Update ELISPOT assay to match new instrument format

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+# Maintain dependencies for GitHub Actions
+ - package-ecosystem: "github-actions"
+directory: "/"
+schedule:
+interval: "daily"

.github/workflows/build.yml

@@ -0,0 +1,19 @@
+name: Build DISCVR
+on:
+ push:
+ pull_request:
+jobs:
+ build-modules:
+ # See: https://help.github.com/en/actions/reference/contexts-and-expression-syntax-for-github-actions#github-context
+ # https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables#default-environment-variables
+ if: github.repository == 'BimberLabInternal/BimberLabKeyModules'
+ runs-on: ubuntu-latest
+ steps:
+ - name: "Build DISCVR"
+ uses: bimberlabinternal/DevOps/githubActions/discvr-build@master
+ with:
+ artifactory_user: ${{secrets.artifactory_user}}
+ artifactory_password: ${{secrets.artifactory_password}}
+ # NOTE: permissions are limited on the default secrets.GITHUB_TOKEN, including updating workflows, so use a personal access token
+ github_token: ${{ secrets.PAT }}
+

.github/workflows/sync-repos.yml

@@ -31,4 +31,4 @@ jobs:
  source_repo: "labkey/BimberLabKeyModules"
  source_branch: "develop"
  destination_branch: "develop"
- github_token: ${{ secrets.GITHUB_TOKEN }}
+ github_token: ${{ secrets.PAT }}

GenotypeAssays/module.properties

@@ -1,3 +1,2 @@
 ModuleClass: org.labkey.genotypeassays.GenotypeAssaysModule
-ConsolidateScripts: false
 ManageVersion: false

LabPurchasing/module.properties

@@ -0,0 +1,6 @@
+ModuleClass: org.labkey.labpurchasing.LabPurchasingModule
+Label: Lab Purchacing
+Description: A module designed to assist with purchasing supplies for academic labs
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ManageVersion: false

LabPurchasing/resources/schemas/dbscripts/postgresql/labpurchasing-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 LabPurchasing module here
+-- All SQL VIEW definitions should be created in labpurchasing-create.sql and dropped in labpurchasing-drop.sql
+CREATE SCHEMA labpurchasing;

LabPurchasing/resources/schemas/dbscripts/sqlserver/labpurchasing-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 LabPurchasing module here
+-- All SQL VIEW definitions should be created in labpurchasing-create.sql and dropped in labpurchasing-drop.sql
+CREATE SCHEMA labpurchasing;
+GO

LabPurchasing/resources/schemas/labpurchasing.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"/>

LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingController.java

@@ -0,0 +1,37 @@
+/*
+ * 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.labpurchasing;
+
+import org.labkey.api.action.SimpleViewAction;
+import org.labkey.api.action.SpringActionController;
+import org.labkey.api.security.RequiresPermission;
+import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.view.JspView;
+import org.labkey.api.view.NavTree;
+import org.springframework.validation.BindException;
+import org.springframework.web.servlet.ModelAndView;
+
+public class LabPurchasingController extends SpringActionController
+{
+ private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(LabPurchasingController.class);
+ public static final String NAME = "labpurchasing";
+
+ public LabPurchasingController()
+ {
+ setActionResolver(_actionResolver);
+ }
+}

LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingManager.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.labpurchasing;
+
+public class LabPurchasingManager
+{
+ private static final LabPurchasingManager _instance = new LabPurchasingManager();
+
+ private LabPurchasingManager()
+ {
+ // prevent external construction with a private default constructor
+ }
+
+ public static LabPurchasingManager get()
+ {
+ return _instance;
+ }
+}

LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingModule.java

@@ -0,0 +1,85 @@
+/*
+ * 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.labpurchasing;
+
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
+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 LabPurchasingModule extends DefaultModule
+{
+ public static final String NAME = "LabPurchasing";
+
+ @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(LabPurchasingController.NAME, LabPurchasingController.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(LabPurchasingSchema.NAME);
+ }
+}

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