diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 000000000..583decfd1
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+ # Maintain dependencies for GitHub Actions
+ - package-ecosystem: "github-actions"
+ directory: "/"
+ schedule:
+ interval: "daily"
\ No newline at end of file
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 000000000..aca42609f
--- /dev/null
+++ b/.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 }}
+
diff --git a/.github/workflows/sync-repos.yml b/.github/workflows/sync-repos.yml
index 199e5f75a..e5201d176 100644
--- a/.github/workflows/sync-repos.yml
+++ b/.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 }}
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 4f4ef89f4..000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-language: java
-dist: trusty
-git:
- depth: 9999999
-jdk:
- - openjdk13
-
-before_cache:
- - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
- - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
-
-cache:
- directories:
- - $HOME/.gradle/caches/
- - $HOME/.gradle/wrapper/
- - $HOME/.m2
- - $HOME/site-library
-
-install: skip
-script:
- - wget -O ./travis.sh https://github.com/bimberlabinternal/DevOps/raw/master/travisci/travis.sh
- - bash ./travis.sh
\ No newline at end of file
diff --git a/GenotypeAssays/module.properties b/GenotypeAssays/module.properties
index 9a8f3c517..26b7527df 100644
--- a/GenotypeAssays/module.properties
+++ b/GenotypeAssays/module.properties
@@ -1,3 +1,2 @@
ModuleClass: org.labkey.genotypeassays.GenotypeAssaysModule
-ConsolidateScripts: false
ManageVersion: false
diff --git a/LabPurchasing/module.properties b/LabPurchasing/module.properties
new file mode 100644
index 000000000..cf4adca31
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/LabPurchasing/resources/schemas/dbscripts/postgresql/labpurchasing-0.00-20.000.sql b/LabPurchasing/resources/schemas/dbscripts/postgresql/labpurchasing-0.00-20.000.sql
new file mode 100644
index 000000000..fe2e39c0f
--- /dev/null
+++ b/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;
diff --git a/LabPurchasing/resources/schemas/dbscripts/sqlserver/labpurchasing-0.00-20.000.sql b/LabPurchasing/resources/schemas/dbscripts/sqlserver/labpurchasing-0.00-20.000.sql
new file mode 100644
index 000000000..35a4a8574
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/LabPurchasing/resources/schemas/labpurchasing.xml b/LabPurchasing/resources/schemas/labpurchasing.xml
new file mode 100644
index 000000000..2bba6c71d
--- /dev/null
+++ b/LabPurchasing/resources/schemas/labpurchasing.xml
@@ -0,0 +1,20 @@
+
+
+
\ No newline at end of file
diff --git a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingController.java b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingController.java
new file mode 100644
index 000000000..e53cbc6c5
--- /dev/null
+++ b/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);
+ }
+}
diff --git a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingManager.java b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingManager.java
new file mode 100644
index 000000000..43b0d9543
--- /dev/null
+++ b/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;
+ }
+}
\ No newline at end of file
diff --git a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingModule.java b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingModule.java
new file mode 100644
index 000000000..230a72130
--- /dev/null
+++ b/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 createWebPartFactories()
+ {
+ return Collections.emptyList();
+ }
+
+ @Override
+ protected void init()
+ {
+ addController(LabPurchasingController.NAME, LabPurchasingController.class);
+ }
+
+ @Override
+ public void doStartup(ModuleContext moduleContext)
+ {
+
+ }
+
+ @Override
+ @NotNull
+ public Collection getSummary(Container c)
+ {
+ return Collections.emptyList();
+ }
+
+ @Override
+ @NotNull
+ public Set getSchemaNames()
+ {
+ return Collections.singleton(LabPurchasingSchema.NAME);
+ }
+}
\ No newline at end of file
diff --git a/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingSchema.java b/LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingSchema.java
new file mode 100644
index 000000000..d4425241d
--- /dev/null
+++ b/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();
+ }
+}
diff --git a/LabPurchasing/test/src/org/labkey/test/components/labpurchasing/LabPurchasingWebPart.java b/LabPurchasing/test/src/org/labkey/test/components/labpurchasing/LabPurchasingWebPart.java
new file mode 100644
index 000000000..eaa9965df
--- /dev/null
+++ b/LabPurchasing/test/src/org/labkey/test/components/labpurchasing/LabPurchasingWebPart.java
@@ -0,0 +1,69 @@
+/*
+ * 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.test.components.labpurchasing;
+
+import org.labkey.test.Locator;
+import org.labkey.test.components.BodyWebPart;
+import org.labkey.test.components.html.Input;
+import org.labkey.test.pages.LabKeyPage;
+import org.openqa.selenium.WebDriver;
+import org.openqa.selenium.WebElement;
+
+import static org.labkey.test.components.html.Input.Input;
+
+/**
+ * TODO: Component for a hypothetical webpart containing an input and a save button
+ * Component classes should handle all timing and functionality for a component
+ */
+public class LabPurchasingWebPart extends BodyWebPart
+{
+ public LabPurchasingWebPart(WebDriver driver)
+ {
+ this(driver, 0);
+ }
+
+ public LabPurchasingWebPart(WebDriver driver, int index)
+ {
+ super(driver, "LabPurchasing", index);
+ }
+
+ public LabPurchasingWebPart setInput(String value)
+ {
+ elementCache().input.set(value);
+ // TODO: Methods that don't navigate should return this object
+ return this;
+ }
+
+ public LabKeyPage clickSave()
+ {
+ getWrapper().clickAndWait(elementCache().button);
+ // TODO: Methods that navigate should return an appropriate page object
+ return new LabKeyPage(getDriver());
+ }
+
+ @Override
+ protected ElementCache newElementCache()
+ {
+ return new ElementCache();
+ }
+
+ protected class ElementCache extends BodyWebPart.ElementCache
+ {
+ protected final WebElement button = Locator.tag("button").withText("Save").findWhenNeeded(this);
+ protected final Input input = Input(Locator.tag("input"), getDriver()).findWhenNeeded(this);
+ }
+}
\ No newline at end of file
diff --git a/LabPurchasing/test/src/org/labkey/test/pages/labpurchasing/BeginPage.java b/LabPurchasing/test/src/org/labkey/test/pages/labpurchasing/BeginPage.java
new file mode 100644
index 000000000..7e36f3e45
--- /dev/null
+++ b/LabPurchasing/test/src/org/labkey/test/pages/labpurchasing/BeginPage.java
@@ -0,0 +1,59 @@
+/*
+ * 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.test.pages.labpurchasing;
+
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.WebDriverWrapper;
+import org.labkey.test.Locator;
+import org.labkey.test.WebTestHelper;
+import org.labkey.test.pages.LabKeyPage;
+import org.openqa.selenium.WebElement;
+
+public class BeginPage extends LabKeyPage
+{
+ public BeginPage(WebDriverWrapper driver)
+ {
+ super(driver);
+ }
+
+ public static BeginPage beginAt(WebDriverWrapper driver)
+ {
+ return beginAt(driver, driver.getCurrentContainerPath());
+ }
+
+ public static BeginPage beginAt(WebDriverWrapper driver, String containerPath)
+ {
+ driver.beginAt(WebTestHelper.buildURL("labpurchasing", containerPath, "begin"));
+ return new BeginPage(driver);
+ }
+
+ public String getHelloMessage()
+ {
+ return elementCache().helloMessage.getText();
+ }
+
+ @Override
+ protected ElementCache newElementCache()
+ {
+ return new ElementCache();
+ }
+
+ protected class ElementCache extends LabKeyPage.ElementCache
+ {
+ protected final WebElement helloMessage = Locator.tagWithName("div", "helloMessage").findWhenNeeded(this);
+ }
+}
diff --git a/LabPurchasing/test/src/org/labkey/test/tests/labpurchasing/LabPurchasingTest.java b/LabPurchasing/test/src/org/labkey/test/tests/labpurchasing/LabPurchasingTest.java
new file mode 100644
index 000000000..1fa717924
--- /dev/null
+++ b/LabPurchasing/test/src/org/labkey/test/tests/labpurchasing/LabPurchasingTest.java
@@ -0,0 +1,88 @@
+/*
+ * 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.test.tests.labpurchasing;
+
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.TestTimeoutException;
+import org.labkey.test.categories.InDevelopment;
+import org.labkey.test.pages.labpurchasing.BeginPage;
+
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
+@Category({InDevelopment.class})
+public class LabPurchasingTest extends BaseWebDriverTest
+{
+ @Override
+ protected void doCleanup(boolean afterTest) throws TestTimeoutException
+ {
+ _containerHelper.deleteProject(getProjectName(), afterTest);
+ }
+
+ @BeforeClass
+ public static void setupProject()
+ {
+ LabPurchasingTest init = (LabPurchasingTest)getCurrentTest();
+
+ init.doSetup();
+ }
+
+ private void doSetup()
+ {
+ _containerHelper.createProject(getProjectName(), null);
+ }
+
+ @Before
+ public void preTest()
+ {
+ goToProjectHome();
+ }
+
+ @Test
+ public void testLabPurchasingModule()
+ {
+ _containerHelper.enableModule("LabPurchasing");
+ BeginPage beginPage = BeginPage.beginAt(this, getProjectName());
+ assertEquals(200, getResponseCode());
+ final String expectedHello = "Hello, and welcome to the LabPurchasing module.";
+ assertEquals("Wrong hello message", expectedHello, beginPage.getHelloMessage());
