Added e2e tests

DNAstack · Oct 20, 2023 · 6d27bac · 6d27bac
1 parent dc8436a
commit 6d27bac
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Showing 4 changed files with 222 additions and 15 deletions.
diff --git a/e2e-tests/src/main/java/com/dnastack/wes/service/WesE2ETest.java b/e2e-tests/src/main/java/com/dnastack/wes/service/WesE2ETest.java
@@ -7,7 +7,6 @@
 import com.google.auth.oauth2.GoogleCredentials;
 import io.restassured.builder.MultiPartSpecBuilder;
 import io.restassured.http.ContentType;
-import io.restassured.http.Header;
 import io.restassured.specification.MultiPartSpecification;
 import org.awaitility.core.ConditionFactory;
 import org.junit.jupiter.api.*;
@@ -20,7 +19,6 @@
 import java.util.*;
 
 import static io.restassured.RestAssured.given;
-import static java.lang.String.format;
 import static org.awaitility.Awaitility.with;
 import static org.hamcrest.Matchers.*;
 
@@ -433,6 +431,7 @@ public void uploadWorkflowAttachmentWithRunSubmission() throws Exception {
         public class RunMethodsWithExistingJobs {
 
             String workflowJobId;
+            String workflowJobIdWithAllOutputTypes;
 
             @BeforeAll
             public void setup() throws InterruptedException {
@@ -452,6 +451,22 @@ public void setup() throws InterruptedException {
                   .multiPart(getJsonMultipart("tags", tags))
                   .multiPart(getJsonMultipart("workflow_params", inputs))
                 .post(path)
+                .then()
+                    .assertThat()
+                    .statusCode(200)
+                    .body("run_id",is(notNullValue()))
+                    .extract()
+                    .jsonPath()
+                    .getString("run_id");
+
+                workflowJobIdWithAllOutputTypes = given()
+                  .log().uri()
+                  .log().method()
+                  .header(getHeader(getResource(path)))
+                  .multiPart(getWorkflowUrlMultipart("echo.wdl"))
+                  .multiPart(getMultipartAttachment("echo.wdl",supplier.getFileContent(WdlSupplier.WORKFLOW_WITH_ALL_OUTPUT_TYPES).getBytes()))
+                  .multiPart(getJsonMultipart("workflow_params", inputs))
+                .post(path)
                 .then()
                     .assertThat()
                     .statusCode(200)
@@ -569,6 +584,139 @@ public void listRunsReturnsReturnsNonEmptyCollection() {
                 //@formatter:on
             }
 
