Link samples to study

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

@@ -16,18 +16,38 @@
 
 package org.labkey.api.query;
 
+import jakarta.servlet.http.HttpSession;
 import org.apache.commons.collections4.SetValuedMap;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.audit.AuditHandler;
 import org.labkey.api.audit.DetailedAuditTypeEvent;
+import org.labkey.api.data.ColumnHeaderType;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DisplayColumn;
+import org.labkey.api.data.Filter;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MethodInfo;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.ParameterDescription;
+import org.labkey.api.data.ParameterDescriptionImpl;
+import org.labkey.api.data.QueryLogging;
+import org.labkey.api.data.Results;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
+import org.labkey.api.module.Module;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.query.column.ColumnInfoTransformer;
-import org.labkey.api.data.*;
-import org.labkey.api.data.dialect.SqlDialect;
-import org.labkey.api.module.Module;
 import org.labkey.api.query.column.ConceptURIColumnInfoTransformer;
 import org.labkey.api.query.snapshot.QuerySnapshotDefinition;
 import org.labkey.api.security.User;
@@ -41,7 +61,6 @@
 import org.labkey.data.xml.TableType;
 import org.springframework.web.servlet.mvc.Controller;
 
-import jakarta.servlet.http.HttpSession;
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -653,6 +672,13 @@ default MutableColumnInfo applyColumnTransformer(MutableColumnInfo col)
     @Nullable
     ContainerFilter getContainerFilterForLookups(Container container, User user);
 
+    /**
+     * Provides the configured ContainerFilter to utilize when requesting data that is being read
+     * within a folder context. Equivalent to the client side function in @labkey/components
+     */
+    @Nullable
+    ContainerFilter getContainerFilterForFolder(Container container, User user);
+
 
     interface SelectBuilder
     {

query/src/org/labkey/query/QueryServiceImpl.java

@@ -3516,6 +3516,40 @@ public ContainerFilter getContainerFilterForLookups(Container container, User us
         return type.create(container, user);
     }
 
+    @Override
+    @Nullable
+    public ContainerFilter getContainerFilterForFolder(Container container, User user)
+    {
+        // Check to see if product folders support is enabled.
+        if (container == null || !container.isProductFoldersEnabled())
+            return null;
+
+        if (isProductFoldersDataListingScopedToProject())
+        {
+            // When requesting data from a top-level folder context the ContainerFilter filters
+            // "down" the folder hierarchy for data.
+            if (container.isProject())
+            {
+                if (isProductFoldersAllFolderScopeEnabled())
+                    return ContainerFilter.Type.AllInProjectPlusShared.create(container, user);
+                return ContainerFilter.Type.CurrentAndSubfoldersPlusShared.create(container, user);
+            }
+
+            // When listing data in a folder scope return data scoped to the current
+            // folder when the experimental feature is enabled.
+            return ContainerFilter.Type.Current.create(container, user);
+        }
+
+        // When requesting data from a top-level folder context the ContainerFilter filters
+        // "down" the folder hierarchy for data.
+        if (container.isProject())
+            return ContainerFilter.Type.CurrentAndSubfoldersPlusShared.create(container, user);
+
+        // When requesting data from a sub-folder context the ContainerFilter filters
+        // "up" the folder hierarchy for data.
+        return ContainerFilter.Type.CurrentPlusProjectAndShared.create(container, user);
+    }
+
     @Override
     @Nullable
     public ContainerFilter.Type getContainerFilterTypeForLookups(Container container)

study/src/org/labkey/study/assay/StudyPublishManager.java

@@ -1126,6 +1126,11 @@ public void autoLinkDerivedSamples(ExpSampleType sampleType, List<Long> keys, Co
                 qs.setQueryName(sampleType.getName());
                 qs.setBaseFilter(new SimpleFilter().addInClause(FieldKey.fromParts("RowId"), keys));
 
+                // issue GH901 : lineage sourced subject or timepoint information are not resolving in cross folder configurations
+                ContainerFilter cf = QueryService.get().getContainerFilterForFolder(container, user);
+                if (cf != null)
+                    qs.setContainerFilterName(cf.getType().name());
+
                 Map<StudyPublishService.LinkToStudyKeys, FieldKey> fieldKeyMap = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
                 UserSchema userSchema = QueryService.get().getUserSchema(user, container, SamplesSchema.SCHEMA_NAME);
                 QueryView view = new QueryView(userSchema, qs, null);
@@ -1231,15 +1236,18 @@ public void autoLinkSamples(ExpSampleType sampleType, List<Map<FieldKey, Object>
                             for (Map<FieldKey, Object> row : results)
                             {
                                 Object timePointValue = getTimepointValue(row, publishKeys, visitBased, translateMap);
-                                if (row.containsKey(publishKeys.get(LinkToStudyKeys.ParticipantId)) && timePointValue != null)
+                                Object subjectId = row.get(publishKeys.get(LinkToStudyKeys.ParticipantId));
+                                if (subjectId != null  && timePointValue != null)
                                 {
                                     dataMaps.add(Map.of(
-                                            LinkToStudyKeys.ParticipantId.name(), row.get(publishKeys.get(LinkToStudyKeys.ParticipantId)),
+                                            LinkToStudyKeys.ParticipantId.name(), subjectId,
                                             timePointPropName, timePointValue,
                                             StudyPublishService.ROWID_PROPERTY_NAME, row.get(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME)),
                                             StudyPublishService.SOURCE_LSID_PROPERTY_NAME, sampleType.getLSID()
                                     ));
                                 }
+                                else
+                                    LOG.error("Failed to auto link samples to study for folder {}. Timepoint and subject ID were both not resolved.", container.getPath());
                             }
                         }