Clean up exporting and README example

Author: illusional

README.md

@@ -14,68 +14,60 @@ The library works for both Python 2.7.12+ and 3.6.0.
 ------------------------
 
 
-
-I've forked this repository to try and get my use of this repository working quickly without 
-worrying too much about proper code etiquette. I have and will continue to submit merge requests 
-back to the [original repository](https://github.com/common-workflow-language/python-cwlgen).
-
-[![Build Status](https://travis-ci.org/illusional/python-cwlgen.svg?branch=master)](https://travis-ci.org/common-workflow-language/python-cwlgen)
-[![codecov](https://codecov.io/gh/illusional/python-cwlgen/branch/master/graph/badge.svg)](https://codecov.io/gh/illusional/python-cwlgen)
-[![PyPI version](https://badge.fury.io/py/illusional.cwlgen.svg)](https://badge.fury.io/py/illusional.cwlgen)
-
 # Common Workflow Language
 
-[Common Workflow Language (CWL)](https://www.commonwl.org/v1.0/index.html) is a method to describe workflows,
- and any tools (software) that it may use. The [user guide](http://www.commonwl.org/user_guide/01-introduction/index.html)
- gives a gentle (and better) explanation of what its goals are, and how they are achieved, but broadly:
+[Common Workflow Language (CWL)](https://www.commonwl.org/v1.0/index.html) is a language to describe workflows. 
+The [user guide](http://www.commonwl.org/user_guide/01-introduction/index.html)
+ gives a gentle explanation of what its goals are, but broadly:
 
  1. Stop writing bash scripts for long complex jobs.
  2. Take pipelines anywhere (portability).
- 3. Try to enforce reproducibility guidelines.
+ 3. Enforce reproducibility guidelines.
 
-This python repository is simply a python wrapper for _most_ of the classes (work in progress), 
+This python repository is a python wrapper for _most_ of the classes (work in progress), 
 allowing you to build the structure of the workflow in Python and have this module generate and export CWL for you.
 
 **Nb:** This isn't going to sanity or quality check Workflows or CommandLineTools for you, use 
 [CWLTool](https://github.com/common-workflow-language/cwltool) or [WOMTool](https://cromwell.readthedocs.io/en/develop/WOMtool/) for that.
 
 ## Quick-start guide
 
-This is available through PIP!
+You can install python-cwlgen through pip with the following command:
 
 ```
-pip install illusional.cwlgen
+pip install cwlgen
 ```
 
 ## How it works ?
 
 There's a pretty close copy of the cwl specifications ([Workflow](https://www.commonwl.org/v1.0/Workflow.html)| 
 [CommandLineTool](https://www.commonwl.org/v1.0/CommandLineTool.html)), where the Python classes mirror the CWL spec. 
-This repository also includes some of the docstrings to give you context of classes and their properties.
-
-I've tried to include direct links to a classes documentation, however this isn't always possible.
+This repository also includes docstrings to give you context of classes and their properties.
 
-There are some small examples in the `examples/` folder, however for whatever class you need, you simply just init 
-that class, for example:
+The `examples/` folder contains some simple examples, however , 
+you can simply initialise that class, for example:
 
