def get(self):
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_kit.html", projects=project_names,
currentuser=self.current_user, msg="", kitinfo=[],
fields="", remaining=remaining)
def get(self):
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_kit.html", projects=project_names,
currentuser=self.current_user, msg="", kitinfo=[],
fields="", remaining=remaining)
def post(self):
tag = self.get_argument("tag")
if not tag:
tag = None
projects = self.get_arguments("projects")
num_swabs = map(int, self.get_arguments("swabs"))
num_kits = map(int, self.get_arguments("kits"))
kits = []
fields = ""
try:
kits = db.create_ag_kits(zip(num_swabs, num_kits), tag, projects)
fields = ','.join(kits[0]._fields)
except Exception as e:
msg = "ERROR: %s" % str(e)
else:
msg = "Kits created! Please wait for downloads."
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_kit.html",
projects=project_names,
currentuser=self.current_user,
msg=msg,
kitinfo=dumps(kits),
remaining=remaining,
fields=fields)
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# the barcode is obsolete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_get(self):
self.mock_login_admin()
response = self.get('/ag_new_kit/')
self.assertEqual(response.code, 200)
for project in db.getProjectNames():
self.assertIn("<option value='%s'>%s</option>" %
(project, project), response.body)
self.assertIn("%i</span> unassigned barcodes" %
len(db.get_unassigned_barcodes()), response.body)
def test_get(self):
self.mock_login()
response = self.get('/projects/summary/')
self.assertEqual(response.code, 200)
# check that correct information is printed on HTML page.
for project_name in db.getProjectNames():
num_barcodes = len(db.get_barcodes_for_projects([project_name]))
self.assertIn('<tr><td>%s</td>' % project_name, response.body)
self.assertIn('<td>%s</td></tr>' % num_barcodes, response.body)
def test_get(self):
self.mock_login_admin()
response = self.get('/ag_new_kit/')
self.assertEqual(response.code, 200)
obs = response.body.decode('utf-8')
for project in db.getProjectNames():
self.assertIn("<option value='%s'>%s</option>" %
((xhtml_escape(project),) * 2), obs)
self.assertIn("%i</span> unassigned barcodes" %
len(db.get_unassigned_barcodes()), obs)
def test_get(self):
self.mock_login_admin()
response = self.get('/ag_new_kit/')
self.assertEqual(response.code, 200)
obs = response.body.decode('utf-8')
for project in db.getProjectNames():
self.assertIn(
"<option value='%s'>%s</option>" %
((xhtml_escape(project), ) * 2), obs)
self.assertIn(
"%i</span> unassigned barcodes" %
len(db.get_unassigned_barcodes()), obs)
def get(self):
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_barcode.html",
currentuser=self.current_user,
projects=project_names,
barcodes=[],
remaining=remaining,
msg="",
newbc=[],
assignedbc=[],
assign_projects="")
def test_get(self):
self.mock_login()
response = self.get('/projects/summary/')
self.assertEqual(response.code, 200)
obs = response.body.decode('utf-8')
# check that correct information is printed on HTML page.
for project_name in db.getProjectNames():
num_barcodes = len(db.get_barcodes_for_projects([project_name]))
self.assertIn('<tr><td>%s</td>' % xhtml_escape(project_name),
obs)
self.assertIn('<td>%s</td></tr>' % num_barcodes, obs)
def post(self):
# create barcodes
msg = ""
newbc = []
assignedbc = []
projects = []
action = self.get_argument("action")
num_barcodes = int(self.get_argument('numbarcodes'))
if action == "create":
newbc = db.create_barcodes(num_barcodes)
msg = ("%d Barcodes created! Please wait for barcode download" %
num_barcodes)
elif action == "assign":
projects = [
url_unescape(p).encode('utf-8')
for p in self.get_arguments('projects')
]
new_project = self.get_argument('newproject').strip()
try:
if new_project:
db.create_project(new_project)
projects.append(new_project)
assignedbc = db.assign_barcodes(num_barcodes, projects)
except ValueError as e:
msg = u"ERROR! %s" % e.message
else:
projects = [p.decode('utf-8') for p in projects]
tmp = u"%d barcodes assigned to %s, please wait for download."