+ }
+
+ @Override
+ protected BrowserType bestBrowser()
+ {
+ return BrowserType.CHROME;
+ }
+
+ @Override
+ protected String getProjectName()
+ {
+ return "LabPurchasingTest Project";
+ }
+
+ @Override
+ public List getAssociatedModules()
+ {
+ return Collections.singletonList("LabPurchasing");
+ }
+}
\ No newline at end of file
diff --git a/README.md b/README.md
index c498f9a50..b5f6334a8 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[](https://travis-ci.com/BimberLab/DiscvrLabKeyModules)
+
## Overview
diff --git a/elispot_assay/module.properties b/elispot_assay/module.properties
index 77a02d564..4f2d4f3f5 100644
--- a/elispot_assay/module.properties
+++ b/elispot_assay/module.properties
@@ -1,3 +1,2 @@
ModuleClass: org.labkey.elispot_assay.ELISPOT_AssayModule
-ConsolidateScripts: false
ManageVersion: false
diff --git a/elispot_assay/resources/credits/dependencies.txt b/elispot_assay/resources/credits/dependencies.txt
new file mode 100644
index 000000000..2b459f3fc
--- /dev/null
+++ b/elispot_assay/resources/credits/dependencies.txt
@@ -0,0 +1,2 @@
+# direct external dependencies for project :server:modules:BimberLabKeyModules:elispot_assay
+commons-math3-3.6.1.jar
diff --git a/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java b/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java
index 6606c1593..f99393759 100644
--- a/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java
+++ b/elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java
@@ -22,6 +22,8 @@
import java.io.IOException;
import java.io.StringWriter;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.ListIterator;
@@ -291,17 +293,19 @@ protected List> processRows(List> rows,
private enum PLATE
{
- spot("Spot counts:", "spots"),
- saturation("Well's saturation values (%)", "saturation"),
- cytokine("Cytokine Activities:", "cytokine");
+ spot("Spot counts:", "spots", Collections.singletonList("Number of Spots:")),
+ saturation("Well's saturation values (%)", "saturation", Collections.singletonList("Well's saturation values (%)")),
+ cytokine("Cytokine Activities:", "cytokine", Collections.singletonList("Activity:"));
private String description;
private String field;
+ private Collection aliases;
- PLATE(String description, String field)
+ PLATE(String description, String field, Collection aliases)
{
this.description = description;
this.field = field;
+ this.aliases = aliases;
}
public static PLATE getByDescription(String description)
@@ -310,6 +314,16 @@ public static PLATE getByDescription(String description)
{
if (t.description.equalsIgnoreCase(description))
return t;
+ else if (t.aliases != null)
+ {
+ for (String alias : t.aliases)
+ {
+ if (alias.equals(description))
+ {
+ return t;
+ }
+ }
+ }
}
return null;
}
diff --git a/flowassays/module.properties b/flowassays/module.properties
index 384050e17..df44cb72e 100644
--- a/flowassays/module.properties
+++ b/flowassays/module.properties
@@ -1,3 +1,2 @@
ModuleClass: org.labkey.flowassays.FlowAssaysModule
-ConsolidateScripts: false
ManageVersion: false
diff --git a/mGAP/module.properties b/mGAP/module.properties
index 5378792a1..18b50ca5b 100644
--- a/mGAP/module.properties
+++ b/mGAP/module.properties
@@ -1,5 +1,4 @@
ModuleClass: org.labkey.mgap.mGAPModule
License: Apache 2.0
LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-ConsolidateScripts: false
ManageVersion: false
diff --git a/mGAP/resources/credits/jars.txt b/mGAP/resources/credits/jars.txt
index b3fbb0b53..0a2c7d2f9 100644
--- a/mGAP/resources/credits/jars.txt
+++ b/mGAP/resources/credits/jars.txt
@@ -1,4 +1,4 @@
{table}
Filename|Component|Version|Source|License|LabKey Dev|Purpose
-htsjdk-2.21.3.jar|htsjdk|2.21.3|{link:htsjdk|http://samtools.github.io/htsjdk/}|{link:MIT License|http://opensource.org/licenses/MIT}|bbimber|Description A Java API for high-throughput sequencing data (HTS) formats
+htsjdk-2.21.3.jar|htsjdk|2.21.3|{link:htsjdk|http://samtools.github.io/htsjdk/}|{link:MIT License|http://opensource.org/licenses/MIT}|bbimber|A Java API for high-throughput sequencing data (HTS) formats
{table}
\ No newline at end of file
diff --git a/mGAP/resources/etls/prime-seq.xml b/mGAP/resources/etls/prime-seq.xml
index da78c21a3..fa21db466 100644
--- a/mGAP/resources/etls/prime-seq.xml
+++ b/mGAP/resources/etls/prime-seq.xml
@@ -143,7 +143,7 @@
af
-
+
@@ -167,6 +167,6 @@
-
+
diff --git a/mGAP/resources/folderTypes/mGAP.folderType.xml b/mGAP/resources/folderTypes/mGAP.folderType.xml
index bee390d74..bf7576130 100644
--- a/mGAP/resources/folderTypes/mGAP.folderType.xml
+++ b/mGAP/resources/folderTypes/mGAP.folderType.xml
@@ -84,6 +84,10 @@
mGAP Variant Releasesbody
+
+ mGAP Release Notes
+ body
+ mGAP Gene Searchright
diff --git a/mGAP/resources/referenceStudy/datasets/datasets_metadata.xml b/mGAP/resources/referenceStudy/datasets/datasets_metadata.xml
index 6c5f22112..6375977ad 100644
--- a/mGAP/resources/referenceStudy/datasets/datasets_metadata.xml
+++ b/mGAP/resources/referenceStudy/datasets/datasets_metadata.xml
@@ -241,7 +241,7 @@
http://cpas.labkey.com/Study#VisitDate
- Gender
+ Sexvarchar
diff --git a/mGAP/resources/schemas/mgap.xml b/mGAP/resources/schemas/mgap.xml
index fd75ef2c4..e55e9ffca 100644
--- a/mGAP/resources/schemas/mgap.xml
+++ b/mGAP/resources/schemas/mgap.xml
@@ -1000,7 +1000,7 @@
- Gender
+ Sexlaboratorygenders
diff --git a/mGAP/resources/views/contact.html b/mGAP/resources/views/contact.html
index 1b110d8cc..e1f2f6b53 100644
--- a/mGAP/resources/views/contact.html
+++ b/mGAP/resources/views/contact.html
@@ -49,7 +49,7 @@
success: function(response){
console.log(response);
- Ext4.Msg.alert('Success', 'An account has been requested. You should receive a reply shortly.', function(){
+ Ext4.Msg.alert('Success', 'Your request has been sent. You should receive a reply shortly.', function(){
window.location = LABKEY.ActionURL.getContextPath() + '/';
});
},
diff --git a/mGAP/resources/views/geneSearch.html b/mGAP/resources/views/geneSearch.html
index 7aaa583a2..515e90b9e 100644
--- a/mGAP/resources/views/geneSearch.html
+++ b/mGAP/resources/views/geneSearch.html
@@ -170,7 +170,7 @@
}
});
- url = Object.keys(unique)[0] + ':' + minStart + '..' + maxStop;
+ url = Object.keys(uniqueRef)[0] + ':' + minStart + '..' + maxStop;
}
if (!url) {
diff --git a/mGAP/resources/views/releaseNotes.html b/mGAP/resources/views/releaseNotes.html
new file mode 100644
index 000000000..110244e37
--- /dev/null
+++ b/mGAP/resources/views/releaseNotes.html
@@ -0,0 +1,12 @@
+
Release 2.0:
+
+
Substantial revamp of all data. All samples have been realigned to the MMul_10 reference genome, followed by our standard GenotypeGVCFs pipeline. The MMul_10 is the most complete rhesus macaque assembly to date, and we expect this should improve accuracy of variant calls. Further, because our data are now aligned to the same assembly as NCBI/Ensembl, it should be easier to translate between mGAP and other databases.
+
Our internal variant calling process has switched to use GATK's GenomicsDB to pre-aggregate data prior to calling with GenotypeGVCFs, as opposed to CombineGVCFs, which was used in prior releases. This should be a purely technical difference with no change in the resulting data
+
+
+
Future Plans:
+
+
We expect to upgrade the genome browser to use the redesigned JBrowse 2 browser. This should provide general performance improvements and will make future mGAP-specific customization easier.
+
We will support other modes of viewing and downloading variant data, in particular tabular views by gene.
+
We recognize that the mGAP release VCF can be enormous, particularly because of all the site-specific functional annotation. To support different types of users, upcoming releases will include 'slim' versions of the data, which will be downloadable files with certain information removed to save file size.
+
\ No newline at end of file
diff --git a/mGAP/resources/views/releaseNotes.view.xml b/mGAP/resources/views/releaseNotes.view.xml
new file mode 100644
index 000000000..c9a2b3e33
--- /dev/null
+++ b/mGAP/resources/views/releaseNotes.view.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mGAP/resources/views/releaseNotes.webpart.xml b/mGAP/resources/views/releaseNotes.webpart.xml
new file mode 100644
index 000000000..f7f58d800
--- /dev/null
+++ b/mGAP/resources/views/releaseNotes.webpart.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mGAP/resources/views/variants.html b/mGAP/resources/views/variants.html
index 3d66a6667..f59586d79 100644
--- a/mGAP/resources/views/variants.html
+++ b/mGAP/resources/views/variants.html
@@ -9,7 +9,7 @@
title: 'Variant Catalog Releases',
schemaName: 'mgap',
queryName: 'variantCatalogReleases',
- maxRows: 50,
+ maxRows: 3,
showRecordSelectors: false,
showDetailsColumn: false,
buttonBar: {position: 'none', includeStandardButtons: false, items: []}
diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
index 8493d435c..a9a8d57ae 100644
--- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
+++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
@@ -309,6 +309,6 @@ protected String getDatabaseName()
protected String getTrackJson()
{
- return "{\"category\":\"mGAP Variant Catalog\",\"visibleByDefault\": true,\"ensemblUrl\":\"jul2019.archive.ensembl.org\",\"ensemblId\":\"Macaca_mulatta\",\"additionalFeatureMsg\":\"
