CWL to graph endpoint (#241)

stain · fbacall · kinow · web-flow · commit 7b8eb6764222 · 2021-09-30T13:52:28.000+02:00
Co-authored-by: Finn Bacall &lt;finn.bacall@manchester.ac.uk&gt;
Co-authored-by: Bruno P. Kinoshita &lt;kinow@users.noreply.github.com&gt;
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM maven:3.5-jdk-8-alpine
+FROM maven:3.6-jdk-8-alpine
 MAINTAINER Stian Soiland-Reyes <stain@apache.org>
 
 # Build-time metadata as defined at http://label-schema.org
diff --git a/src/main/java/org/commonwl/view/cwl/CWLService.java b/src/main/java/org/commonwl/view/cwl/CWLService.java
@@ -169,7 +169,7 @@ public List<WorkflowOverview> getWorkflowOverviewsFromPacked(File packedFile) th
      * Note, the length of the stream is not checked.
      *  
      * @param workflowStream The workflow stream to be parsed
-     * @param packedWorkflowId The ID of the workflow object if the file is packed
+     * @param packedWorkflowId The ID of the workflow object if the file is packed. <code>null</code> means the workflow is not expected to be packed, while "" means the first workflow found is used, packed or non-packed.
      * @param defaultLabel Label to give workflow if not set
      * @return The constructed workflow object
      */
@@ -178,29 +178,31 @@ public Workflow parseWorkflowNative(InputStream workflowStream, String packedWor
         JsonNode cwlFile = yamlStreamToJson(workflowStream);
 
         // Check packed workflow occurs
+        boolean found = false;
         if (packedWorkflowId != null) {
-            boolean found = false;
             if (cwlFile.has(DOC_GRAPH)) {
                 for (JsonNode jsonNode : cwlFile.get(DOC_GRAPH)) {
                     if (extractProcess(jsonNode) == CWLProcess.WORKFLOW) {
                         String currentId = jsonNode.get(ID).asText();
                         if (currentId.startsWith("#")) {
                             currentId = currentId.substring(1);
                         }
-                        if (currentId.equals(packedWorkflowId)) {
+                        if (packedWorkflowId.isEmpty() || currentId.equals(packedWorkflowId)) {
                             cwlFile = jsonNode;
                             found = true;
                             break;
                         }
                     }
                 }
             }
-            if (!found) throw new WorkflowNotFoundException();
-        } else {
-            // Check the current json node is a workflow
-            if (extractProcess(cwlFile) != CWLProcess.WORKFLOW) {
-                throw new WorkflowNotFoundException();
-            }
+            if (!found && ! packedWorkflowId.isEmpty()) throw new WorkflowNotFoundException();
+        }
+        if (! found && extractProcess(cwlFile) == CWLProcess.WORKFLOW) {
+        	// Check the current json node is a workflow
+        	found = true;
+        }
+        if (! found) {
+            throw new WorkflowNotFoundException();
         }
 
         // Use filename for label if there is no defined one
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowController.java b/src/main/java/org/commonwl/view/workflow/WorkflowController.java
@@ -20,16 +20,24 @@
 package org.commonwl.view.workflow;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.Path;
+import java.io.InputStream;
+import java.security.DigestInputStream;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
 import java.util.List;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.validation.Valid;
 
+import org.apache.commons.codec.binary.Hex;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.commonwl.view.WebConfig;
+import org.commonwl.view.cwl.CWLService;
 import org.commonwl.view.cwl.CWLToolStatus;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.graphviz.GraphVizService;
@@ -40,6 +48,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.FileSystemResource;
+import org.springframework.core.io.InputStreamResource;
 import org.springframework.core.io.PathResource;
 import org.springframework.core.io.Resource;
 import org.springframework.data.domain.Pageable;
@@ -48,11 +57,7 @@
 import org.springframework.ui.Model;
 import org.springframework.validation.BeanPropertyBindingResult;
 import org.springframework.validation.BindingResult;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.*;
 import org.springframework.web.servlet.HandlerMapping;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
@@ -64,6 +69,7 @@ public class WorkflowController {
 
     private final WorkflowFormValidator workflowFormValidator;
     private final WorkflowService workflowService;
+    private final CWLService cwlService;
     private final GraphVizService graphVizService;
 
     /**
@@ -79,10 +85,11 @@ public class WorkflowController {
     @Autowired
     public WorkflowController(WorkflowFormValidator workflowFormValidator,
                               WorkflowService workflowService,
-            GraphVizService graphVizService) {
+            GraphVizService graphVizService, CWLService cwlService) {
         this.workflowFormValidator = workflowFormValidator;
         this.workflowService = workflowService;
         this.graphVizService = graphVizService;
+        this.cwlService = cwlService;
     }
 
     /**
@@ -396,6 +403,32 @@ public PathResource getTempGraphAsPng(@PathVariable("queueID") String queueID,
         return new PathResource(out);
     }
 
