Merge discvr-23.3 to develop

Author: bbimber

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

@@ -144,7 +144,7 @@ private void customizeSummaryByLineage(AbstractTableInfo ti)
             ti.addColumn(newCol);
 
             String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
+            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult.").append(d.getStorageTableName()).append(" a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = ").append(ti.getSqlDialect().getBooleanTRUE()).append(") WHERE a.analysisId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".analysis_id AND a.result IS NULL AND hs.name = ").append(ExprColumn.STR_TABLE_ALIAS).append(".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");
             ti.addColumn(newCol3);

IDR/build.gradle

@@ -0,0 +1,19 @@
+import org.labkey.gradle.util.BuildUtils;
+
+plugins {
+    id 'org.labkey.build.module'
+}
+
+dependencies
+        {
+            implementation "com.sun.mail:jakarta.mail:${javaMailVersion}"
+            implementation project(path: ':server:modules:LabDevKitModules:LDK')
+            BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
+            BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "apiJarFile")
+
+            BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: 'published', depExtension: 'module')
+            BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: 'published', depExtension: 'module')
+            BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: 'published', depExtension: 'module')
+            BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premium", depProjectConfig: 'published', depExtension: 'module')
+            BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: 'published', depExtension: 'module')
+        }

IDR/module.properties

@@ -0,0 +1,5 @@
+ModuleClass: org.labkey.idr.IDRModule
+Label: IDR
+Description: This module will support the ONPRC IDR
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0

IDR/resources/schemas/dbscripts/postgresql/idr-0.00-23.000.sql

@@ -0,0 +1,4 @@
+
+-- Create schema, tables, indexes, and constraints used for IDR module here
+-- All SQL VIEW definitions should be created in idr-create.sql and dropped in idr-drop.sql
+CREATE SCHEMA idr;

IDR/resources/schemas/dbscripts/sqlserver/idr-0.00-23.000.sql

@@ -0,0 +1,20 @@
+/*
+ * Copyright (c) 2023 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+-- Create schema, tables, indexes, and constraints used for IDR module here
+-- All SQL VIEW definitions should be created in idr-create.sql and dropped in idr-drop.sql
+CREATE SCHEMA idr;
+GO

IDR/resources/schemas/idr.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<tables xsi:schemaLocation="http://labkey.org/data/xml ..\..\..\..\schemas\tableInfo.xsd"
+        xmlns="http://labkey.org/data/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"/>

IDR/src/org/labkey/idr/IDRController.java

@@ -0,0 +1,15 @@
+package org.labkey.idr;
+
+import org.labkey.api.action.SpringActionController;
+
+public class IDRController extends SpringActionController
+{
+    private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(IDRController.class);
+    public static final String NAME = "idr";
+
+    public IDRController()
+    {
+        setActionResolver(_actionResolver);
+    }
+
+}

IDR/src/org/labkey/idr/IDRManager.java

@@ -0,0 +1,16 @@
+package org.labkey.idr;
+
+public class IDRManager
+{
+    private static final IDRManager _instance = new IDRManager();
+
+    private IDRManager()
+    {
+        // prevent external construction with a private default constructor
+    }
+
+    public static IDRManager get()
+    {
+        return _instance;
+    }
+}

IDR/src/org/labkey/idr/IDRModule.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright (c) 2023 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.labkey.idr;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.ehr.EHRService;
+import org.labkey.api.ldk.ExtendedSimpleModule;
+import org.labkey.api.module.ModuleContext;
+
+public class IDRModule extends ExtendedSimpleModule
+{
+    public static final String NAME = "IDR";
+
+    @Override
+    public String getName()
+    {
+        return NAME;
+    }
+
+    @Override
+    protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
+    {
+        registerEHRResources();
+    }
+
+    private void registerEHRResources()
+    {
+        EHRService.get().registerModule(this);
+    }
+
+    @Override
+    public @Nullable Double getSchemaVersion()
+    {
+        return 23.000;
+    }
+
+    @Override
+    public boolean hasScripts()
+    {
+        return true;
+    }
+
+    @Override
+    protected void init()
+    {
+        addController(IDRController.NAME, IDRController.class);
+    }
+}

IDR/src/org/labkey/idr/IDRSchema.java

@@ -0,0 +1,33 @@
+package org.labkey.idr;
+
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.dialect.SqlDialect;
+
+public class IDRSchema
+{
+    private static final IDRSchema _instance = new IDRSchema();
+    public static final String NAME = "idr";
+
+    public static IDRSchema getInstance()
+    {
+        return _instance;
+    }
+
+    private IDRSchema()
+    {
+        // private constructor to prevent instantiation from
+        // outside this class: this singleton should only be
+        // accessed via org.labkey.idr.IDRSchema.getInstance()
+    }
+
+    public DbSchema getSchema()
+    {
+        return DbSchema.get(NAME, DbSchemaType.Module);
+    }
+
+    public SqlDialect getSqlDialect()
+    {
+        return getSchema().getSqlDialect();
+    }
+}