Merge remote-tracking branch 'origin/develop' into fb_event_handlers

data/GPAT/plate-metadata-1.json

@@ -1,12 +1,12 @@
 {
   "control" : {
     "positive" : {"dilution":  0.005},
-    "negative" : {"dilution":  1.0}
+    "negative" : {"dilution":  1.01}
   },
   "sample" : {
-    "SA01" : {"dilution": 1.0, "ID" : 111, "Barcode" : "BC_111", "Concentration" : 0.0125},
-    "SA02" : {"dilution": 2.0, "ID" : 222, "Barcode" : "BC_222"},
-    "SA03" : {"dilution": 3.0, "ID" : 333, "Barcode" : "BC_333"},
-    "SA04" : {"dilution": 4.0, "ID" : 444, "Barcode" : "BC_444"}
+    "SA01" : {"dilution": 1.01, "ID" : 111, "Barcode" : "BC_111", "Concentration" : 0.0125},
+    "SA02" : {"dilution": 2.01, "ID" : 222, "Barcode" : "BC_222"},
+    "SA03" : {"dilution": 3.01, "ID" : 333, "Barcode" : "BC_333"},
+    "SA04" : {"dilution": 4.01, "ID" : 444, "Barcode" : "BC_444"}
   }
 }

data/qc/build.gradle

@@ -43,13 +43,30 @@ project.tasks.register('transformJar', Jar) {
     archiveFileName.set("transform.jar")
     destinationDirectory = project.projectDir
     manifest {
-        attributes 'Implementation-Title': 'Assay Validator Jar',
+        attributes 'Implementation-Title': 'Assay Transform Testing Jar',
                 'Implementation-Version': project.version,
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayTransform'
     }
 }
 
+project.tasks.register('transformNoopJar', Jar) {
+    group = "QC"
+    description = "Builds no-op transform jar for testing assay transforms"
+
+    from sourceSets.main.output
+    from { configurations.compileClasspath.collect { it.isDirectory() ? it : zipTree(it) } }
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+    archiveFileName.set("transformNoop.jar")
+    destinationDirectory = project.projectDir
+    manifest {
+        attributes 'Implementation-Title': 'Assay No-Op Transform Jar',
+                'Implementation-Version': project.version,
+                'Built-By': System.getProperty("user.name"),
+                'Main-Class': 'org.labkey.AssayTransformNoOp'
+    }
+}
+
 project.tasks.register('transformWarningJar', Jar) {
     group = "QC"
     description = "Builds jar for doing assay transform warnings"
@@ -60,7 +77,7 @@ project.tasks.register('transformWarningJar', Jar) {
     archiveFileName.set("transformWarning.jar")
     destinationDirectory = project.projectDir
     manifest {
-        attributes 'Implementation-Title': 'Assay Validator Jar',
+        attributes 'Implementation-Title': 'Assay Transform Warning Jar',
                 'Implementation-Version': project.version,
                 'Built-By': System.getProperty("user.name"),
                 'Main-Class': 'org.labkey.AssayTransformWarning'
@@ -72,6 +89,7 @@ var jarTask = project.tasks.named('jar')
 jarTask.configure {
     dependsOn(project.tasks.validatorJar)
     dependsOn(project.tasks.transformJar)
+    dependsOn(project.tasks.transformNoopJar)
     dependsOn(project.tasks.transformWarningJar)
 }
 

data/qc/src/org/labkey/AssayTransformNoOp.java

@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2015-2019 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;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class AssayTransformNoOp extends AbstractAssayValidator
+{
+    public static void main(String[] args)
+    {
+        if (args.length < 4)
+            throw new IllegalArgumentException("Input data file not passed in");
+
+        File runProperties = new File(args[0]);
+        if (runProperties.exists())
+        {
+            AssayTransformNoOp transform = new AssayTransformNoOp();
+
+            transform.runTransform(runProperties, args[1], args[2], args[3]);
+        }
+        else
+            throw new IllegalArgumentException("Input data file does not exist");
+    }
+
+    public void runTransform(File inputFile, String username, String password, String host)
+    {
+        setEmail(username);
+        setPassword(password);
+        setHost(host);
+        parseRunProperties(inputFile);
+    }
+
+}

src/org/labkey/test/TestFileUtils.java

@@ -308,6 +308,13 @@ public static File getTestTempDir()
         return new File(buildDir, "testTemp");
     }
 
