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View Code? Open in Web Editor NEWUsing BioSamples as an entry point for data source in Galaxy
Using BioSamples as an entry point for data source in Galaxy
To make the demo more robust, modify template to take in a search term or identifier dynamically.
Test new code update with small list of sample accessions to sort out issue.
Processed data such as count tables come as a zip when downloaded from ArrayExpress. How to unzip these ?
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)
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
Create basic template to mimic BioSamples page listing sample summary information.
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
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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