Reduce DB queries queries by reusing study visits, NAb runs and sampl…

…e properties
LabKey · Sep 15, 2023 · 34843a9 · 34843a9
1 parent 1e20ade
commit 34843a9
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Showing 8 changed files with 45 additions and 79 deletions.
diff --git a/nab/src/org/labkey/nab/NabAssayRun.java b/nab/src/org/labkey/nab/NabAssayRun.java
@@ -50,7 +50,7 @@
 
 public abstract class NabAssayRun extends DilutionAssayRun
 {
-    public NabAssayRun(DilutionAssayProvider provider, ExpRun run,
+    public NabAssayRun(DilutionAssayProvider<?> provider, ExpRun run,
                        User user, List<Integer> cutoffs, StatsService.CurveFitType renderCurveFitType)
     {
         super(provider, run, user, cutoffs, renderCurveFitType);

diff --git a/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java b/nab/src/org/labkey/nab/SinglePlateNabAssayRun.java
@@ -24,6 +24,7 @@
 import org.labkey.api.assay.plate.WellGroup;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
@@ -52,20 +53,20 @@
  */
 public class SinglePlateNabAssayRun extends NabAssayRun
 {
-    protected Plate _plate;
-    private DilutionSummary[] _dilutionSummaries;
+    protected final Plate _plate;
+    private final DilutionSummary[] _dilutionSummaries;
     public static final String SAMPLE_WELL_GROUP_NAME = "SampleWellGroupName";
 
-    private Map<Position, WellGroup> _positionToVirusMap = new HashMap<>();
-    private Map<String, Map<WellGroup, WellGroup>> _virusGroupToControlMap = new HashMap<>();
+    private final Map<Position, WellGroup> _positionToVirusMap = new HashMap<>();
+    private final Map<String, Map<WellGroup, WellGroup>> _virusGroupToControlMap = new HashMap<>();
 
-    public SinglePlateNabAssayRun(DilutionAssayProvider provider, ExpRun run, Plate plate,
+    public SinglePlateNabAssayRun(DilutionAssayProvider<?> provider, ExpRun run, Plate plate,
                                   User user, List<Integer> cutoffs, StatsService.CurveFitType renderCurveFitType)
     {
         super(provider, run, user, cutoffs, renderCurveFitType);
         _plate = plate;
         List<? extends WellGroup> specimenGroups = _plate.getWellGroups(WellGroup.Type.SPECIMEN);
-        _dilutionSummaries = getDilutionSumariesForWellGroups(specimenGroups);
+        _dilutionSummaries = getDilutionSummariesForWellGroups(specimenGroups, run.getContainer());
     }
 
     @Override
@@ -81,7 +82,7 @@ public List<Plate> getPlates()
     }
 
     @Override
-    protected DilutionSummary[] getDilutionSumariesForWellGroups(List<? extends WellGroup> specimenGroups)
+    protected DilutionSummary[] getDilutionSummariesForWellGroups(List<? extends WellGroup> specimenGroups, Container container)
     {
         List<WellGroup> specimenVirusGroups = new ArrayList<>();
         for (WellGroup specimenGroup : specimenGroups)
@@ -116,7 +117,7 @@ protected DilutionSummary[] getDilutionSumariesForWellGroups(List<? extends Well
                 specimenVirusGroups.add(specimenGroup);
         }
 
-        return super.getDilutionSumariesForWellGroups(specimenVirusGroups);
+        return super.getDilutionSummariesForWellGroups(specimenVirusGroups, container);
     }
 
 
@@ -205,9 +206,6 @@ public WellGroup getVirusControlWells(Plate plate, @Nullable List<Position> data
 
     /**
      * Returns the virus well group that contains the specified positions.
-     * @param plate
-     * @param positions
-     * @return
      */
     @Nullable
     private WellGroup getVirusGroupForPositions(Plate plate, List<Position> positions)
@@ -267,7 +265,7 @@ private WellGroup getControlWellsForVirus(Plate plate, WellGroup virusGroup, Str
                     if (virus.contains(pos))
                     {
                         if (!virusToControlPositions.containsKey(virus))
-                            virusToControlPositions.put(virus, new ArrayList<Position>());
+                            virusToControlPositions.put(virus, new ArrayList<>());
 
