Conditionalize more specimen checks

Author: labkey-tchad

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

@@ -193,8 +193,11 @@ protected void setupEnvironment()
         _containerHelper.createProject(getProjectName(), null);
         goToProjectHome(getProjectName());
 
-        // Some test use a stand alone specimen file. Before the file can be imported the Specimen module needs to be enabled.
-        _containerHelper.enableModule("Specimen");
+        if (_studyHelper.isSpecimenModulePresent())
+        {
+            // Some test use a stand alone specimen file. Before the file can be imported the Specimen module needs to be enabled.
+            _containerHelper.enableModule("Specimen");
+        }
 
         log("Setting up groups, users and initial permissions");
         ApiPermissionsHelper permissionsHelper = new ApiPermissionsHelper(this);

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

@@ -22,7 +22,6 @@
 import org.labkey.test.Locator;
 import org.labkey.test.TestTimeoutException;
 import org.labkey.test.WebTestHelper;
-import org.labkey.test.categories.Daily;
 import org.labkey.test.categories.Specimen;
 import org.labkey.test.util.AbstractDataRegionExportOrSignHelper.ColumnHeaderType;
 
@@ -33,7 +32,7 @@
 /**
  * Test exporting rows from a specimen grid (not folder/study specimen export.)
  */
-@Category({Daily.class, Specimen.class})
+@Category({Specimen.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 7)
 public class SpecimenGridExportTest extends AbstractExportTest
 {

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

@@ -26,7 +26,6 @@
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.WebTestHelper;
-import org.labkey.test.categories.Daily;
 import org.labkey.test.categories.Specimen;
 import org.labkey.test.components.ext4.RadioButton;
 import org.labkey.test.util.DataRegionTable;
@@ -43,7 +42,7 @@
 
 import static org.junit.Assert.assertEquals;
 
-@Category({Daily.class, Specimen.class})
+@Category({Specimen.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class SpecimenImportTest extends SpecimenBaseTest
 {

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

@@ -58,7 +58,6 @@
 public abstract class StudyBaseTest extends BaseWebDriverTest
 {
     protected static final File ARCHIVE_TEMP_DIR = StudyHelper.getStudyTempDir();
-    private static Boolean _specimenModulePresent;
 
     protected int datasetCount = getDatasetCount();
     protected int visitCount = 65;
@@ -76,14 +75,6 @@ protected void setupRequestStatuses()
         new SpecimenHelper(this).setupRequestStatuses();
     }
 
-    public boolean isSpecimenModulePresent()
-    {
-        if (null == _specimenModulePresent)
-            _specimenModulePresent = _containerHelper.getAllModules().contains("specimen");
-
-        return _specimenModulePresent;
-    }
-
     protected final AuditLogHelper _auditLogHelper = new AuditLogHelper(this);
 
     @Override
@@ -140,7 +131,7 @@ protected void startSpecimenImport(int completeJobsExpected)
 
     protected void startSpecimenImport(int completeJobsExpected, File specimenArchive)
     {
-        if (isSpecimenModulePresent())
+        if (_studyHelper.isSpecimenModulePresent())
         {
             _specimenImporter = new SpecimenImporter(new File(StudyHelper.getStudySubfolderPath()), specimenArchive, ARCHIVE_TEMP_DIR, getFolderName(), completeJobsExpected);
             _specimenImporter.startImport();
@@ -149,7 +140,7 @@ protected void startSpecimenImport(int completeJobsExpected, File specimenArchiv
 
     protected void waitForSpecimenImport()
     {
-        if (isSpecimenModulePresent())
+        if (_studyHelper.isSpecimenModulePresent())
         {
             _specimenImporter.waitForComplete();
         }

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

@@ -283,7 +283,8 @@ private void doTestContainerTabConversion()
         goToProjectHome();
         _containerHelper.createSubfolder(getProjectName(), COLLAB_FOLDER, "Collaboration");
         _containerHelper.createSubfolder(COLLABFOLDER_PATH, STUDY_FOLDER_TAB_NAME, "Study");
-        _containerHelper.enableModule("Specimen");
+        if (_studyHelper.isSpecimenModulePresent())
+            _containerHelper.enableModule("Specimen");
         _containerHelper.createSubfolder(COLLABFOLDER_PATH, ASSAY_FOLDER_TAB_NAME, "Assay");
         clickFolder(COLLAB_FOLDER);
         clickFolder(STUDY_FOLDER_TAB_NAME);
@@ -317,8 +318,11 @@ private void doTestContainerTabConversion()
         clickAndWait(Locator.linkWithText(STUDY_FOLDER_TAB_LABEL));
         assertTextPresent("Study Overview");
         studyContainerTab = PortalTab.finder(getDriver()).withTabText(STUDY_FOLDER_TAB_LABEL).find();
-        studyContainerTab.goToTabContainer("Specimen Data");
-        assertTextPresent("Vial Search", "Import Specimens");
+        if (_studyHelper.isSpecimenModulePresent())
+        {
+            studyContainerTab.goToTabContainer("Specimen Data");
+            assertTextPresent("Vial Search", "Import Specimens");
+        }
         clickAndWait(Locator.linkWithText(ASSAY_FOLDER_TAB_LABEL));
         assertTextPresent("Assay List", EXTRA_ASSAY_WEBPART);
 
