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 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 metadata_xml_generator(request, compress=False):
"""
Return metadata xml for all cart items.
:param request: django Request object
:param compress: set to True to enable compression
"""
cart = Cart(request.session)
zipper = Gzipper(filename='metadata.xml', compress=compress)
items = cart.cart.items.all()
zipper.write(render_to_string('xml/analysis_xml_header.xml', {
'date': datetime.datetime.strftime(
timezone.now(), '%Y-%d-%m %H:%M:%S'),
'len': items.count()}))
counter = 0
downloadable_size = 0
result_template = get_template('xml/metadata_xml_result.xml')
for item in items:
analysis = item.analysis
try:
xml, files_size = get_analysis_xml(
analysis_id=analysis.analysis_id,
last_modified=analysis.last_modified)
except AnalysisException as e:
cart_logger.error('Error while composing metadata xml. %s' % str(e))
add_message(
request=request,
level='error',
content='An error occured while composing metadata/manifest xml file.')
request.session.save()
return
counter += 1
downloadable_size += analysis.files_size
zipper.write(result_template.render(Context({
'counter': counter,
'xml': xml.strip()})))
yield zipper.read()
zipper.write(render_to_string('xml/analysis_xml_summary.xml', {
'counter': counter,
'size': str(round(downloadable_size / 1073741824. * 100) / 100)}))
yield zipper.close()
def urls_tsv_generator(request, compress=False):
"""
Returns analysis_data_uri urls 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='urls.txt', compress=compress)
iterator = cart.cart.items.all().iterator()
count_all = cart.all_count
count = 0
while True:
urls_list = []
for i in xrange(settings.MAX_ITEMS_IN_QUERY):
try:
urls_list.append(next(iterator).analysis.analysis_id)
except StopIteration:
break
if not urls_list:
break
for i in urls_list:
zipper.write('%s/cghub/data/analysis/download/%s\n' % (
settings.CGHUB_DOWNLOAD_SERVER,
i
))
count += 1
yield zipper.read()
if count != count_all:
cart_logger.error('Error while composing urls tsv.')
add_message(
request=request,
level='error',
content='An error occured while composing urls tsv.')
request.session.save()
zipper.write(u'\nError!')
yield zipper.close()
