Mock githubService to allow testing without network

Author: Mark Robinson

src/test/java/org/commonwl/view/cwl/CWLServiceTest.java

@@ -1,34 +1,48 @@
 package org.commonwl.view.cwl;
 
+import org.apache.commons.io.FileUtils;
+import org.commonwl.view.github.GitHubService;
 import org.commonwl.view.github.GithubDetails;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowOverview;
 import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.context.junit4.SpringRunner;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
 
+import java.io.File;
 import java.util.Map;
 
 import static org.junit.Assert.*;
+import static org.mockito.Matchers.anyObject;
+import static org.mockito.Mockito.when;
 
-@RunWith(SpringRunner.class)
-@SpringBootTest
 public class CWLServiceTest {
 
-    /**
-     * Create a service to test
-     */
-    @Autowired
-    private CWLService cwlService;
-
     /**
      * Test main parsing of a the LobSTR workflow CWL version draft-3
      */
     @Test
     public void parseLobSTRDraft3Workflow() throws Exception {
 
+        // Mock githubService class
+        GitHubService githubService = Mockito.mock(GitHubService.class);
+        Answer fileAnswer = new Answer<String>() {
+            @Override
+            public String answer(InvocationOnMock invocation) throws Throwable {
+                Object[] args = invocation.getArguments();
+                GithubDetails details = (GithubDetails) args[0];
+                File workflowFile = new File("src/test/resources/cwl/lobstr-draft3/"
+                        + details.getPath().replace("workflows/lobSTR/", ""));
+                return FileUtils.readFileToString(workflowFile);
+            }
+        };
+        when(githubService.downloadFile(anyObject())).thenAnswer(fileAnswer);
+        when(githubService.downloadFile(anyObject(), anyObject())).thenAnswer(fileAnswer);
+
+        // Test cwl service
+        CWLService cwlService = new CWLService(githubService, 5242880);
+
         // Get workflow from community repo by commit ID so it will not change
         GithubDetails lobSTRDraft3Details = new GithubDetails("common-workflow-language",
                 "workflows", null, "workflows/lobSTR/lobSTR-workflow.cwl");
@@ -46,6 +60,24 @@ public void parseLobSTRDraft3Workflow() throws Exception {
     @Test
     public void parseLobSTRv1Workflow() throws Exception {
 
+        // Mock githubService class
+        GitHubService githubService = Mockito.mock(GitHubService.class);
+        Answer fileAnswer = new Answer<String>() {
+            @Override
+            public String answer(InvocationOnMock invocation) throws Throwable {
+                Object[] args = invocation.getArguments();
+                GithubDetails details = (GithubDetails) args[0];
+                File workflowFile = new File("src/test/resources/cwl/lobstr-v1/"
+                        + details.getPath().replace("workflows/lobSTR/", ""));
+                return FileUtils.readFileToString(workflowFile);
+            }
+        };
+        when(githubService.downloadFile(anyObject())).thenAnswer(fileAnswer);
+        when(githubService.downloadFile(anyObject(), anyObject())).thenAnswer(fileAnswer);
+
+        // Test cwl service
+        CWLService cwlService = new CWLService(githubService, 5242880);
+
         // Get workflow from community repo by commit ID so it will not change
         GithubDetails lobSTRv1Details = new GithubDetails("common-workflow-language",
                 "workflows", null, "workflows/lobSTR/lobSTR-workflow.cwl");
@@ -104,6 +136,15 @@ private void testLobSTRWorkflow(Workflow lobSTR) throws Exception {
     @Test
     public void getHelloWorkflowOverview() throws Exception {
 
+        // Mock githubService class
+        GitHubService githubService = Mockito.mock(GitHubService.class);
+        File workflowFile = new File("src/test/resources/cwl/hello/hello.cwl");
+        when(githubService.downloadFile(anyObject()))
+                .thenReturn(FileUtils.readFileToString(workflowFile));
+
+        // Test cwl service
+        CWLService cwlService = new CWLService(githubService, 5242880);
+
         // Get workflow from community repo by commit ID so it will not change
         GithubDetails helloDetails = new GithubDetails("common-workflow-language",
                 "workflows", "8296e92d358bb5da4dc3c6e7aabefa89726e3409", "workflows/hello/hello.cwl");

