Sample type color field and color configuration (#7866)

Author: XingY

api/src/org/labkey/api/audit/SampleTimelineAuditEvent.java

@@ -20,6 +20,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
+import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.qc.DataState;
 import org.labkey.api.qc.SampleStatusService;
 import org.labkey.api.query.QueryService;
@@ -224,46 +225,42 @@ public Map<String, Object> getAuditLogMessageElements()
         return elements;
     }
 
-    /**
-     * If the sample state changed, explicitly add in the Status Label value to the map so that it will render in the
-     * audit log timeline event even if the DataState row is later deleted.  Also, remove the aliquot rollup calculated
-     * fields from the data.
-     */
     @Override
     public void setOldRecordMap(String oldRecordMap, Container container)
     {
-        if (oldRecordMap != null)
-        {
-            Map<String, String> row = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(oldRecordMap));
-            EXCLUDED_DETAIL_FIELDS.forEach(row::remove);
-            String label = getStatusLabel(row, container);
-            if (label != null)
-            {
-                row.put("samplestatelabel", label);
-                oldRecordMap = AbstractAuditTypeProvider.encodeForDataMap(row);
-            }
-        }
-        super.setOldRecordMap(oldRecordMap);
+        super.setOldRecordMap(withResolvedLabels(oldRecordMap, container));
     }
 
-    /**
-     * If the sample state changed, explicitly add in the Status Label value to the map so that it will render in the
-     * audit log timeline event even if the DataState row is later deleted. Also, remove the aliquot rollup calculated
-     * fields from the data.
-     */
     @Override
     public void setNewRecordMap(String newRecordMap, Container container)
     {
-        if (newRecordMap != null)
+        super.setNewRecordMap(withResolvedLabels(newRecordMap, container), container);
+    }
+
+    /**
+     * If the sample state or color changed, explicitly add the resolved Status/Color label to the map so it renders in
+     * the audit log timeline event even if the DataState/DataColor row is later deleted. Also removes the aliquot rollup
+     * calculated fields from the data.
+     */
+    private String withResolvedLabels(String recordMap, Container container)
+    {
+        if (recordMap == null)
+            return null;
+
+        Map<String, String> row = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(recordMap));
+        EXCLUDED_DETAIL_FIELDS.forEach(row::remove);
+
+        String statusLabel = getStatusLabel(row, container);
+        if (row.containsKey("samplestate"))
+            row.put("samplestatelabel", statusLabel);
+
+        if (row.containsKey(ExpMaterialColor.name()))
         {
-            Map<String, String> row = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(newRecordMap));
-            EXCLUDED_DETAIL_FIELDS.forEach(row::remove);
-            String label = getStatusLabel(row, container);
-            if (label != null)
-                row.put("samplestatelabel", label);
-            newRecordMap = AbstractAuditTypeProvider.encodeForDataMap(row);
+            String colorLabel = getColorLabel(row, container);
+            row.put("expmaterialcolorlabel", colorLabel);
         }
-        super.setNewRecordMap(newRecordMap, container);
+
+        return AbstractAuditTypeProvider.encodeForDataMap(row);
     }
 
     private String getStatusLabel(Map<String, String> row, Container container)
@@ -276,4 +273,12 @@ private String getStatusLabel(Map<String, String> row, Container container)
         }
         return null;
     }
+
+    private String getColorLabel(Map<String, String> row, Container container)
+    {
+        String value = row.get(ExpMaterialColor.name());
+        if (!StringUtils.isBlank(value))
+            return ExperimentService.get().getDataColorLabel(container, Long.parseLong(value));
+        return null;
+    }
 }

api/src/org/labkey/api/data/ContainerManager.java

@@ -1951,10 +1951,6 @@ private static boolean delete(final Container c, User user, @Nullable String com
             // and delete all container-based sequences
             DbSequenceManager.deleteAll(c);
 
-            ExperimentService experimentService = ExperimentService.get();
-            if (experimentService != null)
-                experimentService.removeContainerDataTypeExclusions(c.getId());
-
             // Issue 17015: After we've committed the transaction, be sure that we remove this container from the cache
             tx.addCommitTask(() ->
             {

api/src/org/labkey/api/exp/api/ExpMaterial.java

@@ -85,6 +85,10 @@ public interface ExpMaterial extends ExpRunItem
 
     void setSampleStateId(Long stateId);
 
+    Long getSampleColorId();
+
+    void setSampleColorId(Long colorId);
+
     Date getMaterialExpDate();
 
     ActionURL detailsURL(Container container, boolean checkForOverride);

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -134,6 +134,8 @@ public interface ExperimentService extends ExperimentRunTypeSource
 
     String EXPERIMENTAL_FEATURE_ALLOW_ROW_ID_MERGE = "org.labkey.experiment.api.SampleTypeUpdateServiceDI#ALLOW_ROW_ID_SAMPLE_MERGE";
 
