Merge basic visualisation

Author: Mark Robinson

src/main/java/org/commonwl/viewer/domain/ROBundle.java

@@ -26,6 +26,8 @@
 import org.commonwl.viewer.services.GitHubService;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.eclipse.egit.github.core.User;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.net.URI;
@@ -40,6 +42,8 @@
  */
 public class ROBundle {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     private GitHubService githubService;
 
     private Bundle bundle;
@@ -87,7 +91,7 @@ public ROBundle(GitHubService githubService, GithubDetails githubInfo,
             manifest.setAuthoredBy(authorList);
 
         } catch (URISyntaxException ex) {
-            System.out.println("Incorrect URI Syntax");
+            logger.error(ex.getMessage());
         }
 
         // Make a directory in the RO bundle to store the files

src/main/java/org/commonwl/viewer/services/ROBundleFactory.java

@@ -21,6 +21,8 @@
 
 import org.commonwl.viewer.domain.GithubDetails;
 import org.commonwl.viewer.domain.ROBundle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.scheduling.annotation.EnableAsync;
@@ -38,6 +40,8 @@
 @EnableAsync
 public class ROBundleFactory {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     @Value("${applicationName}")
     private String applicationName;
     @Value("${applicationURL}")
@@ -53,8 +57,10 @@ public class ROBundleFactory {
     @Async
     void workflowROFromGithub(GitHubService githubService, GithubDetails githubInfo) throws IOException {
         // TODO: Add the bundle link to the page when it is finished being created
+        logger.info("Creating Research Object Bundle");
         ROBundle bundle = new ROBundle(githubService, githubInfo,
                 applicationName, applicationURL);
         bundle.saveToTempFile();
+        logger.info("Successfully saved Research Object Bundle");
     }
-}
+}

src/main/java/org/commonwl/viewer/services/WorkflowFactory.java

@@ -22,6 +22,8 @@
 import org.commonwl.viewer.domain.CWLCollection;
 import org.commonwl.viewer.domain.GithubDetails;
 import org.commonwl.viewer.domain.Workflow;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -31,6 +33,8 @@
 @Service
 public class WorkflowFactory {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     private final GitHubService githubService;
     private final ROBundleFactory ROBundleFactory;
     private final WorkflowRepository workflowRepository;
@@ -60,10 +64,6 @@ public Workflow workflowFromGithub(String githubURL) {
                 // Set up CWL utility to collect the documents
                 CWLCollection cwlFiles = new CWLCollection(githubService, githubInfo);
 
-                // Create a new research object bundle from Github details
-                // This is Async so cannot just call constructor, needs intermediate as per Spring framework
-                ROBundleFactory.workflowROFromGithub(githubService, githubInfo);
-
                 // Get the workflow model
                 Workflow workflowModel = cwlFiles.getWorkflow();
                 if (workflowModel != null) {
@@ -72,19 +72,25 @@ public Workflow workflowFromGithub(String githubURL) {
                     workflowModel.setRetrievedFrom(githubInfo);
 
                     // Save to the MongoDB database
+                    logger.info("Storing workflow in DB");
                     workflowRepository.save(workflowModel);
 
+                    // Create a new research object bundle from Github details
+                    // This is Async so cannot just call constructor, needs intermediate as per Spring framework
+                    ROBundleFactory.workflowROFromGithub(githubService, githubInfo);
+
                     // Return this model to be displayed
                     return workflowModel;
 
                 } else {
-                    System.out.println("Error: no workflow could be found");
+                    logger.error("No workflow could be found");
                 }
             } catch (IOException ex) {
-                System.out.println("Error: " + ex.getMessage());
+                logger.error(ex.getMessage());
             }
         } else {
-            System.out.println("Error should never happen, already passed validation");
+            // TODO: Refactor validator so this redundant step can be removed?
+            logger.error("Error should never happen, already passed URL validation");
         }
 
         return null;