msg = tmp % (num_barcodes, ", ".join(projects))
else:
raise HTTPError(400, 'Unknown action: %s' % action)
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_barcode.html",
currentuser=self.current_user,
projects=project_names,
remaining=remaining,
msg=msg,
newbc=newbc,
assignedbc=assignedbc,
assign_projects=", ".join(projects))
def post(self):
# create barcodes
msg = ""
newbc = []
assignedbc = []
projects = []
action = self.get_argument("action")
num_barcodes = int(self.get_argument('numbarcodes'))
if action == "create":
newbc = db.create_barcodes(num_barcodes)
msg = ("%d Barcodes created! Please wait for barcode download"
% num_barcodes)
elif action == "assign":
projects = [url_unescape(p).encode('utf-8')
for p in self.get_arguments('projects')]
new_project = self.get_argument('newproject').strip()
try:
if new_project:
db.create_project(new_project)
projects.append(new_project)
assignedbc = db.assign_barcodes(num_barcodes, projects)
except ValueError as e:
msg = u"ERROR! %s" % e.message
else:
projects = [p.decode('utf-8') for p in projects]
tmp = u"%d barcodes assigned to %s, please wait for download."
msg = tmp % (num_barcodes, ", ".join(projects))
else:
raise HTTPError(400, 'Unknown action: %s' % action)
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_barcode.html", currentuser=self.current_user,
projects=project_names, remaining=remaining,
msg=msg, newbc=newbc, assignedbc=assignedbc,
assign_projects=", ".join(projects))
def post(self):
tag = self.get_argument("tag")
if not tag:
tag = None
projects = self.get_arguments("projects")
num_swabs = map(int, self.get_arguments("swabs"))
num_kits = map(int, self.get_arguments("kits"))
kits = []
fields = ""
try:
kits = db.create_ag_kits(zip(num_swabs, num_kits), tag, projects)
fields = ','.join(kits[0]._fields)
except Exception as e:
msg = "ERROR: %s" % str(e)
else:
msg = "Kits created! Please wait for downloads."
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_kit.html", projects=project_names,
currentuser=self.current_user, msg=msg,
kitinfo=dumps(kits), remaining=remaining,
fields=fields)
def test_post(self):
self.mock_login_admin()
kits = [1, 2]
swabs = [2, 2]
tag = 'abc'
# check for correct results
projects = db.getProjectNames()
project1 = projects[0].encode('utf-8')
project2 = projects[1].encode('utf-8')
response = self.post('/ag_new_kit/',
{'tag': tag,
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
kitinfo = loads(response.body)
self.assertEqual(len(kitinfo['kitinfo']), sum(kits))
for k in kitinfo['kitinfo']:
self.assertIn(tag, k[0])
self.assertEqual(len(kitinfo['kitinfo'][0][-1]), swabs[0])
self.assertEqual(len(kitinfo['kitinfo'][1][-1]), swabs[1])
self.assertEqual(kitinfo['fields'],
"kit_id,password,verification_code,barcodes")
# missing argument
response = self.post('/ag_new_kit/',
{'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 400)
# too long tag
response = self.post('/ag_new_kit/',
{'tag': 'toolongtag',
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
# TODO: we should find more speaking ways to report an error to the
# user, see issue: #113
self.assertEqual(response.code, 500)
self.assertIn("Tag must be 4 or less characters", response.body)
