Refactor TabbedReport to allow a distributed provider model

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

@@ -236,17 +236,17 @@ public List<TabbedReportItem> getTabbedReportItems(Container c, User u)
         TabbedReportItem analyses = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_ANALYSES, "Sequence Analyses", category);
         analyses.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         analyses.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        analyses.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        analyses.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        analyses.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        analyses.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         analyses.setOwnerKey(owner.getPropertyManagerKey());
         analyses.setVisible(owner.isVisible(c, u));
         items.add(analyses);
 
         TabbedReportItem outputs = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_OUTPUTFILES, "Sequence Outputs", category);
         outputs.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         outputs.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        outputs.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        outputs.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        outputs.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        outputs.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         outputs.setOwnerKey(owner.getPropertyManagerKey());
         outputs.setVisible(owner.isVisible(c, u));
         items.add(outputs);

Studies/resources/web/studies/panel/StudiesFilterType.js

@@ -0,0 +1,127 @@
+Ext4.define('Laboratory.panel.StudiesFilterType', {
+    extend: 'LDK.panel.AbstractFilterType',
+    alias: 'widget.studies-filtertype',
+
+    statics: {
+        filterName: 'study',
+        label: 'Studies'
+    },
+
+    initComponent: function(){
+        this.items = this.getItems();
+
+        this.callParent();
+    },
+
+    getItems: function(){
+        var ctx = this.filterContext;
+        var toAdd = [];
+
+        toAdd.push({
+            width: 200,
+            html: 'Choose Study:',
+            style: 'margin-bottom:10px'
+        });
+
+        toAdd.push({
+            xtype: 'panel',
+            items: [{
+                xtype: 'combo',
+                width: 265,
+                itemId: 'studyField',
+                displayField: 'studyName',
+                valueField: 'studyName',
+                multiSelect: false,
+                store: {
+                    type: 'labkey-store',
+                    schemaName: 'studies',
+                    queryName: 'studies',
+                    autoLoad: true
+                },
+                value: Ext4.isArray(ctx.studies) ? ctx.studies.join(';') : ctx.studies
+            }]
+        });
+
+        return toAdd;
+    },
+
+    getFilters: function(){
+        return {
+            studies: this.getStudies()
+        }
+    },
+
+    getFilterArray: function(tab){
+        var filterArray = {
+            removable: [],
+            nonRemovable: []
+        };
+
+        if (this.reportQCStates?.length) {
+            filterArray.nonRemovable.push(LABKEY.Filter.create('qcstate/label', this.reportQCStates, LABKEY.Filter.Types.EQUALS_ONE_OF));
+        }
+
+        var filters = this.getFilters();
+        var report = tab.report;
+        var studyFieldName = report.additionalFieldKeys?.studyAssignmentFieldKey;
+        if (!studyFieldName){
+            LDK.Utils.logToServer({
+                message: 'A TabbedReport is attempting to load a study filter when it should have been stopped upstream',
+                level: 'ERROR',
+                includeContext: true
+            });
+
+            return filterArray;
+        }
+
+        var studyName = filters.studies[0];
+        filterArray.nonRemovable.push(LABKEY.Filter.create(studyFieldName, studyName, LABKEY.Filter.Types.CONTAINS));
+
+        return filterArray;
+    },
+
+    isValid: function(){
+        var val = this.down('#studyField').getValue();
+        if (!val || !val.length){
+            return false;
+        }
+
+        return true;
+    },
+
+    getFilterInvalidMessage: function(){
+        return 'Error: Must choose a study';
+    },
+
+    validateReportForFilterType: function(report){
+        if (!report.additionalFieldKeys?.studyAssignmentFieldKey){
+            return 'This report cannot be used with the selected filter type, because the report does not contain a field with study assignment information';
+        }
+
+        return null;
+    },
+
+    getTitle: function(){
+        var studies = this.getStudies();
+
+        if (studies && studies.length){
+            return studies.join(', ');
+        }
+
+        return '';
+    },
+
+    getStudies: function(){
+        var projectArray = this.down('#studyField').getValue();
+        if (projectArray && !Ext4.isArray(projectArray)) {
+            projectArray = [projectArray];
+        }
+
+        if (projectArray && projectArray.length > 0){
+            projectArray = Ext4.unique(projectArray);
+            projectArray.sort();
+        }
+
+        return projectArray;
+    }
+});

