Merge pull request #229 from common-workflow-language/fix-package-errror

Fix package errror

Author: mr-c

cwltool/expression.py

@@ -19,6 +19,7 @@ def jshead(engineConfig, rootvars):
     # type: (List[Text], Dict[Text, Any]) -> Text
     return u"\n".join(engineConfig + [u"var %s = %s;" % (k, json.dumps(v, indent=4)) for k, v in rootvars.items()])
 
+
 seg_symbol = r"""\w+"""
 seg_single = r"""\['([^']|\\')+'\]"""
 seg_double = r"""\["([^"]|\\")+"\]"""

cwltool/main.py

@@ -756,5 +756,6 @@ def locToPath(p):
         _logger.removeHandler(stderr_handler)
         _logger.addHandler(defaultStreamHandler)
 
+
 if __name__ == "__main__":
     sys.exit(main(sys.argv[1:]))

cwltool/pack.py

@@ -35,8 +35,6 @@ def replace_refs(d, rewrite, stem, newstem):
             else:
                 replace_refs(v, rewrite, stem, newstem)
     elif isinstance(d, dict):
-        if "package" in d:
-            raise Exception("where the fuck did this come from %s" % json.dumps(d, indent=4))
         if "run" in d and isinstance(d["run"], (str, unicode)):
             d["run"] = rewrite[d["run"]]
         for s,v in d.items():
@@ -75,7 +73,7 @@ def loadref(b, u):
         v = rewrite[r]
         dc = cast(Dict[Text, Any], copy.deepcopy(document_loader.idx[r]))
         dc["id"] = v
-        for n in ("name", "package", "cwlVersion"):
+        for n in ("name", "cwlVersion"):
             if n in dc:
                 del dc[n]
         replace_refs(dc, rewrite, r+"/" if "#" in r else r+"#", v+"/")

cwltool/process.py

@@ -592,6 +592,7 @@ def empty_subtree(dirpath):  # type: (Text) -> bool
                 raise
     return True
 
+
 _names = set()  # type: Set[Text]
 
 

cwltool/sandboxjs.py

@@ -14,6 +14,7 @@
 class JavascriptException(Exception):
     pass
 
+
 _logger = logging.getLogger("cwltool")
 
 JSON = Union[Dict[Text,Any], List[Any], Text, int, long, float, bool, None]

cwltool/schemas/README.md

@@ -40,16 +40,18 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 
 ## Implementations
 
-|Software|Description|CWL support|Platform support|Maturity|
+|Software|Description|CWL support|Platform support|Platform Maturity|
 |--------|-----------|-----------|--------|--------|
 |[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|Production|
 |[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|Production|
 |[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, GCP, Azure, OpenStack, Grid Engine, Mesos|Production|
+|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|[![Build Status](https://ci.commonwl.org/buildStatus/icon?job=rabix-conformance)](https://ci.commonwl.org/job/rabix-conformance/)|Java|alpha|
 |[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|Production|
 |[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|Production|
 |[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|Production|
 |[Funnel](https://github.com/bmeg/funnel)|Use Google Genomics Pipeline API with CWL|alpha|GCP|alpha|
-|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|alpha|Java|alpha|
+|[xenon-cwl-runner](https://github.com/NLeSC/xenon-cwl-runner)|Run CWL workflows using Xenon|alpha|[any Xenon backend](http://nlesc.github.io/Xenon/): local, ssh, SLURM, Torque, Grid Engine|Production|
+
 
 ## Repositories of CWL Tools and Workflows
 
@@ -64,10 +66,12 @@ Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 |--------|-----------|
 |[cwltest](https://github.com/common-workflow-language/cwltest)|CWL testing framework,  automated testing of tools and workflows written with CWL|
 |[cwl-upgrader](https://github.com/common-workflow-language/cwl-upgrader)|Upgrade CWL documents from draft-3 to v1.0|
-|[argparse2cwl](https://github.com/common-workflow-language/gxargparse#argparse2cwl)|Generate CWL CommandLineTool wrapper from Python programs that use argparse.  Also supports [click](http://click.pocoo.org/5/) argument parser.|
+|[argparse2tool](https://github.com/erasche/argparse2tool#cwl-specific-functionality)|Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse.  Also supports the [click](http://click.pocoo.org/5/) argument parser.|
 |[cwl2argparse](https://github.com/common-workflow-language/cwl2argparse)|Generate Python argparse code from CWL CommandLineTool description.|
 |[pypi2cwl](https://github.com/common-workflow-language/pypi2cwl)|Automatically run argparse2cwl on any package in PyPi|
 |[cwlavro](https://github.com/common-workflow-language/cwlavro)|Java classes for loading CWL documents|
+|[acd2cwl](https://github.com/common-workflow-language/acd2cwl)|CWL generator for ACD (EMBOSS) files |
+|[CWLviewer](https://github.com/MarkRobbo/CWLViewer)|A web application to view and share Common Workflow Language workflows|
 
 ## Support, Community and Contributing
 

cwltool/schemas/draft-2/draft-2/binding-test.cwl

@@ -22,7 +22,11 @@ inputs:
     inputBinding:
       position: -1
 
-outputs: []
+outputs:
+  - id: "#args"
+    type:
+      type: array
+      items: string
 
 baseCommand: python
 arguments: ["bwa", "mem"]

cwltool/schemas/draft-2/draft-2/cat1-testcli.cwl

@@ -17,18 +17,24 @@
             }
         },
         {
-        id: "#args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
-        },
-        inputBinding: {
-          position: -1
-        }
+            "id": "#args.py",
+            "type": "File",
+            "default": {
+              "class": "File",
+              "path": "args.py"
+            },
+            "inputBinding": {
+              "position": -1
+            }
       }
     ],
-    "outputs": [],
+    "outputs": [{
+      "id": "#args",
+      "type": {
+          "type": "array",
+          "items": "string"
+      }
+    }],
     "baseCommand": "python",
     "arguments": ["cat"]
 }

cwltool/schemas/draft-2/draft-2/tmap-tool.cwl

@@ -18,14 +18,14 @@
             }
         },
         {
-        id: "#args.py",
-        type: File,
-        default: {
-          class: File,
-          path: args.py
+        "id": "#args.py",
+        "type": "File",
+        "default": {
+          "class": "File",
+          "path": "args.py"
         },
-        inputBinding: {
-          position: -1
+        "inputBinding": {
+          "position": -1
         }
       }
     ],
@@ -36,6 +36,13 @@
                 "glob": "output.sam"
             },
             "type": ["null", "File"]
+        },
+        {
+            "id": "#args",
+            "type": {
+                "type": "array",
+                "items": "string"
+            }
         }
     ],
     "requirements": [

cwltool/schemas/draft-3/draft-3/binding-test.cwl

@@ -23,7 +23,11 @@ inputs:
     inputBinding:
       position: -1
 
-outputs: []
+outputs:
+  - id: args
+    type:
+      type: array
+      items: string
 
 baseCommand: python
 arguments: ["bwa", "mem"]