Refactor packed workflow ID to be part of retrievedFrom ID

MarkRobbo · MarkRobbo · commit 80462d06d894 · 2017-08-17T13:08:41.000+01:00
diff --git a/src/main/java/org/commonwl/view/cwl/CWLService.java b/src/main/java/org/commonwl/view/cwl/CWLService.java
@@ -189,7 +189,6 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
             // Construct the rest of the workflow model
             Workflow workflowModel = new Workflow(label, extractDoc(cwlFile), getInputs(cwlFile),
                     getOutputs(cwlFile), getSteps(cwlFile), null);
-            workflowModel.setPackedWorkflowID(packedWorkflowId);
 
             workflowModel.setCwltoolVersion(cwlTool.getVersion());
 
@@ -223,7 +222,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
                                              File workflowFile) throws CWLValidationException {
         GitDetails gitDetails = basicModel.getRetrievedFrom();
         String latestCommit = basicModel.getLastCommit();
-        String packedWorkflowID = basicModel.getPackedWorkflowID();
+        String packedWorkflowID = gitDetails.getPackedId();
 
         // Get paths to workflow
         String url = gitDetails.getUrl(latestCommit).replace("https://", "");
@@ -488,13 +487,19 @@ public WorkflowOverview getWorkflowOverview(File file) throws IOException {
             JsonNode cwlFile = yamlStringToJson(readFileToString(file));
 
             // If the CWL file is packed there can be multiple workflows in a file
+            int packedCount = 0;
             if (cwlFile.has(DOC_GRAPH)) {
                 // Packed CWL, find the first subelement which is a workflow and take it
                 for (JsonNode jsonNode : cwlFile.get(DOC_GRAPH)) {
                     if (extractProcess(jsonNode) == CWLProcess.WORKFLOW) {
                         cwlFile = jsonNode;
+                        packedCount++;
                     }
                 }
+                if (packedCount > 1) {
+                    return new WorkflowOverview("/" + file.getName(), "Packed file",
+                            "contains " + packedCount + " workflows");
+                }
             }
 
             // Can only make an overview if this is a workflow
diff --git a/src/main/java/org/commonwl/view/cwl/CWLToolRunner.java b/src/main/java/org/commonwl/view/cwl/CWLToolRunner.java
@@ -79,7 +79,6 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow, File workflo
             newWorkflow.setRetrievedFrom(tempWorkflow.getRetrievedFrom());
             newWorkflow.setRetrievedOn(new Date());
             newWorkflow.setLastCommit(tempWorkflow.getLastCommit());
-            newWorkflow.setPackedWorkflowID(tempWorkflow.getPackedWorkflowID());
             newWorkflow.setCwltoolVersion(cwlToolVersion);
 
             workflowRepository.save(newWorkflow);
diff --git a/src/main/java/org/commonwl/view/git/GitDetails.java b/src/main/java/org/commonwl/view/git/GitDetails.java
@@ -34,6 +34,7 @@ public class GitDetails implements Serializable {
     private String repoUrl;
     private String branch;
     private String path;
+    private String packedId;
 
     public GitDetails(String repoUrl, String branch, String path) {
         this.repoUrl = repoUrl;
@@ -67,6 +68,14 @@ public void setBranch(String branch) {
         this.branch = branch;
     }
 
+    public String getPackedId() {
+        return packedId;
+    }
+
+    public void setPackedId(String packedId) {
+        this.packedId = packedId;
+    }
+
     public String getPath() {
         return path;
     }
@@ -139,13 +148,14 @@ public String getUrl() {
      * @return The URL
      */
     public String getInternalUrl() {
+        String packedPart = packedId == null ? "" : "%23" + packedId;
         String pathPart = path.equals("/") ? "" : "/" + path;
         switch (getType()) {
             case GITHUB:
             case GITLAB:
-                return "/workflows/" + normaliseUrl(repoUrl).replace(".git", "") + "/blob/" + branch + pathPart;
+                return "/workflows/" + normaliseUrl(repoUrl).replace(".git", "") + "/blob/" + branch + pathPart + packedPart;
             default:
-                return "/workflows/" + normaliseUrl(repoUrl) + "/" + branch + pathPart;
+                return "/workflows/" + normaliseUrl(repoUrl) + "/" + branch + pathPart + packedPart;
         }
     }
 
diff --git a/src/main/java/org/commonwl/view/researchobject/ROBundleService.java b/src/main/java/org/commonwl/view/researchobject/ROBundleService.java
@@ -171,7 +171,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
 
             // Get URL to run cwltool
             String rawUrl = wfDetails.getRawUrl();
-            String packedWorkflowID = workflow.getPackedWorkflowID();
+            String packedWorkflowID = wfDetails.getPackedId();
             if (packedWorkflowID != null) {
                 if (packedWorkflowID.charAt(0) != '#') {
                     rawUrl += "#";
diff --git a/src/main/java/org/commonwl/view/workflow/Workflow.java b/src/main/java/org/commonwl/view/workflow/Workflow.java
@@ -54,9 +54,6 @@ public class Workflow {
     // Used for caching purposes
     private String lastCommit;
 
-    // If schema salad packed, the workflow ID
-    private String packedWorkflowID;
-
     // A String which represents the path to a RO bundle
     // Path types cannot be stored using Spring Data, unfortunately
     private String roBundlePath;
@@ -164,14 +161,6 @@ public void setLastCommit(String lastCommit) {
         this.lastCommit = lastCommit;
     }
 