+
+            @Test
+            @DisplayName("Get Run Files for existing run returns all files")
+            public void getRunFilesReturnsNonEmptyCollection() throws Exception {
+                String path = getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes + "/files";
+                pollUntilJobCompletes(workflowJobIdWithAllOutputTypes);
+
+                //@formatter:off
+                given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes)))
+                    .accept(ContentType.JSON)
+                    .get(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(200)
+                    .body("runFiles.size()", greaterThan(0))
+                    .body("runFiles.every { it.path != null && it.file_type in ['FINAL', 'SECONDARY', 'LOG'] }", equalTo(true));
+                //@formatter:on
+            }
+
+
+            @Test
+            @DisplayName("Get Run Files for non-existent run fails with status 401 or 404")
+            public void getRunFilesForNonExistentRunShouldFail() {
+                String resourcePath = getRootPath() + "/runs/" + UUID.randomUUID();
+                String path = resourcePath + "/files";
+
+                //@formatter:off
+                given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(resourcePath)))
+                    .accept(ContentType.JSON)
+                    .get(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(anyOf(equalTo(404), equalTo(401)));
+                //@formatter:on
+            }
+
+
+            @Test
+            @DisplayName("Delete Run Files for existing run returns all deleted files")
+            public void deleteRunFilesReturnsNonEmptyCollection() throws Exception {
+                reRunWorkflowWithAllOutputTypes();
+                String path = getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes + "/files";
+                pollUntilJobCompletes(workflowJobIdWithAllOutputTypes);
+
+                //@formatter:off
+                given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes)))
+                    .accept(ContentType.JSON)
+                    .delete(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(200)
+                    .body("deletions.size()", greaterThan(0))
+                    .body("deletions.every { it.path != null && it.file_type == 'SECONDARY' && it.state == 'DELETED' }", equalTo(true));
+                //@formatter:on
+            }
+
+
+            @Test
+            @DisplayName("Delete Run Files for existing run asynchronously returns all deleted files")
+            public void deleteRunFilesAsyncReturnsNonEmptyCollection() throws Exception {
+                reRunWorkflowWithAllOutputTypes();
+                String path = getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes + "/files";
+                pollUntilJobCompletes(workflowJobIdWithAllOutputTypes);
+
+                //@formatter:off
+                given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(getRootPath() + "/runs/" + workflowJobIdWithAllOutputTypes)))
+                    .accept(ContentType.JSON)
+                    .queryParam("async", true)
+                    .delete(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(200)
+                    .body("deletions.size()", greaterThan(0))
+                    .body("deletions.every { it.path != null && it.file_type == 'SECONDARY' && it.state == 'ASYNC' }", equalTo(true));
+                //@formatter:on
+            }
+
+
+            @Test
+            @DisplayName("Delete Run Files for non-existent run fails with status 401 or 404")
+            public void deleteRunFilesForNonExistentRunShouldFail() {
+                String resourcePath = getRootPath() + "/runs/" + UUID.randomUUID();
+                String path = resourcePath + "/files";
+
+                //@formatter:off
+                given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(resourcePath)))
+                    .accept(ContentType.JSON)
+                    .delete(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(anyOf(equalTo(404),equalTo(401)));
+                //@formatter:on
+            }
+
+
+            private void reRunWorkflowWithAllOutputTypes() {
+                String path = getRootPath() + "/runs";
+                Map<String, String> inputs = Collections.singletonMap("hello_world.name", "Some sort of String");
+
+                //@formatter:off
+                workflowJobIdWithAllOutputTypes = given()
+                    .log().uri()
+                    .log().method()
+                    .header(getHeader(getResource(path)))
+                    .multiPart(getWorkflowUrlMultipart("echo.wdl"))
+                    .multiPart(getMultipartAttachment("echo.wdl",supplier.getFileContent(WdlSupplier.WORKFLOW_WITH_ALL_OUTPUT_TYPES).getBytes()))
+                    .multiPart(getJsonMultipart("workflow_params", inputs))
+                    .post(path)
+                    .then()
+                    .assertThat()
+                    .statusCode(200)
+                    .body("run_id",is(notNullValue()))
+                    .extract()
+                    .jsonPath()
+                    .getString("run_id");
+                //@formatter:on
+            }
+
         }
 
     }

diff --git a/e2e-tests/src/main/java/com/dnastack/wes/service/wdl/WdlSupplier.java b/e2e-tests/src/main/java/com/dnastack/wes/service/wdl/WdlSupplier.java
@@ -10,6 +10,7 @@
 public class WdlSupplier {
 
     public static final String WORKFLOW_WITHOUT_FILE = "workflow_without_file.wdl";
+    public static final String WORKFLOW_WITH_ALL_OUTPUT_TYPES = "workflow_with_all_output_types.wdl";
     public static final String WORKFLOW_WITH_IMPORTS_1 = "workflow_with_imports_1.wdl";
     public static final String WORKFLOW_WITH_IMPORTS_2 = "workflow_with_imports_2.wdl";
     public static final String WORKFLOW_WITH_IMPORTS_INPUTS = "workflow_with_imports.json";

diff --git a/e2e-tests/src/main/resources/com/dnastack/wes/service/wdl/workflow_with_all_output_types.wdl b/e2e-tests/src/main/resources/com/dnastack/wes/service/wdl/workflow_with_all_output_types.wdl
@@ -0,0 +1,29 @@
+task echo {
+    String name
+    command {
+        echo "Hello ${name}"
+        >&2 echo "Goodbye ${name}"
+        echo "Bye" > "test.txt"
+    }
+
+    runtime {
+        docker: "ubuntu"
+    }
+
+    output {
+        File out = stdout()
+        File out2 = "test.txt"
+        Array[File] arrayOut = [out, out2]
+    }
+}
+
+workflow hello_world {
+    String name
+    call echo {
+        input:
+            name = name
+    }
+    output {
+        File out = echo.out
+    }
+}
diff --git a/src/test/java/com/dnastack/wes/storage/client/local/LocalBlobStorageClientTest.java b/src/test/java/com/dnastack/wes/storage/client/local/LocalBlobStorageClientTest.java
@@ -15,6 +15,9 @@
 