**The annotations below are primarily derived from human data sources (not macaque), and must be viewed in that context.
+
+
+
+
+
+
+
+
+
+ ehr
+ project
+ project
+
+
+
+ Assign Date
+ Date
+
+
+ Projected Release Date
+
+
+ Release Date
+ false
+ true
+ true
+ Date
+
+
+ true
+
+
+
+
+
+
+
+
+
+ Condition At Assignment
+
+ ehr_lookups
+ animal_condition
+ code
+
+
+
+ Projected Release Condition
+
+ ehr_lookups
+ animal_condition
+ code
+
+
+
+ Condition At Release
+
+ ehr_lookups
+ animal_condition
+ code
+
+
+
+ true
+
+
+ Release Type
+
+ ehr_lookups
+ assignmentReleaseType
+ value
+
+
+
+ Date Assignment End Entered
+ This records the date the end of the assignment was actually entered, which may differ from the enddate itself
+ true
+
+
+ CoAssignments
+ false
+ true
+
+ study
+ assignmentTotalCoAssigned
+ lsid
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/assignment/.qview.xml b/mcc/resources/queries/study/assignment/.qview.xml
new file mode 100644
index 000000000..4c0c2fdb7
--- /dev/null
+++ b/mcc/resources/queries/study/assignment/.qview.xml
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/birth/.qview.xml b/mcc/resources/queries/study/birth/.qview.xml
new file mode 100644
index 000000000..f1449329f
--- /dev/null
+++ b/mcc/resources/queries/study/birth/.qview.xml
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/clinremarks.xml b/mcc/resources/queries/study/clinremarks.xml
new file mode 100644
index 000000000..0bda2a18e
--- /dev/null
+++ b/mcc/resources/queries/study/clinremarks.xml
@@ -0,0 +1,22 @@
+
+
+
+
+ Clinical Remarks
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/mcc/resources/queries/study/clinremarks/.qview.xml b/mcc/resources/queries/study/clinremarks/.qview.xml
new file mode 100644
index 000000000..78d39cdfc
--- /dev/null
+++ b/mcc/resources/queries/study/clinremarks/.qview.xml
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/deaths.js b/mcc/resources/queries/study/deaths.js
new file mode 100644
index 000000000..9dda9861c
--- /dev/null
+++ b/mcc/resources/queries/study/deaths.js
@@ -0,0 +1,97 @@
+/*
+ * Copyright (c) 2018-2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+require("ehr/triggers").initScript(this);
+EHR.Server.Utils = require("ehr/utils").EHR.Server.Utils;
+
+var demographicsUpdates = [];
+var validIds = [];
+
+function onInit(event, helper){
+ helper.setScriptOptions({
+ requiresStatusRecalc: true
+ });
+
+ helper.decodeExtraContextProperty('deathsInTransaction');
+
+ // Cache valid Ids for check on each row
+ LABKEY.Query.selectRows({
+ requiredVersion: 9.1,
+ schemaName: 'study',
+ queryName: 'demographics',
+ columns: ['Id'],
+ scope: this,
+ success: function (results) {
+ if (!results || !results.rows || results.rows.length < 1)
+ return;
+
+ for(var i=0; i 0) {
+ console.log('updating demographics death date for ' + demographicsUpdates.length + " animals");
+ helper.getJavaHelper().updateDemographicsRecord(demographicsUpdates);
+ }
+
+ var deaths = helper.getDeaths();
+ if (deaths){
+ var ids = [];
+ for (var id in deaths){
+ ids.push(id);
+ }
+
+ if (!helper.isETL()) {
+ console.log('sending death notification');
+ helper.getJavaHelper().sendDeathNotification(ids);
+ }
+ }
+}
\ No newline at end of file
diff --git a/mcc/resources/queries/study/deaths.query.xml b/mcc/resources/queries/study/deaths.query.xml
new file mode 100644
index 000000000..25e309e6e
--- /dev/null
+++ b/mcc/resources/queries/study/deaths.query.xml
@@ -0,0 +1,93 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Time of Death
+
+
+ Type of Death
+
+ ehr_lookups
+ death_cause
+ value
+
+
+
+ Manner of Death
+
+ ehr_lookups
+ death_manner
+ value
+
+
+
+ Necropsy Case No
+ /query/executeQuery.view?schemaName=study&
+ query.queryName=Necropsies&
+ query.caseno~eq=${necropsy}&
+
+
+
+
+ 110
+ textarea
+
+
+ Cage At Time
+
+
+ Key
+ false
+ false
+ false
+ true
+
+
+
+ Tattoo/Tag Number
+
+
+ Dam (infants only)
+
+
+ Entered By
+
+
+ Room At Time
+
+
+
+
+
+ ehr_lookups
+ rooms
+ room
+
+
+
+ Death Was Not At Center
+
+
+ Final Condition
+ true
+
+ ehr_lookups
+ animal_condition
+ code
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/deaths/.qview.xml b/mcc/resources/queries/study/deaths/.qview.xml
new file mode 100644
index 000000000..fa7420819
--- /dev/null
+++ b/mcc/resources/queries/study/deaths/.qview.xml
@@ -0,0 +1,16 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/queries/study/demographics.js b/mcc/resources/queries/study/demographics.js
new file mode 100644
index 000000000..992138d43
--- /dev/null
+++ b/mcc/resources/queries/study/demographics.js
@@ -0,0 +1,23 @@
+/*
+ * Copyright (c) 2010-2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+require("ehr/triggers").initScript(this);
+
+function onInit(event, helper){
+ helper.setScriptOptions({
+ allowAnyId: true,
+ requiresStatusRecalc: false,
+ allowDatesInDistantPast: true
+ });
+}
+
+function onUpsert(helper, scriptErrors, row, oldRow){
+ //NOTE: this should be getting set by the birth, death, arrival & departure tables
+ //ALSO: it should be rare to insert directly into this table. usually this record will be created by inserting into either birth or arrival
+ if (!row.calculated_status && !helper.isETL()){
+ row.calculated_status = helper.getJavaHelper().getCalculatedStatusValue(row.Id);
+ }
+}
\ No newline at end of file
diff --git a/mcc/resources/queries/study/demographics.query.xml b/mcc/resources/queries/study/demographics.query.xml
new file mode 100644
index 000000000..48d852b41
--- /dev/null
+++ b/mcc/resources/queries/study/demographics.query.xml
@@ -0,0 +1,242 @@
+
+
+
+
+
+
+
diff --git a/mcc/resources/queries/study/parentageConflicts.sql b/mcc/resources/queries/study/parentageConflicts.sql
new file mode 100644
index 000000000..dd879cac8
--- /dev/null
+++ b/mcc/resources/queries/study/parentageConflicts.sql
@@ -0,0 +1,47 @@
+/*
+ * Copyright (c) 2013-2014 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.
+ */
+SELECT
+ p.Id,
+ p.relationship,
+
+ group_concat(distinct p.parent) as parents,
+ group_concat(distinct p.method) as method,
+ 'Duplicate Parents With Same Relationship' as type,
+ count(p.Id) as totalRecords
+
+FROM study.parentage p
+WHERE p.qcstate.publicdata = true and p.enddateCoalesced <= now()
+AND p.relationship != 'Surrogate Dam' and p.relationship != 'Foster Dam' and p.enddateCoalesced >= curdate()
+
+GROUP BY p.Id, p.relationship
+HAVING COUNT(DISTINCT p.parent) > 1
+
+-- UNION ALL
+--
+-- SELECT
+-- p.Id,
+-- p.relationship,
+-- p.parent as parents,
+-- group_concat(distinct p.method) as method,
+-- 'Duplicate Methods For The Same Parent' as type,
+-- count(p.Id) as totalRecords
+--
+-- FROM study.parentage p
+-- WHERE p.qcstate.publicdata = true and p.enddateCoalesced <= now()
+-- AND p.relationship != 'Surrogate Dam' and p.relationship != 'Foster Dam' and p.enddateCoalesced >= curdate()
+--
+-- GROUP BY p.Id, p.relationship, p.parent
+-- HAVING COUNT(distinct p.method) > 1
\ No newline at end of file
diff --git a/mcc/resources/queries/study/parentageSummary.query.xml b/mcc/resources/queries/study/parentageSummary.query.xml
new file mode 100644
index 000000000..1efefbcd2
--- /dev/null
+++ b/mcc/resources/queries/study/parentageSummary.query.xml
@@ -0,0 +1,25 @@
+
+
+
+
+
+
+
diff --git a/mcc/resources/queries/study/parentageSummary.sql b/mcc/resources/queries/study/parentageSummary.sql
new file mode 100644
index 000000000..46086a185
--- /dev/null
+++ b/mcc/resources/queries/study/parentageSummary.sql
@@ -0,0 +1,36 @@
+/*
+ * Copyright (c) 2013-2017 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.
+ */
+SELECT
+ p.Id,
+ p.date,
+ p.parent,
+ p.relationship,
+ p.method
+
+FROM study.parentage p
+WHERE p.qcstate.publicdata = true and p.enddateCoalesced <= now()
+
+UNION ALL
+
+SELECT
+ b.Id,
+ b.date,
+ b.dam,
+ 'Dam' as relationship,
+ 'Observed' as method
+
+FROM study.birth b
+WHERE b.dam is not null and b.qcstate.publicdata = true
\ No newline at end of file
diff --git a/mcc/resources/queries/study/samples.js b/mcc/resources/queries/study/samples.js
new file mode 100644
index 000000000..64a117a3e
--- /dev/null
+++ b/mcc/resources/queries/study/samples.js
@@ -0,0 +1,7 @@
+/*
+ * Copyright (c) 2011-2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+require("ehr/triggers").initScript(this);
\ No newline at end of file
diff --git a/mcc/resources/queries/study/samples.query.xml b/mcc/resources/queries/study/samples.query.xml
new file mode 100644
index 000000000..9e0f58f4c
--- /dev/null
+++ b/mcc/resources/queries/study/samples.query.xml
@@ -0,0 +1,70 @@
+
+
+
+
+
diff --git a/mcc/resources/referenceStudy/study.xml b/mcc/resources/referenceStudy/study.xml
new file mode 100644
index 000000000..8f84d3259
--- /dev/null
+++ b/mcc/resources/referenceStudy/study.xml
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/mcc/resources/referenceStudy/studyPolicy.xml b/mcc/resources/referenceStudy/studyPolicy.xml
new file mode 100644
index 000000000..61b6c973c
--- /dev/null
+++ b/mcc/resources/referenceStudy/studyPolicy.xml
@@ -0,0 +1,10 @@
+
+
+ ADVANCED_WRITE
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/schemas/dbscripts/postgresql/mcc-0.00-20.000.sql b/mcc/resources/schemas/dbscripts/postgresql/mcc-0.00-20.000.sql
new file mode 100644
index 000000000..53628e9d3
--- /dev/null
+++ b/mcc/resources/schemas/dbscripts/postgresql/mcc-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 Mcc module here
+-- All SQL VIEW definitions should be created in mcc-create.sql and dropped in mcc-drop.sql
+CREATE SCHEMA mcc;
diff --git a/mcc/resources/schemas/dbscripts/postgresql/mcc-20.000-20.001.sql b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.000-20.001.sql
new file mode 100644
index 000000000..567bfef27
--- /dev/null
+++ b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.000-20.001.sql
@@ -0,0 +1,18 @@
+CREATE TABLE mcc.userRequests (
+ rowid serial,
+ email varchar(1000),
+ firstName varchar(1000),
+ lastName varchar(1000),
+ title varchar(1000),
+ institution varchar(1000),
+ reason varchar(4000),
+ userid userid,
+
+ container entityid,
+ created timestamp,
+ createdby userid,
+ modified timestamp,
+ modifiedby userid,
+
+ CONSTRAINT PK_userRequests PRIMARY KEY (rowid)
+);
\ No newline at end of file
diff --git a/mcc/resources/schemas/dbscripts/sqlserver/mcc-0.00-20.000.sql b/mcc/resources/schemas/dbscripts/sqlserver/mcc-0.00-20.000.sql
new file mode 100644
index 000000000..5609630ff
--- /dev/null
+++ b/mcc/resources/schemas/dbscripts/sqlserver/mcc-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 Mcc module here
+-- All SQL VIEW definitions should be created in mcc-create.sql and dropped in mcc-drop.sql
+CREATE SCHEMA mcc;
+GO
\ No newline at end of file
diff --git a/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.000-20.001.sql b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.000-20.001.sql
new file mode 100644
index 000000000..de27af5ef
--- /dev/null
+++ b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.000-20.001.sql
@@ -0,0 +1,18 @@
+CREATE TABLE mcc.userRequests (
+ rowid int identity(1,1),
+ email varchar(1000),
+ firstName varchar(1000),
+ lastName varchar(1000),
+ title varchar(1000),
+ institution varchar(1000),
+ reason varchar(4000),
+ userid userid,
+
+ container entityid,
+ created datetime,
+ createdby userid,
+ modified datetime,
+ modifiedby userid,
+
+ CONSTRAINT PK_userRequests PRIMARY KEY (rowid)
+);
\ No newline at end of file
diff --git a/mcc/resources/schemas/mcc.xml b/mcc/resources/schemas/mcc.xml
new file mode 100644
index 000000000..e69524513
--- /dev/null
+++ b/mcc/resources/schemas/mcc.xml
@@ -0,0 +1,108 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/_footer.html b/mcc/resources/views/_footer.html
new file mode 100644
index 000000000..93de7faf0
--- /dev/null
+++ b/mcc/resources/views/_footer.html
@@ -0,0 +1,3 @@
+
+ The MCC is supported by NIH/BRAIN Initiative U24 XXXXXXXXX
+
\ No newline at end of file
diff --git a/mcc/resources/views/about.html b/mcc/resources/views/about.html
new file mode 100644
index 000000000..436f532b2
--- /dev/null
+++ b/mcc/resources/views/about.html
@@ -0,0 +1,3 @@
+MCC is supported by NIH U24 xxxxxxx.
