Fix package errror

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"]

cwltool/schemas/draft-3/draft-3/cat1-testcli.cwl

@@ -18,18 +18,24 @@
             }
         },
         {
-        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
         }
       }
     ],
-    "outputs": [],
+    "outputs": [{
+        "id": "args",
+        "type": {
+            "type": "array",
+            "items": "string"
+        }
+    }],
     "baseCommand": "python",
     "arguments": ["cat"]
 }

cwltool/schemas/draft-3/draft-3/tmap-tool.cwl

@@ -20,15 +20,15 @@
             }
         },
         {
-        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": [
@@ -38,6 +38,13 @@
                 "glob": "output.sam"
             },
             "type": ["null", "File"]
+        },
+        {
+            "id": "args",
+            "type": {
+                "type": "array",
+                "items": "string"
+            }
         }
     ],
     "requirements": [

cwltool/schemas/v1.0/CommandLineTool.yml

@@ -694,7 +694,6 @@ $graph:
     - name: package
       type: string
       doc: "The common name of the software to be configured."
-      jsonldPredicate: "@id"
     - name: version
       type: string[]?
       doc: "The (optional) version of the software to configured."

cwltool/schemas/v1.0/UserGuide.yml

@@ -290,8 +290,8 @@
     - |
       ## Parameter references
 
-      In a previous example, we used extracted a file using the "tar" program.
-      However, that example was very limited becuase it assumed that the file
+      In a previous example, we extracted a file using the "tar" program.
+      However, that example was very limited because it assumed that the file
       we were interested in was called "hello.txt".  In this example, you will
       see how to reference the value of input parameters dynamically from other
       fields.

cwltool/schemas/v1.0/concepts.md

@@ -89,7 +89,7 @@ preprocessing steps described in the
 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html).
 An implementation may formally validate the structure of a CWL document using
 SALAD schemas located at
-https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-4
+https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.0
 
 ## Identifiers