+    public static File ensureTestTempDir() throws IOException
+    {
+        File file = getTestTempDir();
+        FileUtils.forceMkdir(file);
+        return file;
+    }
+
     public static void delete(File file)
     {
         LOG.info("Deleting from filesystem: " + file.toString());

src/org/labkey/test/tests/GpatPlateTemplateTest.java

@@ -1,28 +1,39 @@
 package org.labkey.test.tests;
 
+import org.apache.commons.io.FileUtils;
 import org.jetbrains.annotations.Nullable;
+import org.json.JSONObject;
+import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.remoteapi.assay.ImportRunCommand;
+import org.labkey.remoteapi.assay.ImportRunResponse;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
 import org.labkey.test.TestTimeoutException;
 import org.labkey.test.categories.Assays;
 import org.labkey.test.categories.Daily;
+import org.labkey.test.pages.ReactAssayDesignerPage;
 import org.labkey.test.pages.assay.plate.PlateDesignerPage;
 import org.labkey.test.util.APIAssayHelper;
 import org.labkey.test.util.DataRegionTable;
+import org.labkey.test.util.QCAssayScriptHelper;
+import org.labkey.test.util.UIAssayHelper;
 
 import java.io.File;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 @Category({Assays.class, Daily.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 7)
 public class GpatPlateTemplateTest extends BaseWebDriverTest
 {
+    private static final File TRANSFORM_SCRIPT = TestFileUtils.getSampleData("qc/transformNoop.jar");
     private static final File TEST_PLATE_DATA = TestFileUtils.getSampleData("GPAT/plateData.xlsx");
+    // Issue 48470: Conversion error during assay API import with plate metadata
     private static final File TEST_PLATE_METADATA = TestFileUtils.getSampleData("GPAT/plate-metadata-1.json");
     private static final String ASSAY_NAME = "Assay with plate template";
     private static final String templateName = "GPAT";
@@ -36,12 +47,18 @@ public static void setUpProject()
 
     private void doSetup()
     {
+        new QCAssayScriptHelper(this).ensureEngineConfig();
+
         _containerHelper.createProject(getProjectName(), "Assay");
         setPipelineRoot(TestFileUtils.getSampleData("GPAT").getAbsolutePath(), false);
 
         goToProjectHome();
-        APIAssayHelper assayHelper = new APIAssayHelper(this);
-        assayHelper.createAssayWithPlateSupport(ASSAY_NAME);
+        new UIAssayHelper(this)
+                .createAssayDesign("General", ASSAY_NAME)
+                .setPlateMetadata(true)
+                // Regression check for Issue 48293: Standard Assay with Plate Metadata & Transformation Script throws an error
+                .addTransformScript(TRANSFORM_SCRIPT)
+                .clickFinish();
         createPlateTemplate(templateName, "blank", "Standard", true);
     }
 
@@ -69,6 +86,23 @@ public void doCleanup(boolean afterTest) throws TestTimeoutException
         _containerHelper.deleteProject(getProjectName(), afterTest);
     }
 
+    @Test
+    public void testApiWithPlateTemplateAndPlateMetadata() throws Exception
+    {
+        String runName = "ImportRun API with plate template and plate metadata";
+        int assayId = new APIAssayHelper(this).getIdFromAssayName(ASSAY_NAME, getProjectName());
+        File plateDataCopy = new File(TestFileUtils.ensureTestTempDir(), "API_" + TEST_PLATE_DATA.getName());
+
+        FileUtils.copyFile(TEST_PLATE_DATA, plateDataCopy);
+        ImportRunCommand importRunCommand = new ImportRunCommand(assayId, plateDataCopy);
+        importRunCommand.setProperties(Map.of("PlateTemplate", new APIAssayHelper(this).getPlateTemplateLsid(getProjectName(), templateName)));
+        importRunCommand.setPlateMetadata(new JSONObject(TestFileUtils.getFileContents(TEST_PLATE_METADATA)));
+        importRunCommand.setName(runName);
+        ImportRunResponse response = importRunCommand.execute(createDefaultConnection(), getProjectName());
+
+        Assert.assertTrue((Boolean)response.getParsedData().get("success"));
+    }
+
     @Test
     public void testWithPlateTemplateAndPlateMetadata()
     {
@@ -83,15 +117,17 @@ public void testWithPlateTemplateAndPlateMetadata()
 