+
+Please remember to cite this funding source in all publications that make use of MCC data.
\ No newline at end of file
diff --git a/mcc/resources/views/about.view.xml b/mcc/resources/views/about.view.xml
new file mode 100644
index 000000000..48ca9ced8
--- /dev/null
+++ b/mcc/resources/views/about.view.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/about.webpart.xml b/mcc/resources/views/about.webpart.xml
new file mode 100644
index 000000000..f40c189c7
--- /dev/null
+++ b/mcc/resources/views/about.webpart.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/contact.html b/mcc/resources/views/contact.html
new file mode 100644
index 000000000..714f95170
--- /dev/null
+++ b/mcc/resources/views/contact.html
@@ -0,0 +1,75 @@
+
\ No newline at end of file
diff --git a/mcc/resources/views/contact.view.xml b/mcc/resources/views/contact.view.xml
new file mode 100644
index 000000000..0fc3bfa31
--- /dev/null
+++ b/mcc/resources/views/contact.view.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/dashboard.html b/mcc/resources/views/dashboard.html
new file mode 100644
index 000000000..a50a225e3
--- /dev/null
+++ b/mcc/resources/views/dashboard.html
@@ -0,0 +1,31 @@
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/dashboard.view.xml b/mcc/resources/views/dashboard.view.xml
new file mode 100644
index 000000000..6779a9525
--- /dev/null
+++ b/mcc/resources/views/dashboard.view.xml
@@ -0,0 +1,11 @@
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/dashboard.webpart.xml b/mcc/resources/views/dashboard.webpart.xml
new file mode 100644
index 000000000..4e56bf8c1
--- /dev/null
+++ b/mcc/resources/views/dashboard.webpart.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/helpMenu.html b/mcc/resources/views/helpMenu.html
new file mode 100644
index 000000000..932f848cc
--- /dev/null
+++ b/mcc/resources/views/helpMenu.html
@@ -0,0 +1 @@
+We'd love to hear your feedback! Click here to send a help or feature request, or email mcc@ohsu.edu for any questions.
\ No newline at end of file
diff --git a/mcc/resources/views/helpMenu.view.xml b/mcc/resources/views/helpMenu.view.xml
new file mode 100644
index 000000000..3960a69c1
--- /dev/null
+++ b/mcc/resources/views/helpMenu.view.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/helpMenu.webpart.xml b/mcc/resources/views/helpMenu.webpart.xml
new file mode 100644
index 000000000..3f4624d6a
--- /dev/null
+++ b/mcc/resources/views/helpMenu.webpart.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/login.html b/mcc/resources/views/login.html
new file mode 100644
index 000000000..71bcbf7d3
--- /dev/null
+++ b/mcc/resources/views/login.html
@@ -0,0 +1,40 @@
+
+
+
+
Or Sign In using:
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/login.view.xml b/mcc/resources/views/login.view.xml
new file mode 100644
index 000000000..7ce47abe2
--- /dev/null
+++ b/mcc/resources/views/login.view.xml
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/overview.html b/mcc/resources/views/overview.html
new file mode 100644
index 000000000..f03b886bc
--- /dev/null
+++ b/mcc/resources/views/overview.html
@@ -0,0 +1 @@
+This will hold the overview information for MCC.
\ No newline at end of file
diff --git a/mcc/resources/views/overview.view.xml b/mcc/resources/views/overview.view.xml
new file mode 100644
index 000000000..f9e80a68a
--- /dev/null
+++ b/mcc/resources/views/overview.view.xml
@@ -0,0 +1,10 @@
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/overview.webpart.xml b/mcc/resources/views/overview.webpart.xml
new file mode 100644
index 000000000..c81f56bb6
--- /dev/null
+++ b/mcc/resources/views/overview.webpart.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/views/requestLogin.html b/mcc/resources/views/requestLogin.html
new file mode 100644
index 000000000..6c3b1fb7f
--- /dev/null
+++ b/mcc/resources/views/requestLogin.html
@@ -0,0 +1,117 @@
+
\ No newline at end of file
diff --git a/mcc/resources/views/requestLogin.view.xml b/mcc/resources/views/requestLogin.view.xml
new file mode 100644
index 000000000..13c485f9f
--- /dev/null
+++ b/mcc/resources/views/requestLogin.view.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mcc/resources/web/mcc/Security.js b/mcc/resources/web/mcc/Security.js
new file mode 100644
index 000000000..5ab385833
--- /dev/null
+++ b/mcc/resources/web/mcc/Security.js
@@ -0,0 +1,49 @@
+Ext4.namespace('MCC.Security');
+
+MCC.Security = new function(){
+ return {
+ approveUserRequests: function(dataRegionName){
+ var dr = LABKEY.DataRegions[dataRegionName];
+ if (!dr){
+ alert('Unable to find DataRegion with name: ' + dataRegionName);
+ return;
+ }
+
+ var rowIds = dr.getChecked();
+ if (!rowIds.length){
+ alert('Must select one or more rows');
+ return;
+ }
+
+ Ext4.Msg.confirm('Approve Requests', 'You are able to approve ' + rowIds.length + ' user requests. Continue?', function(val){
+ if (val === 'yes'){
+ Ext4.Msg.wait('Loading...');
+ LABKEY.Ajax.request({
+ method: 'POST',
+ url: LABKEY.ActionURL.buildURL('mcc', 'approveUserRequests'),
+ params: {
+ requestIds: rowIds
+ },
+ success: function(){
+ Ext4.Msg.hide();
+ Ext4.Msg.alert('Success', 'Requests approved!', function(){
+ //note: drop view, so we see the newly added user(s)
+ LABKEY.DataRegions[dataRegionName].changeView(null);
+ });
+ },
+ failure: LDK.Utils.getErrorCallback({
+ showAlertOnError: false,
+ scope: this,
+ callback: function(responseObj){
+ if (responseObj.errorMsg){
+ Ext4.Msg.alert('Error', responseObj.errorMsg);
+ }
+ }
+ })
+ });
+
+ }
+ }, this);
+ }
+ }
+};
\ No newline at end of file
diff --git a/mcc/resources/web/mcc/dashboard.js b/mcc/resources/web/mcc/dashboard.js
new file mode 100644
index 000000000..1a387e0c7
--- /dev/null
+++ b/mcc/resources/web/mcc/dashboard.js
@@ -0,0 +1,20 @@
+var MCC = {};
+
+MCC.Dashboard = new function() {
+ return {
+ loadDataAndRender: function (wrapperDivId) {
+ LABKEY.Query.selectRows({
+ schemaName: 'study',
+ queryName: 'demographics',
+ columns: 'Id,birth,death,gender,species,Id/age/AgeFriendly',
+ success: function(results) {
+ console.log(results.rows);
+ },
+ failure: function(response) {
+ alert('It didnt work!');
+ },
+ scope: this
+ });
+ }
+ }
+};
diff --git a/mcc/src/org/labkey/mcc/MccController.java b/mcc/src/org/labkey/mcc/MccController.java
new file mode 100644
index 000000000..ea84cef04
--- /dev/null
+++ b/mcc/src/org/labkey/mcc/MccController.java
@@ -0,0 +1,523 @@
+/*
+ * 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.mcc;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.labkey.api.action.ApiSimpleResponse;
+import org.labkey.api.action.MutatingApiAction;
+import org.labkey.api.action.SpringActionController;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.CoreSchema;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.module.AllowedDuringUpgrade;
+import org.labkey.api.query.DetailsURL;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.IgnoresTermsOfUse;
+import org.labkey.api.security.MutableSecurityPolicy;
+import org.labkey.api.security.RequiresNoPermission;
+import org.labkey.api.security.RequiresPermission;
+import org.labkey.api.security.SecurityManager;
+import org.labkey.api.security.SecurityPolicyManager;
+import org.labkey.api.security.User;
+import org.labkey.api.security.UserManager;
+import org.labkey.api.security.ValidEmail;
+import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.security.roles.ReaderRole;
+import org.labkey.api.settings.AppProps;
+import org.labkey.api.settings.LookAndFeelProperties;
+import org.labkey.api.util.ConfigurationException;
+import org.labkey.api.util.ExceptionUtil;
+import org.labkey.api.util.MailHelper;
+import org.labkey.api.util.PageFlowUtil;
+import org.springframework.validation.BindException;
+import org.springframework.validation.Errors;
+
+import javax.mail.Address;
+import javax.mail.Message;
+import javax.mail.internet.InternetAddress;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class MccController extends SpringActionController
+{
+ private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(MccController.class);
+ public static final String NAME = "mcc";
+
+ private static final Logger _log = LogManager.getLogger(MccController.class);
+
+ public MccController()
+ {
+ setActionResolver(_actionResolver);
+ }
+
+ @RequiresNoPermission
+ @IgnoresTermsOfUse
+ @AllowedDuringUpgrade
+ public class RequestUserAction extends MutatingApiAction
+ {
+ @Override
+ public void validateForm(RequestUserForm form, Errors errors)
+ {
+ Container mccContainer = MccManager.get().getMCCContainer();
+ if (mccContainer == null)
+ {
+ errors.reject(ERROR_MSG, "The MCC project has not been set on this server. This is an administrator error.");
+ return;
+ }
+
+ if (StringUtils.isEmpty(form.getEmail()) || StringUtils.isEmpty(form.getEmailConfirmation()))
+ {
+ errors.reject(ERROR_REQUIRED, "No email address provided");
+ }
+ else if (StringUtils.isEmpty(form.getFirstName()) || StringUtils.isEmpty(form.getLastName()) || StringUtils.isEmpty(form.getTitle()) || StringUtils.isEmpty(form.getInstitution()) || StringUtils.isEmpty(form.getReason()))
+ {
+ errors.reject(ERROR_REQUIRED, "You must provide your first and last name, title, institution, and reason for requesting access");
