Cleanup

thehyve · Jan 22, 2024 · 4b0ff1f · 4b0ff1f
1 parent 217e878
commit 4b0ff1f
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Showing 4 changed files with 11 additions and 8 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java b/src/main/java/org/cbioportal/persistence/cachemaputil/StaticRefCacheMapUtil.java
@@ -64,7 +64,6 @@ public class StaticRefCacheMapUtil implements CacheMapUtil {
     static Map<String, MolecularProfile> molecularProfileCache;
     static Map<String, SampleList> sampleListCache;
     static Map<String, CancerStudy> cancerStudyCache;
-    static Map<String, String> genericAssayStableIdToMolecularProfileIdCache;
 
     @PostConstruct
     private void init() {

diff --git a/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java b/src/main/java/org/cbioportal/service/impl/CacheServiceImpl.java
@@ -8,6 +8,7 @@
 import org.cbioportal.persistence.util.CacheUtils;
 import org.cbioportal.service.CacheService;
 import org.cbioportal.service.exception.CacheOperationException;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.CacheManager;
 import org.springframework.stereotype.Component;

diff --git a/src/test/java/org/cbioportal/test/integration/security/AbstractContainerTest.java b/src/test/java/org/cbioportal/test/integration/security/AbstractContainerTest.java
@@ -38,9 +38,6 @@ public class AbstractContainerTest {
     public final static int MOCKSERVER_PORT = 8085;
     public final static String DOWNLOAD_FOLDER = "/tmp/browser_downloads";
 
-    @Value("${user.home:/tmp/chrome_vids}")
-    private String chromeVidsFolder;
-
     private static final String SESSION_IMAGE_VERSION = "docker.io/cbioportal/session-service:0.6.1";
     private static final String MONGO_IMAGE_VERSION = "docker.io/mongo:3.7.9";
     private static final String KEYCLOAK_IMAGE_VERSION = "quay.io/keycloak/keycloak:23.0";
@@ -103,10 +100,10 @@ public class AbstractContainerTest {
         options.setExperimentalOption("prefs", prefs);
 
         chromedriverContainer = new BrowserWebDriverContainer<>()
+            .withCapabilities(options)
             // activate this to record movies of the tests (great for debugging)
-//            .withRecordingMode(RECORD_ALL, new File(chromeVidsFolder))
-            .withAccessToHost(true)
-            .withCapabilities(options);
+            .withRecordingMode(RECORD_ALL, new File("/home/pnp300/"))
+            .withAccessToHost(true);
 
         sessionServiceContainer.start();
         mongoContainer.start();

diff --git a/src/test/java/org/cbioportal/test/integration/security/util/Util.java b/src/test/java/org/cbioportal/test/integration/security/util/Util.java
@@ -48,6 +48,8 @@ public static void testLogin(String cbioUrl, BrowserWebDriverContainer chromedri
         performLogin(cbioUrl, driver);
         WebElement loggedInButton = driver.findElement(By.id("dat-dropdown"));
         Assertions.assertEquals("Logged in as testuser@thehyve.nl", loggedInButton.getText());
+        new WebDriverWait(driver, Duration.ofSeconds(20)).until(
+            ExpectedConditions.presenceOfElementLocated(By.xpath("//span[.='Breast Invasive Carcinoma (TCGA,Nature 2012)']")));
         Assertions.assertDoesNotThrow(
             () -> driver.findElement(By.xpath("//span[.='Breast Invasive Carcinoma (TCGA,Nature 2012)']")),
             "Study could not be found on the landing page. Permissions are not correctly passed from IDP to client.");
@@ -100,6 +102,7 @@ public static void testLoginAgain(String cbioUrl, BrowserWebDriverContainer chro
 
     private static void performLogin(String url, RemoteWebDriver driver) {
         driver.get(url);
+//        driver.manage().timeouts().implicitlyWait(10, TimeUnit.SECONDS);
         try {
             // when the cbioportal logo is visible, skip login
             driver.findElement(By.id("cbioportal-logo"));
@@ -112,6 +115,7 @@ private static void performLogin(String url, RemoteWebDriver driver) {
             loginButton.click();
         }
         // wait for the page to load
+//        driver.manage().timeouts().implicitlyWait(10, TimeUnit.SECONDS);
         new WebDriverWait(driver, Duration.ofSeconds(20)).until(
             ExpectedConditions.presenceOfElementLocated(By.xpath("//*[@data-test='cancerTypeListContainer']")));
     }
@@ -124,7 +128,9 @@ private static boolean containerFileExists(
         Container.ExecResult r = container.execInContainer("/bin/sh", "-c",
             "if [ -f " + path
                 + " ] ; then echo '0' ; else (>&2 echo '1') ; fi");
-        return !r.getStderr().contains("1");
+        boolean fileNotFound = r.getStderr().contains("1");
+        container.execInContainer("rm -f " + path);
+        return !fileNotFound;
     }
 
     private static Callable<Boolean> downloadedFile(GenericContainer chromedriverContainer) {