Merge pull request #61 from common-workflow-language/docker-requirement

Parse DockerRequirement and add DockerHub link to page

Author: MarkRobbo

LICENSE.md

@@ -212,3 +212,11 @@ been federally registered with the United States Copyright Office.
 All rights reserved.
 
 Use rules apply: https://github.com/logos
+
+---------------------------------------------------------
+
+./src/main/resources/static/img/Docker-logo.png
+
+Copyright 2013-2015 Docker, Inc. All rights reserved.
+
+Use rules apply: https://www.docker.com/brand-guidelines

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

@@ -24,12 +24,15 @@
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.databind.node.TextNode;
+import org.commonwl.viewer.services.DockerService;
 import org.eclipse.egit.github.core.RepositoryContents;
 import org.commonwl.viewer.services.GitHubService;
 import org.yaml.snakeyaml.Yaml;
 
 import java.io.IOException;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Provides CWL parsing for workflows to gather an overview
@@ -74,6 +77,14 @@ public class CWLCollection {
     private final String ARRAY = "array";
     private final String ARRAY_ITEMS = "items";
     private final String LOCATION = "location";
+    private final String REQUIREMENTS = "requirements";
+    private final String HINTS = "hints";
+    private final String DOCKER_REQUIREMENT = "DockerRequirement";
+    private final String DOCKER_PULL = "dockerPull";
+
+    // URL validation for docker pull id
+    private final String DOCKERHUB_ID_REGEX = "^([0-9a-z]{4,30})(?:\\/([a-zA-Z0-9_-]+))?(?:\\:[a-zA-Z0-9_-]+)?$";
+    private final Pattern dockerhubPattern = Pattern.compile(DOCKERHUB_ID_REGEX);
 
     /**
      * Creates a new collection of CWL files from a Github repository
@@ -197,7 +208,7 @@ public Workflow getWorkflow() {
         }
 
         return new Workflow(label, extractDoc(mainWorkflow), getInputs(mainWorkflow),
-                            getOutputs(mainWorkflow), getSteps(mainWorkflow));
+                            getOutputs(mainWorkflow), getSteps(mainWorkflow), getDockerLink(mainWorkflow));
     }
 
     /**
@@ -371,6 +382,69 @@ private CWLElement getDetails(JsonNode inputOutput) {
         return null;
     }
 
+    /**
+     * Get the docker link from a workflow node
+     * @param node The overall workflow node
+     * @return A string with a dockerhub or image link
+     */
+    private String getDockerLink(JsonNode node) {
+        if (node != null) {
+            if (node.has(REQUIREMENTS)) {
+                String dockerLink = extractDockerLink(node.get(REQUIREMENTS));
+                if (dockerLink != null) {
+                    return extractDockerLink(node.get(REQUIREMENTS));
+                }
+            }
+            if (node.has(HINTS)) {
+                String dockerLink = extractDockerLink(node.get(HINTS));
+                if (dockerLink != null) {
+                    return extractDockerLink(node.get(HINTS));
+                }
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Get the docker link from a workflow hints or requriements node
+     * @param hintReq A hints or requirements node
+     * @return A string with a dockerhub or image link
+     */
+    private String extractDockerLink(JsonNode hintReq) {
+        // ArrayNode syntax using yaml lists
+        if (hintReq.getClass() == ArrayNode.class) {
+            for (JsonNode requirement : hintReq) {
+                if (requirement.has(CLASS)
+                        && requirement.get(CLASS).asText().equals(DOCKER_REQUIREMENT)) {
+                    if (requirement.has(DOCKER_PULL)) {
+                        // Format dockerPull string as a dockerhub URL
+                        return DockerService.getDockerHubURL(requirement.get(DOCKER_PULL).asText());
+                    } else {
+                        // Indicate that the docker requirement exists, but we cannot
+                        // provide a link to dockerhub as docker pull is not used
+                        return "true";
+                    }
+                }
+            }
+            // v1.0 object syntax with requirement class as key
+        } else if (hintReq.getClass() == ObjectNode.class) {
+            // Look for DockerRequirement
+            if (hintReq.has(DOCKER_REQUIREMENT)) {
+                JsonNode dockerReq = hintReq.get(DOCKER_REQUIREMENT);
+                if (dockerReq.has(DOCKER_PULL)) {
+                    // Format dockerPull string as a dockerhub URL
+                    String dockerPull = dockerReq.get(DOCKER_PULL).asText();
+                    return DockerService.getDockerHubURL(dockerPull);
+                } else {
+                    // Indicate that the docker requirement exists, but we cannot
+                    // provide a link to dockerhub as docker pull is not used
+                    return "true";
+                }
+            }
+        }
+        return null;
+    }
+
     /**
      * Extract the id from a node
      * @param node The node to have the id extracted from

