Add stubs for DISCVR-Core module. Also update module.properties on many modules

bbimber · bbimber · commit cfbca08f3cd0 · 2020-12-28T11:00:07.000-08:00
diff --git a/OpenLdapSync/module.properties b/OpenLdapSync/module.properties
@@ -4,3 +4,4 @@ Description: This module can be used to sync LabKey users with an LDAP server
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
+URL: https://github.com/BimberLab/DiscvrLabKeyModules
diff --git a/SequenceAnalysis/module.properties b/SequenceAnalysis/module.properties
@@ -1,2 +1,7 @@
 ModuleClass: org.labkey.sequenceanalysis.SequenceAnalysisModule
 ManageVersion: false
+Label: DISCVR-seq
+Description: This is the core module for DISCVR-seq, which is a suite of modules to manage and analyze sequence data using LabKey. 
+URL: https://github.com/BimberLab/DiscvrLabKeyModules
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
diff --git a/blast/module.properties b/blast/module.properties
@@ -1,2 +1,7 @@
 ModuleClass: org.labkey.blast.BLASTModule
-ManageVersion: false
+Label: BLAST
+Description: This module provides a wrapper about NCBI's BLAST, allowing the server to maintain and search using custom BLAST databases. 
+ManageVersion: false
+URL: https://github.com/BimberLab/DiscvrLabKeyModules
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
diff --git a/cluster/module.properties b/cluster/module.properties
@@ -1,6 +1,7 @@
 ModuleClass: org.labkey.cluster.ClusterModule
 Label: Cluster
 Description: This module enables integration between the LabKey pipeline and clusters, including HTCondor and Slurm clusters
+URL: https://github.com/BimberLab/DiscvrLabKeyModules
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ManageVersion: false
diff --git a/discvrcore/build.gradle b/discvrcore/build.gradle
@@ -0,0 +1,5 @@
+import org.labkey.gradle.util.BuildUtils;
+
+dependencies {
+
+}
diff --git a/discvrcore/module.properties b/discvrcore/module.properties
@@ -0,0 +1,6 @@
+ModuleClass: org.labkey.discvrcore.DiscvrCoreModule
+Label: DISCVR Core
+Description: This is the base module for the DISCVR familiy of modules. It contains low-level dependencies and is not meant to be used on its own.
+URL: https://github.com/BimberLab/DiscvrLabKeyModules
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
diff --git a/discvrcore/resources/schemas/dbscripts/postgresql/discvrcore-0.00-20.000.sql b/discvrcore/resources/schemas/dbscripts/postgresql/discvrcore-0.00-20.000.sql
@@ -0,0 +1,19 @@
+/*
+ * Copyright (c) 2020 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 DiscvrCore module here
+-- All SQL VIEW definitions should be created in discvrcore-create.sql and dropped in discvrcore-drop.sql
+CREATE SCHEMA discvrcore;
diff --git a/discvrcore/resources/schemas/dbscripts/sqlserver/discvrcore-0.00-20.000.sql b/discvrcore/resources/schemas/dbscripts/sqlserver/discvrcore-0.00-20.000.sql
@@ -0,0 +1,20 @@
+/*
+ * Copyright (c) 2020 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 DiscvrCore module here
+-- All SQL VIEW definitions should be created in discvrcore-create.sql and dropped in discvrcore-drop.sql
+CREATE SCHEMA discvrcore;
+GO
diff --git a/discvrcore/resources/schemas/discvrcore.xml b/discvrcore/resources/schemas/discvrcore.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- 
+
+ * Copyright (c) 2020 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.