                         virusToControlPositions.get(virus).add(pos);
                         break;
@@ -322,7 +320,7 @@ public Map<String, Object> getVirusNames()
     protected String getVirusName(String virusWellGroupName)
     {
         List<? extends ExpData> outputDatas = _run.getOutputDatas(null);
-        if (outputDatas.size() > 0)
+        if (!outputDatas.isEmpty())
         {
             Lsid virusLsid = DilutionDataHandler.createVirusWellGroupLsid(outputDatas.get(0), virusWellGroupName);
             AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _run.getContainer(), _protocol, null);
@@ -356,8 +354,8 @@ private WellGroup getControlWellGroupForVirus(Plate plate, String virusWellGroup
             return plate.getWellGroup(WellGroup.Type.CONTROL, controlGroupName);
     }
 
-    private CaseInsensitiveHashMap<WellGroup> _cellControls = new CaseInsensitiveHashMap<>();
-    private CaseInsensitiveHashMap<WellGroup> _virusControls = new CaseInsensitiveHashMap<>();
+    private final CaseInsensitiveHashMap<WellGroup> _cellControls = new CaseInsensitiveHashMap<>();
+    private final CaseInsensitiveHashMap<WellGroup> _virusControls = new CaseInsensitiveHashMap<>();
 
     private boolean ensureCellControl(Plate plate, String virusWellGroupName)
     {

diff --git a/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java b/nab/src/org/labkey/nab/SinglePlateNabDataHandler.java
@@ -94,7 +94,7 @@ public DataType getDataType()
     }
 
     @Override
-    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider provider, ExpRun run, List<Plate> plates, User user,
+    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider<?> provider, ExpRun run, List<Plate> plates, User user,
                                                       List<Integer> sortedCutoffs, StatsService.CurveFitType fit)
     {
         return new SinglePlateNabAssayRun(provider, run, plates.get(0), user, sortedCutoffs, fit);
@@ -175,7 +175,7 @@ DataLoader createGrid() throws IOException, ExperimentException
 
     // Excel can only handle single sheets so this helper class abstracts away creating the loader for a specific sheet.
     // In addition we need to configure the loaders differently for parsing a list of data versus a grid of data without headers.
-    protected abstract class Load
+    protected abstract static class Load
     {
         abstract DataLoader createList() throws IOException, ExperimentException;
         abstract DataLoader createGrid() throws IOException, ExperimentException;
@@ -313,11 +313,11 @@ protected void prepareWellGroups(List<WellGroup> groups, ExpMaterial sampleInput
                             virusData.add(well);
                     }
                 }
-                applyDilution(virusData, sampleInput, properties, reverseDirection);
+                applyDilution(virusData, sampleInput, properties, reverseDirection, sampleProperties);
             }
         }
         else
-            applyDilution(wells, sampleInput, properties, reverseDirection);
+            applyDilution(wells, sampleInput, properties, reverseDirection, sampleProperties);
     }
 
     @Override
@@ -363,11 +363,11 @@ public void beforeDeleteData(List<ExpData> datas, User user) throws ExperimentEx
                     AssayProvider provider = AssayService.get().getProvider(protocol);
                     AssayProtocolSchema protocolSchema = provider.createProtocolSchema(null, protocol.getContainer(), protocol, null);
                     TableInfo virusTable = protocolSchema.createTable(DilutionManager.VIRUS_TABLE_NAME, null);
-                    if (virusTable instanceof FilteredTable)
+                    if (virusTable instanceof FilteredTable ft)
                     {
                         if (virusTable.getColumn(FieldKey.fromParts(NabVirusDomainKind.DATLSID_COLUMN_NAME)) != null)
                         {
-                            TableInfo table = ((FilteredTable) virusTable).getRealTable();
+                            TableInfo table = ft.getRealTable();
                             SimpleFilter dataLsidFilter = new SimpleFilter(FieldKey.fromString(NabVirusDomainKind.DATLSID_COLUMN_NAME), data.getLSID());
 