Studies/src/org/labkey/studies/StudiesModule.java

@@ -3,15 +3,17 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.ldk.ExtendedSimpleModule;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.query.DefaultSchema;
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.security.roles.RoleManager;
 import org.labkey.api.studies.StudiesService;
-import org.labkey.studies.query.StudiesUserSchema;
 import org.labkey.api.studies.security.StudiesDataAdminRole;
+import org.labkey.studies.query.StudiesUserSchema;
+import org.labkey.studies.study.StudiesFilterProvider;
 import org.labkey.studies.study.StudyEnrollmentEventProvider;
 
 import java.util.Collection;
@@ -42,6 +44,7 @@ protected void init()
         StudiesService.setInstance(StudiesServiceImpl.get());
         StudiesService.get().registerEventProvider(new StudyEnrollmentEventProvider());
         RoleManager.registerRole(new StudiesDataAdminRole());
+        LaboratoryService.get().registerTabbedReportFilterProvider(new StudiesFilterProvider());
     }
 
     @Override

Studies/src/org/labkey/studies/study/StudiesFilterProvider.java

@@ -0,0 +1,73 @@
+package org.labkey.studies.study;
+
+import org.jetbrains.annotations.NotNull;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.laboratory.TabbedReportItem;
+import org.labkey.api.laboratory.query.TabbedReportFilterProvider;
+import org.labkey.api.module.Module;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.view.template.ClientDependency;
+import org.labkey.studies.StudiesModule;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class StudiesFilterProvider implements TabbedReportFilterProvider
+{
+    @Override
+    public Module getOwningModule()
+    {
+        return ModuleLoader.getInstance().getModule(StudiesModule.class);
+    }
+
+    @Override
+    public Collection<ClientDependency> getClientDependencies()
+    {
+        return List.of(ClientDependency.fromPath("studies/panel/StudiesFilterType.js"));
+    }
+
+    @Override
+    public String getXType()
+    {
+        return "studies-filtertype";
+    }
+
+    @Override
+    public String getLabel()
+    {
+        return "Study";
+    }
+
+    @Override
+    public String getInputValue()
+    {
+        return "studies";
+    }
+
+    @Override
+    public @NotNull Map<String, FieldKey> getAdditionalFieldKeys(TableInfo ti, TabbedReportItem tri, Map<String, FieldKey> overrides)
+    {
+        Map<String, FieldKey> ret = new HashMap<>();
+
+        if (overrides.get("studyAssignmentFieldKey") == null)
+        {
+            FieldKey subject = tri.getSubjectIdFieldKey();
+            if (subject != null)
+            {
+                subject = subject.getParent();
+            }
+
+            FieldKey fk = FieldKey.fromString(subject, "projects/allStudies");
+            Map<FieldKey, ColumnInfo> colMap = tri.getQueryCache().getColumns(ti, PageFlowUtil.set(fk));
+            if (colMap.containsKey(fk))
+                ret.put("studyAssignmentFieldKey", colMap.get(fk).getFieldKey());
+        }
+
+        return ret;
+    }
+}

singlecell/src/org/labkey/singlecell/SingleCellProvider.java

@@ -173,15 +173,15 @@ public List<TabbedReportItem> getTabbedReportItems(Container c, User u)
         TabbedReportItem sorts = new QueryTabbedReportItem(cache, this, SingleCellSchema.NAME, SingleCellSchema.TABLE_SORTS, "Single Cell Sorts", category);
         sorts.setSubjectIdFieldKey(FieldKey.fromString("sampleId/subjectId"));
         sorts.setSampleDateFieldKey(FieldKey.fromString("sampleId/date"));
-        sorts.setAllProjectsFieldKey(FieldKey.fromString("sampleId/allProjectsPivot"));
-        sorts.setOverlappingProjectsFieldKey(FieldKey.fromString("sampleId/overlappingProjectsPivot"));
+        sorts.setKeyOverride("allProjectsFieldName", FieldKey.fromString("sampleId/allProjectsPivot"));
+        sorts.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("sampleId/overlappingProjectsPivot"));
         items.add(sorts);
 
         TabbedReportItem cdnas = new QueryTabbedReportItem(cache, this, SingleCellSchema.NAME, SingleCellSchema.TABLE_CDNAS, "Single Cell Libraries", category);
         cdnas.setSubjectIdFieldKey(FieldKey.fromString("sortId/sampleId/subjectId"));
         cdnas.setSampleDateFieldKey(FieldKey.fromString("sortId/sampleId/date"));
-        cdnas.setAllProjectsFieldKey(FieldKey.fromString("sortId/sampleId/allProjectsPivot"));
-        cdnas.setOverlappingProjectsFieldKey(FieldKey.fromString("sortId/sampleId/overlappingProjectsPivot"));
+        cdnas.setKeyOverride("allProjectsFieldName", FieldKey.fromString("sortId/sampleId/allProjectsPivot"));
+        cdnas.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("sortId/sampleId/overlappingProjectsPivot"));
         items.add(cdnas);
 
         return items;