 class LocalBlobStorageClientTest {
 
+    private final String toWrite = "Test String";
+    private final String directory = "test";
+    private final String fileName = "test.txt";
 
     @Test
     public void testCreateStorageClient_noStagingPath() throws IOException {
@@ -36,10 +39,6 @@ public void testCreateStorageClient_withStagingPath() throws IOException {
     @Test
     public void testWritingBytesToFile() throws IOException {
         LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
-        String toWrite = "Test String";
-        String directory = "test";
-        String fileName = "test.txt";
-
         Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
         storageClient.writeBytes(new ByteArrayInputStream(toWrite.getBytes()), toWrite.length(), directory, fileName);
 
@@ -51,9 +50,6 @@ public void testWritingBytesToFile() throws IOException {
     @Test
     public void testWritingBytesToFile_existingFileThrowsError() throws IOException {
         LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
-        String toWrite = "Test String";
-        String directory = "test";
-        String fileName = "test.txt";
         Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
         Files.createDirectory(targetPath.getParent());
         Files.write(targetPath, toWrite.getBytes(), StandardOpenOption.CREATE_NEW);
@@ -66,9 +62,6 @@ public void testWritingBytesToFile_existingFileThrowsError() throws IOException
     @Test
     public void testReadingFile() throws IOException {
         LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
-        String toWrite = "Test String";
-        String directory = "test";
-        String fileName = "test.txt";
         Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
         Files.createDirectory(targetPath.getParent());
         Files.write(targetPath, toWrite.getBytes(), StandardOpenOption.CREATE_NEW);
@@ -83,9 +76,6 @@ public void testReadingFile() throws IOException {
     @Test
     public void testReadingFile_withTruncation() throws IOException {
         LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
-        String toWrite = "Test String";
-        String directory = "test";
-        String fileName = "test.txt";
         Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
         Files.createDirectory(targetPath.getParent());
         Files.write(targetPath, toWrite.getBytes(), StandardOpenOption.CREATE_NEW);
@@ -97,4 +87,43 @@ public void testReadingFile_withTruncation() throws IOException {
         Assertions.assertEquals(toWrite.substring(5), readValue);
     }
 
+    @Test
+    public void testIsFile() throws IOException {
+        LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
+        Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
+        Files.createDirectory(targetPath.getParent());
+        Files.write(targetPath, toWrite.getBytes(), StandardOpenOption.CREATE_NEW);
+
+        Assertions.assertTrue(storageClient.isFile(targetPath.toString()));
+    }
+
+    @Test
+    public void testIsFile_noFileExists() throws IOException {
+        LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
+        Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
+
+        Assertions.assertFalse(storageClient.isFile(targetPath.toString()));
+    }
+
+    @Test
+    public void testDeletingFile() throws IOException {
+        LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
+        Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
+        Files.createDirectory(targetPath.getParent());
+        Files.write(targetPath, toWrite.getBytes(), StandardOpenOption.CREATE_NEW);
+
+        Assertions.assertTrue(Files.exists(targetPath));
+        storageClient.deleteFile(targetPath.toString());
+        Assertions.assertFalse(Files.exists(targetPath));
+    }
+
+    @Test
+    public void testDeletingFile_throwsError() throws IOException {
+        LocalBlobStorageClient storageClient = new LocalBlobStorageClient();
+        Path targetPath = Path.of(storageClient.getStagingPath() + "/" + directory + "/" + fileName);
+
+        Assertions.assertFalse(Files.exists(targetPath));
+        Assertions.assertThrows(IOException.class, () -> storageClient.deleteFile(targetPath.toString()));
+    }
+
 }