def get(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
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=None,
currentuser=self.current_user)
return
# 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
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 = ""
if (barcode_details['obsolete'] == "Y"):
# the barcode is obsolete
div_id = "obsolete"
message = "Barcode is Obsolete"
# get project info for div
ag_details = []
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)
def post(self):
term = self.get_argument('search_term')
results = {}
# search participant info
logins = db.search_participant_info(term)
results = set(logins)
# search kit info and add to resluts
logins = db.search_kits(term)
results = results | set(logins)
# search barcode and add to results
logins = db.search_barcodes(term)
results = results | set(logins)
# search handout kits
handouts = db.search_handout_kits(term)
# now take the ag_login_ids and collect the information to display
display_results = [] # list of dictionatries
for login in results:
login_display = {}
login_display['login_info'] = db.get_login_info(login)
login_display['humans'] = db.getHumanParticipants(
login)
login_display['animals'] = db.getAnimalParticipants(
login)
login_display['kit'] = db.get_kit_info_by_login(login)
for kit in login_display['kit']:
barcode_info = {}
ag_barcodes = db.get_barcode_info_by_kit_id(
kit['ag_kit_id'])
barcode_info = {}
for ag_barcode in ag_barcodes:
barcode_info[ag_barcode['barcode']] = {}
barcode_info[ag_barcode['barcode']]['ag_info'] = ag_barcode
lab_barcode_info = db.get_barcode_details(
ag_barcode['barcode'])
plate = db.get_plate_for_barcode(
ag_barcode['barcode'])
barcode_info[ag_barcode['barcode']]['barcode_info'] = \
lab_barcode_info
barcode_info[ag_barcode['barcode']]['plate'] = plate
kit['barcode_info'] = barcode_info
display_results.append(login_display)
# now render the page
self.render("ag_search.html",
results=display_results,
handouts=handouts,
currentuser=self.current_user)
def post(self):
term = self.get_argument('search_term')
results = {}
# search participant info
logins = db.search_participant_info(term)
results = set(logins)
# search kit info and add to resluts
logins = db.search_kits(term)
results = results | set(logins)
# search barcode and add to results
logins = db.search_barcodes(term)
results = results | set(logins)
# search handout kits
handouts = db.search_handout_kits(term)
# now take the ag_login_ids and collect the information to display
display_results = [] # list of dictionatries
for login in results:
login_display = {}
login_display['login_info'] = db.get_login_info(login)
login_display['humans'] = db.getHumanParticipants(
login)
login_display['animals'] = db.getAnimalParticipants(
login)
login_display['kit'] = db.get_kit_info_by_login(login)
for kit in login_display['kit']:
barcode_info = {}
ag_barcodes = db.get_barcode_info_by_kit_id(
kit['ag_kit_id'])
barcode_info = {}
for ag_barcode in ag_barcodes:
barcode_info[ag_barcode['barcode']] = {}
barcode_info[ag_barcode['barcode']]['ag_info'] = ag_barcode
lab_barcode_info = db.get_barcode_details(
ag_barcode['barcode'])
plate = db.get_plate_for_barcode(
ag_barcode['barcode'])
barcode_info[ag_barcode['barcode']]['barcode_info'] = \
lab_barcode_info
barcode_info[ag_barcode['barcode']]['plate'] = plate
kit['barcode_info'] = barcode_info
display_results.append(login_display)
# now render the page
self.render("ag_search.html", results=display_results,
handouts=handouts, currentuser=self.current_user)
def test_post(self):
data = {
'barcode': '000029153',
'parent_project': 'American+Gut',
'postmark_date': '2015-06-25',
'scan_date': '2015-07-01',
'bstatus': 'Recieved',
'biomass_remaining': 'Unknown',
'sequencing_status': 'WAITING',
'obsolete_status': 'N',
'sent_date': '2015-01-07',
'login_user': '******',
'login_email': 'REMOVED',
'email_type': '1',
'sample_date': '2015-06-24',
'sample_time': '22%3A50%3A00',
'sample_site': 'Stool',
'other_text': 'REMOVED',
'send_mail': 'send_mail',
}
self.mock_login_admin()
# check normal behaviour
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn('Barcode %s general details updated' % data['barcode'],
response.body)
self.assertIn('Project successfully changed', response.body)
dbInfo = db.get_barcode_details(data['barcode'])
self.assertEqual(date(2015, 6, 25), dbInfo['sample_postmark_date'])
self.assertEqual(date(2015, 7, 1), dbInfo['scan_date'])
# check that postmark_date and scan_date is set to None
# if missed as an argument
del data['postmark_date']
del data['scan_date']
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
dbInfo = db.get_barcode_details(data['barcode'])
self.assertEqual(None, dbInfo['sample_postmark_date'])
self.assertEqual(None, dbInfo['scan_date'])
data['postmark_date'] = '2015-06-25'
data['scan_date'] = '2015-07-01'