 _Creating a CommandLineTool_
 ```python
-# if using gitsubmodules, you can use the following import statement
-import cwlgen as cwl
+import cwlgen
 
-tool_object = cwl.CommandLineTool(cwltool_id="echo-tool", base_command="echo", label=None, doc=None,
+tool_object = cwlgen.CommandLineTool(tool_id="echo-tool", base_command="echo", label=None, doc=None,
                  cwl_version="v1.0", stdin=None, stderr=None, stdout=None, path=None)
-tool_object.inputs.append(cwl.CommandInputParameter("myParamId", label=None, secondary_files=None, param_format=None,
-                 streamable=None, doc=None, input_binding=None, default=None, param_type=None))
-                 
-# fill in the fields as required
+tool_object.inputs.append(
+    cwlgen.CommandInputParameter("myParamId", param_type="string", label=None, secondary_files=None, param_format=None,
+                 streamable=None, doc=None, input_binding=None, default=None)
+)
 
 # to get the dictionary representation:
 dict_to_export = tool_object.get_dict()
 
-# dump using a yaml exporter
-yaml.dump(dict_to_export)
-```
+# to get the string representation (YAML)
+yaml_export = tool_object.export_string()
+
+# print to console
+tool_object.export()
 
-All of the classes should work in a similar way. I've removed the `literal` representation from my fork as I 
-didn't want to use _ruamel_ at the moment. Otherwise file an issue and I'll have a look into it.
+# print to file
+with open("echotool.cwl", "w") as f:
+    tool_object.export(f)
+```

cwlgen/commandlinetool.py

@@ -92,23 +92,25 @@ def get_dict(self):
             d['requirements'] = {r.get_class(): r.get_dict() for r in self.requirements}
         return d
 
+    def export_string(self):
+        ruamel.yaml.add_representer(literal, literal_presenter)
+        cwl_tool = self.get_dict()
+        return ruamel.yaml.dump(cwl_tool, default_flow_style=False)
+
     def export(self, outfile=None):
         """
         Export the tool in CWL either on STDOUT or in outfile.
         """
-        # First add representer (see .utils.py) for multiline writting
-        ruamel.yaml.add_representer(literal, literal_presenter)
-
-        cwl_tool = self.get_dict()
+        rep = self.export_string()
 
         # Write CWL file in YAML
         if outfile is None:
             six.print_(CWL_SHEBANG, "\n", sep='')
-            six.print_(ruamel.yaml.dump(cwl_tool))
+            six.print_(rep)
         else:
             out_write = open(outfile, 'w')
             out_write.write(CWL_SHEBANG + '\n\n')
-            out_write.write(ruamel.yaml.dump(cwl_tool))
+            out_write.write(rep)
             out_write.close()
 
 

cwlgen/common.py

@@ -126,7 +126,7 @@ def __init__(self):
         self.s = "http://schema.org/"
 
 
-class Metadata(object):
+class Metadata(Serializable):
     """
     Represent metadata described by http://schema.org.
     """

cwlgen/workflow.py

@@ -110,23 +110,25 @@ def get_dict(self):
 
         return cwl_workflow
 
+    def export_string(self):
+        ruamel.yaml.add_representer(literal, literal_presenter)
+        cwl_tool = self.get_dict()
+        return ruamel.yaml.dump(cwl_tool, default_flow_style=False)
+
     def export(self, outfile=None):
         """
         Export the workflow in CWL either on STDOUT or in outfile.
         """
-        # First add representer (see .utils.py) for multiline writting
-        ruamel.yaml.add_representer(literal, literal_presenter)
-
-        cwl_workflow = self.get_dict()
+        rep = self.export_string()
 
         # Write CWL file in YAML
         if outfile is None:
             six.print_(CWL_SHEBANG, "\n", sep='')
-            six.print_(ruamel.yaml.dump(cwl_workflow))
+            six.print_(rep)
         else:
             out_write = open(outfile, 'w')
             out_write.write(CWL_SHEBANG + '\n\n')
-            out_write.write(ruamel.yaml.dump(cwl_workflow))
+            out_write.write(rep)
             out_write.close()
 
     # def add(self, step_id, tool, params):

examples/grep.cwl

@@ -1,25 +1,31 @@
 #!/usr/bin/env cwl-runner
 
-$namespaces: {s: http://schema.org/}
-arguments: []
+$namespaces:
+  s: http://schema.org/
 baseCommand: grep
 class: CommandLineTool
 cwlVersion: v1.0
-doc: |-
-  grep searches for a pattern in a file.
+doc: grep searches for a pattern in a file.
 id: grep
 inputs:
-  input_file:
-    doc: input file from which you want to look for the pattern
-    inputBinding: {loadContents: false, position: 2, separate: true, shellQuote: true}
-    type: File
-  pattern:
-    doc: pattern to find in the input file
-    inputBinding: {loadContents: false, position: 1, separate: true, shellQuote: true}
-    type: string
+- doc: input file from which you want to look for the pattern
+  id: input_file
+  inputBinding:
+    position: 2
+  type: File
+- doc: pattern to find in the input file
+  id: pattern
+  inputBinding:
+    position: 1
+  type: string
 label: print lines matching a pattern
+metadata:
+  about: grep searches for a pattern in a file.
+  name: grep
 outputs:
-  output: {doc: lines found with the pattern, type: stdout}
+- doc: lines found with the pattern
+  id: output
+  type: stdout
 s:about: grep searches for a pattern in a file.
 s:name: grep
 stdout: grep.txt

examples/grep_example.py

@@ -46,10 +46,10 @@
 
     # Add Metadata
     metadata = {'name': 'grep',
-                'about' : 'grep searches for a pattern in a file.'}
+                'about': 'grep searches for a pattern in a file.'}
     cwl_tool.metadata = cwlgen.Metadata(**metadata)
     cwl_tool.metadata = cwlgen.Metadata(**metadata)
 
     # Write in an output file
-    #cwl_tool.export()
-    cwl_tool.export("grep.cwl")
+    cwl_tool.export()
+    # cwl_tool.export("grep.cwl")

examples/readme_example.py

@@ -0,0 +1,17 @@
+import cwlgen
+
+tool_object = cwlgen.CommandLineTool(tool_id="echo-tool", base_command="echo", label=None, doc=None,
+                                     cwl_version="v1.0", stdin=None, stderr=None, stdout=None, path=None)
+tool_object.inputs.append(
+    cwlgen.CommandInputParameter("myParamId", label=None, secondary_files=None, param_format=None,
+                                 streamable=None, doc=None, input_binding=None, default=None, param_type="string")
+)
+
+# to get the dictionary representation:
+dict_to_export = tool_object.get_dict()
+
+# to get the string representation (YAML)
+yaml_export = tool_object.export_string()
+
+# print to console
+tool_object.export()