Merge pull request #14 from david4096/updates

Updates, HCA feedback

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "task-execution-schemas"]
-	path = task-execution-schemas
-	url = https://github.com/ga4gh/task-execution-schemas.git

CWLFile

@@ -2,8 +2,8 @@ includes:
   - class: Directory
     location: proto
   - class: Directory
-    location: task-execution-schemas/proto
+    location: proto
 proto:
   class: File
-  location: proto/workflow_execution.proto
+  location: proto/workflow_execution_service.proto
 cwl:tool: protoc.cwl

README.md

@@ -1,49 +1,44 @@
-![ga4gh logo](http://genomicsandhealth.org/files/logo_ga.png)
+<img src="https://www.ga4gh.org/gfx/GA-logo-horizontal-tag-RGB.svg" alt="GA4GH Logo" style="width: 100px;"/>
 
 Schemas for the Workflow Execution Service (WES) API
 ====================================================
 
-This is used by the Data Working Group - Containers and Workflows Task Team
-
-<img src="swagger_editor.png" width="48">[View in Swagger](http://editor.swagger.io/#/?import=https://raw.githubusercontent.com/ga4gh/workflow-execution-schemas/0.1.0/swagger/proto/workflow_execution.swagger.json)
-
 The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international
 coalition, formed to enable the sharing of genomic and clinical data.
 
-Containers and Workflows Task Team
-----------------------------------
+Cloud Work Stream
+-----------------
 
-The [Data Working Group](http://ga4gh.org/#/) concentrates on data representation, storage,
+The [Cloud Work Stream](https://ga4gh/cloud) concentrates on data representation, storage,
 and analysis, including working with platform development partners and
 industry leaders to develop standards that will facilitate
-interoperability.  The Containers & Workflows working group is an informal, multi-vendor working group focused on standards for exchanging Docker-based tools and CWL/WDL workflows, execution of Docker-based tools and workflows on clouds, and abstract access to cloud object stores.
+interoperability.  The Cloud Work Stream is an informal, multi-vendor working group focused on standards for exchanging Docker-based tools and CWL/WDL workflows, execution of Docker-based tools and workflows on clouds, and abstract access to cloud object stores.
 
 What is WES?
 ============
 
-This is the home of the Workflow Execution Schema proposal. The Workflow
-Execution Schema is a minimal common API describing how a user can submit
-workflow requests to workflow execution systems in a standardized ways.
+The Workflow Execution Schema is a minimal common API describing how a user can submit
+workflow requests to workflow execution systems in standardized ways.
 Workflow execution engines (SevenBridges, FireCloud, etc) can support this API so users can make workflow requests
 programmatically, adding the ability to scale up.  In addition, these workflow services could have (and probably do have)
 UIs that would (possibly) use this API under the hood to facilitate workflow execution requests.
 
 Having this standard API supported by multiple execution engines will give people options of processing
 the same workflow (CWL or WDL) across different workflow execution platforms running across various clouds/environments.
 As an example use case, one can find a workflow in CWL on [Dockstore.org](http://dockstore.org), use Dockstore to
-generate a JSON parameterization file, and submit this a GA4GH-compliant
+generate a JSON parameterization file, and submit this to a GA4GH-compliant
 workflow execution service.
 
 Key features of the current API proposal:
 
 * ability to request a workflow run using CWL or WDL (and maybe future formats)
 * ability to parameterize that workflow using a JSON schema (ideally a future version would be in common between CWL and WDL)
-* ability to get information about running workflows, status, errors, output file locations etc
+* ability to get information about running workflows, status, errors, output file locations, etc.
 * to search for workflows by arbitrary key/values
 
 Outstanding questions:
 
-* a common JSON parameterization format, see work by Peter, is that checked in?
+* a common JSON parameterization format
 * standardizing terms, job, workflow, steps, tools, etc
 * reference implementation at https://github.com/common-workflow-language/cwltool-service/tree/ga4gh-wes
 * validation service for testing WES implementations' conformance to the spec
@@ -54,9 +49,9 @@ Outstanding questions:
 How to view
 ------------
 
-See the swagger editor to view our [schema in progress](http://editor.swagger.io/#/?import=https://raw.githubusercontent.com/ga4gh/workflow-execution-schemas/develop/src/main/resources/swagger/ga4gh-tool-discovery.yaml).
+The file `swagger/workflow_execution_service.swagger.json` contains the API description.
 
-If the current schema fails to validate, visit [debugging](http://online.swagger.io/validator/debug?url=https://raw.githubusercontent.com/ga4gh/workflow-execution-schemas/develop/src/main/resources/swagger/ga4gh-tool-discovery.yaml)
+Please visit http://ga4gh.github.io/workflow-execution-schemas to view this document in Swagger UI.
 
 Building Documents
 ------------------
@@ -65,24 +60,14 @@ Make sure you have Docker installed for your platform and the `cwltool`.
 
     virtualenv env
     source env/bin/activate
-    pip install setuptools==28.8.0
-    pip install cwl-runner cwltool==1.0.20161114152756 schema-salad==1.18.20161005190847 avro==1.8.1
-
-Make sure you have the [submodule](http://stackoverflow.com/questions/3939055/submodules-files-are-not-checked-out) checked out:
-
-    git submodule update --init --recursive
+    pip install -r requirements.txt
 
-You can generate the [Swagger](http://swagger.io/) YAML from the Protocol Buffers:
+You can generate the [Swagger](http://swagger.io/) from the Protocol Buffers:
 
     cwltool CWLFile
+    sh tools/prepare_openapi.sh
 
-Find the output in `workflow_execution.swagger.json` and this can be loaded in the [Swagger editor](http://swagger.io/swagger-editor/).  Use the GitHub raw feature to generate a URL you can load.
-
-When you're happy with the changes, checkin this file:
-
-    mv workflow_execution.swagger.json swagger/proto/
-
-And commit your changes.
+The resulting OpenAPI description will be in the `swagger` directory.
 
 How to contribute changes
 -------------------------
@@ -100,4 +85,4 @@ More Information
 ----------------
 
 * [Global Alliance for Genomics and Health](http://genomicsandhealth.org)
-* [Google Forum](https://groups.google.com/forum/#!forum/ga4gh-dwg-containers-workflows)
+* [GA4GH Cloud Work Stream)[https://ga4gh.cloud]