                             // delete the rows in the virus table associated with this run

diff --git a/nab/src/org/labkey/nab/multiplate/CrossPlateDilutionNabAssayRun.java b/nab/src/org/labkey/nab/multiplate/CrossPlateDilutionNabAssayRun.java
@@ -36,10 +36,10 @@
  */
 public class CrossPlateDilutionNabAssayRun extends NabAssayRun
 {
-    protected List<Plate> _plates;
-    private DilutionSummary[] _dilutionSummaries;
+    protected final List<Plate> _plates;
+    private final DilutionSummary[] _dilutionSummaries;
 
-    public CrossPlateDilutionNabAssayRun(DilutionAssayProvider provider, ExpRun run, List<Plate> plates,
+    public CrossPlateDilutionNabAssayRun(DilutionAssayProvider<?> provider, ExpRun run, List<Plate> plates,
                                          User user, List<Integer> cutoffs, StatsService.CurveFitType renderCurveFitType)
     {
         super(provider, run, user, cutoffs, renderCurveFitType);
@@ -52,18 +52,13 @@ public CrossPlateDilutionNabAssayRun(DilutionAssayProvider provider, ExpRun run,
         {
             for (WellGroup sample : plate.getWellGroups(WellGroup.Type.SPECIMEN))
             {
-                List<WellGroup> groups = sampleGroups.get(sample.getName());
-                if (groups == null)
-                {
-                    groups = new ArrayList<>();
-                    sampleGroups.put(sample.getName(), groups);
-                }
+                List<WellGroup> groups = sampleGroups.computeIfAbsent(sample.getName(), k -> new ArrayList<>());
                 groups.add(sample);
             }
         }
         int index = 0;
         for (Map.Entry<String, List<WellGroup>> sample : sampleGroups.entrySet())
-            _dilutionSummaries[index++] = new DilutionSummary(this, sample.getValue(), null, _renderedCurveFitType);
+            _dilutionSummaries[index++] = new DilutionSummary(this, sample.getValue(), null, _renderedCurveFitType, run.getContainer());
     }
 
     @Override

diff --git a/nab/src/org/labkey/nab/multiplate/CrossPlateDilutionNabDataHandler.java b/nab/src/org/labkey/nab/multiplate/CrossPlateDilutionNabDataHandler.java
@@ -49,7 +49,7 @@ public DataType getDataType()
     }
 
     @Override
-    protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(DilutionAssayProvider provider, List<Plate> plates, Map<ExpMaterial,String> sampleInputs) throws ExperimentException
+    protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(DilutionAssayProvider<?> provider, List<Plate> plates, Map<ExpMaterial,String> sampleInputs) throws ExperimentException
     {
         Map<String, ExpMaterial> nameToMaterial = new HashMap<>();
         for (Map.Entry<ExpMaterial,String> e : sampleInputs.entrySet())
@@ -81,7 +81,7 @@ protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(Dilution
     }
 
     @Override
-    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider provider, ExpRun run, List<Plate> plates, User user, List<Integer> sortedCutoffs, StatsService.CurveFitType fit)
+    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider<?> provider, ExpRun run, List<Plate> plates, User user, List<Integer> sortedCutoffs, StatsService.CurveFitType fit)
     {
         return new CrossPlateDilutionNabAssayRun(provider, run, plates, user, sortedCutoffs, fit);
     }

diff --git a/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java b/nab/src/org/labkey/nab/multiplate/HighThroughputNabDataHandler.java
@@ -85,7 +85,7 @@ protected List<Plate> createPlates(File dataFile, Plate template) throws Experim
             final int expectedCols = template.getColumns();
 
