AbDisc: Plate Templates (Part 1)

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -24,7 +24,6 @@
 import org.labkey.api.assay.actions.UploadWizardAction;
 import org.labkey.api.assay.pipeline.AssayRunAsyncContext;
 import org.labkey.api.assay.plate.AssayPlateMetadataService;
-import org.labkey.api.assay.plate.PlateMetadataDataHandler;
 import org.labkey.api.assay.security.DesignAssayPermission;
 import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.data.ActionButton;
@@ -143,10 +142,6 @@
 import static org.labkey.api.data.CompareType.IN;
 import static org.labkey.api.util.PageFlowUtil.jsString;
 
-/**
- * User: jeckels
- * Date: Sep 14, 2007
- */
 public abstract class AbstractAssayProvider implements AssayProvider
 {
     public static final String ASSAY_NAME_SUBSTITUTION = "${AssayName}";
@@ -911,15 +906,13 @@ public List<Pair<Domain, Map<DomainProperty, Object>>> getDomains(ExpProtocol pr
         sortDomainList(domains);
 
         // see if there is a plate metadata domain associated with this protocol
-        if (AssayPlateMetadataService.getService(PlateMetadataDataHandler.DATA_TYPE) != null)
+        Domain plateDomain = AssayPlateMetadataService.get().getPlateDataDomain(protocol);
+        if (plateDomain != null)
         {
-            Domain plateDomain = AssayPlateMetadataService.getService(PlateMetadataDataHandler.DATA_TYPE).getPlateDataDomain(protocol);
-            if (plateDomain != null)
-            {
-                Map<DomainProperty, Object> values = DefaultValueService.get().getDefaultValues(plateDomain.getContainer(), plateDomain);
-                domains.add(new Pair<>(plateDomain, values));
-            }
+            Map<DomainProperty, Object> values = DefaultValueService.get().getDefaultValues(plateDomain.getContainer(), plateDomain);
+            domains.add(new Pair<>(plateDomain, values));
         }
+
         return domains;
     }
 

api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java

@@ -97,10 +97,6 @@
 import static java.util.stream.Collectors.toList;
 import static org.labkey.api.gwt.client.ui.PropertyType.SAMPLE_CONCEPT_URI;
 
-/**
- * User: jeckels
- * Date: Jan 3, 2008
- */
 public abstract class AbstractAssayTsvDataHandler extends AbstractExperimentDataHandler implements ValidationDataHandler
 {
     protected static final Object ERROR_VALUE = new Object() {
@@ -210,18 +206,14 @@ public Map<DataType, List<Map<String, Object>>> getValidationDataMap(ExpData dat
             List<Map<String, Object>> dataRows = loader.load();
             boolean skipFirstRowAdjustment = dataRows.isEmpty();
 
-            if (plateMetadataEnabled)
+            if (plateMetadataEnabled && AssayPlateMetadataService.isExperimentalAppPlateEnabled())
             {
-                AssayPlateMetadataService svc = AssayPlateMetadataService.getService(PlateMetadataDataHandler.DATA_TYPE);
-                if (AssayPlateMetadataService.isExperimentalAppPlateEnabled() && svc != null)
-                {
-                    Pair<String, Boolean> plateIdAdded = new Pair<>("PlateIdAdded", false);
-                    Integer plateSetId = getPlateSetValueFromRunProps(context, provider, protocol);
-                    dataRows = svc.parsePlateData(context.getContainer(), context.getUser(), provider, protocol, plateSetId, dataFile, dataRows, plateIdAdded);
+                Pair<String, Boolean> plateIdAdded = new Pair<>("PlateIdAdded", false);
+                Integer plateSetId = getPlateSetValueFromRunProps(context, provider, protocol);
+                dataRows = AssayPlateMetadataService.get().parsePlateData(context.getContainer(), context.getUser(), provider, protocol, plateSetId, dataFile, dataRows, plateIdAdded);
 
-                    // need to do this otherwise the added plateID may get stripped
-                    skipFirstRowAdjustment = plateIdAdded.second;
-                }
+                // need to do this otherwise the added plateID may get stripped
+                skipFirstRowAdjustment = plateIdAdded.second;
             }
 