+    String EXPERIMENTAL_SAMPLE_COLORS = "org.labkey.api.exp.api.ExperimentService#SAMPLE_COLORS";
+
     int SIMPLE_PROTOCOL_FIRST_STEP_SEQUENCE = 1;
     int SIMPLE_PROTOCOL_CORE_STEP_SEQUENCE = 10;
     int SIMPLE_PROTOCOL_EXTRA_STEP_SEQUENCE = 15;
@@ -710,6 +712,8 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
 
     SampleStatusTable createSampleStatusTable(ExpSchema expSchema, ContainerFilter cf);
 
+    TableInfo createDataColorTable(ExpSchema expSchema, ContainerFilter cf);
+
     ExpUnreferencedSampleFilesTable createUnreferencedSampleFilesTable(ExpSchema expSchema, ContainerFilter cf);
 
     FilteredTable<ExpSchema> createFieldsTable(ExpSchema expSchema, ContainerFilter cf);
@@ -1139,6 +1143,25 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
 
     String getDisabledDataTypeAuditMsg(DataTypeForExclusion type, List<Long> ids, boolean isUpdate);
 
+    @NotNull Set<Long> getDataTypeExcludedColors(DataTypeForExclusion dataType, long dataTypeId);
+
+    /** The data type rowIds (e.g. sample type rowIds) that currently exclude the given color. Inverse of {@link #getDataTypeExcludedColors}. */
+    @NotNull Set<Long> getDataTypesExcludingColor(DataTypeForExclusion dataType, long colorRowId);
+
+    @NotNull Set<Long> getActiveDataTypeColors(@NotNull Container container, DataTypeForExclusion dataType, long dataTypeId);
+
+    @Nullable String getDataColorLabel(@NotNull Container container, long colorRowId);
+
+    boolean ensureDataColorExclusions(long dataTypeId, DataTypeForExclusion dataType, @Nullable Collection<Long> disabledColorRowIds, @NotNull Container container, User user);
+
+    @NotNull Set<Long> updateColorDataTypeExclusions(long colorRowId, DataTypeForExclusion dataType, @Nullable Collection<Long> newlyDisabledDataTypeIds, @Nullable Collection<Long> newlyEnabledDataTypeIds, @NotNull Container container, User user);
+
+    void removeDataColorExclusionsForColor(long colorRowId);
+
+    void removeDataColorExclusionsForDataType(long dataTypeId, DataTypeForExclusion dataType);
+
+    void removeContainerDataColors(String containerId);
+
     void registerRunInputsViewProvider(QueryViewProvider<ExpRun> provider);
 
     void registerRunOutputsViewProvider(QueryViewProvider<ExpRun> providers);

api/src/org/labkey/api/exp/api/SampleTypeDomainKind.java

@@ -535,6 +535,8 @@ public Domain createDomain(GWTDomain<GWTPropertyDescriptor> domain, @Nullable Sa
         Map<String, Map<String, Object>> aliases = null;
         List<String> excludedContainerIds = null;
         List<String> excludedDashboardContainerIds = null;
+        List<Integer> excludedSampleColorIds = null;
+
 
         if (arguments != null)
         {
@@ -556,12 +558,13 @@ public Domain createDomain(GWTDomain<GWTPropertyDescriptor> domain, @Nullable Sa
             aliases = arguments.getImportAliases();
             excludedContainerIds = arguments.getExcludedContainerIds();
             excludedDashboardContainerIds = arguments.getExcludedDashboardContainerIds();
+            excludedSampleColorIds = arguments.getDisabledSampleColorRowIds();
         }
         ExpSampleType st;
         try
         {
             st = SampleTypeService.get().createSampleType(container, user, name, description, properties, indices, idCol1, idCol2, idCol3, parentCol, nameExpression, aliquotNameExpression,
-                    templateInfo, aliases, labelColor, metricUnit, autoLinkTargetContainer, autoLinkCategory, category, domain.getDisabledSystemFields(), excludedContainerIds, excludedDashboardContainerIds, arguments != null ? arguments.getAuditRecordMap() : null);
+                    templateInfo, aliases, labelColor, metricUnit, autoLinkTargetContainer, autoLinkCategory, category, domain.getDisabledSystemFields(), excludedContainerIds, excludedDashboardContainerIds, excludedSampleColorIds, arguments != null ? arguments.getAuditRecordMap() : null);
         }
         catch (ExperimentException e)
         {

api/src/org/labkey/api/exp/api/SampleTypeDomainKindProperties.java

@@ -87,6 +87,7 @@ public SampleTypeDomainKindProperties(ExpSampleType st)
     private String category;
     private List<String> excludedContainerIds;
     private List<String> excludedDashboardContainerIds;
+    private List<Integer> disabledSampleColorRowIds;
 
     //Ignored on import/save, use Domain.name & Domain.description instead
     private String name;
@@ -285,6 +286,16 @@ public List<String> getExcludedDashboardContainerIds()
         return excludedDashboardContainerIds;
     }
 