-    public String getPackedWorkflowID() {
-        return packedWorkflowID;
-    }
-
-    public void setPackedWorkflowID(String packedWorkflowID) {
-        this.packedWorkflowID = packedWorkflowID;
-    }
-
     public String getDockerLink() {
         return dockerLink;
     }
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowController.java b/src/main/java/org/commonwl/view/workflow/WorkflowController.java
@@ -413,7 +413,13 @@ public static GitDetails getGitDetails(String domain, String owner, String repoN
             default:
                 throw new WorkflowNotFoundException();
         }
-        return new GitDetails(repoUrl, branch, path);
+        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]);
+        }
+        return details;
     }
 
     /**
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowFormValidator.java b/src/main/java/org/commonwl/view/workflow/WorkflowFormValidator.java
@@ -70,6 +70,7 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
         if (!e.hasErrors()) {
 
             // Override if specific branch or path is given in the form
+            String repoUrl = null;
             String branch = null;
             String path = null;
             if (!isEmptyOrWhitespace(form.getBranch())) {
@@ -82,37 +83,44 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
             // Github URL
             Matcher m = githubCwlPattern.matcher(form.getUrl());
             if (m.find()) {
-                String repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
+                repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
                 if (branch == null) branch = m.group(3);
                 if (path == null) path = m.group(4);
-                return new GitDetails(repoUrl, branch, path);
             }
 
             // Gitlab URL
             m = gitlabCwlPattern.matcher(form.getUrl());
             if (m.find()) {
-                String repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
+                repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
                 if (branch == null) branch = m.group(3);
                 if (path == null) path = m.group(4);
-                return new GitDetails(repoUrl, branch, path);
             }
 
             // Github Dir URL
             m = githubDirPattern.matcher(form.getUrl());
             if (m.find()) {
-                String repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
+                repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
                 if (branch == null) branch = m.group(3);
                 if (path == null) path = m.group(4);
-                return new GitDetails(repoUrl, branch, path);
             }
 
             // Gitlab Dir URL
             m = gitlabDirPattern.matcher(form.getUrl());
             if (m.find()) {
-                String repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
+                repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
                 if (branch == null) branch = m.group(3);
                 if (path == null) path = m.group(4);
-                return new GitDetails(repoUrl, branch, path);
+            }
+
+            // 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]);
+                }
+                return details;
             }
 
             // General Git details if didn't match the above
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowService.java b/src/main/java/org/commonwl/view/workflow/WorkflowService.java
@@ -328,6 +328,7 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
 
             // Set origin details
             basicModel.setRetrievedOn(new Date());
+            gitInfo.setPackedId(packedWorkflowId);
             basicModel.setRetrievedFrom(gitInfo);
             basicModel.setLastCommit(latestCommit);
 
diff --git a/src/main/resources/templates/workflow.html b/src/main/resources/templates/workflow.html
@@ -233,7 +233,7 @@ <h2>Steps</h2>
                             <td th:text="${step.key}">ID</td>
                             <td>
                                 <div th:if="${step.value.runType != null}">
-                                    <a th:if="${step.value.runType.name() == 'WORKFLOW'}" th:href="${step.value.run}" th:text="${step.value.run}" class="subworkflow">workflow.cwl</a>
+                                    <a th:if="${step.value.runType.name() == 'WORKFLOW'}" th:href="@{${step.value.run}}" th:text="${step.value.run}" class="subworkflow">workflow.cwl</a>
                                     <span th:unless="${step.value.runType.name() == 'WORKFLOW'}" th:text="${step.value.run}">cmdlinetool.cwl</span>
                                     (<span th:text="${step.value.runType}">Workflow</span>)
                                 </div>
diff --git a/src/test/java/org/commonwl/view/cwl/CWLServiceTest.java b/src/test/java/org/commonwl/view/cwl/CWLServiceTest.java
@@ -128,7 +128,7 @@ public void parseWorkflowWithCwltool() throws Exception {
                 "549c973ccc01781595ce562dea4cedc6c9540fe0", "workflows/make-to-cwl/dna.cwl");
         Workflow basicModel = new Workflow(null, null, null, null, null, null);
         basicModel.setRetrievedFrom(gitInfo);
-        basicModel.setPackedWorkflowID("main");
+        gitInfo.setPackedId("main");
         basicModel.setLastCommit("549c973ccc01781595ce562dea4cedc6c9540fe0");
 
         // Parse the workflow

Original file line number	Diff line number	Diff line change
`@@ -413,7 +413,13 @@ public static GitDetails getGitDetails(String domain, String owner, String repoN`
`413`	`413`	`default:`
`414`	`414`	`throw new WorkflowNotFoundException();`
`415`	`415`	`}`
`416`		`- return new GitDetails(repoUrl, branch, path);`
	`416`	`+ String[] pathSplit = path.split("#");`
	`417`	`+ GitDetails details = new GitDetails(repoUrl, branch, path);`
	`418`	`+ if (pathSplit.length > 1) {`
	`419`	`+ details.setPath(pathSplit[pathSplit.length - 2]);`
	`420`	`+ details.setPackedId(pathSplit[pathSplit.length - 1]);`
	`421`	`+ }`
	`422`	`+ return details;`
`417`	`423`	`}`
`418`	`424`
`419`	`425`	`/**`