def post(self):
# Do nothing if no file given
if 'barcodes' not in self.request.files:
surveys = db.list_external_surveys()
self.render("ag_pulldown.html", currentuser=self.current_user,
barcodes='', blanks='', external='', surveys=surveys,
errors="No barcode file given, thus nothing could "
"be pulled down.")
return
# Get file information, ignoring commented out lines
fileinfo = self.request.files['barcodes'][0]['body']
lines = fileinfo.splitlines()
# barcodes must be in first column, stripping in case extra spaces
samples = [l.split('\t')[0].strip() for l in lines
if not l.startswith('#')]
barcodes = [b for b in samples if not b.upper().startswith('BLANK')]
blanks = [b for b in samples if b.upper().startswith('BLANK')]
hold = self.get_arguments('external', [])
if hold:
external = ','.join(hold)
else:
external = ''
surveys = db.list_external_surveys()
self.render("ag_pulldown.html", currentuser=self.current_user,
barcodes=",".join(barcodes), blanks=",".join(blanks),
surveys=surveys, external=external, errors='')
def test_post(self):
self.mock_login_admin()
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001448', '000001447',
'100001449', '000001445',
'000015296', '000015297',
'000015298', '000015299',
'000016180', '000016280',
'000016281', '000016283',
'000016284'],
'blanks': ['BLANK000001449', 'BLANK000001453',
'BLANK100001453'],
'external': db.list_external_surveys()[:1],
'selected_ag_surveys': [-1, -2, -3, -4, -5],
'merged': 'True'})
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
self.assertIn('failures.txt', response.body)
self.assertIn('survey_Personal_Information_md.txt', response.body)
# store the resulting zip archive to disc ...
tmpfile = NamedTemporaryFile(mode='w', delete=False,
prefix='metadata_pulldown_single_',
suffix='.zip')
tmpfile.write(response.body)
tmpfile.close()
# ... and read the content as dict of strings
result = extract_zip(tmpfile.name)
os.remove(tmpfile.name)
# read in the true content from data dir for comparison
truth = extract_zip(join(dirname(realpath(__file__)), 'data',
'results_barcodes.zip'))
self.maxDiff = None
self.assertEqual(sneak_files(result), sneak_files(truth))
def post(self):
form = ThirdPartyData()
form.survey.choices = [(x, x) for x in db.list_external_surveys()]
msg = ''
seperators = {'comma': ',', 'tab': '\t', 'space': ' '}
args = {a: v[0] for a, v in viewitems(self.request.arguments)}
form.process(data=args)
# Validate form and make sure upload happened
if not form.validate() or 'file_in' not in self.request.files:
self.render("ag_third_party.html", the_form=form, errors=msg)
return
# Format file for stringIO
file_body = self.request.files['file_in'][0]['body'].replace(
"\r\n", "\n").replace("\r", "\n")
file_body = StringIO(unicode(file_body), newline=None)
try:
count = db.store_external_survey(
file_body,
form.survey.data,
separator=seperators[form.seperator.data],
survey_id_col=form.survey_id.data,
trim=form.trim.data)
except KeyError as e:
msg = 'Header column not found: %s' % str(e)
except Exception as e:
# Print any error that happens to the page
msg = str(e)
else:
msg = "%d surveys added to '%s' successfully" % \
(count, form.survey.data)
self.render("ag_third_party.html", the_form=form, errors=msg)
def post(self):
# Do nothing if no file given
if 'barcodes' not in self.request.files:
self.render("ag_pulldown.html",
currentuser=self.current_user,
barcodes='',
blanks='',
external='')
return
# Get file information, ignoring commented out lines
fileinfo = self.request.files['barcodes'][0]['body']
lines = fileinfo.splitlines()
# barcodes must be in first column, stripping in case extra spaces
samples = [
l.split('\t')[0].strip() for l in lines if not l.startswith('#')
]
barcodes = [b for b in samples if not b.upper().startswith('BLANK')]
blanks = [b for b in samples if b.upper().startswith('BLANK')]
hold = self.get_arguments('external', [])
if hold:
external = ','.join(hold)
else:
external = ''
surveys = db.list_external_surveys()
self.render("ag_pulldown.html",
currentuser=self.current_user,
barcodes=",".join(barcodes),
blanks=",".join(blanks),
surveys=surveys,
external=external)