+
+ -->
+<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"/>
diff --git a/discvrcore/src/org/labkey/discvrcore/DiscvrCoreController.java b/discvrcore/src/org/labkey/discvrcore/DiscvrCoreController.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright (c) 2020 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.discvrcore;
+
+import org.labkey.api.action.SpringActionController;
+
+public class DiscvrCoreController extends SpringActionController
+{
+    private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(DiscvrCoreController.class);
+    public static final String NAME = "discvrcore";
+
+    public DiscvrCoreController()
+    {
+        setActionResolver(_actionResolver);
+    }
+}
diff --git a/discvrcore/src/org/labkey/discvrcore/DiscvrCoreManager.java b/discvrcore/src/org/labkey/discvrcore/DiscvrCoreManager.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright (c) 2020 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.discvrcore;
+
+public class DiscvrCoreManager
+{
+    private static final DiscvrCoreManager _instance = new DiscvrCoreManager();
+
+    private DiscvrCoreManager()
+    {
+        // prevent external construction with a private default constructor
+    }
+
+    public static DiscvrCoreManager get()
+    {
+        return _instance;
+    }
+}
diff --git a/discvrcore/src/org/labkey/discvrcore/DiscvrCoreModule.java b/discvrcore/src/org/labkey/discvrcore/DiscvrCoreModule.java
@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2020 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.discvrcore;
+
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.module.DefaultModule;
+import org.labkey.api.module.ModuleContext;
+import org.labkey.api.view.WebPartFactory;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Set;
+
+public class DiscvrCoreModule extends DefaultModule
+{
+    public static final String NAME = "DiscvrCore";
+
+    @Override
+    public String getName()
+    {
+        return NAME;
+    }
+
+    @Override
+    public @Nullable Double getSchemaVersion()
+    {
+        return 20.000;
+    }
+
+    @Override
+    public boolean hasScripts()
+    {
+        return true;
+    }
+
+    @Override
+    @NotNull
+    protected Collection<WebPartFactory> createWebPartFactories()
+    {
+        return Collections.emptyList();
+    }
+
+    @Override
+    protected void init()
+    {
+        addController(DiscvrCoreController.NAME, DiscvrCoreController.class);
+    }
+
+    @Override
+    public void doStartup(ModuleContext moduleContext)
+    {
+
+    }
+
+    @Override
+    @NotNull
+    public Collection<String> getSummary(Container c)
+    {
+        return Collections.emptyList();
+    }
+
+    @Override
+    @NotNull
+    public Set<String> getSchemaNames()
+    {
+        return Collections.singleton(DiscvrCoreSchema.NAME);
+    }
+}
diff --git a/discvrcore/src/org/labkey/discvrcore/DiscvrCoreSchema.java b/discvrcore/src/org/labkey/discvrcore/DiscvrCoreSchema.java
@@ -0,0 +1,49 @@
+/*
+ * Copyright (c) 2020 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.discvrcore;
+
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.dialect.SqlDialect;
+
+public class DiscvrCoreSchema
+{
+    private static final DiscvrCoreSchema _instance = new DiscvrCoreSchema();
+    public static final String NAME = "discvrcore";
+
+    public static DiscvrCoreSchema getInstance()
+    {
+        return _instance;
+    }
+
+    private DiscvrCoreSchema()
+    {
+        // private constructor to prevent instantiation from
+        // outside this class: this singleton should only be
+        // accessed via org.labkey.discvrcore.DiscvrCoreSchema.getInstance()
+    }
+
+    public DbSchema getSchema()
+    {
+        return DbSchema.get(NAME, DbSchemaType.Module);
+    }
+
+    public SqlDialect getSqlDialect()
+    {
+        return getSchema().getSqlDialect();
+    }
+}
diff --git a/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java b/discvrcore/test/src/org/labkey/test/tests/discvrcore/DiscvrCoreTest.java
diff --git a/jbrowse/module.properties b/jbrowse/module.properties
diff --git a/omerointegration/module.properties b/omerointegration/module.properties

-Original file line number
+Diff line change
@@ @@ -0,0 +1,5 @@ @@
 +import org.labkey.gradle.util.BuildUtils;
++
 +dependencies {
++
 +}