Fixed empty items list issue

[rhpvorderman]

Sometimes no items are needed for run-data-managers, see the following file:

data_managers:
    - id: all_fasta_by_path_manager
      params:
        - 'dbkey': 'GRCh38/hg38'
        - 'name': 'Human Genome Assembly GRCh38/hg38'
        - 'path': '/export/genomes/hg38.fa'
      data_table_reload:
        - all_fasta
        - __dbkeys__

However, run-data-managers throws the following error when the file is run:

Traceback (most recent call last):
  File "/home/ruben/ephemeris/.venv/bin/run-data-managers", line 11, in <module>
    load_entry_point('ephemeris==0.6.2.dev0', 'console_scripts', 'run-data-managers')()
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/ephemeris-0.6.2.dev0-py2.7.egg/ephemeris/run_data_managers.py", line 80, in main
    run_dm(args)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/ephemeris-0.6.2.dev0-py2.7.egg/ephemeris/run_data_managers.py", line 52, in run_dm
    value = re.sub(r'{{\s*item\s*}}', item, value, flags=re.IGNORECASE)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/re.py", line 155, in sub
    return _compile(pattern, flags).sub(repl, string, count)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/re.py", line 286, in _subx
    template = _compile_repl(template, pattern)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/re.py", line 271, in _compile_repl
    p = sre_parse.parse_template(repl, pattern)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/sre_parse.py", line 737, in parse_template
    s = Tokenizer(source)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/sre_parse.py", line 192, in __init__
    self.__next()
  File "/home/ruben/ephemeris/.venv/lib/python2.7/sre_parse.py", line 194, in __next
    if self.index >= len(self.string):
TypeError: object of type 'NoneType' has no len()

The fix is to default items to empty string instead of None.

[rhpvorderman]

I just tested for item in dm.get('items',[]): It gives the following error:

Traceback (most recent call last):
  File "/home/ruben/ephemeris/.venv/bin/run-data-managers", line 11, in <module>
    load_entry_point('ephemeris==0.6.2.dev0', 'console_scripts', 'run-data-managers')()
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/ephemeris-0.6.2.dev0-py2.7.egg/ephemeris/run_data_managers.py", line 80, in main
    run_dm(args)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/ephemeris-0.6.2.dev0-py2.7.egg/ephemeris/run_data_managers.py", line 56, in run_dm
    job = gi.tools.run_tool(history_id=None, tool_id=dm_id, tool_inputs=inputs)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/bioblend-0.8.0-py2.7.egg/bioblend/galaxy/tools/__init__.py", line 113, in run_tool
    return self._tool_post(payload)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/bioblend-0.8.0-py2.7.egg/bioblend/galaxy/tools/__init__.py", line 219, in _tool_post
    return Client._post(self, payload, files_attached=files_attached)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/bioblend-0.8.0-py2.7.egg/bioblend/galaxy/client.py", line 157, in _post
    files_attached=files_attached)
  File "/home/ruben/ephemeris/.venv/lib/python2.7/site-packages/bioblend-0.8.0-py2.7.egg/bioblend/galaxyclient.py", line 134, in make_post_request
    body=r.text, status_code=r.status_code)
bioblend.ConnectionError: Unexpected HTTP status code: 400: {"err_data": {"all_fasta_source": "Parameter all_fasta_source requires a value, but has no legal values defined."}, "err_msg": "Parameter all_fasta_source requires a value, but has no legal values defined.", "err_code": 0}

for item in dm.get('items',['']): works fine. I believe there has to be an item in the list in order for the for item statement to work. It just skips the code block when there are no items defined (which is the most logical behaviour). But the code block should not be skipped, so an empty string is a good placeholder.

[afgane]

Thanks for trying it out.