src/test/resources/cwl/hello/README.md

@@ -0,0 +1,70 @@
+A simple CWL workflow printing "Hello World" into a File.
+
+See : https://github.com/common-workflow-language/workflows/pull/2
+
+## echo 'Hello'
+
+Execute:
+
+```bash
+$ cwl-runner  hello.cwl 
+cwl-runner 1.0.20150728161219
+Must provide input in the form of a json file or command line parameters.
+[job 177019500] exec echo 'Hello World' > /tmp/tmpz9BXNP/messageout.txt
+[workflow 177019180] outdir is /path/to/workflows/workflows/hello
+Final process status is success
+{
+    "output": {
+        "path": "//path/to/workflows/workflows/hello/messageout.txt", 
+        "checksum": "sha1$648a6a6ffffdaa0badb23b8baf90b6168dd16b3a", 
+        "class": "File", 
+        "size": 12
+    }
+}
+
+
+$ cat /path/to/workflows/workflows/hello/messageout.txt
+Hello World
+```
+
+## echo 'Hello' with parameters
+
+```bash
+$ cwl-runner  hello-param.cwl params.json
+cwl-runner 1.0.20150728161219
+[job 153175084] exec echo -n -e 'Hello, CWL !
+Hello World !' > /tmp/tmp1er8QF/useroutput.txt
+[workflow 153177196] outdir is workflows/hello
+Final process status is success
+{
+    "output": {
+        "path": "workflows/hello/useroutput.txt", 
+        "checksum": "sha1$e8bb28df025c10299db8e73281fbf96d402a1bc0", 
+        "class": "File", 
+        "size": 26
+    }
+}
+
+$ cat useroutput.txt 
+Hello, CWL !
+Hello World !
+```
+
+with parameters specified on the command line:
+
+```bash
+$ cwl-runner  hello-param.cwl --usermessage "Yellow submarine" --useroutput song.txt
+cwl-runner 1.0.20150728161219
+[job 154935692] exec echo -n -e 'Yellow submarine' > /tmp/tmpljSIiy/song.txt
+[workflow 154938540] outdir is workflows/hello
+Final process status is success
+{
+    "output": {
+        "path": "workflows/hello/song.txt", 
+        "checksum": "sha1$72fd47e534c95ce205f8fa1d2f78ab144e6a04ff", 
+        "class": "File", 
+        "size": 16
+    }
+}lindenb@hardyweinberg:~/src/cwl-workflows/workflows/hello$ cat song.txt 
+Yellow submarine
+```

src/test/resources/cwl/hello/hello-param.cwl

@@ -0,0 +1,46 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+$graph:
+- id: echocmd
+  class: CommandLineTool
+  inputs:
+    echo-in-message:
+      type: string
+      label: "Message"
+      doc: "The message to print"
+      default: "Hello World"
+      inputBinding: {}
+    echo-in-outputfile:
+      type: string
+      label: "Output file"
+      doc: "The file containing the message"
+  outputs:
+    echo-out-filename:
+      type: stdout
+      label: "Printed Message"
+      doc: "The file containing the message"
+  baseCommand: echo
+  arguments:
+     - "-n"
+     - "-e"
+  stdout: $(inputs['echo-in-outputfile'])
+
+- id: main
+  class: Workflow
+  label: "Hello World"
+  doc: "Puts a message into a file using echo"
+  inputs:
+     usermessage: string
+     useroutput: string
+  outputs:
+    output:
+      type: File
+      outputSource: step0/echo-out-filename
+  steps :
+    - id: step0
+      run: "#echocmd"
+      in:
+        echo-in-message: usermessage
+        echo-in-outputfile: useroutput
+      out: [echo-out-filename]

src/test/resources/cwl/hello/hello.cwl

@@ -0,0 +1,35 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+$graph:
+- id: echocmd
+  class: CommandLineTool
+  inputs:
+    echo-in:
+      type: string
+      label: "Message"
+      doc: "The message to print"
+      default: "Hello World"
+      inputBinding: {}
+  outputs:
+    echo-out:
+      type: stdout
+      label: "Printed Message"
+      doc: "The file containing the message"
+  baseCommand: echo
+  stdout: messageout.txt
+
+- id: main
+  class: Workflow
+  label: "Hello World"
+  doc: "Puts a message into a file using echo"
+  inputs: []
+  outputs:
+    output:
+      type: File
+      outputSource: step0/echo-out
+  steps:
+    step0:
+      run: "#echocmd"
+      in: []
+      out: [echo-out]