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

@@ -65,16 +65,20 @@ public class Workflow {
     private Map<String, CWLElement> outputs;
     private Map<String, CWLStep> steps;
 
+    // Currently only DockerRequirement is parsed for this
+    private String dockerLink;
+
     // DOT graph of the contents
     private String dotGraph;
 
     public Workflow(String label, String doc, Map<String, CWLElement> inputs,
-                    Map<String, CWLElement> outputs, Map<String, CWLStep> steps) {
+                    Map<String, CWLElement> outputs, Map<String, CWLStep> steps, String dockerLink) {
         this.label = label;
         this.doc = doc;
         this.inputs = inputs;
         this.outputs = outputs;
         this.steps = steps;
+        this.dockerLink = dockerLink;
 
         // Create a DOT graph for this workflow and store it
         StringWriter graphWriter = new StringWriter();
@@ -172,4 +176,12 @@ public String getLastCommit() {
     public void setLastCommit(String lastCommit) {
         this.lastCommit = lastCommit;
     }
+
+    public String getDockerLink() {
+        return dockerLink;
+    }
+
+    public void setDockerLink(String dockerLink) {
+        this.dockerLink = dockerLink;
+    }
 }

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

@@ -0,0 +1,32 @@
+package org.commonwl.viewer.services;
+
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Handles DockerHub functionality
+ */
+public class DockerService {
+
+    // URL validation for docker pull id
+    private static final String DOCKERHUB_ID_REGEX = "^([0-9a-z]{4,30})(?:\\/([a-zA-Z0-9_-]+))?(?:\\:[a-zA-Z0-9_-]+)?$";
+    private static final Pattern dockerhubPattern = Pattern.compile(DOCKERHUB_ID_REGEX);
+
+    /**
+     * Get a DockerHub URL from a dockerPull ID
+     * @param dockerPull The repository and ID as a string
+     * @return A docker hub link
+     */
+    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);
+            } else {
+                return "https://hub.docker.com/r/" + m.group(1) + "/" + m.group(2);
+            }
+        }
+        return null;
+    }
+
+}

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

@@ -55,6 +55,11 @@ body {
     margin-right: 5px;
 }
 
+#dockerLogo {
+    height: 75px;
+    margin-left: 10px;
+}
+
 #fullscreen-open, #fullscreen-close {
     cursor: pointer;
     font-size: 25px;

src/main/resources/static/img/Docker-logo.png

@@ -151,6 +151,13 @@ <h2>Workflow: <span th:text="${workflow.label}">Workflow Name</span></h2>
                     <img th:src="@{'/workflows/' + ${workflow.id} + '/graph/png'}" alt="workflow graph" />
                 </object>
             </div>
+            <div th:if="${workflow.dockerLink != null}">
+                <h2 style="float:left;">Requires: </h2>
+                <a th:unless="${workflow.dockerLink == 'true'}" th:href="${workflow.dockerLink}">
+                    <img id="dockerLogo" src="/img/Docker-logo.png" alt="docker logo" />
+                </a>
+                <img th:if="${workflow.dockerLink == 'true'}" id="dockerLogo" src="/img/Docker-logo.png" alt="docker logo" />
+            </div>
             <h2>Inputs</h2>
             <div th:if="${workflow.inputs.isEmpty()}" class="alert alert-info">
                 <p>There are no inputs in this workflow</p>