             // loader did not parse any rows
@@ -249,29 +241,27 @@ private List<Map<String, Object>> mergePlateMetadata(XarContext context, AssayPr
                                                          Map<String, AssayPlateMetadataService.MetadataLayer> rawPlateMetadata, File plateMetadataFile)
             throws ExperimentException
     {
-        AssayPlateMetadataService svc = AssayPlateMetadataService.getService(PlateMetadataDataHandler.DATA_TYPE);
-        if (svc != null)
+        Map<String, AssayPlateMetadataService.MetadataLayer> plateMetadata = null;
+        if (plateMetadataFile != null || rawPlateMetadata != null)
         {
-            Map<String, AssayPlateMetadataService.MetadataLayer> plateMetadata = null;
-            if (plateMetadataFile != null || rawPlateMetadata != null)
-            {
-                plateMetadata = plateMetadataFile != null
-                        ? svc.parsePlateMetadata(plateMetadataFile)
-                        : rawPlateMetadata;
-            }
+            if (plateMetadataFile != null)
+                plateMetadata = AssayPlateMetadataService.get().parsePlateMetadata(plateMetadataFile);
+            else
+                plateMetadata = rawPlateMetadata;
+        }
 
-            Domain runDomain = provider.getRunDomain(protocol);
-            DomainProperty propertyPlateTemplate = runDomain.getPropertyByName(AssayPlateMetadataService.PLATE_TEMPLATE_COLUMN_NAME);
-            DomainProperty propertyPlateSet = runDomain.getPropertyByName(AssayPlateMetadataService.PLATE_SET_COLUMN_NAME);
-            if (propertyPlateTemplate != null || propertyPlateSet != null)
-            {
-                Map<DomainProperty, String> runProps = ((AssayUploadXarContext)context).getContext().getRunProperties();
-                Object lsid = runProps.getOrDefault(propertyPlateTemplate, null);
-                Lsid templateLsid = lsid != null && !StringUtils.isEmpty(String.valueOf(lsid)) ? Lsid.parse(String.valueOf(lsid)) : null;
-                Integer plateSetId = getPlateSetValueFromRunProps(context, provider, protocol);
-                return svc.mergePlateMetadata(context.getContainer(), context.getUser(), templateLsid, plateSetId, dataRows, plateMetadata, provider, protocol);
-            }
+        Domain runDomain = provider.getRunDomain(protocol);
+        DomainProperty propertyPlateTemplate = runDomain.getPropertyByName(AssayPlateMetadataService.PLATE_TEMPLATE_COLUMN_NAME);
+        DomainProperty propertyPlateSet = runDomain.getPropertyByName(AssayPlateMetadataService.PLATE_SET_COLUMN_NAME);
+        if (propertyPlateTemplate != null || propertyPlateSet != null)
+        {
+            Map<DomainProperty, String> runProps = ((AssayUploadXarContext)context).getContext().getRunProperties();
+            Object lsid = runProps.getOrDefault(propertyPlateTemplate, null);
+            Lsid templateLsid = lsid != null && !StringUtils.isEmpty(String.valueOf(lsid)) ? Lsid.parse(String.valueOf(lsid)) : null;
+            Integer plateSetId = getPlateSetValueFromRunProps(context, provider, protocol);
+            return AssayPlateMetadataService.get().mergePlateMetadata(context.getContainer(), context.getUser(), templateLsid, plateSetId, dataRows, plateMetadata, provider, protocol);
         }
+
         return dataRows;
     }
 
@@ -293,8 +283,6 @@ private Integer getPlateSetValueFromRunProps(XarContext context, AssayProvider p
     /**
      * Creates a DataLoader that can handle missing value indicators if the columns on the domain
      * are configured to support it.
-     *
-     * @throws ExperimentException
      */
     public static DataLoader createLoaderForImport(File dataFile, @Nullable Domain dataDomain, DataLoaderSettings settings, boolean shouldInferTypes) throws ExperimentException
     {
@@ -310,7 +298,7 @@ public static DataLoader createLoaderForImport(File dataFile, @Nullable Domain d
             {
                 if (col.isMvEnabled())
                 {
-                    // Check for all of the possible names for the column in the incoming data when deciding if we should
+                    // Check for all possible names for the column in the incoming data when deciding if we should
                     // check it for missing values
                     Set<String> columnAliases = ImportAliasable.Helper.createImportMap(Collections.singletonList(col), false).keySet();
                     mvEnabledColumns.addAll(columnAliases);
@@ -689,22 +677,16 @@ private void addAssayPlateMetadata(
         if (datas.size() == 1)
         {
             ExpData plateData = datas.get(0);
-            AssayPlateMetadataService svc = AssayPlateMetadataService.getService((AssayDataType)plateData.getDataType());
-            if (svc != null)
-            {
-                Map<String, AssayPlateMetadataService.MetadataLayer> plateMetadata;
-
-                if (plateData.getFile() != null)
-                    plateMetadata = svc.parsePlateMetadata(plateData.getFile());
-                else if (getRawPlateMetadata() != null)
-                    plateMetadata = getRawPlateMetadata();
-                else
-                    throw new ExperimentException("There was no plate metadata JSON available for this run");
+            Map<String, AssayPlateMetadataService.MetadataLayer> plateMetadata;
 
