def test_post_update_ag_project_change(self):
db.alter_access_levels("test", [3])
self.data["project"] = "UNKNOWN"
self.mock_login()
response = self.post("/barcode_util/", data=self.data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details updated" % self.ag_good, response.body)
self.assertIn("Project successfully changed", response.body)
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, "UNKNOWN")
self.assertEqual(parent_project, "American Gut")
# reset back
db.setBarcodeProjects(self.ag_good, rem_projects=["UNKNOWN"])
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, "")
self.assertEqual(parent_project, "American Gut")
def test_post_update_ag_project_change(self):
db.alter_access_levels('test', [3])
self.data['project'] = 'UNKNOWN'
self.mock_login()
response = self.post('/barcode_util/', data=self.data)
self.assertEqual(response.code, 200)
self.assertIn('Barcode %s general details updated' % self.ag_good,
response.body)
self.assertIn('Project successfully changed', response.body)
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, 'UNKNOWN')
self.assertEqual(parent_project, 'American Gut')
# reset back
db.setBarcodeProjects(self.ag_good, rem_projects=['UNKNOWN'])
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, '')
self.assertEqual(parent_project, 'American Gut')
def test_post_update_ag_project_change(self):
db.alter_access_levels('test', [3])
self.data['project'] = 'UNKNOWN'
self.mock_login()
response = self.post('/barcode_util/', data=self.data)
self.assertEqual(response.code, 200)
self.assertIn('Barcode %s general details updated' % self.ag_good,
response.body)
self.assertIn('Project successfully changed', response.body)
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, 'UNKNOWN')
self.assertEqual(parent_project, 'American Gut')
# reset back
db.setBarcodeProjects(self.ag_good, rem_projects=['UNKNOWN'])
barcode_projects, parent_project = db.getBarcodeProjType(self.ag_good)
self.assertEqual(barcode_projects, '')
self.assertEqual(parent_project, 'American Gut')
def post(self):
barcode = self.get_argument('barcode')
postmark_date = self.get_argument('postmark_date', None)
scan_date = self.get_argument('scan_date', None)
biomass_remaining_value = self.get_argument('biomass_remaining_value',
None)
sequencing_status = self.get_argument('sequencing_status', None)
obsolete_status = self.get_argument('obsolete_status', None)
projects = set(self.get_arguments('project'))
sent_date = self.get_argument('sent_date', None)
login_user = self.get_argument('login_user',
'American Gut participant')
send_mail = self.get_argument('send_mail', None)
login_email = self.get_argument('login_email', None)
other_text = self.get_argument('other_text', None)
email_type = self.get_argument('email_type', None)
sample_time = self.get_argument('sample_time', None)
sample_date = self.get_argument('sample_date', None)
# now we collect data and update based on forms
# first update general barcode info
# Set to non to make sure no conflicts with new date typing in DB
if not postmark_date:
postmark_date = None
if not scan_date:
scan_date = None
try:
db.updateBarcodeStatus('Received', postmark_date, scan_date,
barcode, biomass_remaining_value,
sequencing_status, obsolete_status)
gen_update_msg = "Barcode %s general details updated" % barcode
except: # noqa
gen_update_msg = "Barcode %s general details failed" % barcode
email_msg = ag_update_msg = project_msg = None
exisiting_proj, parent_project = db.getBarcodeProjType(barcode)
# This WILL NOT let you remove a sample from being in AG if it is
# part of AG to begin with
exisiting_proj = set(exisiting_proj.split(', '))
if exisiting_proj != projects:
try:
add_projects = projects.difference(exisiting_proj)
rem_projects = exisiting_proj.difference(projects)
db.setBarcodeProjects(barcode, add_projects, rem_projects)
project_msg = "Project successfully changed"
except: # noqa
project_msg = "Error changing project"
new_proj, parent_project = db.getBarcodeProjType(barcode)
if parent_project == 'American Gut':
db.push_barcode_to_qiita_buffer(barcode)
email_msg, ag_update_msg = self.update_ag_barcode(
barcode, login_user, login_email, email_type, sent_date,
send_mail, sample_date, sample_time, other_text)
self.render("barcode_util.html",
div_and_msg=None,
barcode_projects=[],
parent_project=None,
project_names=[],
barcode=None,
email_type=None,
barcode_info=None,
proj_barcode_info=None,
msgs=(gen_update_msg, email_msg, ag_update_msg,
project_msg),
currentuser=self.current_user)
def post(self):
barcode = self.get_argument('barcode')
postmark_date = self.get_argument('postmark_date', None)
scan_date = self.get_argument('scan_date', None)