# TODO: Stefan Janssen: looks like we can successfully update a non
# existing barcode!!
data['barcode'] = 'rdskjmxykgrlyh'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertTrue(
'<p> Barcode %s general details updated </p>' % data['barcode'],
response.body)
data['barcode'] = '000029153'
# check that update failes for wrong data types
data['postmark_date'] = 'invalid date'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details failed" % data['barcode'],
response.body)
# test changing the barcode's project to a non existing one
# TODO: Stefan Janssen: I think this should not result in a positive
# message like 'Project successfully changed', because this does not
# trigger the creation of a new project!
data['project'] = 'NotAProject'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertTrue(
'<p> Barcode %s general details updated </p>' % data['barcode'],
response.body)
self.assertIn('Project successfully changed', response.body)
# check updating a AGP barcode
del data['project']
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn(
"Barcode %s AG info was successfully updated" % data['barcode'],
response.body)
data = {
'barcode': db.ut_get_arbitrary_non_ag_barcode(),
'parent_project': db.getProjectNames()[1],
'scan_date': '2014-12-15',
'bstatus': 'Recieved',
'biomass_remaining': 'Unknown',
'sequencing_status': 'WAITING',
'obsolete_status': 'N',
'project': 'UNKNOWN',
}
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertNotIn(
"Barcode %s AG info was successfully updated" % data['barcode'],
response.body)
self.assertTrue(
'<p> Barcode %s general details updated </p>' % data['barcode'],
response.body)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
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=None,
currentuser=self.current_user)
return
# 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
barcode_projects, parent_project = db.getBarcodeProjType(barcode)
project_names = db.getProjectNames()
# barcode exists get general info
# TODO (Stefan Janssen): check spelling of "received", i.e. tests in
# the template check for 'Recieved'. I think the logic is broken due
# to that.
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 = ""
if (barcode_details['obsolete'] == "Y"):
# the barcode is obsolete
div_id = "obsolete"
# TODO: Stefan: why is that set here, as far as I see, this
# message will in all cases be overwritten!
message = "Barcode is Obsolete"
# get project info for div
ag_details = []
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)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
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=None,
currentuser=self.current_user)
return
# 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
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 = ""
if (barcode_details['obsolete'] == "Y"):
# the barcode is obsolete
div_id = "obsolete"
message = "Barcode is Obsolete"
# get project info for div
ag_details = []
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)
def test_post(self):
data = {
"barcode": "000029153",
"parent_project": "American+Gut",
"postmark_date": "2015-06-25",
"scan_date": "2015-07-01",
"bstatus": "Recieved",
"biomass_remaining": "Unknown",
"sequencing_status": "WAITING",
"obsolete_status": "N",
"sent_date": "2015-01-07",
"login_user": "******",
"login_email": "REMOVED",
"email_type": "1",
"sample_date": "2015-06-24",
"sample_time": "22%3A50%3A00",
"sample_site": "Stool",
"other_text": "REMOVED",
"send_mail": "send_mail",
}
self.mock_login_admin()
# check normal behaviour
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details updated" % data["barcode"], response.body)
self.assertIn("Project successfully changed", response.body)
dbInfo = db.get_barcode_details(data["barcode"])
self.assertEqual(date(2015, 6, 25), dbInfo["sample_postmark_date"])
self.assertEqual(date(2015, 7, 1), dbInfo["scan_date"])
# check that postmark_date and scan_date is set to None
# if missed as an argument
del data["postmark_date"]
del data["scan_date"]
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
dbInfo = db.get_barcode_details(data["barcode"])
self.assertEqual(None, dbInfo["sample_postmark_date"])
self.assertEqual(None, dbInfo["scan_date"])
data["postmark_date"] = "2015-06-25"
data["scan_date"] = "2015-07-01"
# TODO: Stefan Janssen: looks like we can successfully update a non
# existing barcode!!
data["barcode"] = "rdskjmxykgrlyh"
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertTrue("<p> Barcode %s general details updated </p>" % data["barcode"], response.body)
data["barcode"] = "000029153"
# check that update failes for wrong data types
data["postmark_date"] = "invalid date"
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details failed" % data["barcode"], response.body)
