Major refactor of underlying SBT SQL queries (#212)

* Major refactor of underlying SBT SQL queries

* Small code cleanup

Author: bbimber

GenotypeAssays/resources/views/sbtReview.html

@@ -159,11 +159,9 @@
                             //sort: '-percent',
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
                             removeableFilters: [
-                                LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE)
+                                LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
+                                LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUALS)
                             ],
-                            parameters: {
-                                AnalysisId: analysisId
-                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -180,12 +178,10 @@
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
                             removeableFilters: [
                                 LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
-                                LABKEY.Filter.create('total_reads', 5, LABKEY.Filter.Types.GT),
-                                LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL)
+                                LABKEY.Filter.create('total_reads_from_locus', 5, LABKEY.Filter.Types.GT),
+                                LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL),
+                                LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)
                             ],
-                            parameters: {
-                                AnalysisId: analysisId
-                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -195,7 +191,7 @@
                         title: 'Haplotype Matches',
                         items: [{
                             xtype: 'genotypeassays-haplotypepanel',
-                            analysisId: [analysisId]
+                            analysisIds: [analysisId]
                         }]
                     },{
                         xtype: 'ldk-querypanel',

GenotypeAssays/resources/web/genotypeassays/buttons.js

@@ -28,7 +28,7 @@ GenotypeAssays.buttons = new function(){
 
             var newForm = Ext4.DomHelper.append(document.getElementsByTagName('body')[0],
                     '<form method="POST" action="' + LABKEY.ActionURL.buildURL("genotypeassays", "bulkHaplotype", null) + '">' +
-                    '<input type="hidden" name="analysisId" value="' + Ext4.htmlEncode(checked[0]) + '" />' +
+                    '<input type="hidden" name="analysisIds" value="' + Ext4.htmlEncode(checked.join(';')) + '" />' +
                     '</form>');
             newForm.submit();
         }

GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js

@@ -1,7 +1,7 @@
 Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
     extend: 'Ext.panel.Panel',
     alias: 'widget.genotypeassays-haplotypepanel',
-    analysisId: null,
+    analysisIds: null,
     showCheckBoxes: false,
 
     initComponent: function(){
@@ -461,13 +461,11 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             schemaName: 'sequenceanalysis',
             queryName: 'alignment_summary_by_lineage',
             columns: 'analysis_id,analysis_id/readset,analysis_id/readset/subjectId,lineages,loci,total,total_reads,percent,total_reads_from_locus,percent_from_locus',
-            parameters: {
-                AnalysisId: this.analysisId
-            },
             apiVersion: 13.2,
             scope: this,
             filterArray: [
-                LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE)
+                LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE),
+                LABKEY.Filter.create('analysis_id', this.analysisIds, LABKEY.Filter.Types.IN)
             ],
             failure: LDK.Utils.getErrorCallback(),
             success: function(results){
@@ -501,13 +499,13 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             schemaName: 'sequenceanalysis',
             queryName: 'alignment_summary_grouped',
             columns: 'analysis_id,lineages,loci,alleles,total_reads,percent,total_reads_from_locus,percent_from_locus',
+            filterArray: [
+                LABKEY.Filter.create('analysis_id', this.analysisIds, LABKEY.Filter.Types.IN)
+            ],
             // This is designed to remove the view-level sorts:
             sort: 'analysis_id',
             apiVersion: 13.2,
             scope: this,
-            parameters: {
-                AnalysisId: this.analysisId
-            },
             failure: LDK.Utils.getErrorCallback(),
             success: function(results){
                 this.lineageToAlleleMap = {};

GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js

@@ -11,17 +11,8 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
                 return;
             }
 
-            const analysisId = dr.getParameters()?.AnalysisId;
-            if (!analysisId) {
-                Ext4.Msg.alert('Error', 'Error: unable to find analysisId. This should not occur.');
-                LDK.Assert.assertNotEmpty('Unable to find AnalysisId parameter from the DataRegion in PublishResultsWindow');
-
-                return;
-            }
-
             Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
                 dataRegionName: dataRegionName,
-                analysisId: analysisId,
                 actionName: 'cacheAnalyses'
             }).show();
         }
@@ -116,7 +107,6 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
             scope: this,
             jsonData: {
                 alleleNames: alleleNames,
-                analysisId: this.analysisId,
                 json: Ext4.encode(this.json),
                 protocolId: protocol
             },

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java

@@ -24,13 +24,15 @@
 import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.HtmlView;
@@ -53,7 +55,7 @@ public GenotypeAssaysController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class MigrateLegacySSPAction extends ConfirmAction<Object>
+    public static class MigrateLegacySSPAction extends ConfirmAction<Object>
     {
         @Override
         public void validateCommand(Object form, Errors errors)
@@ -64,19 +66,19 @@ public void validateCommand(Object form, Errors errors)
         @Override
         public ModelAndView getConfirmView(Object form, BindException errors) throws Exception
         {
-            DbSchema schema = DbSchema.get("SSP_Assay");
+            DbSchema schema = DbSchema.get("SSP_Assay", DbSchemaType.Module);
             if (schema == null)
-                return new HtmlView("Either the legacy SSP module has not been installed, or it has already been removed");
+                return new HtmlView(HtmlString.of("Either the legacy SSP module has not been installed, or it has already been removed"));
             else
-                return new HtmlView("This allows an admin to copy any primers stored in the original SSP Assay module into the new genotyping module.  Any data has already been copied.  Do you want to continue?");
+                return new HtmlView(HtmlString.of("This allows an admin to copy any primers stored in the original SSP Assay module into the new genotyping module.  Any data has already been copied.  Do you want to continue?"));
         }
 
