def test_append(self):
exp_contents = 'argh'
mem = InMemoryZip()
mem2 = mem.append(self.test_fname, exp_contents)
self.assertIn(
'test.zip',
mem2.in_memory_data.getvalue(),
)
def test_write_to_buffer(self):
exp_contents = 'argh'
mem = InMemoryZip()
mem2 = mem.append(self.test_fname, exp_contents)
res = mem2.write_to_buffer()
# http://stackoverflow.com/a/34162395/1167475
zhandle = zipfile.ZipFile(io.BytesIO(res))
res_contents = zhandle.read(self.test_fname)
self.assertEqual(res_contents, exp_contents)
def test_writetofile(self):
exp_contents = 'argh'
mem = InMemoryZip()
mem2 = mem.append(self.test_fname, exp_contents)
mem2.writetofile(self.test_out_fname)
self.assertTrue(os.path.exists(self.test_out_fname))
zhandle = zipfile.ZipFile(self.test_out_fname, 'r')
res_contents = zhandle.read(self.test_fname)
self.assertEqual(res_contents, exp_contents)
def post(self):
participants = db.participant_names()
participants = "\n".join(["\t".join(r) for r in participants])
meta_zip = InMemoryZip()
meta_zip.append("participants.txt", participants)
# write out zip file
self.add_header("Content-type", "application/octet-stream")
self.add_header("Content-Transfer-Encoding", "binary")
self.add_header("Accept-Ranges", "bytes")
self.add_header("Content-Encoding", "none")
self.add_header("Content-Disposition", "attachment; filename=participants.zip")
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
kitinfo = loads(self.get_argument('kitinfo'))
fields = self.get_argument('fields').split(',')
table = ['\t'.join(fields)]
table.extend(['\t'.join(map(str, kit)) for kit in kitinfo])
kit_zip = InMemoryZip()
kit_zip.append('kit_printouts.txt', get_printout_data(kitinfo)).append(
'kit_table.txt', '\n'.join(table))
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition', 'attachment; filename=kitinfo.zip')
self.write(kit_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
participants = db.participant_names()
participants = '\n'.join(['\t'.join(r) for r in participants])
meta_zip = InMemoryZip()
meta_zip.append('participants.txt', participants)
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=participants.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
participants = db.participant_names()
participants = '\n'.join(['\t'.join(r) for r in participants])
meta_zip = InMemoryZip()
meta_zip.append('participants.txt', participants)
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=participants.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
barcodes = self.get_argument('barcodes').split(',')
if self.get_argument('blanks'):
blanks = self.get_argument('blanks').split(',')
else:
blanks = []
if self.get_argument('external'):
external = self.get_argument('external').split(',')
else:
external = []
# Get metadata and create zip file
metadata, failures = db.pulldown(barcodes, blanks, external)
meta_zip = InMemoryZip()
failed = '\n'.join(['\t'.join(bc) for bc in viewitems(failures)])
failtext = ("The following barcodes were not retrieved "
"for any survey:\n%s" % failed)
meta_zip.append("failures.txt", failtext)
for survey, meta in viewitems(metadata):
meta_zip.append('survey_%s_md.txt' % survey, meta)
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=metadata.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
kitinfo = loads(self.get_argument('kitinfo'))
fields = self.get_argument('fields').split(',')
table = ['\t'.join(fields)]
table.extend(['\t'.join(map(str, kit)) for kit in kitinfo])
kit_zip = InMemoryZip()
kit_zip.append('kit_printouts.txt', get_printout_data(kitinfo)).append(
'kit_table.txt', '\n'.join(table))
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=kitinfo.zip')
self.write(kit_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
barcodes = self.get_argument('barcodes').split(',')
if self.get_argument('blanks'):
blanks = self.get_argument('blanks').split(',')
else:
blanks = []
if self.get_argument('external'):
external = self.get_argument('external').split(',')
else:
external = []
# Get metadata and create zip file
metadata, failures = db.pulldown(barcodes, blanks, external)
meta_zip = InMemoryZip()
failed = '\n'.join(['\t'.join(bc) for bc in viewitems(failures)])
failtext = ("The following barcodes were not retrieved "
"for any survey:\n%s" % failed)
meta_zip.append("failures.txt", failtext)
for survey, meta in viewitems(metadata):
meta_zip.append('survey_%s_md.txt' % survey, meta)
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=metadata.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def post(self):
barcodes = listify(self.get_arguments('barcodes'))
blanks = listify(self.get_arguments('blanks'))
# query which surveys have been selected by the user
selected_ag_surveys = listify(
self.get_arguments('selected_ag_surveys'))
external = listify(self.get_arguments('external'))
selected_ag_surveys = list(map(int, selected_ag_surveys))
# Get metadata and create zip file
metadata, failures = db.pulldown(barcodes, blanks, external)
meta_zip = InMemoryZip()
failed = '\n'.join(['\t'.join(bc) for bc in viewitems(failures)])
failtext = ("The following barcodes were not retrieved "
"for any survey:\n%s" % failed)
meta_zip.append("failures.txt", failtext)
# check database about what surveys are available
available_agsurveys = {}
for (_id, name, _) in db.list_ag_surveys():
available_agsurveys[_id] = name.replace(' ', '_')
results_as_pd = []
for survey, meta in viewitems(metadata):
