends AbstractPipelineStepProvider<StepType> implements AlignmentStepProvider
+abstract public class AbstractAlignmentStepProvider<StepType extends AlignmentStep> extends AbstractPipelineStepProvider<StepType> implements AlignmentStepProvider<StepType>
 {
     public static String ALIGNMENT_MODE_PARAM = "alignmentMode";
     public static String SUPPORT_MERGED_UNALIGNED = "supportsMergeUnaligned";

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java

@@ -31,7 +31,7 @@
  * Date: 6/14/2014
  * Time: 12:37 PM
  */
-abstract public class AbstractPipelineStepProvider<StepType extends PipelineStep> implements PipelineStepProvider
+abstract public class AbstractPipelineStepProvider<StepType extends PipelineStep> implements PipelineStepProvider<StepType>
 {
     private final String _name;
     private final String _label;
@@ -145,7 +145,7 @@ public Class<StepType> getStepClass()
     }
 
     @Override
-    public PipelineStepProvider<StepType> combineSteps(int existingStepIdx, PipelineStepCtx toCombine)
+    public PipelineStepProvider<StepType> combineSteps(int existingStepIdx, PipelineStepCtx<StepType> toCombine)
     {
         return null;
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignmentStepProvider.java

@@ -1,6 +1,6 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
-public interface AlignmentStepProvider extends PipelineStepProvider
+public interface AlignmentStepProvider<StepType extends PipelineStep> extends PipelineStepProvider<StepType>
 {
     default boolean shouldRunIdxstats()
     {

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PedigreeToolParameterDescriptor.java

@@ -0,0 +1,20 @@
+package org.labkey.api.sequenceanalysis.pipeline;
+
+import org.json.JSONObject;
+
+public class PedigreeToolParameterDescriptor extends ToolParameterDescriptor
+{
+    public static String NAME = "pedigreeSource";
+
+    public PedigreeToolParameterDescriptor()
+    {
+        super(null, NAME, "Pedigree Source", "This is the table used for pedigree data", "laboratory-pedigreeselectorfield", "laboratory.subjects", new JSONObject(){{
+            put("allowBlank", false);
+        }});
+    }
+
+    public static String getClientDependencyPath()
+    {
+        return "/laboratory/field/PedigreeSelectorField.js";
+    }
+}

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/PipelineStepProvider.java

@@ -94,5 +94,5 @@ default boolean hasParameter(String name)
      * Allows a given step to combine itself w/ a neighboring step to save compute time.  Should return a new provider, which will
      * replace both original provider.  Return null for no changes.
      */
-    PipelineStepProvider<StepType> combineSteps(int existingStepIdx, PipelineStepCtx toCombine);
+    PipelineStepProvider<StepType> combineSteps(int existingStepIdx, PipelineStepCtx<StepType> toCombine);
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -53,9 +53,9 @@ static public void setInstance(SequencePipelineService instance)
 
     abstract public void registerPipelineStepType(Class<? extends PipelineStep> clazz, String paramName);
 
-    abstract public void registerPipelineStep(PipelineStepProvider provider);
+    abstract public void registerPipelineStep(PipelineStepProvider<?> provider);
 
-    abstract public Set<PipelineStepProvider> getAllProviders();
+    abstract public Set<PipelineStepProvider<?>> getAllProviders();
 
     abstract public <StepType extends PipelineStep> Set<PipelineStepProvider<StepType>> getProviders(Class<StepType> stepType);
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java

@@ -17,8 +17,11 @@
 
 import htsjdk.samtools.util.Interval;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.laboratory.DemographicsProvider;
+import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 
 import java.io.File;
@@ -70,7 +73,20 @@ interface Output extends PipelineStepOutput
 
     interface RequiresPedigree
     {
+        default String getDemographicsProviderName(PipelineStepProvider<?> provider, PipelineJob job, int stepIdx)
+        {
+            return provider.getParameterByName(PedigreeToolParameterDescriptor.NAME).extractValue(job, provider, stepIdx, String.class);
+        }
 
+        default DemographicsProvider getDemographicsProvider(PipelineStepProvider<?> provider, PipelineJob job, int stepIdx)
+        {
+            if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+            {
+                throw new IllegalStateException("getDemographicsProvider() can only be run from the webserver");
+            }
+
+            return LaboratoryService.get().getDemographicsProviderByName(job.getContainer(), job.getUser(), getDemographicsProviderName(provider, job, stepIdx));
+        }
     }
 
     interface SupportsScatterGather

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisServiceImpl.java

@@ -12,12 +12,12 @@
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.laboratory.DemographicsProvider;
 import org.labkey.api.laboratory.NavItem;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
@@ -57,8 +57,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.sql.ResultSet;
-import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -361,25 +359,20 @@ public Integer getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) thro
     }
 
     @Override
-    public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u)
+    public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u, DemographicsProvider d)
     {
         final List<PedigreeRecord> pedigreeRecords = new ArrayList<>();
 
