Merge pull request #95 from common-workflow-language/tests

Addition of Unit Testing

Author: MarkRobbo

.travis.yml

@@ -4,3 +4,7 @@ dist: trusty
 language: java
 
 services: mongodb
+
+before_install:
+  - sudo apt-get -qq update
+  - sudo apt-get install graphviz

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

@@ -282,7 +282,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
                 // Explicit ID and other fields within each input list
                 for (JsonNode step : steps) {
                     CWLStep stepObject = new CWLStep(extractLabel(step), extractDoc(step),
-                            extractTypes(step), extractRun(step), getInputs(step), getOutputs(step));
+                            extractRun(step), getInputs(step));
                     returnMap.put(extractID(step), stepObject);
                 }
             } else if (steps.getClass() == ObjectNode.class) {
@@ -292,8 +292,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
                     Map.Entry<String, JsonNode> stepNode = iterator.next();
                     JsonNode stepJson = stepNode.getValue();
                     CWLStep stepObject = new CWLStep(extractLabel(stepJson), extractDoc(stepJson),
-                            extractTypes(stepJson), extractRun(stepJson), getInputs(stepJson),
-                            getOutputs(stepJson));
+                            extractRun(stepJson), getInputs(stepJson));
                     returnMap.put(stepNode.getKey(), stepObject);
                 }
             }
@@ -311,7 +310,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
     private Map<String, CWLElement> getInputs(JsonNode cwlDoc) {
         if (cwlDoc != null) {
             if (cwlDoc.has(INPUTS)) {
-                // For workflow/draft steps
+                // For all version workflow inputs/outputs and draft steps
                 return getInputsOutputs(cwlDoc.get(INPUTS));
             } else if (cwlDoc.has(IN)) {
                 // For V1.0 steps
@@ -328,13 +327,11 @@ private Map<String, CWLElement> getInputs(JsonNode cwlDoc) {
      */
     private Map<String, CWLElement> getOutputs(JsonNode cwlDoc) {
         if (cwlDoc != null) {
+            // For all version workflow inputs/outputs and draft steps
             if (cwlDoc.has(OUTPUTS)) {
-                // For workflow/draft steps
                 return getInputsOutputs(cwlDoc.get(OUTPUTS));
-            } else if (cwlDoc.has(OUT)) {
-                // For V1.0 steps
-                return getStepInputsOutputs(cwlDoc.get(OUT));
             }
+            // Outputs are not gathered for v1 steps
         }
         return null;
     }
@@ -668,7 +665,7 @@ private String extractTypes(JsonNode typeNode) {
                 }
 
                 // Add optional if null was included in the multiple types
-                if (optional) typeDetails.append(" (Optional)");
+                if (optional) typeDetails.append("?");
 
                 // Set the type to the constructed string
                 return typeDetails.toString();

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

@@ -28,20 +28,16 @@ public class CWLStep {
 
     private String label;
     private String doc;
-    private String type;
     private String run;
     private CWLProcess runType;
-    private Map<String, CWLElement> inputs;
-    private Map<String, CWLElement> outputs;
+    private Map<String, CWLElement> sources;
 
-    public CWLStep(String label, String doc, String type, String run,
-                   Map<String, CWLElement> inputs, Map<String, CWLElement> outputs) {
+    public CWLStep(String label, String doc, String run,
+                   Map<String, CWLElement> sources) {
         this.label = label;
         this.doc = doc;
-        this.type = type;
         this.run = run;
-        this.inputs = inputs;
-        this.outputs = outputs;
+        this.sources = sources;
     }
 
     public String getLabel() {
@@ -60,14 +56,6 @@ public void setDoc(String doc) {
         this.doc = doc;
     }
 
-    public String getType() {
-        return type;
-    }
-
-    public void setType(String type) {
-        this.type = type;
-    }
-
     public String getRun() {
         return run;
     }
@@ -84,20 +72,8 @@ public void setRunType(CWLProcess runType) {
         this.runType = runType;
     }
 
-    public Map<String, CWLElement> getInputs() {
-        return inputs;
-    }
-
-    public void setInputs(Map<String, CWLElement> inputs) {
-        this.inputs = inputs;
-    }
-
-    public Map<String, CWLElement> getOutputs() {
-        return outputs;
-    }
-
-    public void setOutputs(Map<String, CWLElement> outputs) {
-        this.outputs = outputs;
+    public Map<String, CWLElement> getSources() {
+        return sources;
     }
 
 }

src/main/java/org/commonwl/view/docker/DockerService.java

@@ -20,8 +20,8 @@ public class DockerService {
     public static String getDockerHubURL(String dockerPull) {
         Matcher m = dockerhubPattern.matcher(dockerPull);
         if (m.find()) {
-            if (m.group(1).isEmpty()) {
-                return "https://hub.docker.com/r/_/" + m.group(2);
+            if (m.group(2) == null) {
+                return "https://hub.docker.com/r/_/" + m.group(1);
             } else {
                 return "https://hub.docker.com/r/" + m.group(1) + "/" + m.group(2);
             }

src/main/java/org/commonwl/view/github/GitHubService.java

@@ -54,12 +54,12 @@ public class GitHubService {
     private final CommitService commitService;
 