             List<double[][]> matrices = parse(dataFile, loader.getColumns(), loader.load(), expectedRows, expectedCols);
-            if (matrices == null || matrices.size() == 0)
+            if (matrices == null || matrices.isEmpty())
                 throw createParseError(dataFile, "No plate data found");
 
             int plateNumber = 1;
@@ -184,11 +184,13 @@ protected void prepareWellGroups(List<WellGroup> groups, ExpMaterial sampleInput
         List<WellData> wells = new ArrayList<>();
         // All well groups use the same plate template, so it's okay to just check the dilution direction of the first group:
         boolean reverseDirection = Boolean.parseBoolean((String) groups.get(0).getProperty(SampleProperty.ReverseDilutionDirection.name()));
+
+        Map<PropertyDescriptor,Object> sampleProperties = sampleInput.getPropertyValues();
+
         for (WellGroup group : groups)
         {
-            Map<PropertyDescriptor,Object> map = sampleInput.getPropertyValues();
             for (DomainProperty property : properties.values())
-                group.setProperty(property.getName(), map.get(property.getPropertyDescriptor()));
+                group.setProperty(property.getName(), sampleProperties.get(property.getPropertyDescriptor()));
 
             boolean hasExplicitOrder = true;
             List<? extends WellData> wellData = group.getWellData(true);
@@ -230,7 +232,7 @@ protected void prepareWellGroups(List<WellGroup> groups, ExpMaterial sampleInput
             wells.addAll(wellData);
         }
 
-        applyDilution(wells, sampleInput, properties, reverseDirection);
+        applyDilution(wells, sampleInput, properties, reverseDirection, sampleProperties);
     }
 
     @Override

diff --git a/nab/src/org/labkey/nab/multiplate/SinglePlateDilutionNabAssayRun.java b/nab/src/org/labkey/nab/multiplate/SinglePlateDilutionNabAssayRun.java
@@ -19,6 +19,7 @@
 import org.labkey.api.assay.dilution.DilutionSummary;
 import org.labkey.api.assay.nab.Luc5Assay;
 import org.labkey.api.assay.plate.WellGroup;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.statistics.StatsService;
 import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.api.ExpMaterial;
@@ -40,10 +41,10 @@
  */
 public class SinglePlateDilutionNabAssayRun extends NabAssayRun
 {
-    protected List<Plate> _plates;
-    private DilutionSummary[] _dilutionSummaries;
+    protected final List<Plate> _plates;
+    private final DilutionSummary[] _dilutionSummaries;
 
-    public SinglePlateDilutionNabAssayRun(DilutionAssayProvider provider, ExpRun run, List<Plate> plates,
+    public SinglePlateDilutionNabAssayRun(DilutionAssayProvider<?> provider, ExpRun run, List<Plate> plates,
                                   User user, List<Integer> cutoffs, StatsService.CurveFitType renderCurveFitType)
     {
         super(provider, run, user, cutoffs, renderCurveFitType);
@@ -56,21 +57,16 @@ public SinglePlateDilutionNabAssayRun(DilutionAssayProvider provider, ExpRun run
             {
                 String virusName = plate.getProperty(NabAssayProvider.VIRUS_NAME_PROPERTY_NAME).toString();
                 String key = SinglePlateDilutionSamplePropertyHelper.getKey(virusName, sample.getName());
-                List<WellGroup> groups = sampleGroups.get(key);
-                if (groups == null)
-                {
-                    groups = new ArrayList<>();
-                    sampleGroups.put(key, groups);
-                }
+                List<WellGroup> groups = sampleGroups.computeIfAbsent(key, k -> new ArrayList<>());
                 groups.add(sample);
             }
         }
         List<DilutionSummary> dilutionSummaries = new ArrayList<>();
 
         for (Map.Entry<String, List<WellGroup>> sample : sampleGroups.entrySet())
-            dilutionSummaries.add(new MultiVirusDilutionSummary(this, sample.getValue(), null, _renderedCurveFitType));
+            dilutionSummaries.add(new MultiVirusDilutionSummary(this, sample.getValue(), null, _renderedCurveFitType, _run.getContainer()));
 
-        _dilutionSummaries = dilutionSummaries.toArray(new DilutionSummary[dilutionSummaries.size()]);
+        _dilutionSummaries = dilutionSummaries.toArray(new DilutionSummary[0]);
     }
 
     @Override
@@ -87,8 +83,6 @@ public List<Plate> getPlates()
 
     /**
      * Generate a key for the sample level property map
-     * @param material
-     * @return
      */
     @Override
     protected String getSampleKey(ExpMaterial material)
@@ -105,8 +99,6 @@ protected String getSampleKey(ExpMaterial material)
 
