Parameterise packed ID in API

Author: MarkRobbo

src/main/java/org/commonwl/view/workflow/WorkflowForm.java

@@ -28,6 +28,7 @@ public class WorkflowForm {
     private String url;
     private String branch;
     private String path;
+    private String packedId;
 
     public WorkflowForm() {}
 
@@ -41,6 +42,13 @@ public WorkflowForm(String url, String branch, String path) {
         this.path = path;
     }
 
+    public WorkflowForm(String url, String branch, String path, String packedId) {
+        setUrl(url);
+        this.branch = branch;
+        this.path = path;
+        this.packedId = packedId;
+    }
+
     public String getUrl() {
         return url;
     }
@@ -67,6 +75,14 @@ public void setPath(String path) {
         this.path = path;
     }
 
+    public String getPackedId() {
+        return packedId;
+    }
+
+    public void setPackedId(String packedId) {
+        this.packedId = packedId;
+    }
+
     /**
      * Cuts any trailing slashes off a string
      * @param url The string to cut the slashes off

src/main/java/org/commonwl/view/workflow/WorkflowFormValidator.java

@@ -73,12 +73,16 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
             String repoUrl = null;
             String branch = null;
             String path = null;
+            String packedId = null;
             if (!isEmptyOrWhitespace(form.getBranch())) {
                 branch = form.getBranch();
             }
             if (!isEmptyOrWhitespace(form.getPath())) {
                 path = form.getPath();
             }
+            if (!isEmptyOrWhitespace(form.getPackedId())) {
+                packedId = form.getPackedId();
+            }
 
             // Github URL
             Matcher m = githubCwlPattern.matcher(form.getUrl());
@@ -114,11 +118,15 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
 
             // Split off packed ID if present
             if (repoUrl != null) {
-                String[] pathSplit = path.split("#");
                 GitDetails details = new GitDetails(repoUrl, branch, path);
-                if (pathSplit.length > 1) {
-                    details.setPath(pathSplit[pathSplit.length - 2]);
-                    details.setPackedId(pathSplit[pathSplit.length - 1]);
+                if (packedId != null) {
+                    details.setPackedId(packedId);
+                } else {
+                    String[] pathSplit = path.split("#");
+                    if (pathSplit.length > 1) {
+                        details.setPath(pathSplit[pathSplit.length - 2]);
+                        details.setPackedId(pathSplit[pathSplit.length - 1]);
+                    }
                 }
                 return details;
             }
@@ -128,7 +136,9 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
             if (!e.hasErrors()) {
                 m = gitRepoPattern.matcher(form.getUrl());
                 if (m.find()) {
-                    return new GitDetails(form.getUrl(), form.getBranch(), form.getPath());
+                    GitDetails details = new GitDetails(form.getUrl(), form.getBranch(), form.getPath());
+                    details.setPackedId(form.getPackedId());
+                    return details;
                 }
             }
 

src/main/java/org/commonwl/view/workflow/WorkflowRESTController.java

@@ -89,16 +89,18 @@ public Page<Workflow> searchWorkflowsJson(Model model,
      * @param url The URL of the workflow
      * @param branch The branch where the workflow can be found
      * @param path The path within the repository to the workflow file
+     * @param packedId The ID of the workflow if the file is packed
      * @return Appropriate response code and optional JSON string with message
      */
     @PostMapping(value = "/workflows", produces = MediaType.APPLICATION_JSON_UTF8_VALUE)
     public ResponseEntity<?> newWorkflowFromGitURLJson(@RequestParam(value="url") String url,
                                                        @RequestParam(value="branch", required=false) String branch,
                                                        @RequestParam(value="path", required=false) String path,
+                                                       @RequestParam(value="packedId", required=false) String packedId,
                                                        HttpServletResponse response) {
 
         // Run validator which checks the URL is valid
-        WorkflowForm workflowForm = new WorkflowForm(url, branch, path);
+        WorkflowForm workflowForm = new WorkflowForm(url, branch, path, packedId);
         BeanPropertyBindingResult errors = new BeanPropertyBindingResult(workflowForm, "errors");
         GitDetails gitInfo = workflowFormValidator.validateAndParse(workflowForm, errors);
 
@@ -130,14 +132,15 @@ public ResponseEntity<?> newWorkflowFromGitURLJson(@RequestParam(value="url") St
                                 }
                             } else {
                                 // Error with alternatives suggested
+                                List<WorkflowOverview> test = queued.getWorkflowList();
                                 List<String> workflowUris = new ArrayList<>();
                                 for (WorkflowOverview overview : queued.getWorkflowList()) {
-                                    workflowUris.add(overview.getFileName());
+                                    workflowUris.add(overview.getFileName().substring(1));
                                 }
                                 Map<String, Object> responseMap = new HashMap<>();
                                 responseMap.put("message", "This workflow file is packed and contains multiple workflow " +
-                                        "descriptions. Please choose one to add");
-                                responseMap.put("workflows", workflowUris);
+                                        "descriptions. Please provide a packedId parameter with one of the following");
+                                responseMap.put("packedId", workflowUris);
                                 return new ResponseEntity<Map>(responseMap, HttpStatus.UNPROCESSABLE_ENTITY);
                             }
                         }

