[WIP] Draft 4.dev1

cwltool/process.py

@@ -73,12 +73,12 @@
 def get_schema():  # type: () -> Tuple[Loader,avro.schema.Names,List[Dict[str,Any]]]
     cache = {}
     for f in cwl_files:
-        rs = resource_stream(__name__, 'schemas/draft-3/' + f)
+        rs = resource_stream(__name__, 'schemas/draft-4/' + f)
         cache["https://w3id.org/cwl/" + f] = rs.read()
         rs.close()
 
     for f in salad_files:
-        rs = resource_stream(__name__, 'schemas/draft-3/salad/schema_salad/metaschema/' + f)
+        rs = resource_stream(__name__, 'schemas/draft-4/salad/schema_salad/metaschema/' + f)
         cache["https://w3id.org/cwl/salad/schema_salad/metaschema/" + f] = rs.read()
         rs.close()
 

cwltool/schemas/CITATION

@@ -0,0 +1,21 @@
+To cite the Common Workflow Language standard in a publication, please use:
+
+Amstutz, Peter; Andeer, Robin; Chapman, Brad; Chilton, John; Crusoe, Michael
+R.; Valls Guimerà, Roman; Carrasco Hernandez, Guillermo; Ivkovic, Sinisa;
+Kartashov, Andrey; Kern, John; Leehr, Dan; Ménager, Hervé; Mikheev, Maxim;
+Pierce, Tim; Randall, Josh; Soiland-Reyes, Stian; Stojanovic, Luka; Tijanić,
+Nebojša (2016): Common Workflow Language, draft 3. figshare.
+https://dx.doi.org/10.6084/m9.figshare.3115156.v1
+
+@data{common-workflow-language-draft3,
+  doi = {10.6084/m9.figshare.3115156.v1},
+  url = {http://dx.doi.org/10.6084/m9.figshare.3115156.v1},
+  author = {Peter Amstutz; Robin Andeer; Brad Chapman; John Chilton;
+Michael R. Crusoe; Roman Valls Guimerà; Guillermo Carrasco Hernandez;
+Sinisa Ivkovic; Andrey Kartashov; John Kern; Dan Leehr; Hervé Ménager;
+Maxim Mikheev; Tim Pierce; Josh Randall; Stian Soiland-Reyes; Luka Stojanovic;
+Nebojša Tijanić; },
+  publisher = {Figshare},
+  title = {Common Workflow Language, draft 3},
+  year = {2016}
+}

cwltool/schemas/README.md

@@ -16,11 +16,19 @@ Bioinformatics, Medical Imaging, Chemistry, Physics, and Astronomy.
 
 ## CWL Specification
 
-The current stable specification is [draft 3](http://common-workflow-language.github.io/draft-3/):
+The current stable specification is [draft 3](http://www.commonwl.org/draft-3/):
 
-http://common-workflow-language.github.io/draft-3/
+http://www.commonwl.org/draft-3/
 
-Older drafts: [draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1), [draft-2](http://common-workflow-language.github.io/draft-2/)
+The next work-in-progress specification is [draft 4](http://www.commonwl.org/draft-4/):
+
+http://www.commonwl.org/draft-4/
+
+Older drafts: [draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1), [draft-2](http://www.commonwl.org/draft-2/)
+
+### Citation
+
+Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v1
 
 ## Implementations
 
@@ -44,6 +52,8 @@ Some of the software supporting running Common Workflow Language tools or workfl
   [Airflow wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/SciDAP)
 * [cwl2script](https://github.com/common-workflow-language/cwl2script),
   [cwl2script page](https://github.com/common-workflow-language/common-workflow-language/wiki/cwl2script)
+* [Apache Taverna](http://taverna.incubator.apache.org/),
+  [Apache Taverna wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Taverna)
 
 ## Examples
 
@@ -101,7 +111,6 @@ Conduct](https://github.com/common-workflow-language/common-workflow-language/bl
 * [Apache Taverna](http://taverna.incubator.apache.org/)
 * [Institut Pasteur](http://www.pasteur.fr)
 * [Wellcome Trust Sanger Institute](https://www.sanger.ac.uk/)
-* [University of California Davis](http://ucdavis.edu)
 * [University of California Santa Cruz](https://cbse.soe.ucsc.edu/research/bioinfo)
 * [Harvard Chan School of Public Health](http://www.hsph.harvard.edu/)
 * [Cincinnati Children's Hospital Medical Center](http://www.cincinnatichildrens.org/)

cwltool/schemas/doc/add-new-draft.md

@@ -0,0 +1,21 @@
+How to make a new draft version of the CWL spec
+
+1. Duplicate prior draft-n directory to draft-n+1 in a branch
+2. Update references to the new draft name.
+3. Pull in the latest metaschema
+
+     git subtree add -P draft-4/salad schema_salad_repo/master
+
+4. In the reference implementation (cwltool): make a new branch, and update the
+   subtree checkout of the spec:
+
+     git subtree merge -P cwltool/schemas/ cwl_repo/draft-4
+
+   Where `cwl_repo` is the remote repository for the CWL specifications.
+4. In the reference implementation, teach it about the new draft version:
+
+  a. Edit `cwltool/update.py`: append a new entry to the updates dictionary and
+     change the previous last version to point to an update function
+  b. Edit `cwltool/process.py`: update `get_schema` to look in the new
+     directory
+  c. Edit `setup.py` to include the new schemas in the `package_data` stanza

cwltool/schemas/draft-3/Process.yml

@@ -35,7 +35,7 @@ $graph:
   type: enum
   extends: "sld:PrimitiveType"
   symbols:
-    - File
+    - cwl:File
   doc:
     - "Extends primitive types with the concept of a file as a first class type."
     - "File: A File object"

cwltool/schemas/draft-3/README.md

@@ -2,10 +2,8 @@
 
 The CWL specifications are divided up into several documents.
 
-<!--
 The [User Guide](UserGuide.html) provides a gentle introduction to writing CWL
 command line tools and workflows.
--->
 
 The [Command Line Tool Description Specification](CommandLineTool.html)
 specifies the document schema and execution semantics for wrapping and
@@ -19,3 +17,6 @@ The
 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html)
 specifies the preprocessing steps that must be applied when loading CWL
 documents and the schema language used to write the above specifications.
+
+If you use the CWL specifications or distribute CWL descriptions with a
+publication you should [cite the standard](https://dx.doi.org/10.6084/m9.figshare.3115156.v1)