+ }
+ else
+ {
+ try
+ {
+ ValidEmail email = new ValidEmail(form.getEmail());
+ if (!form.getEmail().equals(form.getEmailConfirmation()))
+ {
+ errors.reject(ERROR_MSG, "The email addresses you have entered do not match. Please verify your email addresses below.");
+ }
+
+ TableInfo ti = MccSchema.getInstance().getSchema().getTable(MccSchema.TABLE_USER_REQUESTS);
+
+ //first check if this email exists:
+ SimpleFilter filter = new SimpleFilter(FieldKey.fromString("email"), form.getEmail());
+ filter.addCondition(FieldKey.fromString("container"), mccContainer.getId());
+ if (new TableSelector(ti, filter, null).exists())
+ {
+ errors.reject(ERROR_MSG, "A login has already been requested for this email. You should receive a reply shortly from the site administrator.");
+ }
+ }
+ catch (ValidEmail.InvalidEmailException e)
+ {
+ errors.reject(ERROR_MSG, "Your email address is not valid. Please verify your email address below.");
+ }
+ }
+ }
+
+ @Override
+ public Object execute(RequestUserForm form, BindException errors) throws Exception
+ {
+ ApiSimpleResponse response = new ApiSimpleResponse();
+
+ try
+ {
+ TableInfo ti = MccSchema.getInstance().getSchema().getTable(MccSchema.TABLE_USER_REQUESTS);
+ Map row = new HashMap<>();
+ row.put("email", form.getEmail());
+ row.put("firstName", form.getFirstName());
+ row.put("lastName", form.getLastName());
+ row.put("title", form.getTitle());
+ row.put("institution", form.getInstitution());
+ row.put("reason", form.getReason());
+ row.put("container", MccManager.get().getMCCContainer().getId());
+
+ Table.insert(UserManager.getGuestUser(), ti, row);
+
+ Set users = MccManager.get().getNotificationUsers();
+ if (users != null && !users.isEmpty())
+ {
+ try
+ {
+ Set emails = new HashSet<>();
+ for (User u : users)
+ {
+ emails.add(new InternetAddress(u.getEmail()));
+ }
+
+ MailHelper.MultipartMessage mail = MailHelper.createMultipartMessage();
+ Container c = MccManager.get().getMCCContainer();
+ if (c == null)
+ {
+ c = getContainer();
+ _log.warn("MCC container was not set, using: " + c.getPath());
+ }
+
+ DetailsURL url = DetailsURL.fromString("/query/executeQuery.view?schemaName=mcc&query.queryName=userRequests&query.viewName=Pending Requests", c);
+ mail.setEncodedHtmlContent("A user requested an account on MCC. Click here to view/approve this request");
+ mail.setFrom(getReplyEmail(getContainer()));
+ mail.setSubject("MCC Account Request");
+ mail.addRecipients(Message.RecipientType.TO, emails.toArray(new Address[0]));
+
+ MailHelper.send(mail, getUser(), c);
+ }
+ catch (Exception e)
+ {
+ ExceptionUtil.logExceptionToMothership(null, e);
+ }
+ }
+
+
+ }
+ catch (ConfigurationException e)
+ {
+ errors.reject(ERROR_MSG, "There was a problem sending the registration email. Please contact your administrator.");
+ _log.error("Error adding self registered user", e);
+ }
+
+ response.put("success", !errors.hasErrors());
+ if (!errors.hasErrors())
+ response.put("email", form.getEmail());
+
+ return response;
+ }
+ }
+
+ public static class RequestUserForm extends Object
+ {
+ private String email;
+ private String emailConfirmation;
+ private String firstName;
+ private String lastName;
+ private String title;
+ private String institution;
+ private String reason;
+
+ public void setEmail(String email)
+ {
+ this.email = email;
+ }
+
+ public String getEmail()
+ {
+ return this.email;
+ }
+
+ public void setEmailConfirmation(String email)
+ {
+ this.emailConfirmation = email;
+ }
+
+ public String getEmailConfirmation()
+ {
+ return this.emailConfirmation;
+ }
+
+ public String getFirstName()
+ {
+ return firstName;
+ }
+
+ public void setFirstName(String firstName)
+ {
+ this.firstName = firstName;
+ }
+
+ public String getLastName()
+ {
+ return lastName;
+ }
+
+ public void setLastName(String lastName)
+ {
+ this.lastName = lastName;
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+
+ public void setTitle(String title)
+ {
+ this.title = title;
+ }
+
+ public String getInstitution()
+ {
+ return institution;
+ }
+
+ public void setInstitution(String institution)
+ {
+ this.institution = institution;
+ }
+
+ public String getReason()
+ {
+ return reason;
+ }
+
+ public void setReason(String reason)
+ {
+ this.reason = reason;
+ }
+ }
+
+ @RequiresPermission(AdminPermission.class)
+ public class ApproveUserRequestsAction extends MutatingApiAction
+ {
+ @Override
+ public void validateForm(ApproveUserRequestsForm form, Errors errors)
+ {
+ Container mccContainer = MccManager.get().getMCCContainer();
+ if (mccContainer == null)
+ {
+ errors.reject(ERROR_MSG, "The MCC project has not been set on this server. This is an administrator error.");
+ return;
+ }
+
+ if (form.getRequestIds() == null || form.getRequestIds().length == 0)
+ {
+ errors.reject(ERROR_MSG, "No request IDs provided");
+ }
+
+ TableInfo ti = MccSchema.getInstance().getSchema().getTable(MccSchema.TABLE_USER_REQUESTS);
+ for (int requestId : form.getRequestIds())
+ {
+ TableSelector ts = new TableSelector(ti, PageFlowUtil.set("userId"), new SimpleFilter(FieldKey.fromString("rowId"), requestId), null);
+ if (!ts.exists())
+ {
+ errors.reject(ERROR_MSG, "No request found for request ID: " + requestId);
+ break;
+ }
+ }
+ }
+
+ @Override
+ public Object execute(ApproveUserRequestsForm form, BindException errors) throws Exception
+ {
+ ApiSimpleResponse response = new ApiSimpleResponse();
+ MutableSecurityPolicy policy = new MutableSecurityPolicy(MccManager.get().getMCCContainer().getPolicy());
+ List newUserStatusList = new ArrayList<>();
+ List existingUsersGivenAccess = new ArrayList<>();
+ try (DbScope.Transaction transaction = CoreSchema.getInstance().getScope().ensureTransaction())
+ {
+ TableInfo ti = MccSchema.getInstance().getSchema().getTable(MccSchema.TABLE_USER_REQUESTS);
+ for (int requestId : form.getRequestIds())
+ {
+ TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowId"), requestId), null);
+ Map map = ts.getMap(requestId);
+
+ User u;
+ if (map.get("userId") != null)
+ {
+ Integer userId = (Integer)map.get("userId");
+ u = UserManager.getUser(userId);
+ existingUsersGivenAccess.add(u);
+ }
+ else
+ {
+ ValidEmail ve = new ValidEmail((String)map.get("email"));
+ u = UserManager.getUser(ve);
+ if (u != null)
+ {
+ existingUsersGivenAccess.add(u);
+ }
+ else
+ {
+ SecurityManager.NewUserStatus st = SecurityManager.addUser(ve, getUser());
+ u = st.getUser();
+ u.setFirstName((String)map.get("firstName"));
+ u.setLastName((String)map.get("lastName"));
+ UserManager.updateUser(getUser(), u);
+
+ if (st.isLdapEmail())
+ {
+ existingUsersGivenAccess.add(st.getUser());
+ }
+ else
+ {
+ newUserStatusList.add(st);
+ }
+ }
+ }
+
+ Map row = new HashMap<>();
+ row.put("rowId", requestId);
+ row.put("userId", u.getUserId());
+ Table.update(getUser(), ti, row, requestId);
+
+ if (!policy.hasPermission(u, ReadPermission.class))
+ {
+ policy.addRoleAssignment(u, ReaderRole.class);
+ }
+ else
+ {
+ _log.info("user already has read permission on MCC container: " + u.getDisplayName(getUser()));
+ }
+ }
+
+ SecurityPolicyManager.savePolicy(policy);
+
+ transaction.commit();
+ }
+
+ //send emails:
+ for (SecurityManager.NewUserStatus st : newUserStatusList)
+ {
+ SecurityManager.sendRegistrationEmail(getViewContext(), st.getEmail(), null, st, null);
+ }
+
+ for (User u : existingUsersGivenAccess)
+ {
+ Container mccContainer = MccManager.get().getMCCContainer();
+ boolean isLDAP = SecurityManager.isLdapEmail(new ValidEmail(u.getEmail()));
+
+ MailHelper.MultipartMessage mail = MailHelper.createMultipartMessage();
+ mail.setEncodedHtmlContent("Your account request has been approved for MCC! " + "Click here to access the site." + (isLDAP ? " Use your normal OHSU email/password to login." : ""));
+ mail.setFrom(getReplyEmail(getContainer()));
+ mail.setSubject("MCC Account Request");
+ mail.addRecipients(Message.RecipientType.TO, u.getEmail());
+
+ MailHelper.send(mail, getUser(), getContainer());
+ }
+
+ response.put("success", !errors.hasErrors());
+
+ return response;
+ }
+ }
+
+ private String getReplyEmail(Container c)
+ {
+ LookAndFeelProperties lfp = LookAndFeelProperties.getInstance(getContainer());
+ String email = lfp.getSystemEmailAddress();
+ if (email == null)
+ {
+ return AppProps.getInstance().getAdministratorContactEmail(true);
+ }
+
+ return email;
+ }
+
+ public static class ApproveUserRequestsForm
+ {
+ private int[] requestIds;
+
+ public int[] getRequestIds()
+ {
+ return requestIds;
+ }
+
+ public void setRequestIds(int[] requestIds)
+ {
+ this.requestIds = requestIds;
+ }
+ }
+
+ @RequiresNoPermission
+ @IgnoresTermsOfUse
+ @AllowedDuringUpgrade
+ public class RequestHelpAction extends MutatingApiAction
+ {
+ @Override
+ public void validateForm(RequestHelpForm form, Errors errors)
+ {
+ Container mccContainer = MccManager.get().getMCCContainer();
+ if (mccContainer == null)
+ {
+ errors.reject(ERROR_MSG, "The MCC project has not been set on this server. This is an administrator error.");
+ return;
+ }
+
+ if (StringUtils.isEmpty(form.getEmail()) || StringUtils.isEmpty(form.getComment()))
+ {