biomass_remaining_value = self.get_argument('biomass_remaining_value',
None)
sequencing_status = self.get_argument('sequencing_status', None)
obsolete_status = self.get_argument('obsolete_status', None)
projects = set(self.get_arguments('project'))
sent_date = self.get_argument('sent_date', None)
login_user = self.get_argument('login_user',
'American Gut participant')
send_mail = self.get_argument('send_mail', None)
login_email = self.get_argument('login_email', None)
other_text = self.get_argument('other_text', None)
email_type = self.get_argument('email_type', None)
sample_time = self.get_argument('sample_time', None)
sample_date = self.get_argument('sample_date', None)
# now we collect data and update based on forms
# first update general barcode info
# Set to non to make sure no conflicts with new date typing in DB
if not postmark_date:
postmark_date = None
if not scan_date:
scan_date = None
try:
db.updateBarcodeStatus('Received',
postmark_date,
scan_date, barcode,
biomass_remaining_value,
sequencing_status,
obsolete_status)
gen_update_msg = "Barcode %s general details updated" % barcode
except:
gen_update_msg = "Barcode %s general details failed" % barcode
email_msg = ag_update_msg = project_msg = None
exisiting_proj, parent_project = db.getBarcodeProjType(
barcode)
# This WILL NOT let you remove a sample from being in AG if it is
# part of AG to begin with
exisiting_proj = set(exisiting_proj.split(', '))
if exisiting_proj != projects:
try:
add_projects = projects.difference(exisiting_proj)
rem_projects = exisiting_proj.difference(projects)
db.setBarcodeProjects(barcode, add_projects, rem_projects)
project_msg = "Project successfully changed"
except:
project_msg = "Error changing project"
new_proj, parent_project = db.getBarcodeProjType(barcode)
if parent_project == 'American Gut':
email_msg, ag_update_msg = self.update_ag_barcode(
barcode, login_user, login_email, email_type, sent_date,
send_mail, sample_date, sample_time, other_text)
self.render("barcode_util.html", div_and_msg=None,
barcode_projects=[],
parent_project=None,
project_names=[], barcode=None,
email_type=None,
barcode_info=None, proj_barcode_info=None,
msgs=(gen_update_msg, email_msg, ag_update_msg,
project_msg),
currentuser=self.current_user)
def post(self):
barcode = self.get_argument('barcode', None)
bstatus = self.get_argument('bstatus', None)
postmark_date = self.get_argument('postmark_date', None)
scan_date = self.get_argument('scan_date', None)
biomass_remaining_value = self.get_argument('biomass_remaining_value',
None)
sequencing_status = self.get_argument('sequencing_status', None)
obsolete_status = self.get_argument('obsolete_status', None)
projects = set(self.get_arguments('project'))
barcode_projects = 'Unknown'
ag_details = {}
if bstatus is None:
# gather info to display
barcode_details = db.get_barcode_details(barcode)
if len(barcode_details) == 0:
div_id = "invalid_barcode"
message = ("Barcode %s does not exist in the database" %
barcode)
self.render("barcode_util.html",
div_and_msg=(div_id, message, barcode),
barcode_projects=[],
parent_project=None,
project_names=[],
barcode=barcode,
email_type=None,
barcode_info=None,
proj_barcode_info=None,
msgs=None,
currentuser=self.current_user)
return
else:
barcode_projects, parent_project = db.getBarcodeProjType(
barcode)
project_names = db.getProjectNames()
# barcode exists get general info
if barcode_details['status'] is None:
barcode_details['status'] = 'Received'
if barcode_details['biomass_remaining'] is None:
barcode_details['biomass_remaining'] = 'Unknown'
if barcode_details['sequencing_status'] is None:
barcode_details['sequencing_status']
if barcode_details['obsolete'] is None:
barcode_details['obsolete'] = 'N'
div_id = message = email_type = ""
ag_details = []
if (barcode_details['obsolete'] == "Y"):
#the barcode is obsolete
div_id = "obsolete"
message = "Barcode is Obsolete"
#get project info for div
if parent_project == 'American Gut':
div_id, message, ag_details = self.get_ag_details(barcode)
else:
div_id = "verified"
message = "Barcode Info is correct"
div_and_msg = (div_id, message, barcode)
self.render("barcode_util.html",
div_and_msg=div_and_msg,
barcode_projects=barcode_projects,
parent_project=parent_project,
project_names=project_names,
barcode=barcode,
email_type=None,
barcode_info=barcode_details,
proj_barcode_info=ag_details,
msgs=None,
currentuser=self.current_user)
else:
#now we collect data and update based on forms
#first update general barcode info
#Set to non to make sure no conflicts with new date typing in DB
if not postmark_date:
postmark_date = None
if not scan_date:
scan_date = None
try:
db.updateBarcodeStatus('Received', postmark_date, scan_date,
barcode, biomass_remaining_value,
sequencing_status, obsolete_status)
msg1 = "Barcode %s general details updated" % barcode
except:
msg1 = "Barcode %s general details failed" % barcode
msg2 = msg3 = msg4 = None
exisiting_proj, parent_project = db.getBarcodeProjType(barcode)
exisiting_proj = set(exisiting_proj.split(','))
if exisiting_proj != projects:
try:
add_projects = projects.difference(exisiting_proj)
rem_projects = exisiting_proj.difference(projects)
print exisiting_proj
print projects
print add_projects
print rem_projects
db.setBarcodeProjects(barcode, add_projects, rem_projects)
msg4 = "Project successfully changed"
except:
msg4 = "Error changing project"
new_proj, parent_project = db.getBarcodeProjType(barcode)
if parent_project == 'American Gut':
msg2, msg3 = self.update_ag_barcode(barcode)
self.render("barcode_util.html",
div_and_msg=None,
barcode_projects=[],
parent_project=None,
project_names=[],
barcode=None,
email_type=None,
barcode_info=None,
proj_barcode_info=None,
msgs=(msg1, msg2, msg3, msg4),
currentuser=self.current_user)
def post(self):
barcode = self.get_argument('barcode', None)
bstatus = self.get_argument('bstatus', None)
postmark_date = self.get_argument('postmark_date', None)
scan_date = self.get_argument('scan_date', None)
biomass_remaining_value = self.get_argument('biomass_remaining_value',
None)
sequencing_status = self.get_argument('sequencing_status', None)
obsolete_status = self.get_argument('obsolete_status', None)
projects = set(self.get_arguments('project'))
barcode_projects = 'Unknown'
ag_details = {}
if bstatus is None:
# gather info to display
barcode_details = db.get_barcode_details(barcode)
if len(barcode_details) == 0:
div_id = "invalid_barcode"
message = ("Barcode %s does not exist in the database" %
barcode)
self.render("barcode_util.html",
div_and_msg=(div_id, message, barcode),
barcode_projects=[], parent_project=None, project_names=[],
barcode=barcode, email_type=None,
barcode_info=None, proj_barcode_info=None,
msgs=None, currentuser=self.current_user)
return
else:
barcode_projects, parent_project = db.getBarcodeProjType(
barcode)
project_names = db.getProjectNames()
# barcode exists get general info
if barcode_details['status'] is None:
barcode_details['status'] = 'Received'
if barcode_details['biomass_remaining'] is None:
barcode_details['biomass_remaining'] = 'Unknown'
if barcode_details['sequencing_status'] is None:
barcode_details['sequencing_status']
if barcode_details['obsolete'] is None:
barcode_details['obsolete'] = 'N'
div_id = message = email_type = ""
ag_details = []
if (barcode_details['obsolete'] == "Y"):
#the barcode is obsolete
div_id = "obsolete"
message = "Barcode is Obsolete"
#get project info for div
if parent_project == 'American Gut':
div_id, message, ag_details = self.get_ag_details(barcode)
else:
div_id = "verified"
message = "Barcode Info is correct"
div_and_msg = (div_id, message, barcode)
self.render("barcode_util.html", div_and_msg=div_and_msg,
barcode_projects=barcode_projects, parent_project=parent_project,
project_names=project_names,
barcode=barcode, email_type=None,
barcode_info=barcode_details,
proj_barcode_info=ag_details, msgs=None,
currentuser=self.current_user)
else:
#now we collect data and update based on forms
#first update general barcode info
#Set to non to make sure no conflicts with new date typing in DB
if not postmark_date:
postmark_date = None
if not scan_date:
scan_date = None
try:
db.updateBarcodeStatus('Received', postmark_date,
scan_date, barcode,
biomass_remaining_value,
sequencing_status,
obsolete_status)
msg1 = "Barcode %s general details updated" % barcode
except:
msg1 = "Barcode %s general details failed" % barcode
msg2 = msg3 = msg4 = None
exisiting_proj, parent_project = db.getBarcodeProjType(
barcode)
exisiting_proj = set(exisiting_proj.split(','))
if exisiting_proj != projects:
try:
add_projects = projects.difference(exisiting_proj)
rem_projects = exisiting_proj.difference(projects)
print exisiting_proj
print projects
print add_projects
print rem_projects
db.setBarcodeProjects(barcode, add_projects, rem_projects)
msg4 = "Project successfully changed"
except:
msg4 = "Error changing project"
new_proj, parent_project = db.getBarcodeProjType(barcode)
if parent_project == 'American Gut':
msg2, msg3 = self.update_ag_barcode(barcode)
self.render("barcode_util.html", div_and_msg=None, barcode_projects=[],
parent_project=None,
project_names=[], barcode=None, email_type=None,
barcode_info=None, proj_barcode_info=None,
msgs=(msg1, msg2, msg3, msg4),
currentuser=self.current_user)