Error with CWL1.0 - Githubissues

denis-yuen commented 6 years ago

This seems to have problems with the CWL 1.0, possibly because it doesn't like the switch from #id to the new map style parameters.

Replicate with https://github.com/dockstore/phylowgs/blob/master/Dockstore.cwl

$ cwl2wdl Dockstore.cwl 
Traceback (most recent call last):
  File "/usr/local/bin/cwl2wdl", line 11, in <module>
    load_entry_point('cwl2wdl==0.1.dev42+gbba7c3c', 'console_scripts', 'cwl2wdl')()
  File "/usr/local/lib/python2.7/dist-packages/cwl2wdl-0.1.dev42+gbba7c3c-py2.7.egg/cwl2wdl/main.py", line 59, in cli
    CwlParser(arguments.FILE).parse_document()
  File "/usr/local/lib/python2.7/dist-packages/cwl2wdl-0.1.dev42+gbba7c3c-py2.7.egg/cwl2wdl/parsers.py", line 33, in parse_document
    tasks = [self.__parse_cwl_task(cwl, sourceDir)]
  File "/usr/local/lib/python2.7/dist-packages/cwl2wdl-0.1.dev42+gbba7c3c-py2.7.egg/cwl2wdl/parsers.py", line 61, in __parse_cwl_task
    inputs = self.__parse_cwl_inputs(cwl_task['inputs'])
  File "/usr/local/lib/python2.7/dist-packages/cwl2wdl-0.1.dev42+gbba7c3c-py2.7.egg/cwl2wdl/parsers.py", line 189, in __parse_cwl_inputs
    cwl_input['id'].strip("#")
TypeError: string indices must be integers, not unicode

ambarishK commented 4 years ago

I am working over Ubuntu 16.04 and Python 3.5

I am getting an error while installation.

error: The 'setuptools>=40.0' distribution was not found and is required by the application

Please fix the issue.

ambarishK commented 4 years ago

One more error while running cwl2wdl command.

cwl_input['id'].strip("#")
TypeError: string indices must be integers

aubreybailey commented 3 years ago

I'm guessing this is abandoned. Same issue :(

adamstruck commented 3 years ago

I'm guessing this is abandoned.

I do not have any plans to work on this again. It was only ever a proof-of-concept. Feel free to fork the repo.

adamstruck / cwl2wdl

Error with CWL1.0 #3