def post(self):
form = ThirdPartyData()
form.survey.choices = [(x, x) for x in db.list_external_surveys()]
msg = ''
seperators = {'comma': ',', 'tab': '\t', 'space': ' '}
args = {a: v[0] for a, v in viewitems(self.request.arguments)}
form.process(data=args)
# Validate form and make sure upload happened
if not form.validate() or 'file_in' not in self.request.files:
self.render("ag_third_party.html", the_form=form,
errors=msg)
return
# Format file for stringIO
file_body = self.request.files['file_in'][0]['body'].replace(
"\r\n", "\n").replace("\r", "\n")
file_body = StringIO(unicode(file_body), newline=None)
try:
count = db.store_external_survey(
file_body, form.survey.data,
separator=seperators[form.seperator.data],
survey_id_col=form.survey_id.data, trim=form.trim.data)
except KeyError as e:
msg = 'Header column not found: %s' % str(e)
except Exception as e:
# Print any error that happens to the page
msg = str(e)
else:
msg = "%d surveys added to '%s' successfully" % \
(count, form.survey.data)
self.render("ag_third_party.html", the_form=form,
errors=msg)
def test_post(self):
self.mock_login_admin()
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001445',
'000001446',
'000001447',
'000001448',
'100001449',
'000016180',
'000015296',
'000015297',
'000015298',
'000015299',
'000015300',
'000016280',
'000016281',
'000016282',
'000016283',
'000016284'],
'blanks': ['BLANK000001449',
'BLANK000001453',
'BLANK100001453'],
'external': db.list_external_surveys()[:1]})
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
self.assertIn('failures.txt', response.body)
self.assertIn('survey_1_md.txt', response.body)
def get(self):
surveys = db.list_external_surveys()
self.render("ag_pulldown.html",
currentuser=self.current_user,
barcodes=[],
surveys=surveys,
errors='')
def test_get(self):
self.mock_login_admin()
response = self.get('/ag_pulldown/')
self.assertEqual(response.code, 200)
for survey in db.list_external_surveys():
self.assertIn("<option value='%s'>%s</option>" % (survey, survey),
response.body)
self.assertNotIn('<input type="submit" disabled>', response.body)
def test_get(self):
self.mock_login_admin()
response = self.get('/ag_pulldown/')
self.assertEqual(response.code, 200)
for survey in db.list_external_surveys():
self.assertIn("<option value='%s'>%s</option>" % (survey, survey),
response.body)
self.assertNotIn('<input type="submit" disabled>', response.body)
def post(self):
# Do nothing if no file given
if 'barcodes' not in self.request.files:
surveys = db.list_external_surveys()
ags = db.list_ag_surveys(map(int, self.get_arguments('agsurveys')))
self.render("ag_pulldown.html",
currentuser=self.current_user,
barcodes='',
blanks='',
external='',
surveys=surveys,
errors="No barcode file given, thus nothing could "
"be pulled down.",
agsurveys=ags,
merged=self.get_argument('merged', default='False'))
return
# Get file information, ignoring commented out lines
fileinfo = self.request.files['barcodes'][0]['body']
lines = fileinfo.splitlines()
# barcodes must be in first column, stripping in case extra spaces
samples = [
l.split('\t')[0].strip() for l in lines if not l.startswith('#')
]
barcodes = [b for b in samples if not b.upper().startswith('BLANK')]
blanks = [b for b in samples if b.upper().startswith('BLANK')]
hold = self.get_arguments('external')
if hold:
external = ','.join(hold)
else:
external = ''
surveys = db.list_external_surveys()
ags = db.list_ag_surveys(map(int, self.get_arguments('agsurveys')))
self.render("ag_pulldown.html",
currentuser=self.current_user,
barcodes=",".join(barcodes),
blanks=",".join(blanks),
surveys=surveys,
external=external,
errors='',
agsurveys=ags,
merged=self.get_argument('merged', default='False'))
def test_get(self):
self.mock_login_admin()
tpsurveys = db.list_external_surveys()
form = ThirdPartyData()
# make sure that at least this third party survey exist in the DB
if len(tpsurveys) == 0:
response = self.post('/ag_third_party/add/',
{'name': 'newTPsurvey',
'description': 'akSJdghcakscmakld fh',
'url': 'www.google.com'})
response = self.get('/ag_third_party/data/')
self.assertEqual(response.code, 200)