+ errors.reject(ERROR_REQUIRED, "Must provide both an email address and question/comment");
+ }
+ else
+ {
+ try
+ {
+ new ValidEmail(form.getEmail());
+ }
+ catch (ValidEmail.InvalidEmailException e)
+ {
+ errors.reject(ERROR_MSG, "Your email address is not valid. Please verify your email address below.");
+ }
+ }
+ }
+
+ @Override
+ public Object execute(RequestHelpForm form, BindException errors) throws Exception
+ {
+ Set users = MccManager.get().getNotificationUsers();
+ if (users != null && !users.isEmpty())
+ {
+ try
+ {
+ Set emails = new HashSet<>();
+ for (User u : users)
+ {
+ emails.add(new InternetAddress(u.getEmail()));
+ }
+
+ MailHelper.MultipartMessage mail = MailHelper.createMultipartMessage();
+ mail.setEncodedHtmlContent("A support request was submitted from MCC by: " + form.getEmail() + "
Message: " + form.getComment());
+ mail.setFrom(form.getEmail());
+ mail.setSubject("MCC Help Request");
+ mail.addRecipients(Message.RecipientType.TO, emails.toArray(new Address[0]));
+
+ MailHelper.send(mail, getUser(), getContainer());
+ }
+ catch (Exception e)
+ {
+ ExceptionUtil.logExceptionToMothership(null, e);
+ }
+ }
+ else
+ {
+ _log.error("A help request was received by MCC, but the admin emails have not been configured. The request from: " + form.getEmail());
+ _log.error(form.getComment());
+ }
+
+ return new ApiSimpleResponse("success", true);
+ }
+ }
+
+ public static class RequestHelpForm
+ {
+ private String _email;
+ private String _comment;
+
+ public String getEmail()
+ {
+ return _email;
+ }
+
+ public void setEmail(String email)
+ {
+ _email = email;
+ }
+
+ public String getComment()
+ {
+ return _comment;
+ }
+
+ public void setComment(String comment)
+ {
+ _comment = comment;
+ }
+ }
+}
diff --git a/mcc/src/org/labkey/mcc/MccManager.java b/mcc/src/org/labkey/mcc/MccManager.java
new file mode 100644
index 000000000..d0f657de9
--- /dev/null
+++ b/mcc/src/org/labkey/mcc/MccManager.java
@@ -0,0 +1,102 @@
+/*
+ * 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.mcc;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.module.Module;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.module.ModuleProperty;
+import org.labkey.api.security.User;
+import org.labkey.api.security.UserManager;
+import org.labkey.api.security.ValidEmail;
+
+import java.util.HashSet;
+import java.util.Set;
+
+public class MccManager
+{
+ private static final Logger _log = LogManager.getLogger(MccManager.class);
+
+ public static final String ContainerPropName = "MCCContainer";
+ public static final String NotifyPropName = "MCCContactUsers";
+
+ private static final MccManager _instance = new MccManager();
+
+ private MccManager()
+ {
+ // prevent external construction with a private default constructor
+ }
+
+ public static MccManager get()
+ {
+ return _instance;
+ }
+
+ public Container getMCCContainer()
+ {
+ Module m = ModuleLoader.getInstance().getModule(MccModule.NAME);
+ ModuleProperty mp = m.getModuleProperties().get(MccManager.ContainerPropName);
+ String path = mp.getEffectiveValue(ContainerManager.getRoot());
+ if (path == null)
+ return null;
+
+ return ContainerManager.getForPath(path);
+ }
+
+ public Set getNotificationUsers()
+ {
+ Module m = ModuleLoader.getInstance().getModule(MccModule.NAME);
+ ModuleProperty mp = m.getModuleProperties().get(MccManager.NotifyPropName);
+ String userNames = mp.getEffectiveValue(ContainerManager.getRoot());
+ userNames = StringUtils.trimToNull(userNames);
+ if (userNames == null)
+ return null;
+
+ Set ret = new HashSet<>();
+ for (String username : userNames.split(","))
+ {
+ User u = UserManager.getUserByDisplayName(username);
+ if (u == null)
+ {
+ try
+ {
+ u = UserManager.getUser(new ValidEmail(username));
+ }
+ catch (ValidEmail.InvalidEmailException e)
+ {
+ //ignore
+ }
+ }
+
+ if (u == null)
+ {
+ _log.error("Unknown user registered for MCC notifcations: " + username);
+ }
+
+ if (u != null)
+ {
+ ret.add(u);
+ }
+ }
+
+ return ret;
+ }
+}
\ No newline at end of file
diff --git a/mcc/src/org/labkey/mcc/MccModule.java b/mcc/src/org/labkey/mcc/MccModule.java
new file mode 100644
index 000000000..ea28010a7
--- /dev/null
+++ b/mcc/src/org/labkey/mcc/MccModule.java
@@ -0,0 +1,90 @@
+/*
+ * 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.mcc;
+
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.ehr.EHRService;
+import org.labkey.api.ldk.ExtendedSimpleModule;
+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 MccModule extends ExtendedSimpleModule
+{
+ public static final String NAME = "MCC";
+
+ @Override
+ public String getName()
+ {
+ return NAME;
+ }
+
+ @Override
+ public @Nullable Double getSchemaVersion()
+ {
+ return 20.001;
+ }
+
+ @Override
+ public boolean hasScripts()
+ {
+ return true;
+ }
+
+ @Override
+ @NotNull
+ protected Collection createWebPartFactories()
+ {
+ return Collections.emptyList();
+ }
+
+ @Override
+ protected void init()
+ {
+ addController(MccController.NAME, MccController.class);
+ }
+
+ @Override
+ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
+ {
+ registerEHRResources();
+ }
+
+ @Override
+ @NotNull
+ public Collection getSummary(Container c)
+ {
+ return Collections.emptyList();
+ }
+
+ @Override
+ @NotNull
+ public Set getSchemaNames()
+ {
+ return Collections.singleton(MccSchema.NAME);
+ }
+
+ private void registerEHRResources()
+ {
+ EHRService.get().registerModule(this);
+ }
+}
\ No newline at end of file
diff --git a/mcc/src/org/labkey/mcc/MccSchema.java b/mcc/src/org/labkey/mcc/MccSchema.java
new file mode 100644
index 000000000..be31ef6f1
--- /dev/null
+++ b/mcc/src/org/labkey/mcc/MccSchema.java
@@ -0,0 +1,51 @@
+/*
+ * 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.mcc;
+
+import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.dialect.SqlDialect;
+
+public class MccSchema
+{
+ private static final MccSchema _instance = new MccSchema();
+ public static final String NAME = "mcc";
+
+ public static final String TABLE_USER_REQUESTS = "userRequests";
+
+ public static MccSchema getInstance()
+ {
+ return _instance;
+ }
+
+ private MccSchema()
+ {
+ // private constructor to prevent instantiation from
+ // outside this class: this singleton should only be
+ // accessed via org.labkey.mcc.MccSchema.getInstance()
+ }
+
+ public DbSchema getSchema()
+ {
+ return DbSchema.get(NAME, DbSchemaType.Module);
+ }
+
+ public SqlDialect getSqlDialect()
+ {
+ return getSchema().getSqlDialect();
+ }
+}
diff --git a/mcc/src/org/labkey/mcc/query/UserRequestCustomizer.java b/mcc/src/org/labkey/mcc/query/UserRequestCustomizer.java
new file mode 100644
index 000000000..7f789d464
--- /dev/null
+++ b/mcc/src/org/labkey/mcc/query/UserRequestCustomizer.java
@@ -0,0 +1,44 @@
+package org.labkey.mcc.query;
+
+import org.labkey.api.data.AbstractTableInfo;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.TableCustomizer;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.ldk.LDKService;
+import org.labkey.api.query.ExprColumn;
+
+public class UserRequestCustomizer implements TableCustomizer
+{
+ @Override
+ public void customize(TableInfo tableInfo)
+ {
+ LDKService.get().getDefaultTableCustomizer().customize(tableInfo);
+
+ if (tableInfo instanceof AbstractTableInfo)
+ {
+ addUserCol((AbstractTableInfo)tableInfo);
+ }
+ }
+
+ public void addUserCol(AbstractTableInfo ti)
+ {
+ String colName = "hasAccess";
+ if (ti.getColumn(colName) != null)
+ {
+ return;
+ }
+
+ ExprColumn col = new ExprColumn(ti, colName, new SQLFragment("(CASE WHEN (exists (" +
+ "select u.rowid from mcc.userrequests u " +
+ "left join core.RoleAssignments ra " +
+ "on (u.userid = ra.UserId AND u.container = ra.ResourceId) " +
+ "WHERE ra.Role = 'org.labkey.api.security.roles.ReaderRole' AND u.rowid = " + ExprColumn.STR_TABLE_ALIAS + ".rowid " +
+ ")) THEN " + ti.getSqlDialect().getBooleanTRUE() + " ELSE " + ti.getSqlDialect().getBooleanFALSE() + " END)"), JdbcType.BOOLEAN, ti.getColumn("userId"));
+ col.setLabel("Has MCC Access?");
+ col.setReadOnly(true);
+ col.setIsUnselectable(true);
+ col.setUserEditable(false);
+ ti.addColumn(col);
+ }
+}
diff --git a/mcc/test/src/org/labkey/test/components/mcc/MccWebPart.java b/mcc/test/src/org/labkey/test/components/mcc/MccWebPart.java
new file mode 100644
index 000000000..a48615354
--- /dev/null
+++ b/mcc/test/src/org/labkey/test/components/mcc/MccWebPart.java
@@ -0,0 +1,69 @@
+/*
+ * 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.test.components.mcc;
+
+import org.labkey.test.Locator;
+import org.labkey.test.components.BodyWebPart;
+import org.labkey.test.components.html.Input;
+import org.labkey.test.pages.LabKeyPage;
+import org.openqa.selenium.WebDriver;
+import org.openqa.selenium.WebElement;
+
+import static org.labkey.test.components.html.Input.Input;
+
+/**
+ * TODO: Component for a hypothetical webpart containing an input and a save button
+ * Component classes should handle all timing and functionality for a component
+ */
+public class MccWebPart extends BodyWebPart
+{
+ public MccWebPart(WebDriver driver)
+ {
+ this(driver, 0);
+ }
+
+ public MccWebPart(WebDriver driver, int index)
+ {
+ super(driver, "Mcc", index);
+ }
+
+ public MccWebPart setInput(String value)
+ {
+ elementCache().input.set(value);