# only create files for those surveys that have been selected by
# the user. Note that ids from the DB are negative, in metadata
# they are positive!
# Currently, I (Stefan Janssen) don't have test data for external
# surveys, thus I don't know their 'survey' value. I expect it to
# be the name of the external survey. In order to not block their
# pulldown I check that a skipped survey ID must be in the set of
# all available surveys.
survey = -1 * survey
if (survey in selected_ag_surveys) or \
(survey not in available_agsurveys):
meta_zip.append(
'survey_%s_md.txt' % available_agsurveys[survey], meta)
# transform each survey into a pandas dataframe for later merge
# read all columns as string to avoid unintened conversions,
# like cutting leading zeros of barcodes
pd_meta = pd.read_csv(StringIO(meta), sep="\t", dtype=str)
# reset the index to barcodes = here sample_name
pd_meta.set_index('sample_name', inplace=True)
results_as_pd.append(pd_meta)
# add the merged table of all selected surveys to the zip archive
if self.get_argument('merged', default='False') == 'True':
pd_all = pd.DataFrame()
if len(results_as_pd) > 0:
pd_all = pd.concat(results_as_pd, join='outer', axis=1)
meta_zip.append(
'surveys_merged_md.txt',
pd_all.to_csv(sep='\t', index_label='sample_name'))
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=metadata.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()
def test_append(self):
exp_contents = 'argh'
mem = InMemoryZip()
mem2 = mem.append(self.test_fname, exp_contents)
self.assertIn('test.zip',
mem2.in_memory_data.getvalue(),)
def test_constructor(self):
mem = InMemoryZip()
self.assertTrue(mem.in_memory_data is not None)
self.assertTrue(mem.in_memory_zip is not None)
self.assertEqual(mem.in_memory_zip.debug, 3)
def post(self):
barcodes = listify(self.get_arguments('barcodes'))
blanks = listify(self.get_arguments('blanks'))
# query which surveys have been selected by the user
selected_ag_surveys = listify(
self.get_arguments('selected_ag_surveys'))
external = listify(self.get_arguments('external'))
selected_ag_surveys = list(map(int, selected_ag_surveys))
# Get metadata and create zip file
metadata, failures = db.pulldown(barcodes, blanks, external)
meta_zip = InMemoryZip()
failed = '\n'.join(['\t'.join(bc) for bc in viewitems(failures)])
failtext = ("The following barcodes were not retrieved "
"for any survey:\n%s" % failed)
meta_zip.append("failures.txt", failtext)
# check database about what surveys are available
available_agsurveys = {}
for (_id, name, _) in db.list_ag_surveys():
available_agsurveys[_id] = name.replace(' ', '_')
results_as_pd = []
for survey, meta in viewitems(metadata):
# only create files for those surveys that have been selected by
# the user. Note that ids from the DB are negative, in metadata
# they are positive!
# Currently, I (Stefan Janssen) don't have test data for external
# surveys, thus I don't know their 'survey' value. I expect it to
# be the name of the external survey. In order to not block their
# pulldown I check that a skipped survey ID must be in the set of
# all available surveys.
survey = -1 * survey
if (survey in selected_ag_surveys) or \
(survey not in available_agsurveys):
meta_zip.append('survey_%s_md.txt' %
available_agsurveys[survey], meta)
# transform each survey into a pandas dataframe for later merge
# read all columns as string to avoid unintened conversions,
# like cutting leading zeros of barcodes
pd_meta = pd.read_csv(StringIO(meta), sep="\t", dtype=str)
# reset the index to barcodes = here sample_name
pd_meta.set_index('sample_name', inplace=True)
results_as_pd.append(pd_meta)
# add the merged table of all selected surveys to the zip archive
if self.get_argument('merged', default='False') == 'True':
pd_all = pd.DataFrame()
if len(results_as_pd) > 0:
pd_all = pd.concat(results_as_pd, join='outer', axis=1)
meta_zip.append('surveys_merged_md.txt',
pd_all.to_csv(sep='\t',
index_label='sample_name'))
# write out zip file
self.add_header('Content-type', 'application/octet-stream')
self.add_header('Content-Transfer-Encoding', 'binary')
self.add_header('Accept-Ranges', 'bytes')
self.add_header('Content-Encoding', 'none')
self.add_header('Content-Disposition',
'attachment; filename=metadata.zip')
self.write(meta_zip.write_to_buffer())
self.flush()
self.finish()