# test that all fields are present in the HTML side.
for key, element in form.__dict__['_fields'].items():
self.assertIn(str(element.label), response.body)
for survey in tpsurveys:
self.assertIn('<option value="%s">%s</option>' % (survey, survey),
response.body)
def test_get(self):
self.mock_login_admin()
tpsurveys = db.list_external_surveys()
form = ThirdPartyData()
# make sure that at least this third party survey exist in the DB
data = {
'name': 'newTPsurvey',
'description': 'akSJdghcakscmakld fh',
'url': 'www.google.com'
}
if len(tpsurveys) == 0:
response = self.post('/ag_third_party/add/', data)
response = self.get('/ag_third_party/data/')
self.assertEqual(response.code, 200)
# test that all fields are present in the HTML side.
for key, element in form.__dict__['_fields'].items():
self.assertIn(str(element.label), response.body)
for survey in tpsurveys:
self.assertIn('<option value="%s">%s</option>' % (survey, survey),
response.body)
# roll back change to the DB
self._clean_up_funcs.append(
partial(db.ut_remove_external_survey, **data))
def test_post_select_surveys(self):
self.mock_login_admin()
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000037555', '000065893',
'000067690', '000037583',
'000066526', '000031568'],
'blanks': [],
'external': [],
'selected_ag_surveys': [-2, -3, -8],
'merged': 'False'})
# store the resulting zip archive to disc ...
tmpfile = NamedTemporaryFile(mode='w', delete=False,
prefix='metadata_pulldown_multiple_sel_',
suffix='.zip')
tmpfile.write(response.body)
tmpfile.close()
# ... and read the content as dict of strings
result = extract_zip(tmpfile.name)
self.assertItemsEqual(result.keys(),
['failures.txt',
'survey_Fermented_Foods_md.txt',
'survey_Pet_Information_md.txt'])
os.remove(tmpfile.name)
# no blanks
response = self.post('/ag_pulldown/download/',
{'barcodes': ('000001445', '000001446',
'000001447', '000001448',
'100001449', '000016180',
'000015296', '000015297',
'000015298', '000015299',
'000015300', '000016280',
'000016281', '000016282',
'000016283', '000016284'),
'blanks': [],
'external': db.list_external_surveys()[:1]})
self.assertEqual(response.code, 200)
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
# no externals
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001445',
'000001446',
'000001447',
'000001448',
'100001449',
'000016180',
'000015296',
'000015297',
'000015298',
'000015299',
'000015300',
'000016280',
'000016281',
'000016282',
'000016283',
'000016284'],
'blanks': ['BLANK000001449',
'BLANK000001453',
'BLANK100001453'],
'external': []})
self.assertEqual(response.code, 200)
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
def get(self):
form = ThirdPartyData()
form.survey.choices = [(x, x) for x in db.list_external_surveys()]
self.render("ag_third_party.html", the_form=form,
errors='')
def get(self):
form = ThirdPartyData()
form.survey.choices = [(x, x) for x in db.list_external_surveys()]
self.render("ag_third_party.html", the_form=form, errors='')
def get(self):
surveys = db.list_external_surveys()
self.render("ag_pulldown.html", currentuser=self.current_user,
barcodes=[], surveys=surveys, errors='')
def test_post(self):
self.mock_login_admin()
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001445',
'000001446',
'000001447',
'000001448',
'100001449',
'000016180',
'000015296',
'000015297',
'000015298',
'000015299',
'000015300',
'000016280',
'000016281',
'000016282',
'000016283',
'000016284'],
'blanks': ['BLANK000001449',
'BLANK000001453',
'BLANK100001453'],
'external': db.list_external_surveys()[:1]})
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
self.assertIn('failures.txt', response.body)
self.assertIn('survey_1_md.txt', response.body)
# no blanks
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001445',
'000001446',
'000001447',
'000001448',
'100001449',
'000016180',
'000015296',
'000015297',
'000015298',
'000015299',
'000015300',
'000016280',
'000016281',
'000016282',
'000016283',
'000016284'],
'blanks': '',
'external': db.list_external_surveys()[:1]})
self.assertEqual(response.code, 200)
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
# no externals
response = self.post('/ag_pulldown/download/',
{'barcodes': ['000001445',
'000001446',
'000001447',
'000001448',
'100001449',
'000016180',
'000015296',
'000015297',
'000015298',
'000015299',
'000015300',
'000016280',
'000016281',
'000016282',
'000016283',
'000016284'],
'blanks': ['BLANK000001449',
'BLANK000001453',
'BLANK100001453'],
'external': ''})
self.assertEqual(response.code, 200)
self.assertEqual(response.headers['Content-Disposition'],
'attachment; filename=metadata.zip')
