Merge pull request #147 from common-workflow-language/api-fixes

API Fixes

Author: stain

src/main/java/org/commonwl/view/cwl/CWLElement.java

@@ -73,14 +73,6 @@ public void setFormat(String format) {
         this.format = format;
     }
 
-    public List<String> getSourceID() {
-        return sourceID;
-    }
-
-    public void setSourceID(List<String> sourceID) {
-        this.sourceID = sourceID;
-    }
-
     public List<String> getSourceIDs() {
         return sourceID;
     }

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

@@ -453,7 +453,7 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
             queued = workflowService.getQueuedWorkflow(gitDetails);
             if (queued == null) {
                 // Validation
-                WorkflowForm workflowForm = new WorkflowForm(gitDetails.getUrl());
+                WorkflowForm workflowForm = new WorkflowForm(gitDetails.getUrl(), gitDetails.getBranch(), gitDetails.getPath());
                 BeanPropertyBindingResult errors = new BeanPropertyBindingResult(workflowForm, "errors");
                 workflowFormValidator.validateAndParse(workflowForm, errors);
                 if (!errors.hasErrors()) {

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

@@ -32,9 +32,13 @@ public class WorkflowForm {
     public WorkflowForm() {}
 
     public WorkflowForm(String url) {
-        if (url != null) {
-            this.url = trimTrailingSlashes(url);
-        }
+        setUrl(url);
+    }
+
+    public WorkflowForm(String url, String branch, String path) {
+        setUrl(url);
+        this.branch = branch;
+        this.path = path;
     }
 
     public String getUrl() {

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

@@ -19,6 +19,7 @@
 
 package org.commonwl.view.workflow;
 
+import org.apache.commons.lang.StringUtils;
 import org.commonwl.view.git.GitDetails;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -68,32 +69,50 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
         // If not null and isn't just whitespace
         if (!e.hasErrors()) {
 
+            // Override if specific branch or path is given in the form
+            String branch = null;
+            String path = null;
+            if (!isEmptyOrWhitespace(form.getBranch())) {
+                branch = form.getBranch();
+            }
+            if (!isEmptyOrWhitespace(form.getPath())) {
+                path = form.getPath();
+            }
+
             // Github URL
             Matcher m = githubCwlPattern.matcher(form.getUrl());
             if (m.find()) {
                 String repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
-                return new GitDetails(repoUrl, m.group(3), m.group(4));
+                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";
-                return new GitDetails(repoUrl, m.group(3), m.group(4));
+                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";
-                return new GitDetails(repoUrl, m.group(3), m.group(4));
+                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";
-                return new GitDetails(repoUrl, m.group(3), m.group(4));
+                if (branch == null) branch = m.group(3);
+                if (path == null) path = m.group(4);
+                return new GitDetails(repoUrl, branch, path);
             }
 
             // General Git details if didn't match the above
@@ -110,4 +129,15 @@ public GitDetails validateAndParse(WorkflowForm form, Errors e) {
         // Errors will stop this being used anyway
         return null;
     }
+
+    /**
+     * Checks if a string is empty or whitespace
+     * @param str The string to be checked
+     * @return Whether the string is empty or whitespace
+     */
+    private boolean isEmptyOrWhitespace(String str) {
+        return (str == null ||
+                str.length() == 0 ||
+                StringUtils.isWhitespace(str));
+    }
 }

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

@@ -88,14 +88,18 @@ public Page<Workflow> searchWorkflowsJson(Model model,
     /**
      * Create a new workflow from the given URL
      * @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
      * @return Appropriate response code and optional JSON string with message
      */
     @PostMapping(value = "/workflows", produces = MediaType.APPLICATION_JSON_UTF8_VALUE)
-    public ResponseEntity<?> newWorkflowFromGithubURLJson(@RequestParam(value="url") String url,
-                                                          HttpServletResponse response) {
+    public ResponseEntity<?> newWorkflowFromGitURLJson(@RequestParam(value="url") String url,
+                                                       @RequestParam(value="branch", required=false) String branch,
+                                                       @RequestParam(value="path", required=false) String path,
+                                                       HttpServletResponse response) {
 
-        // Run validator which checks the github URL is valid
-        WorkflowForm workflowForm = new WorkflowForm(url);
+        // Run validator which checks the URL is valid
+        WorkflowForm workflowForm = new WorkflowForm(url, branch, path);
         BeanPropertyBindingResult errors = new BeanPropertyBindingResult(workflowForm, "errors");
         GitDetails gitInfo = workflowFormValidator.validateAndParse(workflowForm, errors);