+ // TODO: Methods that don't navigate should return this object
+ return this;
+ }
+
+ public LabKeyPage clickSave()
+ {
+ getWrapper().clickAndWait(elementCache().button);
+ // TODO: Methods that navigate should return an appropriate page object
+ return new LabKeyPage(getDriver());
+ }
+
+ @Override
+ protected ElementCache newElementCache()
+ {
+ return new ElementCache();
+ }
+
+ protected class ElementCache extends BodyWebPart.ElementCache
+ {
+ protected final WebElement button = Locator.tag("button").withText("Save").findWhenNeeded(this);
+ protected final Input input = Input(Locator.tag("input"), getDriver()).findWhenNeeded(this);
+ }
+}
\ No newline at end of file
diff --git a/mcc/test/src/org/labkey/test/pages/mcc/BeginPage.java b/mcc/test/src/org/labkey/test/pages/mcc/BeginPage.java
new file mode 100644
index 000000000..3baa4087e
--- /dev/null
+++ b/mcc/test/src/org/labkey/test/pages/mcc/BeginPage.java
@@ -0,0 +1,59 @@
+/*
+ * 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.test.pages.mcc;
+
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.WebDriverWrapper;
+import org.labkey.test.Locator;
+import org.labkey.test.WebTestHelper;
+import org.labkey.test.pages.LabKeyPage;
+import org.openqa.selenium.WebElement;
+
+public class BeginPage extends LabKeyPage
+{
+ public BeginPage(WebDriverWrapper driver)
+ {
+ super(driver);
+ }
+
+ public static BeginPage beginAt(WebDriverWrapper driver)
+ {
+ return beginAt(driver, driver.getCurrentContainerPath());
+ }
+
+ public static BeginPage beginAt(WebDriverWrapper driver, String containerPath)
+ {
+ driver.beginAt(WebTestHelper.buildURL("mcc", containerPath, "begin"));
+ return new BeginPage(driver);
+ }
+
+ public String getHelloMessage()
+ {
+ return elementCache().helloMessage.getText();
+ }
+
+ @Override
+ protected ElementCache newElementCache()
+ {
+ return new ElementCache();
+ }
+
+ protected class ElementCache extends LabKeyPage.ElementCache
+ {
+ protected final WebElement helloMessage = Locator.tagWithName("div", "helloMessage").findWhenNeeded(this);
+ }
+}
diff --git a/mcc/test/src/org/labkey/test/tests/mcc/MccTest.java b/mcc/test/src/org/labkey/test/tests/mcc/MccTest.java
new file mode 100644
index 000000000..1c53ac721
--- /dev/null
+++ b/mcc/test/src/org/labkey/test/tests/mcc/MccTest.java
@@ -0,0 +1,88 @@
+/*
+ * 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.test.tests.mcc;
+
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.TestTimeoutException;
+import org.labkey.test.categories.InDevelopment;
+import org.labkey.test.pages.mcc.BeginPage;
+
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
+@Category({InDevelopment.class})
+public class MccTest extends BaseWebDriverTest
+{
+ @Override
+ protected void doCleanup(boolean afterTest) throws TestTimeoutException
+ {
+ _containerHelper.deleteProject(getProjectName(), afterTest);
+ }
+
+ @BeforeClass
+ public static void setupProject()
+ {
+ MccTest init = (MccTest)getCurrentTest();
+
+ init.doSetup();
+ }
+
+ private void doSetup()
+ {
+ _containerHelper.createProject(getProjectName(), null);
+ }
+
+ @Before
+ public void preTest()
+ {
+ goToProjectHome();
+ }
+
+ @Test
+ public void testMccModule()
+ {
+ _containerHelper.enableModule("Mcc");
+ BeginPage beginPage = BeginPage.beginAt(this, getProjectName());
+ assertEquals(200, getResponseCode());
+ final String expectedHello = "Hello, and welcome to the Mcc module.";
+ assertEquals("Wrong hello message", expectedHello, beginPage.getHelloMessage());
+ }
+
+ @Override
+ protected BrowserType bestBrowser()
+ {
+ return BrowserType.CHROME;
+ }
+
+ @Override
+ protected String getProjectName()
+ {
+ return "MccTest Project";
+ }
+
+ @Override
+ public List getAssociatedModules()
+ {
+ return Collections.singletonList("Mcc");
+ }
+}
\ No newline at end of file
diff --git a/primeseq/build.gradle b/primeseq/build.gradle
index bd248fbf7..b172c8848 100644
--- a/primeseq/build.gradle
+++ b/primeseq/build.gradle
@@ -14,4 +14,7 @@ dependencies {
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:cluster", depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:jbrowse", depProjectConfig: "published", depExtension: "module")
+
+ BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "apiJarFile")
+ BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:dataintegration", depProjectConfig: "published", depExtension: "module")
}
diff --git a/primeseq/module.properties b/primeseq/module.properties
index 6e8b00db6..47985036b 100644
--- a/primeseq/module.properties
+++ b/primeseq/module.properties
@@ -3,5 +3,4 @@ Label: PRIMe-Seq
Description: This module contains code related to our internal server, PRIMe-Seq
License: Apache 2.0
LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-ConsolidateScripts: false
ManageVersion: false
\ No newline at end of file
diff --git a/primeseq/resources/views/geneticsMenu.html b/primeseq/resources/views/geneticsMenu.html
index 3ff3df451..5177cd413 100644
--- a/primeseq/resources/views/geneticsMenu.html
+++ b/primeseq/resources/views/geneticsMenu.html
@@ -44,7 +44,7 @@
'data-qtip="You do not have permission to view this page"',
'style="width: 300px;height: auto;" class="thumb-wrap thumb-wrap-side">',
'',
- '{title:htmlEncode}',
+ '{title:htmlEncode}',
'',
'',
'',
@@ -88,15 +88,15 @@
items: [{
title: 'Public Resources',
itemId: 'public'
- },{
- itemId: 'collaborations',
- title: 'Collaborations'
},{
title: 'Labs',
itemId: 'labs'
},{
itemId: 'internal',
title: 'Internal Projects'
+ },{
+ itemId: 'collaborations',
+ title: 'Bimber Lab Collaborations'
}]
});
diff --git a/primeseq/src/org/labkey/primeseq/PrimeseqController.java b/primeseq/src/org/labkey/primeseq/PrimeseqController.java
index bc680d82c..ee6e01d94 100644
--- a/primeseq/src/org/labkey/primeseq/PrimeseqController.java
+++ b/primeseq/src/org/labkey/primeseq/PrimeseqController.java
@@ -28,8 +28,13 @@
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.ContainerType;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SqlExecutor;
import org.labkey.api.module.Module;
import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineService;
import org.labkey.api.pipeline.PipelineUrls;
import org.labkey.api.security.RequiresPermission;
import org.labkey.api.security.RequiresSiteAdmin;
@@ -39,6 +44,7 @@
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
+import org.labkey.primeseq.pipeline.MhcMigrationPipelineJob;
import org.springframework.validation.BindException;
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;
@@ -68,7 +74,7 @@ public ApiResponse execute(Object form, BindException errors)
{
Map resultProperties = new HashMap<>();
- resultProperties.put("collaborations", getSection("/Public/Collaborations"));
+ resultProperties.put("collaborations", getSection("/Labs/Bimber/Collaborations"));
resultProperties.put("internal", getSection("/Internal"));
resultProperties.put("labs", getSection("/Labs"));
@@ -125,12 +131,6 @@ private List getSection(String path)
{
for (Container c : mainContainer.getChildren())
{
- //NOTE: unlike EHR, omit children if the current user cannot read them
- if (!c.hasPermission(getUser(), ReadPermission.class))
- {
- continue;
- }
-
JSONObject json = new JSONObject();
json.put("name", c.getName());
json.put("title", c.getTitle());
@@ -203,4 +203,239 @@ public URLHelper getSuccessURL(Object o)
}
}
+ @RequiresSiteAdmin
+ public class SyncMhcAction extends ConfirmAction
- tcrdb
- cdnas
+ singlecell
+ cdna_librariesrowidrowid
diff --git a/tcrdb/resources/assay/TCRdb/queries/Data/cDNA Info.qview.xml b/tcrdb/resources/assay/TCRdb/queries/Data/cDNA Info.qview.xml
index d8518ac12..2b3104ee9 100644
--- a/tcrdb/resources/assay/TCRdb/queries/Data/cDNA Info.qview.xml
+++ b/tcrdb/resources/assay/TCRdb/queries/Data/cDNA Info.qview.xml
@@ -2,9 +2,9 @@
-
-
-
+
+
+
diff --git a/tcrdb/resources/external/install.R b/tcrdb/resources/external/install.R
deleted file mode 100644
index 8000b3313..000000000
--- a/tcrdb/resources/external/install.R
+++ /dev/null
@@ -1 +0,0 @@
-install.packages(c("reshape2", "FField", "reshape", "gplots", "gridExtra", "circlize", "ggplot2", "grid", "VennDiagram", "ape", "MASS", "plotrix", "RColorBrewer", "scales"), dependencies=TRUE, repos='http://cran.rstudio.com')
\ No newline at end of file
diff --git a/tcrdb/resources/external/installCiteSeqCount.sh b/tcrdb/resources/external/installCiteSeqCount.sh
deleted file mode 100644
index 286748329..000000000
--- a/tcrdb/resources/external/installCiteSeqCount.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-scl enable rh-python36 bash
-virtualenv /home/groups/prime-seq/pipeline_tools/bin/primeseq-python
-source /home/groups/prime-seq/pipeline_tools/bin/primeseq-python/bin/activate
-pip install --upgrade pip
-pip install CITE-seq-Count
-
-
diff --git a/tcrdb/resources/external/scRNAseq/Seurat3.rmd b/tcrdb/resources/external/scRNAseq/Seurat3.rmd
deleted file mode 100644
index a3911a6c7..000000000
--- a/tcrdb/resources/external/scRNAseq/Seurat3.rmd
+++ /dev/null
@@ -1,183 +0,0 @@
----
-title: 'Seurat scRNA-seq Analysis'
----
-
-```{r Setup}
-
-knitr::opts_chunk$set(message=FALSE, warning=FALSE,echo=TRUE,error = FALSE)
-library(knitr)
-library(OOSAP)
-