src/test/resources/cwl/hello/params.json

@@ -0,0 +1,6 @@
+#!/usr/bin/env cwl-runner
+{
+"cwl:tool"    : "hello-param.cwl#main",
+"usermessage" : "Hello, CWL !\nHello World !",
+"useroutput"  :  "useroutput.txt" 
+}

src/test/resources/cwl/lobstr-draft3/README

@@ -0,0 +1,40 @@
+lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.
+
+This lobSTR workflow is based on http://melissagymrek.com/lobstr-code/usage.html
+
+To run locally, you may install the reference implementation of CWL:
+
+1) Install the reference implementation of cwl-runner with  "pip install cwl-runner".
+
+2)  Download reference data:
+
+$ wget http://files.teamerlich.org/lobstr/v3/ref/lobSTR_v3.0.2_hg19_resource_bundle.tar.gz
+$ tar xvzf lobSTR_v3.0.2_hg19_resource_bundle.tar.gz
+
+3) Ensure your docker version is compatible with the Arvados image ( < 1.10 ):
+
+$ docker --version
+
+4) Run the demo:
+
+$ ./lobSTR-workflow.cwl lobSTR-demo.json
+
+
+Alternately, you may run lobSTR on Curoverse cloud.  This does not require
+downloading the reference data.
+
+1) Install Arvados cwl-runner using "pip install arvados-cwl-runner".
+
+2) Sign up for a Curoverse Cloud account at https://cloud.curoverse.com
+
+3) Navigate to https://cloud.curoverse.com/current_token and follow the
+instructions to set ARVADOS_API_TOKEN and ARVADOS_API_HOST into your shell
+session (these are your Curoverse cloud credentials).
+
+4) You can now run the lobSTR workflow and submit jobs to run on Curoverse
+cloud:
+
+$ ./lobSTR-workflow.cwl lobSTR-arvados-demo.json
+
+Note that the output data will also be stored on Curoverse cloud, and may be
+downloaded through the Workbench web interface or using "arv-get".

src/test/resources/cwl/lobstr-draft3/allelotype.cwl

@@ -0,0 +1,78 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: "cwl:draft-3"
+
+class: CommandLineTool
+
+description: Run lobSTR allelotype classifier.
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+inputs:
+  - id: bam
+    type: File
+    description: |
+      BAM file to analyze. Should have a unique read group and be sorted and indexed.
+    inputBinding:
+      prefix: "--bam"
+    secondaryFiles:
+      - ".bai"
+
+  - id: output_prefix
+    type: string
+    description: "Prefix for output files. will output prefix.vcf and prefix.genotypes.tab"
+    inputBinding:
+      prefix: "--out"
+
+  - id: noise_model
+    type: File
+    description: |
+      File to read noise model parameters from (.stepmodel)
+    inputBinding:
+      prefix: "--noise_model"
+      valueFrom: |
+          ${ return {"path": self.path.match(/(.*)\.stepmodel/)[1], "class": "File"}; }
+    secondaryFiles:
+      - "^.stuttermodel"
+
+  - id: strinfo
+    type: File
+    description: |
+      File containing statistics for each STR.
+    inputBinding:
+      prefix: "--strinfo"
+
+  - id: reference
+    type: File
+    description: "lobSTR's bwa reference files"
+    inputBinding:
+      prefix: "--index-prefix"
+      valueFrom: |
+          ${ return {"path": self.path.match(/(.*)ref\.fasta/)[1], "class": "File"}; }
+
+    secondaryFiles:
+      - ".amb"
+      - ".ann"
+      - ".bwt"
+      - ".pac"
+      - ".rbwt"
+      - ".rpac"
+      - ".rsa"
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1chromsizes.tab")}
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1mergedref.bed")}
+      - ${return self.path.replace(/(.*)ref\.fasta/, "$1ref_map.tab")}
+
+outputs:
+  - id: vcf
+    type: File
+    outputBinding:
+      glob: $(inputs['output_prefix'] + '.vcf')
+  - id: "#vcf_stats"
+    type: File
+    outputBinding:
+      glob: $(inputs['output_prefix'] + '.allelotype.stats')
+
+baseCommand: ["allelotype", "--command", "classify"]
+
+arguments:
+  - "--noweb"