+    public List<Integer> getDisabledSampleColorRowIds()
+    {
+        return disabledSampleColorRowIds;
+    }
+
+    public void setDisabledSampleColorRowIds(List<Integer> disabledSampleColorRowIds)
+    {
+        this.disabledSampleColorRowIds = disabledSampleColorRowIds;
+    }
+
     public void setExcludedDashboardContainerIds(List<String> excludedDashboardContainerIds)
     {
         this.excludedDashboardContainerIds = excludedDashboardContainerIds;

api/src/org/labkey/api/exp/api/SampleTypeService.java

@@ -123,6 +123,8 @@ static void setInstance(SampleTypeService impl)
 
     Map<String, ExpSampleType> getSampleTypesForRoles(Container container, ContainerFilter filter, ExpProtocol.ApplicationType type);
 
+    void auditSampleColorExclusion(Container container, long sampleTypeRowId, @Nullable String auditUserComment, User user);
+
     /**
      * Create a new SampleType with the provided properties.
      * If a 'Name' property exists in the list, it will be used as the 'id' property of the SampleType.
@@ -150,7 +152,7 @@ ExpSampleType createSampleType(Container container, User user, String name, Stri
     ExpSampleType createSampleType(Container c, User u, String name, String description, List<GWTPropertyDescriptor> properties, List<GWTIndex> indices, int idCol1, int idCol2, int idCol3, int parentCol,
                                               String nameExpression, String aliquotNameExpression, @Nullable TemplateInfo templateInfo, @Nullable Map<String, Map<String, Object>> importAliases, @Nullable String labelColor, @Nullable String metricUnit,
                                               @Nullable Container autoLinkTargetContainer, @Nullable String autoLinkCategory, @Nullable String category, @Nullable List<String> disabledSystemField,
-                                              @Nullable List<String> excludedContainerIds, @Nullable List<String> excludedDashboardContainerIds, @Nullable Map<String, Object> changeDetails)
+                                              @Nullable List<String> excludedContainerIds, @Nullable List<String> excludedDashboardContainerIds, @Nullable List<Integer> excludedSampleColorIds, @Nullable Map<String, Object> changeDetails)
             throws ExperimentException;
 
     @NotNull

api/src/org/labkey/api/exp/query/ExpMaterialTable.java

@@ -66,6 +66,7 @@ enum Column
         RunId, // database table only
         RunApplication,
         RunApplicationOutput,
+        ExpMaterialColor,
         SampleSet,
         SampleState,
         SourceApplicationId, // database table only

api/src/org/labkey/api/exp/query/ExpSchema.java

@@ -245,6 +245,14 @@ public TableInfo createTable(ExpSchema expSchema, String queryName, ContainerFil
                 return ExperimentService.get().createSampleStatusTable(expSchema, cf);
             }
         },
+        DataColors
+        {
+            @Override
+            public TableInfo createTable(ExpSchema expSchema, String queryName, ContainerFilter cf)
+            {
+                return ExperimentService.get().createDataColorTable(expSchema, cf);
+            }
+        },
         Fields
         {
             @Override

api/src/org/labkey/api/query/AbstractQueryUpdateService.java

@@ -596,7 +596,8 @@ protected DataIteratorBuilder _toDataIteratorBuilder(String debugName, List<Map<
 
     /** @deprecated switch to using DIB based method */
     @Deprecated
-    protected List<Map<String, Object>> _insertRowsUsingInsertRow(User user, Container container, List<Map<String, Object>> rows, BatchValidationException errors, Map<String, Object> extraScriptContext)
+    protected List<Map<String, Object>> _insertRowsUsingInsertRow(User user, Container container, List<Map<String, Object>> rows, BatchValidationException errors,
+                                                                  @Nullable Map<Enum, Object> configParameters, Map<String, Object> extraScriptContext)
             throws DuplicateKeyException, BatchValidationException, QueryUpdateServiceException, SQLException
     {
         if (!hasInsertRowsPermission(user))
@@ -664,7 +665,7 @@ else if (SqlDialect.isTransactionException(sqlx) && errors.hasErrors())
         if (hasTableScript)
             getQueryTable().fireBatchTrigger(container, user, TableInfo.TriggerType.INSERT, null, false, errors, extraScriptContext);
 
-        addAuditEvent(user, container, QueryService.AuditAction.INSERT, null, result, null, providedValues);
+        addAuditEvent(user, container, QueryService.AuditAction.INSERT, configParameters, result, null, providedValues);
 
         return result;
     }
@@ -715,7 +716,7 @@ public List<Map<String, Object>> insertRows(User user, Container container, List
     {
         try
         {
-            List<Map<String,Object>> ret = _insertRowsUsingInsertRow(user, container, rows, errors, extraScriptContext);
+            List<Map<String,Object>> ret = _insertRowsUsingInsertRow(user, container, rows, errors, configParameters, extraScriptContext);
             afterInsertUpdate(null==ret?0:ret.size(), errors);
             if (errors.hasErrors())
                 return null;