@@ -343,8 +347,11 @@ private void doTestContainerTabConversion()
         assertTextPresent(STUDY_FOLDER_TAB_LABEL, ASSAY_FOLDER_TAB_LABEL);
         clickAndWait(Locator.linkWithText(STUDY_FOLDER_TAB_LABEL));
         assertTextPresent("Study Overview");
-        PortalTab.find(STUDY_FOLDER_TAB_LABEL, getDriver()).goToTabContainer("Specimen Data");
-        assertTextPresent("Vial Search", "Import Specimens");
+        if (_studyHelper.isSpecimenModulePresent())
+        {
+            PortalTab.find(STUDY_FOLDER_TAB_LABEL, getDriver()).goToTabContainer("Specimen Data");
+            assertTextPresent("Vial Search", "Import Specimens");
+        }
         PortalTab.find(ASSAY_FOLDER_TAB_LABEL, getDriver()).activate();
         assertTextPresent("Assay List", EXTRA_ASSAY_WEBPART);
 

src/org/labkey/test/tests/flow/FlowSpecimenTest.java

@@ -15,13 +15,13 @@
  */
 package org.labkey.test.tests.flow;
 
+import org.junit.Assume;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.WebTestHelper;
-import org.labkey.test.categories.Daily;
 import org.labkey.test.categories.Flow;
 import org.labkey.test.categories.Specimen;
 import org.labkey.test.components.assay.AssayConstants;
@@ -38,7 +38,7 @@
 /**
  * This test checks the flow specimen foreign key behavior from flow.FCSFiles and flow.FCSAnalyses.
  */
-@Category({Daily.class, Flow.class, Specimen.class})
+@Category({Flow.class, Specimen.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 8)
 public class FlowSpecimenTest extends BaseFlowTest
 {
@@ -62,6 +62,7 @@ public static void initFlowFolders()
     @LogMethod
     private void initializeStudyFolder()
     {
+        Assume.assumeTrue("Specimen module not present", _studyHelper.isSpecimenModulePresent());
         log("** Initialize Study Folder");
         _containerHelper.createSubfolder(getProjectName(), getProjectName(), STUDY_FOLDER, "Study", null);
         _containerHelper.enableModule("Specimen");

src/org/labkey/test/tests/viability/AbstractViabilityTest.java

@@ -70,7 +70,8 @@ protected void initializeStudyFolder(String... tabs)
     {
         log("** Initialize Folder");
         _containerHelper.createProject(getProjectName(), null);
-        _containerHelper.enableModule("Specimen");
+        if (_studyHelper.isSpecimenModulePresent())
+            _containerHelper.enableModule("Specimen");
         _containerHelper.createSubfolder(getProjectName(), getProjectName(), getFolderName(), "Study", tabs, true);
 
         log("** Create Study");
@@ -86,14 +87,17 @@ protected void importSpecimens()
 
     protected void importSpecimens(String studyFolder, File specimensPath)
     {
-        log("** Import specimens");
-        clickFolder(studyFolder);
-        clickAndWait(Locator.linkWithText("Specimen Data"));
-        waitAndClickAndWait(Locator.linkWithText("Import Specimens"));
-        waitForElement(Locator.id("tsv"));
-        setFormElement(Locator.id("tsv"), TestFileUtils.getFileContents(specimensPath));
-        submit();
-        assertTextPresent("Specimens uploaded successfully");
+        if (_studyHelper.isSpecimenModulePresent())
+        {
+            log("** Import specimens");
+            clickFolder(studyFolder);
+            clickAndWait(Locator.linkWithText("Specimen Data"));
+            waitAndClickAndWait(Locator.linkWithText("Import Specimens"));
+            waitForElement(Locator.id("tsv"));
+            setFormElement(Locator.id("tsv"), TestFileUtils.getFileContents(specimensPath));
+            submit();
+            assertTextPresent("Specimens uploaded successfully");
+        }
     }
 
     protected void createViabilityAssay()