add some basic tests

Author: gijzelaerr

cwl_utils/cite-extract.py renamed to cwl_utils/cite_extract.py

@@ -15,4 +15,7 @@
         'schema_salad',
         'typing_extensions',
     ],
+    setup_requires=['pytest-runner'],
+    tests_require=['pytest'],
+    test_suite='tests',
 )

cwl_utils/docker-extract.py renamed to cwl_utils/docker_extract.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+id: Md5sum
+label: Simple md5sum tool
+cwlVersion: v1.0
+
+$namespaces:
+  dct: http://purl.org/dc/terms/
+  foaf: http://xmlns.com/foaf/0.1/
+
+doc: |
+  [![Docker Repository on Quay.io](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum/status "Docker Repository on Quay.io")](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum)
+  [![Build Status](https://travis-ci.org/briandoconnor/dockstore-tool-md5sum.svg)](https://travis-ci.org/briandoconnor/dockstore-tool-md5sum)
+  A very, very simple Docker container for the md5sum command. See the [README](https://github.com/briandoconnor/dockstore-tool-md5sum/blob/master/README.md) for more information.
+
+
+#dct:creator:
+#  '@id': http://orcid.org/0000-0002-7681-6415
+#  foaf:name: Brian O'Connor
+#  foaf:mbox: [email protected]
+
+requirements:
+- class: DockerRequirement
+  dockerPull: quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4
+- class: InlineJavascriptRequirement
+
+hints:
+- class: ResourceRequirement
+  # The command really requires very little resources.
+  coresMin: 1
+  ramMin: 1024
+  outdirMin: 512
+
+inputs:
+  input_file:
+    type: File
+    inputBinding:
+      position: 1
+    doc: The file that will have its md5sum calculated.
+
+outputs:
+  output_file:
+    type: File
+    format: http://edamontology.org/data_3671
+    outputBinding:
+      glob: md5sum.txt
+    doc: A text file that contains a single line that is the md5sum of the input file.
+
+baseCommand: [/bin/my_md5sum]
+

setup.py

@@ -0,0 +1,18 @@
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+  input_file: File
+
+outputs:
+  output_file:
+    type: File
+    outputSource: md5sum/output_file
+
+steps:
+  md5sum:
+    run: dockstore-tool-md5sum.cwl
+    in:
+      input_file: input_file
+    out: [output_file]
+

testdata/dockstore-tool-md5sum.cwl

@@ -0,0 +1 @@
+hello

testdata/md5sum.cwl

@@ -0,0 +1,2 @@
+{"output_file": {"path": "/tmp/md5sum.txt", "class": "File"},
+ "input_file": {"path": "md5sum.input", "class": "File"}}

testdata/md5sum.input

@@ -0,0 +1,13 @@
+from unittest import TestCase
+from pathlib import Path
+from cwl_utils.cite_extract import traverse_workflow
+import cwl_utils.parser_v1_0 as parser
+
+HERE = Path(__file__).resolve().parent
+TEST_CWL = HERE / "../testdata/md5sum.cwl"
+
+
+class TestCiteExtract(TestCase):
+    def test_traverse_workflow(self):
+        loaded = parser.load_document(str(TEST_CWL.resolve()))
+        traverse_workflow(loaded)

testdata/md5sum.json

@@ -0,0 +1,19 @@
+from unittest import TestCase
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from cwl_utils.docker_extract import traverse, get_image_name, save_docker_image, load_docker_image
+import cwl_utils.parser_v1_0 as parser
+
+HERE = Path(__file__).resolve().parent
+TEST_CWL = HERE / "../testdata/md5sum.cwl"
+
+
+class TestDockerExtract(TestCase):
+    def test_traverse_workflow(self):
+        loaded = parser.load_document(str(TEST_CWL.resolve()))
+
+        with TemporaryDirectory() as tmpdir:
+            for req in set(traverse(loaded)):
+                image_name = get_image_name(req)
+                save_docker_image(req, image_name, tmpdir)
+                _ = load_docker_image(image_name)