src/main/resources/templates/apidocs.html

@@ -59,7 +59,7 @@ <h4>Parameters</h4>
                         <tr>
                             <td>url</td>
                             <td>String</td>
-                            <td>The URL of the repository. Either a Gitlab or Github URL, or any Git repository URL.</td>
+                            <td>The URL of the repository. Either a Gitlab or Github URL, or any Git repository URL. If a Gitlab or Github repository URL is used, the following fields will take priority over those parsed from the URL if provided.</td>
                         </tr>
                         <tr>
                             <td>branch</td>
@@ -71,6 +71,11 @@ <h4>Parameters</h4>
                             <td>String</td>
                             <td>The path within the repository to the workflow file. Required if the URL is not from Gitlab or Github.</td>
                         </tr>
+                        <tr>
+                            <td>packedId</td>
+                            <td>String</td>
+                            <td>The ID of the workflow, to be provided if the workflow file is packed (contains multiple descriptions with <code>$graph</code>).</td>
+                        </tr>
                     </table>
                     <h4>Input</h4>
 <pre class="highlight json">
@@ -93,19 +98,19 @@ <h4>Success</h4>
                     <h4>Already Exists</h4>
 <pre class="highlight http">
 HTTP/1.1 303 See Other
-Location: /workflows/:githubURL
+Location: /workflows/:URL
 </pre>
                     <h4>Packed Workflow with Multiple Choices</h4>
                     <pre class="highlight json">
 HTTP/1.1 422 Unprocessable Entity
 {
-    "message": "This workflow file is packed and contains multiple workflow descriptions. Please choose one to add"
-    "workflows": [
-        "#workflow.cwl",
-        "#main",
-        "#workflow_exome.cwl",
-        "#align.cwl",
-        "#workflow.cwl_2"
+    "message": "This workflow file is packed and contains multiple workflow descriptions. Please provide a packedId parameter with one of the following values"
+    "packedId": [
+        "workflow.cwl",
+        "main",
+        "workflow_exome.cwl",
+        "align.cwl",
+        "workflow.cwl_2"
     ]
 }
 </pre>

src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java

@@ -40,6 +40,7 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import static org.hamcrest.core.Is.is;
@@ -206,11 +207,9 @@ public void directWorkflowURL() throws Exception {
         List<WorkflowOverview> listOfTwoOverviews = new ArrayList<>();
         listOfTwoOverviews.add(new WorkflowOverview("/workflow1.cwl", "label", "doc"));
         listOfTwoOverviews.add(new WorkflowOverview("/workflow2.cwl", "label2", "doc2"));
-        List<WorkflowOverview> listOfOneOverview = new ArrayList<>();
-        listOfOneOverview.add(new WorkflowOverview("/workflow1.cwl", "label", "doc"));
         when(mockWorkflowService.getWorkflowsFromDirectory(anyObject()))
                 .thenReturn(listOfTwoOverviews)
-                .thenReturn(listOfOneOverview);
+                .thenReturn(Collections.singletonList(new WorkflowOverview("/workflow1.cwl", "label", "doc")));
 
         // Mock controller/MVC
         WorkflowController workflowController = new WorkflowController(

src/test/java/org/commonwl/view/workflow/WorkflowRESTControllerTest.java

@@ -31,6 +31,11 @@
 import org.springframework.test.web.servlet.MockMvc;
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.is;
 import static org.mockito.Matchers.*;
 import static org.mockito.Mockito.when;
@@ -67,6 +72,14 @@ public void newWorkflowFromGithubURLJson() throws Exception {
                 .thenReturn("123");
         when(mockQueuedWorkflow.getTempRepresentation())
                 .thenReturn(mockWorkflow);
+        List<WorkflowOverview> listOfTwoOverviews = new ArrayList<>();
+        listOfTwoOverviews.add(new WorkflowOverview("#packedId1", "label", "doc"));
+        listOfTwoOverviews.add(new WorkflowOverview("#packedId2", "label2", "doc2"));
+        when(mockQueuedWorkflow.getWorkflowList())
+                .thenReturn(null)
+                .thenReturn(null)
+                .thenReturn(Collections.singletonList(new WorkflowOverview("#packedId", "Label", "Doc")))
+                .thenReturn(listOfTwoOverviews);
 
         // Mock workflow service returning valid workflow
         WorkflowService mockWorkflowService = Mockito.mock(WorkflowService.class);
@@ -109,11 +122,27 @@ public void newWorkflowFromGithubURLJson() throws Exception {
 
         // Success
         mockMvc.perform(post("/workflows")
-                .param("url", "https://github.com/owner/repoName/tree/branch/path/workflow.cwl")
+                .param("url", "https://github.com/owner/repoName/tree/branch/path/success.cwl")
                 .accept(MediaType.APPLICATION_JSON_UTF8))
                 .andExpect(status().isAccepted())
                 .andExpect(header().string("Location", is("/queue/123")));
 
+        // Packed workflow with one ID is still accepted and parsed using that ID
+        mockMvc.perform(post("/workflows")
+                .param("url", "https://github.com/owner/repoName/tree/branch/path/singlePacked.cwl")
+                .accept(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(status().isAccepted())
+                .andExpect(header().string("Location", is("/queue/123")));
+
+        // Packed workflow with multiple IDs is unprocessable
+        mockMvc.perform(post("/workflows")
+                .param("url", "https://github.com/owner/repoName/tree/branch/path/multiplePacked.cwl")
+                .accept(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(status().isUnprocessableEntity())
+                .andExpect(jsonPath("$.message", is("This workflow file is packed and contains multiple workflow " +
+                        "descriptions. Please provide a packedId parameter with one of the following")))
+                .andExpect(jsonPath("$.packedId", containsInAnyOrder("packedId1", "packedId2")));
+
     }
 
     /**