+    /**
+     * Take a CWL workflow from the POST body and generate a PNG graph for it.
+     * @param in The workflow CWL
+     */
+    @PostMapping(value="/graph/png", produces="image/png", 
+    		consumes={"text/yaml", "text/x-yaml", "text/plain", "application/octet-stream"})
+    @ResponseBody
+    public Resource downloadGraphPngFromFile(InputStream in, HttpServletResponse response)
+            throws IOException, NoSuchAlgorithmException {
+        response.setHeader("Content-Disposition", "inline; filename=\"graph.png\"");
+        return getGraphFromInputStream(in, "png");
+    }
+
+    /**
+     * Take a CWL workflow from the POST body and generate a SVG graph for it.
+     * @param in The workflow CWL as YAML text
+     */
+    @PostMapping(value="/graph/svg", produces="image/svg+xml", 
+    		consumes={"text/yaml", "text/x-yaml", "text/plain", "application/octet-stream"})
+    @ResponseBody
+    public Resource downloadGraphSvgFromFile(InputStream in, HttpServletResponse response)
+            throws IOException, NoSuchAlgorithmException {
+        response.setHeader("Content-Disposition", "inline; filename=\"graph.svg\"");
+        return getGraphFromInputStream(in, "svg");
+    }
+
 
     /**
      * Extract the path from the end of a full request string
@@ -549,4 +582,11 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
                     WebConfig.Format.values());
         }
     }
+
+    private Resource getGraphFromInputStream(InputStream in, String format)
+            throws IOException, NoSuchAlgorithmException {
+        Workflow workflow = cwlService.parseWorkflowNative(in, null, "workflow"); // first workflow will do
+        InputStream out = graphVizService.getGraphStream(workflow.getVisualisationDot(), format);
+        return new InputStreamResource(out);
+    }
 }
diff --git a/src/main/resources/templates/apidocs.html b/src/main/resources/templates/apidocs.html
@@ -39,7 +39,7 @@ <h1>JSON API Documentation</h1>
 
                     <p>If you make anything utilizing our API, please <a href="https://gitter.im/common-workflow-language/cwlviewer" alt="Gitter Chatroom" target="_blank" rel="noopener">let us know about it</a> - we would love to see!</p>
 
-                    <p>All queries require the following header to receive a JSON response:
+                    <p>Except where noted otherwise, all queries require the following header to receive a JSON response:
                         <pre class="highlight http">accept: application/json</pre>
                     </p>
 
@@ -652,6 +652,130 @@ <h4>cwlviewer.py</h4>
 else:
     print('Error adding workflow')
 </pre>
+
+
+                    <h3 id="graphSvg">SVG sketch of CWL workflow</h3>
+                    <div class="alert alert-info"><strong>Note:</strong> This method uses a brief YAML
+                    parsing of the standalone CWL file that does not support annotations
+                    like <kbd>label</kbd> or <kbd>doc</kbd>, and that does not check 
+                    for validity or completeness.
+                    </div>
+                    <span class="method post">POST</span>
+                    <pre>/graph/svg</pre>                    
+                    <h4>Input</h4>
+<pre class="highlight http">
+Content-Type: text/yaml
+</pre>
+<pre class="highlight yaml">
+#!/usr/bin/env cwl-runner
+  
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+  usermessage: string
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]
+</pre>
+<h4>Output</h4>
+<p><samp>Content-Type: image/svg+xml</samp></p>
+<pre class="highlight xml">
+&lt;?xml version="1.0" encoding="UTF-8" standalone="no"?&gt;
+&lt;!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"&gt;
+&lt;svg width="450pt" height="270pt"
+     viewBox="0.00 0.00 463.00 278.00" xmlns="http://www.w3.org/2000/svg"&gt;
+	&lt;!-- ... --&gt;
+&lt;/svg&gt;
+</pre>
+                    <h4>Success</h4>
+<pre class="highlight http">
+HTTP/1.1 200 OK
+Content-Type: image/svg+xml
+</pre>
+                    <h4>Error</h4>
+                    <pre class="highlight http">HTTP/1.1 400 Bad Request</pre>
+
+
+                    <h3 id="graphPng">PNG sketch of CWL workflow</h3>
+                    <div class="alert alert-info"><strong>Note:</strong> This method uses a brief YAML
+                    parsing of the standalone CWL file that does not support annotations
+                    like <kbd>label</kbd> or <kbd>doc</kbd>, and that does not check 
+                    for validity or completeness.
+                    </div>
+                    <span class="method post">POST</span>
+                    <pre>/graph/png</pre>                    
+                    <h4>Input</h4>
+
+<pre class="highlight http">
+Content-Type: text/yaml
+</pre>
+<pre class="highlight yaml">
+#!/usr/bin/env cwl-runner
+  
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+  usermessage: string
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]
+</pre>
+
+<h4>Output</h4>
+
+<pre class="highlight">
+\x89PNG\n\x1a\n\x00\x00 (binary)
+</pre>
+                    <h4>Success</h4>
+<pre class="highlight http">
+HTTP/1.1 200 OK
+Content-Type: image/png
+</pre>
+                    <h4>Error</h4>
+                    <pre class="highlight http">HTTP/1.1 400 Bad Request</pre>
+
+
+
                 </div>
             </div>
         </div>
diff --git a/src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java b/src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-FROM maven:3.5-jdk-8-alpine`
	`1`	`+FROM maven:3.6-jdk-8-alpine`
`2`	`2`	`MAINTAINER Stian Soiland-Reyes <stain@apache.org>`
`3`	`3`
`4`	`4`	`# Build-time metadata as defined at http://label-schema.org`