     /**
      * Generate a key for the sample level property map
-     * @param summary
-     * @return
      */
     @Override
     protected String getSampleKey(DilutionSummary summary)
@@ -119,9 +111,9 @@ protected String getSampleKey(DilutionSummary summary)
 
     private static class MultiVirusDilutionSummary extends DilutionSummary
     {
-        public MultiVirusDilutionSummary(Luc5Assay assay, List<WellGroup> sampleGroups, String lsid, StatsService.CurveFitType curveFitType)
+        public MultiVirusDilutionSummary(Luc5Assay assay, List<WellGroup> sampleGroups, String lsid, StatsService.CurveFitType curveFitType, Container container)
         {
-            super(assay, sampleGroups, lsid, curveFitType);
+            super(assay, sampleGroups, lsid, curveFitType, container);
         }
     }
 }
diff --git a/nab/src/org/labkey/nab/multiplate/SinglePlateDilutionNabDataHandler.java b/nab/src/org/labkey/nab/multiplate/SinglePlateDilutionNabDataHandler.java
@@ -25,10 +25,8 @@
 import org.labkey.api.assay.plate.WellGroup;
 import org.labkey.api.data.statistics.StatsService;
 import org.labkey.api.exp.ExperimentException;
-import org.labkey.api.exp.Lsid;
 import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.api.DataType;
-import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
@@ -167,7 +165,7 @@ protected List<Plate> createPlates(File dataFile, Plate template) throws Experim
     }
 
     @Override
-    protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(DilutionAssayProvider provider, List<Plate> plates, Map<ExpMaterial,String> sampleInputs) throws ExperimentException
+    protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(DilutionAssayProvider<?> provider, List<Plate> plates, Map<ExpMaterial,String> sampleInputs) throws ExperimentException
     {
         Map<String, ExpMaterial> nameToMaterial = new HashMap<>();
         for (Map.Entry<ExpMaterial,String> e : sampleInputs.entrySet())
@@ -189,38 +187,19 @@ protected Map<ExpMaterial, List<WellGroup>> getMaterialWellGroupMapping(Dilution
                     throw new ExperimentException("Unable to find sample metadata for sample well group \"" + name +
                             "\": your sample metadata file may contain incorrect well group names, or it may not list all required samples.");
                 }
-                List<WellGroup> materialWellGroups = mapping.get(material);
-                if (materialWellGroups == null)
-                {
-                    materialWellGroups = new ArrayList<>();
-                    mapping.put(material, materialWellGroups);
-                }
+                List<WellGroup> materialWellGroups = mapping.computeIfAbsent(material, k -> new ArrayList<>());
                 materialWellGroups.add(specimenGroup);
             }
         }
         return mapping;
     }
 
     @Override
-    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider provider, ExpRun run, List<Plate> plates, User user, List<Integer> sortedCutoffs, StatsService.CurveFitType fit)
+    protected DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider<?> provider, ExpRun run, List<Plate> plates, User user, List<Integer> sortedCutoffs, StatsService.CurveFitType fit)
     {
         return new SinglePlateDilutionNabAssayRun(provider, run, plates, user, sortedCutoffs, fit);
     }
 
-    public Lsid getDataRowLSID(ExpData data, String wellGroupName, Map<PropertyDescriptor, Object> sampleProperties)
-    {
-        String virusName = "";
-        for (Map.Entry<PropertyDescriptor, Object> entry : sampleProperties.entrySet())
-        {
-            if (entry.getKey().getName().equals(NabAssayProvider.VIRUS_NAME_PROPERTY_NAME))
-                virusName = entry.getValue().toString();
-        }
-        Lsid.LsidBuilder dataRowLsid = new Lsid.LsidBuilder(data.getLSID());
-        dataRowLsid.setNamespacePrefix(NAB_DATA_ROW_LSID_PREFIX);
-        dataRowLsid.setObjectId(dataRowLsid.getObjectId() + "-" + virusName + "-" + wellGroupName);
-        return dataRowLsid.build();
-    }
-
     @Override
     public Map<DilutionSummary, DilutionAssayRun> getDilutionSummaries(User user, StatsService.CurveFitType fit, int... dataObjectIds) throws ExperimentException
     {