Update to advertise support for WES 1.0. Update README.

Author: Peter Amstutz

README.md

@@ -1,10 +1,9 @@
 # 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.
+This is a client and server implementation of the [GA4GH Workflow
+Execution Service](https://github.com/ga4gh/workflow-execution-schemas) 1.0.0 API.
 
-It provides an [Arvados](https://github.com/curoverse/arvados) backend.  It
+It provides [Arvados](https://arvados.org/) and [Toil](http://toil.ucsc-cgl.org/) backends.  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
 
@@ -16,43 +15,66 @@ pip install wes-service
 
 ## Usage
 
-Run a standalone server with default `cwl-runner` backend:
+### Client configuration
+
+Command line parameter or environment variable.
+
+`--host` or `WES_API_HOST`
+
+The host to contact.
+
+`--proto` or `WES_API_PROTO`
+
+The protocol (http or https) to use.
+
+`--auth` or `WES_API_AUTH`
+
+Credentials.  Format is 'Header: value' or just 'value'.  If header name is not provided, value goes in the 'Authorization'.
+
+### Get service info
 
 ```
-$ wes-server
+$ wes-client --info
 ```
 
 ### Submit a workflow to run:
 
-Note! All inputs files must be accessible from the filesystem.
+Attachments must be accessible from the filesystem.  Workflow runners may also support http URLs or other storage systems.
 
 ```
-$ wes-client --host=localhost:8080 --proto=http --attachments="testdata/dockstore-tool-md5sum.cwl,testdata/md5sum.input" testdata/md5sum.cwl testdata/md5sum.cwl.json
+$ wes-client --attachments="testdata/dockstore-tool-md5sum.cwl,testdata/md5sum.input" testdata/md5sum.cwl testdata/md5sum.cwl.json
 ```
 
 ### List workflows
 
 ```
-$ wes-client --proto http --host=localhost:8080 --list
+$ wes-client --list
 ```
 
 ### Get workflow status
 
 ```
-$ wes-client --proto http --host=localhost:8080 --get <workflow-id>
+$ wes-client --get <run-id>
 ```
 
 ### Get stderr log from workflow:
 
 ```
-$ wes-client --proto http --host=localhost:8080 --log <workflow-id>
+$ wes-client --log <run-id>
 ```
 
 ## Server Configuration
 
+### Run a standalone server with default `cwl-runner` backend:
+
+```
+$ wes-server
+```
+
 ### Run a standalone server with Arvados backend:
 
 ```
+$ pip install arvados-cwl-runner
 $ wes-server --backend=wes_service.arvados_wes
 ```
 
@@ -63,46 +85,21 @@ $ pip install toil[all]
 $ wes-server --backend=wes_service.toil_wes --opt extra=--clean=never
 ```
 
-### Use a different executable with cwl_runner backend
+### Use alternate executable with cwl-runner backend
 
 ```
-$ pip install toil[all]
-$ wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil --opt extra=--logLevel=CRITICAL
+$ pip install cwltool
+$ wes-server --backend=wes_service.cwl_runner --opt runner=cwltool --opt extra=--logLevel=CRITICAL
 ```
 
 ### Pass parameters to cwl-runner
 
-```
-$ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/
-```
-
-## 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:
-
-```
-$ export WES_API_HOST=localhost:8080
-```
-
-Set the value to pass in the `Authorization` header:
+Use "--opt" following by "key=value"
 
 ```
-$ export WES_API_AUTH=my_api_token
+$ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/tmp/work
 ```
 
-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.
-
 ## Development
 If you would like to develop against `workflow-service` make sure you pass the provided test and it is flake8 compliant
 
@@ -113,7 +110,7 @@ $ virtualenv venv && source venv/bin/activate && pip install toil[all] && pip in
 ```
 
 #### Running Tests
-From path `workflow-service` run 
+From path `workflow-service` run
 
 ```
 $ pytest && flake8

wes_client/util.py

@@ -234,7 +234,7 @@ def cancel(self, run_id):
         :param host: Port where the post request will be sent and the wes server listens at (default 8080)
         :return: The body of the delete result as a dictionary.
         """
-        postresult = requests.delete("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
+        postresult = requests.post("%s://%s/ga4gh/wes/v1/runs/%s/cancel" % (self.proto, self.host, run_id),
                                      headers=self.auth)
         return wes_reponse(postresult)
 

wes_service/arvados_wes.py

@@ -72,7 +72,7 @@ def GetServiceInfo(self):
             "workflow_type_versions": {
                 "CWL": {"workflow_type_version": ["v1.0"]}
             },
-            "supported_wes_versions": ["0.3.0"],
+            "supported_wes_versions": ["0.3.0", "1.0.0"],
             "supported_filesystem_protocols": ["http", "https", "keep"],
             "workflow_engine_versions": {
                 "arvados-cwl-runner": stderr

wes_service/cwl_runner.py

@@ -160,15 +160,19 @@ def cancel(self):
 
 class CWLRunnerBackend(WESBackend):
     def GetServiceInfo(self):
+        runner = self.getopt("runner", default="cwl-runner")
+        stdout, stderr = subprocess.Popen([runner, "--version"], stderr=subprocess.PIPE).communicate()
         return {
             "workflow_type_versions": {
                 "CWL": {"workflow_type_version": ["v1.0"]}
             },
-            "supported_wes_versions": ["0.3.0"],
+            "supported_wes_versions": ["0.3.0", "1.0.0"],
             "supported_filesystem_protocols": ["file", "http", "https"],
-            "engine_versions": "cwl-runner",
+            "workflow_engine_versions": {
+                "cwl-runner": stderr
+            },
             "system_state_counts": {},
-            "key_values": {}
+            "tags": {}
         }
 
     def ListRuns(self, page_size=None, page_token=None, state_search=None):