-                svc.addAssayPlateMetadata(resultData, plateMetadata, container, user, run, provider, protocol, inserted, rowIdToLsidMap);
-            }
+            if (plateData.getFile() != null)
+                plateMetadata = AssayPlateMetadataService.get().parsePlateMetadata(plateData.getFile());
+            else if (getRawPlateMetadata() != null)
+                plateMetadata = getRawPlateMetadata();
             else
-                throw new ExperimentException("No PlateMetadataService registered for data type : " + plateData.getDataType().toString());
+                throw new ExperimentException("There was no plate metadata JSON available for this run");
+
+            AssayPlateMetadataService.get().addAssayPlateMetadata(resultData, plateMetadata, container, user, run, provider, protocol, inserted, rowIdToLsidMap);
         }
         else
         {
@@ -720,32 +702,31 @@ protected ParticipantVisitResolver createResolver(User user, ExpRun run, ExpProt
         return AssayService.get().createResolver(user, run, protocol, provider, null);
     }
 
-    /** Insert the data into the database.  Transaction is active. */
-    protected List<Map<String, Object>> insertRowData(ExpData data, User user, Container container, ExpRun run, ExpProtocol protocol, AssayProvider provider,Domain dataDomain, List<Map<String, Object>> fileData, TableInfo tableInfo, boolean autoFillDefaultColumns)
-            throws SQLException, ValidationException, ExperimentException
+    /** Insert the data into the database. Transaction is active. */
+    protected List<Map<String, Object>> insertRowData(
+        ExpData data,
+        User user,
+        Container container,
+        ExpRun run,
+        ExpProtocol protocol,
+        AssayProvider provider,
+        Domain dataDomain,
+        List<Map<String, Object>> fileData,
+        TableInfo tableInfo,
+        boolean autoFillDefaultColumns
+    ) throws SQLException, ValidationException, ExperimentException
     {
         OntologyManager.UpdateableTableImportHelper importHelper = new SimpleAssayDataImportHelper(data);
         if (provider.isPlateMetadataEnabled(protocol))
-        {
-            AssayPlateMetadataService svc = AssayPlateMetadataService.getService(PlateMetadataDataHandler.DATA_TYPE);
-            if (svc != null)
-            {
-                importHelper = svc.getImportHelper(container, user, run, data, protocol, provider);
-            }
-        }
+            importHelper = AssayPlateMetadataService.get().getImportHelper(container, user, run, data, protocol, provider);
 
         if (tableInfo instanceof UpdateableTableInfo)
-        {
             return OntologyManager.insertTabDelimited(tableInfo, container, user, importHelper, fileData, autoFillDefaultColumns, LOG);
-        }
-        else
-        {
-            Integer id = OntologyManager.ensureObject(container, data.getLSID());
-            List<String> lsids = OntologyManager.insertTabDelimited(container, user, id,
-                    importHelper, dataDomain, fileData, false);
-            // TODO: Add LSID values into return value rows
-            return fileData;
-        }
+
+        Integer id = OntologyManager.ensureObject(container, data.getLSID());
+        OntologyManager.insertTabDelimited(container, user, id, importHelper, dataDomain, fileData, false);
+
+        return fileData;
     }
 
     protected abstract boolean shouldAddInputMaterials();

api/src/org/labkey/api/assay/DefaultAssayRunCreator.java

@@ -99,10 +99,6 @@
 
 import static java.util.Collections.unmodifiableCollection;
 
-/**
- * User: jeckels
- * Date: Oct 12, 2011
- */
 public class DefaultAssayRunCreator<ProviderType extends AbstractAssayProvider> implements AssayRunCreator<ProviderType>
 {
     private static final Logger LOG = LogManager.getLogger(DefaultAssayRunCreator.class);
@@ -164,7 +160,7 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
 
             exp = saveExperimentRun(context, exp, run, false);
 
-            // re-fetch the run after is has been fully constructed
+            // re-fetch the run after it has been fully constructed
             run = ExperimentService.get().getExpRun(run.getRowId());
 
             context.uploadComplete(run);

api/src/org/labkey/api/assay/SimpleAssayDataImportHelper.java

@@ -16,18 +16,13 @@
 
 package org.labkey.api.assay;
 
-import org.labkey.api.data.Parameter;
 import org.labkey.api.data.ParameterMapStatement;
 import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.query.ValidationException;
 
 import java.util.Map;
 