         @Override
         public boolean handlePost(Object form, BindException errors) throws Exception
         {
             try
             {
-                DbSchema schema = DbSchema.get("SSP_Assay");
+                DbSchema schema = DbSchema.get("SSP_Assay", DbSchemaType.Module);
                 if (schema == null)
                     return true; //module not installed
 
@@ -113,7 +115,7 @@ public URLHelper getSuccessURL(Object form)
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class CacheAnalysesAction extends MutatingApiAction<CacheAnalysesForm>
+    public static class CacheAnalysesAction extends MutatingApiAction<CacheAnalysesForm>
     {
         @Override
         public ApiResponse execute(CacheAnalysesForm form, BindException errors)
@@ -133,7 +135,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
                     }
 
                     String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
-                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), form.getAnalysisId(), protocol, alleleNames);
+                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
                     resultProperties.put("runsCreated", ret.first);
                     resultProperties.put("runsDeleted", ret.second);
                 }
@@ -159,7 +161,6 @@ public static class CacheAnalysesForm
     {
         private String[] _alleleNames;
         private String _json;
-        private int _analysisId;
         private int _protocolId;
 
         public String[] getAlleleNames()
@@ -191,20 +192,10 @@ public void setJson(String json)
         {
             _json = json;
         }
-
-        public int getAnalysisId()
-        {
-            return _analysisId;
-        }
-
-        public void setAnalysisId(int analysisId)
-        {
-            _analysisId = analysisId;
-        }
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class CacheHaplotypesAction extends MutatingApiAction<CacheAnalysesForm>
+    public static class CacheHaplotypesAction extends MutatingApiAction<CacheAnalysesForm>
     {
         @Override
         public ApiResponse execute(CacheAnalysesForm form, BindException errors)

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -90,7 +90,7 @@ public static GenotypeAssaysManager get()
         return _instance;
     }
 
-    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final int analysisId, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
+    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
     {
         final User u = ctx.getUser();
         final List<Long> runsCreated = new ArrayList<>();
@@ -125,7 +125,6 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final i
 
             AtomicInteger records = new AtomicInteger();
             TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
-            tsAlignments.setNamedParameters(Map.of("AnalysisId", analysisId));
 
             tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
             {

primeseq/src/org/labkey/primeseq/pipeline/MhcCleanupPipelineJob.java

@@ -285,7 +285,6 @@ private void processAnalysis(int analysisId)
                 dataFilter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.GT);
 
                 TableSelector ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
-                ts.setNamedParameters(Map.of("AnalysisId", analysisId));
 
                 ts.forEachResults(rs -> {
                     existingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
@@ -337,7 +336,6 @@ private void processAnalysis(int analysisId)
                     filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getAlleleGroupThreshold(), CompareType.LT);
 
                     ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
-                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
                     List<String> lowFreqRowIdList = ts.getArrayList(String.class);
                     if (!lowFreqRowIdList.isEmpty())
                     {
@@ -373,7 +371,6 @@ private void processAnalysis(int analysisId)
                     filter.addCondition(FieldKey.fromString("loci"), "MHC", CompareType.CONTAINS);
 
                     ts  = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
-                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
                     List<String> rowIdList = ts.getArrayList(String.class);
                     if (!rowIdList.isEmpty())
                     {
@@ -392,7 +389,6 @@ private void processAnalysis(int analysisId)
                     SimpleFilter nAlignmentFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
                     nAlignmentFilter.addCondition(FieldKey.fromString("nAlignments"), 1, CompareType.GT);
                     ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null);
-                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
                     List<String> redundantAlignmentSets = ts.getArrayList(String.class);
                     if (!redundantAlignmentSets.isEmpty())
                     {
@@ -460,7 +456,6 @@ private void processAnalysis(int analysisId)
                 // verify ending data:
                 final Map<String, Double> endingData = new HashMap<>();
                 ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
-                ts.setNamedParameters(Map.of("AnalysisId", analysisId));
                 ts.forEachResults(rs -> {
                     endingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
                 });
@@ -531,7 +526,6 @@ public AlignmentGroupCompare(final int analysisId, Container c, User u)
             this.analysisId = analysisId;
 
             TableSelector ts = new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null);
-            ts.setNamedParameters(Map.of("AnalysisId", analysisId));
             ts.forEachResults(rs -> {
                 if (rs.getString(FieldKey.fromString("alleles")) == null)
                 {