[med-svn] [cwltool] 02/05: Merge tag 'upstream/1.0.20160316204054'

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository cwltool.

commit 34eb81f4ecd2f81e444020c00fae7f0fd1890e3a
Merge: aa7208f 5964045
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Mar 18 06:35:28 2016 -0700

    Merge tag 'upstream/1.0.20160316204054'
    
    Upstream version 1.0.20160316204054

 MANIFEST.in                           |   1 +
 PKG-INFO                              |   2 +-
 cwltool.egg-info/SOURCES.txt          |   3 +
 cwltool.egg-info/requires.txt         |   2 +-
 cwltool/builder.py                    |   3 +-
 cwltool/cwlrdf.py                     | 136 ++++++++++++--
 cwltool/cwltest.py                    |  50 +++--
 cwltool/draft2tool.py                 |  81 +++++++--
 cwltool/expression.py                 |   6 +-
 cwltool/job.py                        |  11 +-
 cwltool/main.py                       |  77 +++++---
 cwltool/pathmapper.py                 |   1 +
 cwltool/process.py                    |  47 +++++
 cwltool/sandboxjs.py                  |  59 +++---
 cwltool/schemas/draft-3/Process.yml   |   1 +
 cwltool/schemas/draft-3/contrib.md    |   3 +
 cwltool/schemas/draft-3/invocation.md |  10 +-
 cwltool/workflow.py                   |  55 +++---
 ez_setup.py                           | 332 ++++++++++++++++++++++++++++++++++
 gittaggers.py                         |  23 +++
 setup.cfg                             |   2 +-
 setup.py                              |   7 +-
 22 files changed, 783 insertions(+), 129 deletions(-)

diff --cc cwltool/main.py
index 832002b,cd27bfc..4108557
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@@ -412,43 -423,17 +423,53 @@@ def load_job_order(args, t, parser, std
  
      return (job_order_object, input_basedir)
  
+ def print_deps(fn):
+     with open(fn) as f:
+         deps = {"class": "File",
+                 "path": fn}
+         sf = process.scandeps(os.path.dirname(fn), yaml.load(f),
+                               set(("$import", "run")),
+                               set(("$include", "$schemas", "path")))
+         if sf:
+             deps["secondaryFiles"] = sf
+         print json.dumps(deps, indent=4)
  
 +def scandeps(base, doc):
 +    r = []
 +    if isinstance(doc, dict):
 +        if "$import" in doc:
 +            p = os.path.join(base, doc["$import"])
 +            with open(p) as f:
 +                r.append({
 +                    "class": "File",
 +                    "path": p,
 +                    "secondaryFiles": scandeps(os.path.dirname(p), yaml.load(f))
 +                })
 +        elif "$include" in doc:
 +            p = os.path.join(base, doc["$include"])
 +            r.append({
 +                "class": "File",
 +                "path": p
 +            })
 +        elif "$schemas" in doc:
 +            for s in doc["$schemas"]:
 +                p = os.path.join(base, s)
 +                r.append({
 +                    "class": "File",
 +                    "path": p
 +                })
 +        else:
 +            for d in doc.itervalues():
 +                r.extend(scandeps(base, d))
 +    elif isinstance(doc, list):
 +        for d in doc:
 +            r.extend(scandeps(base, d))
 +    return r
 +
 +def print_deps(fn):
 +    with open(fn) as f:
 +        print json.dumps(scandeps(os.path.dirname(fn), yaml.load(f)), indent=4)
 +
  def main(args=None,
           executor=single_job_executor,
           makeTool=workflow.defaultMakeTool,

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