Merge pull request #6 from dockstore-testing/develop

Merge to master

Author: garyluu

.travis.yml

@@ -0,0 +1,25 @@
+sudo: required
+
+services:
+  - docker
+
+language: python
+
+python:
+  - "3.6"
+
+before_install:
+  # Download Cromwell
+  - wget -O $TRAVIS_BUILD_DIR/cromwell-42.jar https://github.com/broadinstitute/cromwell/releases/download/42/cromwell-42.jar;
+  - curl -o requirements.txt "https://dockstore.org/api/metadata/runner_dependencies?client_version=1.6.0&python_version=3"
+
+install:
+  - pip install -r requirements.txt
+
+script:
+  - docker build -t test-image -f checker/Dockerfile checker
+  - >-
+    sed 's/dockerPull:.*/dockerPull: test-image:latest/g' checker/md5sum-checker.cwl
+  - >-
+    sed 's/docker:.*/docker: "test-image:latest"/g' checker/md5sum-checker.wdl
+  - python -m unittest discover -s .

checker-fail-cwl.json

@@ -0,0 +1,7 @@
+{
+  "input_file": {
+        "class": "File",
+        "path": "md5sum.input"
+    },
+    "expected_md5": "not a matching md5sum"
+}

checker/bin/check_md5sum

@@ -6,39 +6,41 @@ import json
 import sys
 import os
 
+
 def main():
-  parser = argparse.ArgumentParser(description='Checks to see if a given file contains a certain string and then returns a JSON.', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-  parser.add_argument('--input-file', type=str, help='file input')
-  parser.add_argument('--md5', type=str, help='expected md5')
-  args = parser.parse_args()
+    parser = argparse.ArgumentParser(description='Checks to see if a given file contains a certain string and then returns a JSON.', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--input-file', type=str, help='file input')
+    parser.add_argument('--md5', type=str, help='expected md5')
+    args = parser.parse_args()
+
+    result_code = check_file(args.input_file, args.md5)
 
-  result = check_file(args.input_file, args.md5)
+    results_file = open("results.json", "w")
+    if result_code == 0:
+        results_file.write('{ "overall" : true, "steps" : { "md5sum_check" : true } }')
+    else:
+        results_file.write('{ "overall" : false, "steps" : { "md5sum_check" : false } }')
+    results_file.close()
 
-  results_file  = open("results.json", "w")
-  if (result == 0):
-    results_file.write('{ "overall" : true, "steps" : { "md5sum_check" : true } }')
-  else:
-    results_file.write('{ "overall" : false, "steps" : { "md5sum_check" : false } }')
-  results_file.close()
+    log_file = open("log.txt", "w")
+    log_file.write("")
+    log_file.close()
 
-  log_file  = open("log.txt", "w")
-  log_file.write("")
-  log_file.close()
+    sys.exit(result_code)
 
-  # correct way to do this?
-  return(result)
 
 def check_file(input_file, md5):
-  file = open(input_file, "r")
-  contents = file.read()
-  contents = contents.rstrip()
-  print ("FILE CONTENTS: "+contents)
-  if (contents == md5):
-    print("Contents match")
-    return(0)
-  else:
-    print("Contents DO NOT match")
-    return(1)
+    file = open(input_file, "r")
+    contents = file.read()
+    contents = contents.rstrip()
+    print("FILE CONTENTS: "+contents)
+    if contents == md5:
+        print("Contents match")
+        return 0
+    else:
+        print("Contents DO NOT match")
+        return 1
+
 
 if __name__ == "__main__":
     main()

checker/md5sum-checker.cwl

@@ -7,7 +7,7 @@ cwlVersion: v1.0
 
 requirements:
 - class: DockerRequirement
-  dockerPull: quay.io/agduncan94/checker-md5sum
+  dockerPull: quay.io/dockstore-testing/md5sum-checker:1.0.0
 - class: InlineJavascriptRequirement
 
 hints:

checker/md5sum-checker.wdl

@@ -7,6 +7,6 @@ task checkerTask {
   }
 
   runtime {
-    docker: "quay.io/agduncan94/checker-md5sum"
+    docker: "quay.io/dockstore-testing/md5sum-checker:1.0.0"
   }
 }

md5sum-fail-wdl.json

@@ -0,0 +1,4 @@
+{
+  "checkerWorkflow.inputFile": "md5sum.input",
+  "checkerWorkflow.expectedMd5sum": "not a real md5sum"
+}

md5sum/md5sum-input-cwl.json

@@ -1,6 +1,6 @@
 {
   "input_file": {
         "class": "File",
-        "path": "md5sum.input"
+        "path": "../md5sum.input"
     }
 }

md5sum/md5sum-wdl.json

@@ -1,3 +1,3 @@
 {
- "ga4ghMd5.inputFile": "md5sum.input"
+ "ga4ghMd5.inputFile": "../md5sum.input"
 }

test.py

@@ -0,0 +1,27 @@
+import subprocess
+import unittest
+
+
+class TestMd5sumChecker(unittest.TestCase):
+    # For each workflow, verify that it succeeds when the input file's md5sum matches and fails when it does not
+    def test_cwl_success(self):
+        process = subprocess.call(["cwltool", "checker-workflow-wrapping-tool.cwl", "checker-input-cwl.json"])
+        self.assertEqual(process, 0)
+
+    def test_cwl_failure(self):
+        process = subprocess.call(["cwltool", "checker-workflow-wrapping-tool.cwl", "checker-fail-cwl.json"])
+        self.assertEqual(process, 1)
+
+    def test_wdl_success(self):
+        process = subprocess.call(["java", "-jar", "cromwell-42.jar", "run", "checker-workflow-wrapping-workflow.wdl",
+                                  "-i", "md5sum-wdl.json"])
+        self.assertEqual(process, 0)
+
+    def test_wdl_failure(self):
+        process = subprocess.call(["java", "-jar", "cromwell-42.jar", "run", "checker-workflow-wrapping-workflow.wdl",
+                                  "-i", "md5sum-fail-wdl.json"])
+        self.assertEqual(process, 1)
+
+
+if __name__ == '__main__':
+    unittest.main()