[#186091347] Create endpoints to clean up a run

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
+            }
+
         }
 
     }

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";

e2e-tests/src/main/resources/com/dnastack/wes/service/wdl/workflow_with_all_output_types.wdl

@@ -0,0 +1,30 @@
+task echo {
+    String name
+    command {
+        echo "Hello ${name}"
+        >&2 echo "Goodbye ${name}"
+        echo "Bye" > "test.txt"
+        echo "Bye" > "test2.txt"
+    }
+
+    runtime {
+        docker: "ubuntu"
+    }
+
+    output {
+        File out = stdout()
+        File out2 = "test.txt"
+        Array[File] arrayOut = [out, out2, "test2.txt"]
+    }
+}
+
+workflow hello_world {
+    String name
+    call echo {
+        input:
+            name = name
+    }
+    output {
+        File out = echo.out
+    }
+}

src/main/java/com/dnastack/wes/api/RunFile.java

@@ -0,0 +1,26 @@
+package com.dnastack.wes.api;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.*;
+
+@Getter
+@Setter
+@AllArgsConstructor
+@NoArgsConstructor
+@EqualsAndHashCode
+@ToString
+@Builder
+public class RunFile {
+
+    @JsonProperty(value = "file_type")
+    FileType fileType;
+
+    String path;
+
+    public enum FileType {
+        FINAL,
+        SECONDARY,
+        LOG
+    }
+
+}

src/main/java/com/dnastack/wes/api/RunFileDeletion.java

@@ -0,0 +1,13 @@
+package com.dnastack.wes.api;
+
+import com.fasterxml.jackson.annotation.JsonUnwrapped;
+
+public record RunFileDeletion(@JsonUnwrapped RunFile runFile, DeletionState state, @JsonUnwrapped ErrorResponse errorResponse) {
+
+    public enum DeletionState {
+        DELETED,
+        ASYNC,
+        FAILED
+    }
+
+}

src/main/java/com/dnastack/wes/api/RunFileDeletions.java

@@ -0,0 +1,5 @@
+package com.dnastack.wes.api;
+
+import java.util.List;
+
+public record RunFileDeletions(List<RunFileDeletion> deletions) {}

src/main/java/com/dnastack/wes/api/RunFiles.java

@@ -0,0 +1,5 @@
+package com.dnastack.wes.api;
+
+import java.util.List;
+
+public record RunFiles(List<RunFile> runFiles) {}

src/main/java/com/dnastack/wes/api/WesV1Controller.java

@@ -123,11 +123,28 @@ public RunId cancelRun(@PathVariable("runId") String runId) {
         return adapter.cancel(runId);
     }
 
+    @AuditActionUri("wes:run:files:list")
+    @PreAuthorize("@accessEvaluator.canAccessResource('/ga4gh/wes/v1/runs/' + #runId + '/files', 'wes:runs:read', 'wes')")
+    @GetMapping(value = "/runs/{run_id}/files", produces = { MediaType.APPLICATION_JSON_VALUE })
+    public RunFiles getRunFiles(@PathVariable("run_id") String runId) {
+        return adapter.getRunFiles(runId);
+    }
+
+    @AuditActionUri("wes:run:files:delete")
+    @PreAuthorize("@accessEvaluator.canAccessResource('/ga4gh/wes/v1/runs/' + #runId + '/files', 'wes:runs:write', 'wes')")
+    @DeleteMapping(value = "/runs/{run_id}/files", produces = { MediaType.APPLICATION_JSON_VALUE })
+    public RunFileDeletions deleteRunFiles(
+        @PathVariable("run_id") String runId,
+        @RequestParam(value = "async", required = false) boolean async
+    ) {
+        return adapter.deleteRunFiles(runId, async);
+    }
+
     @AuditActionUri("wes:run:stderr")
     @PreAuthorize("@accessEvaluator.canAccessResource('/ga4gh/wes/v1/runs/' + #runId, 'wes:runs:read', 'wes')")
     @GetMapping(value = "/runs/{runId}/logs/stderr", produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
     public void getStderr(HttpServletResponse response, @RequestHeader HttpHeaders headers, @PathVariable String runId) throws IOException {
-        adapter.getLogBytes(response.getOutputStream(), runId,getRangeFromHeaders(response,headers));
+        adapter.getLogBytes(response.getOutputStream(), runId, getRangeFromHeaders(response, headers));
     }
 
     @AuditActionUri("wes:run:stderr")
@@ -139,7 +156,7 @@ public void getTaskStderr(
         @PathVariable String runId,
         @PathVariable String taskId
     ) throws IOException {
-        adapter.getLogBytes(response.getOutputStream(), runId, taskId, "stderr",getRangeFromHeaders(response,headers));
+        adapter.getLogBytes(response.getOutputStream(), runId, taskId, "stderr", getRangeFromHeaders(response, headers));
     }
 
     @AuditActionUri("wes:run:stdout")
@@ -151,7 +168,7 @@ public void getTaskStdout(
         @PathVariable String runId,
         @PathVariable String taskId
     ) throws IOException {
-        adapter.getLogBytes(response.getOutputStream(), runId, taskId, "stdout",getRangeFromHeaders(response,headers));
+        adapter.getLogBytes(response.getOutputStream(), runId, taskId, "stdout", getRangeFromHeaders(response, headers));
     }
 
     @AuditActionUri("wes:run:stderr")
@@ -164,7 +181,7 @@ public void getTaskStderr(
         @PathVariable String taskName,
         @PathVariable int index
     ) throws IOException {
-        adapter.getLogBytes(response.getOutputStream(), runId, taskName, index, "stderr",getRangeFromHeaders(response,headers));
+        adapter.getLogBytes(response.getOutputStream(), runId, taskName, index, "stderr", getRangeFromHeaders(response, headers));
     }
 
     @AuditActionUri("wes:run:stdout")
@@ -180,9 +197,9 @@ public void getTaskStdout(
         adapter.getLogBytes(response.getOutputStream(), runId, taskName, index, "stdout", getRangeFromHeaders(response, headers));
     }
 
-    private HttpRange getRangeFromHeaders(HttpServletResponse response, HttpHeaders headers){
+    private HttpRange getRangeFromHeaders(HttpServletResponse response, HttpHeaders headers) {
         List<HttpRange> ranges = headers.getRange();
-        if (ranges.isEmpty()){
+        if (ranges.isEmpty()) {
             return null;
         } else if (ranges.size() > 1) {
             // only return the first range parsed

src/main/java/com/dnastack/wes/config/AsyncConfig.java

@@ -0,0 +1,32 @@
+package com.dnastack.wes.config;
+
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.task.TaskExecutor;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+
+import java.util.concurrent.ThreadPoolExecutor;
+
+@Slf4j
+@Configuration
+public class AsyncConfig {
+
+    @Bean
+    public TaskExecutor defaultAsyncOperationExecutor(
+        @Value("${app.executors.default.core-pool-size:8}") int corePoolSize,
+        @Value("${app.executors.default.max-pool-size:16}") int maxPoolSize,
+        @Value("${app.executors.default.queue-capacity:5000}") int queueCapacity
+    ) {
+        final ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
+        executor.setCorePoolSize(corePoolSize);
+        executor.setMaxPoolSize(maxPoolSize);
+        executor.setQueueCapacity(queueCapacity);
+        executor.setThreadNamePrefix("defaultAsyncOp-");
+        executor.setRejectedExecutionHandler(new ThreadPoolExecutor.CallerRunsPolicy());
+        executor.initialize();
+        return executor;
+    }
+
+}