         table.setFilter("Run/PlateTemplate", "Does Not Equal", templateName);
         checker().verifyEquals("Only GPAT should be present", 0, table.getDataRowCount());
+        checker().screenShotIfNewError("rowsWithoutPlateTemplate");
         table.clearAllFilters();
 
         table.setFilter("PlateData/control_well_groups", "Is Not Blank");
         checker().verifyEquals("Control well data is incorrect", Arrays.asList("positive", "negative"),
                 table.getColumnDataAsText("PlateData/control_well_groups"));
         checker().verifyEquals("Well location is incorrect", Arrays.asList("A11", "A12"),
                 table.getColumnDataAsText("WellLocation"));
-        checker().verifyEquals("Dilution is incorrect", Arrays.asList("0.005", "1.0"),
-                table.getColumnDataAsText(" PlateData/dilution"));
+        checker().verifyEquals("Dilution is incorrect", Arrays.asList("0.005", "1.01"),
+                table.getColumnDataAsText("PlateData/dilution"));
+        checker().screenShotIfNewError("rowsInControlWells");
         table.clearAllFilters();
 
         table.setFilter("PlateData/control_well_groups", "Is Blank");
@@ -101,8 +137,9 @@ public void testWithPlateTemplateAndPlateMetadata()
                 table.getColumnDataAsText("PlateData/sample_well_groups"));
         checker().verifyEquals("Barcode is incorrect", Arrays.asList("BC_111", "BC_111", "BC_111", "BC_222", "BC_222", "BC_222", "BC_333", "BC_333", "BC_444", "BC_444"),
                 table.getColumnDataAsText("PlateData/Barcode"));
-        checker().verifyEquals("Dilution is incorrect", Arrays.asList("1.0", "1.0", "1.0", "2.0", "2.0", "2.0", "3.0", "3.0", "4.0", "4.0"),
+        checker().verifyEquals("Dilution is incorrect", Arrays.asList("1.01", "1.01", "1.01", "2.01", "2.01", "2.01", "3.01", "3.01", "4.01", "4.01"),
                 table.getColumnDataAsText(" PlateData/dilution"));
+        checker().screenShotIfNewError("rowsOutsideControlWells");
         table.clearAllFilters();
     }
 

src/org/labkey/test/util/APIAssayHelper.java

@@ -40,6 +40,7 @@
 import org.labkey.test.WebTestHelper;
 import org.labkey.test.pages.ReactAssayDesignerPage;
 import org.labkey.test.params.assay.AssayDesign;
+import org.openqa.selenium.NotFoundException;
 
 import java.io.File;
 import java.io.IOException;
@@ -311,14 +312,36 @@ public void createAssayWithPlateSupport(String name)
 
     public String getPlateTemplateLsid(String folderPath) throws Exception
     {
-        SelectRowsCommand selectRowsCmd = new SelectRowsCommand("assay.General", "PlateTemplate");
-        selectRowsCmd.setColumns(List.of("Lsid"));
-
-        SelectRowsResponse resp = selectRowsCmd.execute(_test.createDefaultConnection(), folderPath);
+        SelectRowsResponse resp = getPlateTemplates(folderPath);
 
         return String.valueOf(resp.getRows().get(0).get("Lsid"));
     }
 
+    public String getPlateTemplateLsid(String folderPath, String name) throws Exception
+    {
+        SelectRowsResponse resp = getPlateTemplates(folderPath);
+        List<String> names = new ArrayList<>();
+        for (Map<String, Object> row : resp.getRows())
+        {
+            String rowName = (String) row.get("name");
+            if (rowName.equals(name))
+            {
+                return (String) row.get("Lsid");
+            }
+            names.add(rowName);
+        }
+
+        throw new NotFoundException("No plate template '%s'. Found: %s".formatted(name, names.toString()));
+    }
+
+    private SelectRowsResponse getPlateTemplates(String folderPath) throws IOException, CommandException
+    {
+        SelectRowsCommand selectRowsCmd = new SelectRowsCommand("assay.General", "PlateTemplate");
+        selectRowsCmd.setColumns(List.of("Name", "Lsid"));
+
+        return selectRowsCmd.execute(_test.createDefaultConnection(), folderPath);
+    }
+
     public List<PropertyDescriptor> inferFieldsFromFile(File file, String containerPath) throws IOException, CommandException
     {
         return new InferDomainCommand(file, "Assay").execute(_test.createDefaultConnection(), containerPath)