Fixes 2.2 (#6)

* Add pypi rst readme
pypi does not like markdown.

* Add md5sum test data from GA4GH dream

* Safely check options, close #3

* Add example using md5sum in test data

* Clarify readme and add cwl-runner reqt thx @achave11

Author: david4096

README.md

@@ -8,63 +8,71 @@ It provides an [Arvados](https://github.com/curoverse/arvados) backend.  It
 also works with any `cwl-runner` that supports the CWL standard command line
 interface: http://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts
 
-Installation:
+## Installation:
 
 ```
 pip install wes-service
 ```
 
+## Usage
+
 Run a standalone server with default `cwl-runner` backend:
 
 ```
 $ wes-server
 ```
 
-Submit a workflow to run:
+### Submit a workflow to run:
+
+Note! All inputs files must be accessible from the filesystem.
 
 ```
-$ wes-client --host=localhost:8080 myworkflow.cwl myjob.json
+$ wes-client --host=localhost:8080 testdata/md5sum.cwl testdata/md5sum.cwl.json
 ```
 
-List workflows:
+### List workflows
 
 ```
-$ wes-client --list
+$ wes-client --proto http --host=locahost:8080 --list
 ```
 
-Get workflow status:
+### Get workflow status
 
 ```
-$ wes-client --get <workflow-id>
+$ wes-client --proto http --host=locahost:8080 --get <workflow-id>
 ```
 
-Get stderr log from workflow:
+### Get stderr log from workflow:
 
 ```
-$ wes-client --log <workflow-id>
+$ wes-client --proto http --host=locahost:8080 --log <workflow-id>
 ```
 
-# Server Options
+## Server Configuration
 
-## Run a standalone server with Arvados backend:
+### Run a standalone server with Arvados backend:
 
 ```
 $ wes-server --backend=wes_service.arvados_wes
 ```
 
-## Use a different executable with cwl_runner backend
+### Use a different executable with cwl_runner backend
 
 ```
 $ wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil
 ```
 
-## Pass parameters to cwl-runner
+### Pass parameters to cwl-runner
 
 ```
 $ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/
 ```
 
-# Client environment options
+## Client Configuration
+
+These options will be read in as defaults when running the client from the
+command line. The default protocol is https, to support secure communications,
+but the server starts using http, to ease development.
 
 Set service endpoint:
 
@@ -83,3 +91,6 @@ Set the protocol (one of http, https)
 ```
 $ export WES_API_PROTO=http
 ```
+
+Then, when you call `wes-client` these defaults will be used in place of the
+flags, `--host`, `--auth`, and `proto` respectively.

README.pypi.rst

@@ -0,0 +1,93 @@
+Workflow as a Service
+=====================
+
+This provides client and server implementations of the `GA4GH Workflow
+Execution
+Service <https://github.com/ga4gh/workflow-execution-schemas>`__ API for
+the Common Workflow Language.
+
+It provides an `Arvados <https://github.com/curoverse/arvados>`__
+backend. It also works with any ``cwl-runner`` that supports the CWL
+standard command line interface:
+http://www.commonwl.org/v1.0/CommandLineTool.html#Executing\_CWL\_documents\_as\_scripts
+
+Installation:
+
+::
+
+    pip install wes-service
+
+Run a standalone server with default ``cwl-runner`` backend:
+
+::
+
+    $ wes-server
+
+Submit a workflow to run:
+
+::
+
+    $ wes-client --host=localhost:8080 myworkflow.cwl myjob.json
+
+List workflows:
+
+::
+
+    $ wes-client --list
+
+Get workflow status:
+
+::
+
+    $ wes-client --get <workflow-id>
+
+Get stderr log from workflow:
+
+::
+
+    $ wes-client --log <workflow-id>
+
+Server Options
+==============
+
+Run a standalone server with Arvados backend:
+---------------------------------------------
+
+::
+
+    $ wes-server --backend=wes_service.arvados_wes
+
+Use a different executable with cwl\_runner backend
+---------------------------------------------------
+
+::
+
+    $ wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil
+
+Pass parameters to cwl-runner
+-----------------------------
+
+::
+
+    $ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/
+
+Client environment options
+==========================
+
+Set service endpoint:
+
+::
+
+    $ export WES_API_HOST=localhost:8080
+
+Set the value to pass in the ``Authorization`` header:
+
+::
+
+    $ export WES_API_AUTH=my_api_token
+
+Set the protocol (one of http, https)
+
+::
+
+    $ export WES_API_PROTO=http

setup.py

@@ -8,12 +8,16 @@
 from setuptools import setup, find_packages
 
 SETUP_DIR = os.path.dirname(__file__)
-README = os.path.join(SETUP_DIR, 'README.md')
+
+long_description = ""
+
+with open("README.pypi.rst") as readmeFile:
+    long_description = readmeFile.read()
 
 setup(name='wes-service',
       version='2.1',
       description='GA4GH Workflow Execution Service reference implementation',
-      long_description=open(README).read(),
+      long_description=long_description,
       author='GA4GH Containers and Workflows task team',
       author_email='[email protected]',
       url="https://github.com/common-workflow-language/cwltool-service",
@@ -26,6 +30,7 @@
           'connexion',
           'bravado',
           'ruamel.yaml >= 0.12.4, < 0.15',
+          'cwl-runner'
         ],
       entry_points={
           'console_scripts': [ "wes-server=wes_service:main",

testdata/dockstore-tool-md5sum.cwl

@@ -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]
+

testdata/md5sum.cwl

@@ -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/md5sum.cwl.json

@@ -0,0 +1,10 @@
+{
+  "input_file": {
+        "class": "File",
+        "path": "../../testdata/md5sum.input"
+    },
+    "output_file": {
+        "class": "File",
+        "path": "/tmp/md5sum.txt"
+    }
+}

testdata/md5sum.input

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

wes_service/util.py

@@ -10,7 +10,7 @@ def visit(d, op):
 class WESBackend(object):
     def __init__(self, opts):
         self.pairs = []
-        for o in opts:
+        for o in opts if opts else []:
             k, v = o.split("=", 1)
             self.pairs.append((k, v))