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biosamples-to-galaxy's Issues

Import not working

Test new code update with small list of sample accessions to sort out issue.

Duplications

For ArrayExpress data each sample seems to have two IDs : one from ArrayExpress and one from ENA. The one from ArrayExpress gets the links to both AE and ENA. The script gets only the fastq data from the ENA one.
Not sure if this is common (was looking at E-MTAB-3173)

Avoid unpacking .gz files

Default behaviour seems to be that the downloaded .gz files (from ENA) are unzipped. As we now have datatypes representing "fastqsanger.gz", unzipping should be an opt-in step

Error when No ENA link found

When no ENA link is found, the Flask app returns:

127.0.0.1 - - [05/Jul/2017 18:00:36] "POST / HTTP/1.1" 302 -
RK:  [u'SAMEA3194620']
Formatted Response:  [u'SAMEA3194620']
** Sample Accession for Data Export:  SAMEA3194620
8
No ENA link found
127.0.0.1 - - [05/Jul/2017 18:00:38] "GET /get_data_for_galaxy/?sample_list=SAMEA3194620 HTTP/1.0" 500 -
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1997, in __call__
    return self.wsgi_app(environ, start_response)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1985, in wsgi_app
    response = self.handle_exception(e)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1540, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
    response = self.full_dispatch_request()
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
    rv = self.dispatch_request()
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/Users/twhetzel/git/biosamples-to-galaxy/sync.py", line 327, in get_data
    sample = _get_data_from_AE(ae_link, sample)
  File "/Users/twhetzel/git/biosamples-to-galaxy/sync.py", line 156, in _get_data_from_AE
    AE_table = AE_table.loc[AE_table['Source Name'] == sample.name]
  File "/usr/local/lib/python2.7/site-packages/pandas/core/ops.py", line 861, in wrapper
    res = na_op(values, other)
  File "/usr/local/lib/python2.7/site-packages/pandas/core/ops.py", line 800, in na_op
    raise TypeError("invalid type comparison")
TypeError: invalid type comparison

dataset_xxx.datfiles

Sometimes a folder dataset_xxx.datfiles is generated, but not always. I'm not sure how that works. Out of 4 files (2 gzip and 2 zip) one of each had the files folder, the other one did not

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