src/main/java/org/commonwl/viewer/services/WorkflowFormValidator.java

@@ -22,6 +22,8 @@
 import org.commonwl.viewer.domain.GithubDetails;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.commonwl.viewer.domain.WorkflowForm;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import org.springframework.validation.Errors;
@@ -37,6 +39,8 @@
 @Component
 public class WorkflowFormValidator implements Validator {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     /**
      * Github API service
      */
@@ -89,16 +93,21 @@ public void validate(Object obj, Errors e) {
                     }
                     if (!foundCWL) {
                         // The URL does not contain any .cwl files
+                        logger.error("No .cwl files found at Github URL");
                         e.rejectValue("githubURL", "githubURL.missingWorkflow");
                     }
                 } catch (IOException ex) {
                     // Given repository/branch/path does not exist or API error occured
+                    logger.error(ex.getMessage());
                     e.rejectValue("githubURL", "githubURL.apiError");
                 }
             } else {
                 // The Github URL is not valid
+                logger.error("The Github URL is not valid");
                 e.rejectValue("githubURL", "githubURL.invalid");
             }
+        } else {
+            logger.error("Github URL is empty");
         }
     }
 }

src/main/java/org/commonwl/viewer/web/WorkflowController.java

@@ -23,17 +23,23 @@
 import org.commonwl.viewer.domain.WorkflowForm;
 import org.commonwl.viewer.services.WorkflowFactory;
 import org.commonwl.viewer.services.WorkflowFormValidator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.validation.BindingResult;
+import org.springframework.validation.ObjectError;
 import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.servlet.ModelAndView;
 
 import javax.validation.Valid;
+import java.util.List;
 
 @Controller
 public class WorkflowController {
 
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
     private final WorkflowFormValidator workflowFormValidator;
     private final WorkflowFactory workflowFactory;
 
@@ -56,6 +62,8 @@ public WorkflowController(WorkflowFormValidator workflowFormValidator, WorkflowF
      */
     @PostMapping("/")
     public ModelAndView newWorkflowFromGithubURL(@Valid WorkflowForm workflowForm, BindingResult bindingResult) {
+        logger.info("Processing new workflow from Github: \"" + workflowForm.getGithubURL() + "\"");
+
         // Run validator which checks the github URL is valid
         workflowFormValidator.validate(workflowForm, bindingResult);
 

src/main/resources/static/css/main.css

@@ -72,13 +72,4 @@ body {
     text-align: center;
     font-style: italic;
     margin-bottom: 30px;
-    margin-top: 15px;
 }
-
-#footer a {
-    color: #939393;
-}
-
-#footer a:hover {
-    color: #494949;
-}

src/main/resources/templates/fragments/footer.html

@@ -19,16 +19,25 @@
   -->
 
 <html xmlns:th="http://www.thymeleaf.org">
+<head>
+    <link rel="stylesheet" type="text/css" href="../../static/css/main.css" />
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css" />
+</head>
 <body>
-    <div th:fragment="copy" id="footer">
-        <a href="https://github.com/common-workflow-language/cwlviewer" rel="noopener" target="_blank">CWL Viewer</a>
-        &copy; 2016 <a href="https://github.com/common-workflow-language/" rel="noopener" target="_blank">Common Workflow Project</a>
-        and <a href="https://github.com/orgs/common-workflow-language/people" rel="noopener" target="_blank">contributors</a>,
-        distributed under <a href="https://www.apache.org/licenses/LICENSE-2.0" rel="noopener" target="_blank">Apache license, version 2.0</a>
-        <br />
-        <span th:if="${workflow != null}">
-            <a th:href="@{'https://github.com/' + ${workflow.retrievedFrom.owner} + '/' + ${workflow.retrievedFrom.repoName}}" href="#" rel="noopener" target="_blank">Shown workflow</a> has separate copyright and license
-        </span>
+    <div th:fragment="copy" id="footer" class="container">
+        <div class="row">
+            <hr />
+            <div class="col-lg-12 muted text-center">
+                <a href="https://github.com/common-workflow-language/cwlviewer" rel="noopener" target="_blank">CWL Viewer</a>
+                &copy; 2016 <a href="https://github.com/common-workflow-language/" rel="noopener" target="_blank">Common Workflow Project</a>
+                and <a href="https://github.com/orgs/common-workflow-language/people" rel="noopener" target="_blank">contributors</a>,
+                distributed under <a href="https://www.apache.org/licenses/LICENSE-2.0" rel="noopener" target="_blank">Apache license, version 2.0</a>
+                <br />
+                <span th:if="${workflow != null}">
+                    <a th:href="@{'https://github.com/' + ${workflow.retrievedFrom.owner} + '/' + ${workflow.retrievedFrom.repoName}}" href="#" rel="noopener" target="_blank">Shown workflow</a> has separate copyright and license
+                </span>
+            </div>
+        </div>
     </div>
 </body>
 </html>