-cores <- Sys.getenv('SEQUENCEANALYSIS_MAX_THREADS')
-if (cores != ''){
- print(paste0('Setting future::plan to ', cores, ' cores'))
- future::plan("multiprocess", workers = as.integer(cores))
- Sys.setenv('OMP_NUM_THREADS' = cores)
-} else {
- print('SEQUENCEANALYSIS_MAX_THREADS not set, will not set cores')
-}
-
-print('Updating future.globals.maxSize')
-options(future.globals.maxSize = Inf)
-
-print('Global variables: ')
-for (v in c('outPrefix', 'resolutionToUse', 'dimsToUse', 'minDimsToUse', 'doCellFilter', 'doCellCycle', 'useSCTransform', 'runSingleR', 'mergeMethod', 'skipProcessing', 'gtfFile')){
- if (exists(v)){
- print(paste0(v, ': ', get(v)))
- } else {
- print(paste0(v, ': not defined'))
- }
-}
-
-```
-
-## Prepare data
-
-```{r PreparingData, fig.width=12}
-
-rawDataSaveFile <- paste0(outPrefix, '.rawData.rds')
-seuratObjs <- list()
-if (file.exists(rawDataSaveFile)) {
- print('resuming from file')
- seuratObjs <- readRDS(rawDataSaveFile)
-} else {
- for (datasetName in names(data)) {
- print(paste0('Loading dataset: ', datasetName))
- seuratObjs[[datasetName]] <- ReadAndFilter10xData(dataDir = data[[datasetName]], datasetName = datasetName, gtfFile = gtfFile)
-
- print(seuratObjs[[datasetName]])
- }
-
- saveRDS(seuratObjs, file = rawDataSaveFile)
-}
-
-```
-
-## Merge data
-
-```{r MergeDatasets}
-
-seuratObj <- NULL
-saveFile <- paste0(outPrefix, '.seurat.rds')
-if (file.exists(saveFile)) {
- print('resuming from file')
- seuratObj <- readRDS(saveFile)
-} else {
- seuratObj <- MergeSeuratObjs(seuratObjs, metadata = data, method = mergeMethod)
- saveRDS(seuratObj, file = saveFile)
- rm(seuratObjs)
-}
-
-print(seuratObj)
-
-```
-
-## Initial Processing
-
-```{r InitialProcessing, fig.width=12}
-
-if (!skipProcessing) {
- seuratObj <- ProcessSeurat1(seuratObj, variableGeneTable = paste0(outPrefix, '.variableGenes.txt'), doCellFilter = doCellFilter, doCellCycle = doCellCycle, useSCTransform = useSCTransform, saveFile = saveFile)
-
- print(seuratObj)
-} else {
- print('Downstream processing will be skipped')
-}
-
-```
-
-## DimRedux
-
-```{r DimRedux, fig.width=12}
-
-if (!skipProcessing) {
- seuratObj <- FindClustersAndDimRedux(seuratObj, dimsToUse = dimsToUse, minDimsToUse = minDimsToUse, saveFile = saveFile)
-
- Find_Markers(seuratObj, resolutionToUse = resolutionToUse, outFile = paste0(outPrefix, '.markers.txt'), saveFileMarkers = paste0(outPrefix, '.markers.rds'))
-
- print(seuratObj)
-}
-
-```
-
-## SingleR
-
-```{r SingleR, fig.width=12}
-
-if (!skipProcessing && runSingleR) {
- tryCatch({
- seuratObj <- RunSingleR(seuratObj = seuratObj, resultTableFile = paste0(outPrefix, '.singleR.txt'))
- saveRDS(seuratObj, file = saveFile)
-
- DimPlot_SingleRClassLabs(seuratObj, plotIndividually = T)
-
- Tabulate_SingleRClassLabs(seuratObj, plotIndividually = T)
- }, error = function(e){
- print('There was an error in SingleR')
-
- saveRDS(e, file = 'error.rds')
- })
-
- print(seuratObj)
-} else {
- print('SingleR will not be run')
-}
-
-```
-
-## Phenotypes
-
-```{r Phenotypes, fig.width=12}
-
-if ( !skipProcessing ) {
- PlotImmuneMarkers(seuratObj, reductions = c('tsne', 'umap'))
-
- if (length(unique(seuratObj$BarcodePrefix)) > 1) {
- print(Seurat::DimPlot(seuratObj, reduction = 'pca', group.by = 'BarcodePrefix', label = T))
- print(Seurat::DimPlot(seuratObj, reduction = 'tsne', group.by = 'BarcodePrefix', label = T))
- print(Seurat::DimPlot(seuratObj, reduction = 'umap', group.by = 'BarcodePrefix', label = T))
-
- t <- table(Cluster = Seurat::Idents(seuratObj), Dataset = seuratObj$BarcodePrefix)
- t <- round(t / colSums(t), 2)
- knitr::kable(t)
- }
-}
-
-```
-
-## Activation
-
-```{r ActivationScore}
-
-if ( !skipProcessing ) {
- seuratObj <- ClassifySGSAndApply(seuratObj = seuratObj, geneSetName = 'HighlyActivated', geneList = OOSAP::Phenotyping_GeneList()$HighlyActivated, positivityThreshold = 0.5, saveFilePath = paste0(outPrefix, '.ha.txt'))
- saveRDS(seuratObj, file = saveFile)
-}
-
-```
-
-## Write Summary
-
-```{r Summary}
-
-saveRDS(seuratObj, file = saveFile)
-unlink(rawDataSaveFile)
-
-WriteSummaryMetrics(seuratObj, file = paste0(outPrefix, '.summary.txt'))
-
-if ( !skipProcessing ) {
- SaveDimRedux(seuratObj, file = paste0(outPrefix, '.DimReduxComps.csv'))
-}
-
-WriteCellBarcodes(seuratObj, file = paste0(outPrefix, '.cellBarcodes.csv'))
-
-```
-
-## Print Session Info
-
-```{r SessionInfo}
-
-sessionInfo()
-
-```
-
diff --git a/tcrdb/resources/external/scRNAseq/seuratWrapper.sh b/tcrdb/resources/external/scRNAseq/seuratWrapper.sh
deleted file mode 100644
index 5a6f2d81b..000000000
--- a/tcrdb/resources/external/scRNAseq/seuratWrapper.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-
-set -e
-set -u
-set -x
-
-WD=`pwd`
-HOME=`echo ~/`
-
-DOCKER=/opt/acc/sbin/exadocker
-LK_ROOT=$1
-
-RAM_OPTS=""
-ENV_OPTS=""
-if [ ! -z $SEQUENCEANALYSIS_MAX_RAM ];then
- RAM_OPTS=" --memory=${SEQUENCEANALYSIS_MAX_RAM}g"
-
- ENV_OPTS=" -e SEQUENCEANALYSIS_MAX_RAM"
-fi
-
-if [ ! -z SEQUENCEANALYSIS_MAX_THREADS ];then
- ENV_OPTS=${ENV_OPTS}" -e SEQUENCEANALYSIS_MAX_THREADS="${SEQUENCEANALYSIS_MAX_THREADS}
-fi
-
-sudo $DOCKER pull bimberlab/oosap
-
-sudo $DOCKER run --rm=true $RAM_OPTS $ENV_OPTS -v "${WD}:/work" -v "${HOME}:/homeDir" -u $UID -e USERID=$UID -w /work -e HOME=/homeDir bimberlab/oosap Rscript --vanilla script.R
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/cdnas/Assay Info.qview.xml b/tcrdb/resources/queries/singlecell/cdna_libraries/Assay Info.qview.xml
similarity index 80%
rename from tcrdb/resources/queries/tcrdb/cdnas/Assay Info.qview.xml
rename to tcrdb/resources/queries/singlecell/cdna_libraries/Assay Info.qview.xml
index 482b26d5d..109d35ad5 100644
--- a/tcrdb/resources/queries/tcrdb/cdnas/Assay Info.qview.xml
+++ b/tcrdb/resources/queries/singlecell/cdna_libraries/Assay Info.qview.xml
@@ -2,10 +2,10 @@
-
-
-
-
+
+
+
+
@@ -13,7 +13,7 @@
-
+
diff --git a/tcrdb/resources/queries/tcrdb/cdnas.js b/tcrdb/resources/queries/tcrdb/cdnas.js
deleted file mode 100644
index e465f71e1..000000000
--- a/tcrdb/resources/queries/tcrdb/cdnas.js
+++ /dev/null
@@ -1,39 +0,0 @@
-var console = require("console");
-var LABKEY = require("labkey");
-var importHelper = org.labkey.tcrdb.ImportHelper.create(LABKEY.Security.currentContainer.id, LABKEY.Security.currentUser.id, 'cdnas');
-
-var wellMap = importHelper.getInitialWells();
-
-function beforeInsert(row, errors){
- beforeUpsert(row, null, errors);
-}
-
-function beforeUpdate(row, oldRow, errors){
- beforeUpsert(row, oldRow, errors);
-}
-
-var rowIdx = -1;
-
-function beforeUpsert(row, oldRow, errors){
- //check for duplicate plate/well
- oldRow = oldRow || {};
- var rowId = row.rowId || oldRow.rowId || rowIdx;
- rowIdx--;
-
- var well = row.well || oldRow.well || '';
- if ('pool' !== well.toLowerCase()) {
- var wellArr = [(row.plateId || oldRow.plateId), well];
- var wellKey = wellArr.join('<>').toUpperCase();
- if (wellMap[wellKey] && wellMap[wellKey] !== rowId) {
- errors.well = 'Duplicate entry for plate/well: ' + wellArr.join('/');
- }
- else {
- wellMap[wellKey] = rowId;
- }
- }
-
- //Note: this will only work if the incoming row has a container property
- //if (row.sortId && !row.container){
- // row.container = importHelper.getContainerForSort(row.sortId);
- //}
-}
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/cdnas/.qview.xml b/tcrdb/resources/queries/tcrdb/cdnas/.qview.xml
deleted file mode 100644
index fafeb6227..000000000
--- a/tcrdb/resources/queries/tcrdb/cdnas/.qview.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/citeseq_panel_names.query.xml b/tcrdb/resources/queries/tcrdb/citeseq_panel_names.query.xml
deleted file mode 100644
index bf5d41a17..000000000
--- a/tcrdb/resources/queries/tcrdb/citeseq_panel_names.query.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-
-
-
-
-
-
- true
-
-
-
-
-
-
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/citeseq_panel_names.sql b/tcrdb/resources/queries/tcrdb/citeseq_panel_names.sql
deleted file mode 100644
index c4140f37f..000000000
--- a/tcrdb/resources/queries/tcrdb/citeseq_panel_names.sql
+++ /dev/null
@@ -1,6 +0,0 @@
-SELECT
- distinct name,
- count(*) as totalMarkers
-
-FROM tcrdb.citeseq_panels
-GROUP BY name
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/citeseq_panels/.qview.xml b/tcrdb/resources/queries/tcrdb/citeseq_panels/.qview.xml
deleted file mode 100644
index 570773573..000000000
--- a/tcrdb/resources/queries/tcrdb/citeseq_panels/.qview.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/hashtag_oligos.sql b/tcrdb/resources/queries/tcrdb/hashtag_oligos.sql
deleted file mode 100644
index 16e695b4c..000000000
--- a/tcrdb/resources/queries/tcrdb/hashtag_oligos.sql
+++ /dev/null
@@ -1,7 +0,0 @@
-SELECT
- b.tag_name,
- b.sequence,
- b.group_name
-
-FROM sequenceanalysis.barcodes b
-WHERE group_name IN ('5p-HTOs', 'MultiSeq Barcodes')
\ No newline at end of file
diff --git a/tcrdb/resources/queries/tcrdb/sortStatusByPlate.query.xml b/tcrdb/resources/queries/tcrdb/sortStatusByPlate.query.xml
deleted file mode 100644
index 6ea09e41f..000000000
--- a/tcrdb/resources/queries/tcrdb/sortStatusByPlate.query.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-
-
-
-