def forwards(self, orm):
for analysis in orm.Analysis.objects.all():
api_request = RequestDetailJSON(query={
'analysis_id': analysis.analysis_id})
try:
result = api_request.call().next()
except StopIteration:
print 'Bad analysis: %s, skipped.' % analysis.analysis_id
continue
analysis.aliquot_id = result.get('aliquot_id')
analysis.analyte_code = result.get('analyte_code')
analysis.center_name = result.get('center_name')
analysis.checksum = result.get('checksum')
analysis.disease_abbr = result.get('disease_abbr')
analysis.filename = result.get('filename')
analysis.legacy_sample_id = result.get('legacy_sample_id')
analysis.library_strategy = result.get('library_strategy')
analysis.published_date = result.get('published_date')
analysis.participant_id = result.get('participant_id')
analysis.platform = result.get('platform')
analysis.refassem_short_name = result.get('refassem_short_name')
analysis.sample_accession = result.get('sample_accession')
analysis.sample_id = result.get('sample_id')
analysis.sample_type = result.get('sample_type')
analysis.study = result.get('study')
analysis.tss_id = result.get('tss_id')
analysis.upload_date = result.get('upload_date')
analysis.save()
def summary_tsv_generator(request, compress=False):
"""
Return summary tsv for all cart items.
:param request: django Request object
:param compress: set to True to enable compression
"""
cart = Cart(request.session)
zipper = Gzipper(filename='summary.tsv', compress=compress)
COLUMNS = settings.TABLE_COLUMNS
stringio = StringIO()
csvwriter = CSVUnicodeWriter(
stringio, quoting=csv.QUOTE_MINIMAL,
dialect='excel-tab', lineterminator='\n')
csvwriter.writerow(
[field.lower().replace(' ', '_') for field in COLUMNS])
count_all = cart.all_count
iterator = cart.cart.items.all().iterator()
count = 0
while True:
ids = []
for i in xrange(settings.MAX_ITEMS_IN_QUERY):
try:
ids.append(next(iterator).analysis.analysis_id)
except StopIteration:
break
if not ids:
break
api_request = RequestDetailJSON(query={'analysis_id': ids})
for result in api_request.call():
fields = field_values(result, humanize_files_size=False)
row = []
for field_name in COLUMNS:
value = fields.get(field_name, '')
row.append(unicode(value))
csvwriter.writerow(row)
count += 1
stringio.seek(0)
line = stringio.read()
stringio.seek(0)
stringio.truncate()
zipper.write(line)
yield zipper.read()
if count != count_all:
cart_logger.error('Error while composing summary tsv.')
add_message(
request=request,
level='error',
content='An error occured while composing summary tsv.')
request.session.save()
zipper.write(u'\nError!')
yield zipper.close()
def manifest_xml_generator(request, compress=False):
"""
Return manifest xml for cart items with state==live.
:param request: django Request object
:param compress: set to True to enable compression
"""
cart = Cart(request.session)
zipper = Gzipper(filename='manifest.xml', compress=compress)
count_live = cart.live_count
zipper.write(render_to_string('xml/analysis_xml_header.xml', {
'date': datetime.datetime.strftime(
timezone.now(), '%Y-%d-%m %H:%M:%S'),
'len': count_live}))
iterator = cart.cart.items.filter(analysis__state='live').iterator()
counter = 0
downloadable_size = 0
result_template = get_template('xml/manifest_xml_result.xml')
while True:
ids = []
for i in xrange(settings.MAX_ITEMS_IN_QUERY):
try:
ids.append(next(iterator).analysis.analysis_id)
except StopIteration:
break
if not ids:
break
api_request = RequestDetailJSON(query={'analysis_id': ids})
for result in api_request.call():
for f in result['files']:
downloadable_size += f['filesize']
counter += 1
zipper.write(result_template.render(Context({
'counter': counter,
'result': result,
'server_url': settings.CGHUB_DOWNLOAD_SERVER})))
yield zipper.read()
if counter != count_live:
cart_logger.error('Error while composing manifest xml.')
add_message(
request=request,
level='error',
content='An error occured while composing manifest xml.')
request.session.save()
else:
zipper.write(render_to_string('xml/analysis_xml_summary.xml', {
'counter': counter,
'size': str(round(downloadable_size / 1073741824. * 100) / 100)}))
yield zipper.close()
def post(self, request, analysis_id):
api_request = RequestDetailJSON(query={'analysis_id': analysis_id})
try:
result = api_request.call().next()
except StopIteration:
raise URLError('No results for analysis_id == %s' % analysis_id)
try:
with transaction.commit_on_success():
cart = Cart(request.session)
cart.add(result)
cart.update_stats()
except DatabaseError:
add_message(
request, 'error',
settings.DATABASE_ERROR_NOTIFICATION,
once=True)
return HttpResponseRedirect(reverse('cart_page'))
def update_analysis(data):
"""
Updates analysis with data.analysis_id.
:param data: Result object (may contains only analysis_id or all attributes).
"""
try:
analysis = Analysis.objects.get(analysis_id=data['analysis_id'])
except Analysis.DoesNotExist:
analysis = Analysis(analysis_id=data['analysis_id'])
if 'platform' in data:
result = data
else:
# get all attributes
api_request = RequestDetailJSON(query={'analysis_id': data['analysis_id']})
result = api_request.call().next()
for attr in CART_SORT_ATTRIBUTES:
setattr(analysis, attr, result.get(attr))
try:
analysis.save()
except Exception as e:
cart_logger.error('Error while creating new Analysis: %s' % str(e))
return None
return analysis