-/**
- * User: jeckels
- * Date: Jul 23, 2007
- */
 public class SimpleAssayDataImportHelper implements OntologyManager.ImportHelper, OntologyManager.UpdateableTableImportHelper
 {
     private int _id = 0;

api/src/org/labkey/api/assay/plate/AssayPlateMetadataService.java

@@ -3,7 +3,6 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
-import org.labkey.api.assay.AssayDataType;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
@@ -15,29 +14,23 @@
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.security.User;
+import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.settings.ExperimentalFeatureService;
 import org.labkey.api.util.Pair;
 
 import java.io.File;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
 public interface AssayPlateMetadataService
 {
     String PLATE_TEMPLATE_COLUMN_NAME = "PlateTemplate";
     String PLATE_SET_COLUMN_NAME = "PlateSet";
-    Map<AssayDataType, AssayPlateMetadataService> _handlers = new HashMap<>();
     String EXPERIMENTAL_APP_PLATE_SUPPORT = "experimental-app-plate-support";
 
-    static void registerService(AssayDataType dataType, AssayPlateMetadataService handler)
+    static void setInstance(AssayPlateMetadataService serviceImpl)
     {
-        if (dataType != null)
-        {
-            _handlers.put(dataType, handler);
-        }
-        else
-            throw new RuntimeException("The specified assay data type is null");
+        ServiceRegistry.get().registerService(AssayPlateMetadataService.class, serviceImpl);
     }
 
     static boolean isExperimentalAppPlateEnabled()
@@ -53,10 +46,9 @@ static boolean isBiologicsFolder(Container container)
         return false;
     }
 
-    @Nullable
-    static AssayPlateMetadataService getService(AssayDataType dataType)
+    static AssayPlateMetadataService get()
     {
-        return _handlers.get(dataType);
+        return ServiceRegistry.get().getService(AssayPlateMetadataService.class);
     }
 
     /**
@@ -75,17 +67,33 @@ static AssayPlateMetadataService getService(AssayDataType dataType)
      * @param inserted the inserted result data
      * @param rowIdToLsidMap a map of result data rowIds to result data lsids
      */
-    void addAssayPlateMetadata(ExpData resultData, Map<String, MetadataLayer> plateMetadata, Container container, User user, ExpRun run, AssayProvider provider,
-                               ExpProtocol protocol, List<Map<String, Object>> inserted, Map<Integer, String> rowIdToLsidMap) throws ExperimentException;
+    void addAssayPlateMetadata(
+        ExpData resultData,
+        Map<String, MetadataLayer> plateMetadata,
+        Container container,
+        User user,
+        ExpRun run,
+        AssayProvider provider,
+        ExpProtocol protocol,
+        List<Map<String, Object>> inserted,
+        Map<Integer, String> rowIdToLsidMap
+    ) throws ExperimentException;
 
     /**
      * Merges the results data with the plate metadata to produce a single row map
      *
      * @return the merged rows
      */
-    List<Map<String, Object>> mergePlateMetadata(Container container, User user, Lsid plateLsid, Integer plateSetId,
-                                                 List<Map<String, Object>> rows, @Nullable Map<String, MetadataLayer> plateMetadata,
-                                                 AssayProvider provider, ExpProtocol protocol) throws ExperimentException;
+    List<Map<String, Object>> mergePlateMetadata(
+        Container container,
+        User user,
+        Lsid plateLsid,
+        Integer plateSetId,
+        List<Map<String, Object>> rows,
+        @Nullable Map<String, MetadataLayer> plateMetadata,
+        AssayProvider provider,
+        ExpProtocol protocol
+    ) throws ExperimentException;
 
     /**
      * Methods to create the metadata model from either a JSON object or a file object
@@ -98,22 +106,29 @@ List<Map<String, Object>> mergePlateMetadata(Container container, User user, Lsi
      * well as cases where plate identifiers have not been supplied.
      */
     List<Map<String, Object>> parsePlateData(
-            Container container,
-            User user,
-            AssayProvider provider,
-            ExpProtocol protocol,
-            Integer plateSetId,
-            File dataFile,
-            List<Map<String, Object>> data,
-            Pair<String, Boolean> plateIdAdded
+        Container container,
+        User user,
+        AssayProvider provider,
+        ExpProtocol protocol,
+        Integer plateSetId,
+        File dataFile,
+        List<Map<String, Object>> data,
+        Pair<String, Boolean> plateIdAdded
     ) throws ExperimentException;
 
     /**
      * Returns an import helper to help join assay results data to well data and metadata that is associated
      * with the plate used in the assay run import
      */
     @NotNull
-    OntologyManager.UpdateableTableImportHelper getImportHelper(Container container, User user, ExpRun run, ExpData data, ExpProtocol protocol, AssayProvider provider) throws ExperimentException;
+    OntologyManager.UpdateableTableImportHelper getImportHelper(
+        Container container,
+        User user,
+        ExpRun run,
+        ExpData data,
+        ExpProtocol protocol,
+        AssayProvider provider
+    ) throws ExperimentException;
 
     interface MetadataLayer
     {