-        TableInfo subjectTable = QueryService.get().getUserSchema(u, (c.isWorkbook() ? c.getParent() : c), "laboratory").getTable("subjects");
-        TableSelector ts = new TableSelector(subjectTable, PageFlowUtil.set("subjectname", "mother", "father", "gender"), new SimpleFilter(FieldKey.fromString("subjectname"), sampleNames, CompareType.IN), null);
-        ts.forEach(new Selector.ForEachBlock<ResultSet>()
-        {
-            @Override
-            public void exec(ResultSet rs) throws SQLException
-            {
-                PedigreeRecord pedigree = new PedigreeRecord();
-                pedigree.setSubjectName(rs.getString("subjectname"));
-                pedigree.setFather(rs.getString("father"));
-                pedigree.setMother(rs.getString("mother"));
-                pedigree.setGender(rs.getString("gender"));
-                if (!StringUtils.isEmpty(pedigree.getSubjectName()))
-                    pedigreeRecords.add(pedigree);
-            }
+        TableInfo subjectTable = QueryService.get().getUserSchema(u, (c.isWorkbook() ? c.getParent() : c), d.getSchema()).getTable(d.getQuery());
+        TableSelector ts = new TableSelector(subjectTable, PageFlowUtil.set(d.getSubjectField(), d.getMotherField(), d.getFatherField(), "gender"), new SimpleFilter(FieldKey.fromString(d.getSubjectField()), sampleNames, CompareType.IN), null);
+        ts.forEach(rs -> {
+            PedigreeRecord pedigree = new PedigreeRecord();
+            pedigree.setSubjectName(rs.getString(d.getSubjectField()));
+            pedigree.setFather(rs.getString(d.getFatherField()));
+            pedigree.setMother(rs.getString(d.getMotherField()));
+            pedigree.setGender(rs.getString(d.getSexField()));
+            if (!StringUtils.isEmpty(pedigree.getSubjectName()))
+                pedigreeRecords.add(pedigree);
         });
 
         //insert record for any missing parents:

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java

@@ -58,7 +58,7 @@ public class SequencePipelineServiceImpl extends SequencePipelineService
     private static final SequencePipelineServiceImpl _instance = new SequencePipelineServiceImpl();
 
     private static final Logger _log = LogManager.getLogger(SequencePipelineServiceImpl.class);
-    private final Set<PipelineStepProvider> _providers = new HashSet<>();
+    private final Set<PipelineStepProvider<?>> _providers = new HashSet<>();
     private final Set<JobResourceSettings> _resourceSettings = new HashSet<>();
 
     private final Map<Class<? extends PipelineStep>, String> _pipelineStepTypeMap = new HashMap<>();
@@ -85,14 +85,14 @@ public void registerPipelineStepType(Class<? extends PipelineStep> clazz, String
     }
 
     @Override
-    public void registerPipelineStep(PipelineStepProvider provider)
+    public void registerPipelineStep(PipelineStepProvider<?> provider)
     {
         _log.info("registering sequence pipeline provider: " + provider.getName());
         _providers.add(provider);
     }
 
     @Override
-    public Set<PipelineStepProvider> getAllProviders()
+    public Set<PipelineStepProvider<?>> getAllProviders()
     {
         return Collections.unmodifiableSet(_providers);
     }
@@ -101,19 +101,40 @@ public Set<PipelineStepProvider> getAllProviders()
     public <StepType extends PipelineStep> Set<PipelineStepProvider<StepType>> getProviders(Class<StepType> stepType)
     {
         Set<PipelineStepProvider<StepType>> ret = new HashSet<>();
-        for (PipelineStepProvider provider : _providers)
+        for (PipelineStepProvider<?> provider : _providers)
         {
-            ParameterizedType parameterizedType = (ParameterizedType)provider.getClass().getGenericSuperclass();
-            Class clazz = (Class)parameterizedType.getActualTypeArguments()[0];
+            Class<?> clazz = findSuperClassParameterType(provider, 0);
+            if (clazz == null)
+            {
+                _log.error("Unable to infer parameter type for provider: " + provider.getName());
+                continue;
+            }
+
             if (stepType.isAssignableFrom(clazz))
             {
-                ret.add(provider);
+                ret.add((PipelineStepProvider<StepType>)provider);
             }
         }
 
         return ret;
     }
 
+    // Based on: https://www.javacodegeeks.com/2013/12/advanced-java-generics-retreiving-generic-type-arguments.html
+    private static Class<?> findSuperClassParameterType(Object instance, int parameterIndex) {
+        Class<?> clazz = instance.getClass();
+        while (clazz != clazz.getSuperclass()) {
+            if (clazz.getGenericSuperclass() instanceof ParameterizedType pt)
+            {
+                return (Class<?>) pt.getActualTypeArguments()[parameterIndex];
+            }
+
+
+            clazz = clazz.getSuperclass();
+        }
+
+        return null;
+    }
+
     @Override
     public <StepType extends PipelineStep> PipelineStepProvider<StepType> getProviderByName(String name, Class<StepType> stepType)
     {