# test changing the barcode's project to a non existing one
# TODO: Stefan Janssen: I think this should not result in a positive
# message like 'Project successfully changed', because this does not
# trigger the creation of a new project!
data["project"] = "NotAProject"
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertTrue("<p> Barcode %s general details updated </p>" % data["barcode"], response.body)
self.assertIn("Project successfully changed", response.body)
# check updating a AGP barcode
del data["project"]
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s AG info was successfully updated" % data["barcode"], response.body)
# check updating a non-AGP barcode
data = {
"barcode": "000033786",
"parent_project": "PROJECT4",
"scan_date": "2016-10-31",
"bstatus": "Recieved",
"biomass_remaining": "Unknown",
"sequencing_status": "WAITING",
"obsolete_status": "N",
"project": "UNKNOWN",
}
response = self.post("/barcode_util/", data)
self.assertEqual(response.code, 200)
self.assertNotIn("Barcode %s AG info was successfully updated" % data["barcode"], response.body)
self.assertTrue("<p> Barcode %s general details updated </p>" % data["barcode"], response.body)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
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=None,
currentuser=self.current_user)
return
# 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
barcode_projects, parent_project = db.getBarcodeProjType(
barcode)
project_names = db.getProjectNames()
# barcode exists get general info
# TODO (Stefan Janssen): check spelling of "received", i.e. tests in
# the template check for 'Recieved'. I think the logic is broken due
# to that.
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 = ""
if (barcode_details['obsolete'] == "Y"):
# the barcode is obsolete
div_id = "obsolete"
# TODO: Stefan: why is that set here, as far as I see, this
# message will in all cases be overwritten!
message = "Barcode is Obsolete"
# get project info for div
ag_details = []
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)
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)
def test_post(self):
data = {
'barcode': '000029153',
'parent_project': 'American+Gut',
'postmark_date': '2015-06-25',
'scan_date': '2015-07-01',
'bstatus': 'Recieved',
'biomass_remaining': 'Unknown',
'sequencing_status': 'WAITING',
'obsolete_status': 'N',
'sent_date': '2015-01-07',
'login_user': '******',
'login_email': 'REMOVED',
'email_type': '1',
'sample_date': '2015-06-24',
'sample_time': '22%3A50%3A00',
'sample_site': 'Stool',
'other_text': 'REMOVED',
'send_mail': 'send_mail',
}
self.mock_login_admin()
# check normal behaviour
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn('Barcode %s general details updated' % data['barcode'],
response.body)
self.assertIn('Project successfully changed', response.body)
dbInfo = db.get_barcode_details(data['barcode'])
self.assertEqual(date(2015, 6, 25), dbInfo['sample_postmark_date'])
self.assertEqual(date(2015, 7, 1), dbInfo['scan_date'])
# check that postmark_date and scan_date is set to None
# if missed as an argument
del data['postmark_date']
del data['scan_date']
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
dbInfo = db.get_barcode_details(data['barcode'])
self.assertEqual(None, dbInfo['sample_postmark_date'])
self.assertEqual(None, dbInfo['scan_date'])
data['postmark_date'] = '2015-06-25'
data['scan_date'] = '2015-07-01'
# TODO: Stefan Janssen: looks like we can successfully update a non
# existing barcode!!
data['barcode'] = 'rdskjmxykgrlyh'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertTrue('<p> Barcode %s general details updated </p>'
% data['barcode'], response.body)
data['barcode'] = '000029153'
# check that update failes for wrong data types
data['postmark_date'] = 'invalid date'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details failed" % data['barcode'],
response.body)
# test changing the barcode's project to a non existing one
# TODO: Stefan Janssen: I think this should not result in a positive
# message like 'Project successfully changed', because this does not
# trigger the creation of a new project!
data['project'] = 'NotAProject'
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertTrue('<p> Barcode %s general details updated </p>'
% data['barcode'], response.body)
self.assertIn('Project successfully changed', response.body)
# check updating a AGP barcode
del data['project']
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s AG info was successfully updated"
% data['barcode'], response.body)
data = {
'barcode': db.ut_get_arbitrary_non_ag_barcode(),
'parent_project': db.getProjectNames()[1],
'scan_date': '2014-12-15',
'bstatus': 'Recieved',
'biomass_remaining': 'Unknown',
'sequencing_status': 'WAITING',
'obsolete_status': 'N',
'project': 'UNKNOWN',
}
response = self.post('/barcode_util/', data)
self.assertEqual(response.code, 200)
self.assertNotIn("Barcode %s AG info was successfully updated"
% data['barcode'], response.body)
self.assertTrue('<p> Barcode %s general details updated </p>'
% data['barcode'], response.body)