     // URL validation for directory links
-    private final String GITHUB_DIR_REGEX = "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree|blob)\\/([^/]+)\\/?(.*)?)?$";
-    private final Pattern githubDirPattern = Pattern.compile(GITHUB_DIR_REGEX);
+    private static final String GITHUB_DIR_REGEX = "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree|blob)\\/([^/]+)\\/?(.*)?)?$";
+    private static final Pattern githubDirPattern = Pattern.compile(GITHUB_DIR_REGEX);
 
     // URL validation for cwl files
-    private final String GITHUB_CWL_REGEX = "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
-    private final Pattern githubCwlPattern = Pattern.compile(GITHUB_CWL_REGEX);
+    private static final String GITHUB_CWL_REGEX = "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
+    private static final Pattern githubCwlPattern = Pattern.compile(GITHUB_CWL_REGEX);
 
     private final boolean downloadWithAPI;
 

src/main/java/org/commonwl/view/github/GithubDetails.java

@@ -97,7 +97,7 @@ public String getURL() {
      */
     public String getURL(String ref) {
         String url = "https://github.com/" + owner + "/" + repoName + "/tree/" + ref;
-        if (path != null) {
+        if (path != null && !path.equals("/")) {
             url += "/" + this.path;
         }
         return url;

src/main/java/org/commonwl/view/graphviz/DotWriter.java

@@ -173,8 +173,8 @@ private void writeSteps(Workflow workflow) throws IOException {
         // Write links between the remaining steps
         int defaultCount = 0;
         for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
-            if (step.getValue().getInputs() != null) {
-                for (Map.Entry<String, CWLElement> input : step.getValue().getInputs().entrySet()) {
+            if (step.getValue().getSources() != null) {
+                for (Map.Entry<String, CWLElement> input : step.getValue().getSources().entrySet()) {
                     List<String> sourceIDs = input.getValue().getSourceIDs();
 
                     // Draw the default value on the graph if there are no step inputs (it is a constant)

src/main/java/org/commonwl/view/researchobject/ROBundleFactory.java

@@ -20,14 +20,13 @@
 package org.commonwl.view.researchobject;
 
 import org.apache.commons.io.FilenameUtils;
-import org.commonwl.view.github.GitHubService;
+import org.apache.taverna.robundle.Bundle;
 import org.commonwl.view.github.GithubDetails;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.stereotype.Component;
@@ -47,34 +46,24 @@ public class ROBundleFactory {
 
     private final Logger logger = LoggerFactory.getLogger(this.getClass());
 
-    private final String applicationName;
-    private final String applicationURL;
-    private final int singleFileSizeLimit;
-    private final Path storageLocation;
     private final WorkflowRepository workflowRepository;
+    private final ROBundleService roBundleService;
 
     @Autowired
-    public ROBundleFactory(@Value("${applicationName}") String applicationName,
-                           @Value("${applicationURL}") String applicationURL,
-                           @Value("${graphvizStorage}") Path graphvizStorage,
-                           @Value("${singleFileSizeLimit}") int singleFileSizeLimit,
+    public ROBundleFactory(ROBundleService roBundleService,
                            WorkflowRepository workflowRepository) {
-        this.applicationName = applicationName;
-        this.applicationURL = applicationURL;
-        this.storageLocation = graphvizStorage;
         this.workflowRepository = workflowRepository;
-        this.singleFileSizeLimit = singleFileSizeLimit;
+        this.roBundleService = roBundleService;
     }
 
     /**
      * Creates a new Workflow Research Object Bundle from a Github URL
      * and saves it to a file
-     * @param githubService The service for Github API functionality
      * @param githubInfo Details of the Github repository
      * @throws IOException Any API errors which may have occurred
      */
     @Async
-    public void workflowROFromGithub(GitHubService githubService, GithubDetails githubInfo)
+    public void workflowROFromGithub(GithubDetails githubInfo)
             throws IOException, InterruptedException {
         logger.info("Creating Research Object Bundle");
 
@@ -83,16 +72,15 @@ public void workflowROFromGithub(GitHubService githubService, GithubDetails gith
                 githubInfo.getBranch(), FilenameUtils.getPath(githubInfo.getPath()));
 
         // Create a new Research Object Bundle with Github contents
-        ROBundle bundle = new ROBundle(githubService, roDetails,
-                applicationName, applicationURL, singleFileSizeLimit);
+        Bundle bundle = roBundleService.newBundleFromGithub(roDetails);
 
         // Save the bundle to the storage location in properties
-        Path bundleLocation = bundle.saveToFile(storageLocation);
+        Path bundleLocation = roBundleService.saveToFile(bundle);
 
         // Add the path to the bundle to the bundle
         Workflow workflow = workflowRepository.findByRetrievedFrom(githubInfo);
 
-        // Chance that this thread could be created before workflow model is saved
+        // Chance that this thread could be done before workflow model is saved
         int attempts = 5;
         while (attempts > 0 && workflow == null) {
             // Delay this thread by 0.5s and try again until success or too many attempts