From b3afe6359eed78509ce76316469c5b89a95b4e76 Mon Sep 17 00:00:00 2001
From: emlys <43770515+emlys@users.noreply.github.com>
Date: Wed, 26 Jun 2019 10:24:33 -0700
Subject: [PATCH 1/3] Checker workflow fails as expected when checksums do not
 match

* set exit code to 1 on failure

dockstore/dockstore#2340
---
 .travis.yml                | 20 ++++++++++++++
 checker-fail-cwl.json      |  7 +++++
 checker/bin/check_md5sum   | 54 ++++++++++++++++++++------------------
 checker/md5sum-checker.cwl |  2 +-
 checker/md5sum-checker.wdl |  2 +-
 md5sum-fail-wdl.json       |  4 +++
 test.py                    | 27 +++++++++++++++++++
 7 files changed, 88 insertions(+), 28 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 checker-fail-cwl.json
 create mode 100644 md5sum-fail-wdl.json
 create mode 100644 test.py

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..adcf9b3
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,20 @@
+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:
+  - python -m unittest discover -s .
\ No newline at end of file
diff --git a/checker-fail-cwl.json b/checker-fail-cwl.json
new file mode 100644
index 0000000..9812490
--- /dev/null
+++ b/checker-fail-cwl.json
@@ -0,0 +1,7 @@
+{
+  "input_file": {
+        "class": "File",
+        "path": "md5sum.input"
+    },
+    "expected_md5": "not a matching md5sum"
+}
\ No newline at end of file
diff --git a/checker/bin/check_md5sum b/checker/bin/check_md5sum
index 4c12b76..bf8c9f8 100644
--- a/checker/bin/check_md5sum
+++ b/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()
diff --git a/checker/md5sum-checker.cwl b/checker/md5sum-checker.cwl
index c90549e..da0b186 100644
--- a/checker/md5sum-checker.cwl
+++ b/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:feature_emlys_DOC-654
 - class: InlineJavascriptRequirement
 
 hints:
diff --git a/checker/md5sum-checker.wdl b/checker/md5sum-checker.wdl
index 7ad8eb7..dc7ff95 100644
--- a/checker/md5sum-checker.wdl
+++ b/checker/md5sum-checker.wdl
@@ -7,6 +7,6 @@ task checkerTask {
   }
 
   runtime {
-    docker: "quay.io/agduncan94/checker-md5sum"
+    docker: "quay.io/dockstore-testing/md5sum-checker:feature_emlys_DOC-654"
   }
 }
diff --git a/md5sum-fail-wdl.json b/md5sum-fail-wdl.json
new file mode 100644
index 0000000..98d8f05
--- /dev/null
+++ b/md5sum-fail-wdl.json
@@ -0,0 +1,4 @@
+{
+  "checkerWorkflow.inputFile": "md5sum.input",
+  "checkerWorkflow.expectedMd5sum": "not a real md5sum"
+}
diff --git a/test.py b/test.py
new file mode 100644
index 0000000..8b49eaa
--- /dev/null
+++ b/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()

From 761499a8329b367d37eb83d180fb762e04ada97f Mon Sep 17 00:00:00 2001
From: emlys <43770515+emlys@users.noreply.github.com>
Date: Fri, 28 Jun 2019 11:18:51 -0700
Subject: [PATCH 2/3] updated to version 1.0.0 (#4)

* updated to version 1.0.0

* replacing test docker image with local version
---
 .travis.yml                | 5 +++++
 checker/md5sum-checker.cwl | 2 +-
 checker/md5sum-checker.wdl | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index adcf9b3..98e1c7f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,4 +17,9 @@ 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 .
\ No newline at end of file
diff --git a/checker/md5sum-checker.cwl b/checker/md5sum-checker.cwl
index da0b186..16887ac 100644
--- a/checker/md5sum-checker.cwl
+++ b/checker/md5sum-checker.cwl
@@ -7,7 +7,7 @@ cwlVersion: v1.0
 
 requirements:
 - class: DockerRequirement
-  dockerPull: quay.io/dockstore-testing/md5sum-checker:feature_emlys_DOC-654
+  dockerPull: quay.io/dockstore-testing/md5sum-checker:1.0.0
 - class: InlineJavascriptRequirement
 
 hints:
diff --git a/checker/md5sum-checker.wdl b/checker/md5sum-checker.wdl
index dc7ff95..637e782 100644
--- a/checker/md5sum-checker.wdl
+++ b/checker/md5sum-checker.wdl
@@ -7,6 +7,6 @@ task checkerTask {
   }
 
   runtime {
-    docker: "quay.io/dockstore-testing/md5sum-checker:feature_emlys_DOC-654"
+    docker: "quay.io/dockstore-testing/md5sum-checker:1.0.0"
   }
 }

From 329a291b2d349b19e94dc456b547c7d38834596a Mon Sep 17 00:00:00 2001
From: garyluu <garylau.work@gmail.com>
Date: Tue, 10 Sep 2019 15:34:38 -0400
Subject: [PATCH 3/3] Move inputs files

---
 md5sum/md5sum-input-cwl.json | 2 +-
 md5sum/md5sum-wdl.json       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/md5sum/md5sum-input-cwl.json b/md5sum/md5sum-input-cwl.json
index c6e6b7b..a254306 100644
--- a/md5sum/md5sum-input-cwl.json
+++ b/md5sum/md5sum-input-cwl.json
@@ -1,6 +1,6 @@
 {
   "input_file": {
         "class": "File",
-        "path": "md5sum.input"
+        "path": "../md5sum.input"
     }
 }
diff --git a/md5sum/md5sum-wdl.json b/md5sum/md5sum-wdl.json
index 4ed090c..125237c 100644
--- a/md5sum/md5sum-wdl.json
+++ b/md5sum/md5sum-wdl.json
@@ -1,3 +1,3 @@
 {
- "ga4ghMd5.inputFile": "md5sum.input"
+ "ga4ghMd5.inputFile": "../md5sum.input"
 }