# test that non existing projects are recognized.
response = self.post('/ag_new_kit/',
{'tag': 'abc',
'projects': ['doesNotExist', 'PROJECT5'],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 500)
self.assertIn("Project(s) given don\'t exist in database:",
response.body)
# check for empty swabs list
response = self.post('/ag_new_kit/',
{'tag': tag,
'projects': [project1, project2],
'swabs': [],
'kits': kits,
})
self.assertEqual(response.code, 500)
self.assertIn("SET assigned_on = NOW() WHERE barcode IN ()",
response.body)
# no kits given
response = self.post('/ag_new_kit/',
{'tag': tag,
'projects': [project1, project2],
'swabs': swabs,
'kits': [],
})
self.assertEqual(response.code, 500)
self.assertIn("SET assigned_on = NOW() WHERE barcode IN ()",
response.body)
# what if tag is None
response = self.post('/ag_new_kit/',
{'tag': '',
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 200)
kitinfo = loads(response.body)
self.assertNotIn('_', kitinfo['kitinfo'][0][0])
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 get(self):
project_names = db.getProjectNames()
remaining = len(db.get_unassigned_barcodes())
self.render("ag_new_barcode.html", currentuser=self.current_user,
projects=project_names, barcodes=[], remaining=remaining,
msg="", newbc=[], assignedbc=[], assign_projects="")
def test_post(self):
self.mock_login_admin()
action = 'unknown'
num_barcodes = 4
projects = [p.encode('utf-8') for p in db.getProjectNames()[:2]]
newProject = 'newProject' + str(os.getpid())
# check that unkown action results in a response code 400
response = self.post('/ag_new_barcode/', {
'action': action,
'numbarcodes': num_barcodes
})
self.assertRaises(HTTPError)
self.assertEqual(response.code, 400)
self.assertIn(
"HTTPError: HTTP %i: Bad Request (Unknown action: %s)" %
(400, action), response.body)
# TODO: test if exception for 0 barcodes to create is raised issue #105
# check creation of new barcodes
response = self.post('/ag_new_barcode/', {
'action': 'create',
'numbarcodes': num_barcodes
})
self.assertIn(
"%i Barcodes created! Please wait for barcode download" %
num_barcodes, response.body)
# check assignment of barcodes
# check that error is raised if project(s) cannot be found in DB
prj_nonexist = 'a non existing project name'
response = self.post(
'/ag_new_barcode/', {
'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects + [prj_nonexist],
'newproject': ""
})
self.assertEqual(response.code, 200)
exp = xhtml_escape('ERROR! Project(s) given don\'t exist in '
'database: %s' % prj_nonexist)
self.assertIn(exp, response.body)
# check correct assignment report on HTML side
response = self.post(
'/ag_new_barcode/', {
'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects,
'newproject': ""
})
self.assertEqual(response.code, 200)
exp = xhtml_escape(
"%i barcodes assigned to %s, please wait for download." %
(num_barcodes, ", ".join(projects)))
self.assertIn(exp, response.body)
# check if SQL error is thrown if number of barcodes is 0.
# See issue: #107
response = self.post(
'/ag_new_barcode/', {
'action': 'assign',
'numbarcodes': 0,
'projects': projects,
'newproject': ""
})
self.assertEqual(response.code, 200)
self.assertIn("Error running SQL query: UPDATE barcodes.barcode",
response.body)
# check recognition of existing projects
response = self.post(
'/ag_new_barcode/', {
'action': 'assign',
'numbarcodes': num_barcodes,
'newproject': projects[0]
})
self.assertEqual(response.code, 200)
self.assertIn(
"ERROR! Project %s already exists!" % xhtml_escape(projects[0]),
response.body)
# check recognition of unkown action
response = self.post('/ag_new_barcode/', {'action': 'unkown'})
self.assertEqual(response.code, 400)
self.assertRaises(HTTPError)
# test that new project is appended to list of projects
response = self.post(
'/ag_new_barcode/', {
'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects,
'newproject': newProject
})
self.assertEqual(response.code, 200)
self.assertIn(
"%i barcodes assigned to %s, please wait for download." %
(num_barcodes, ", ".join(map(
xhtml_escape, projects + [newProject]))), response.body)
def get(self):
projects = db.getProjectNames()
# escape unicode project names for xhtml rendering
info = [(p, len(db.get_barcodes_for_projects([p]))) for p in projects]
self.render('projects_summary.html', proj_counts=info)
def get(self):
projects = db.getProjectNames()
# escape unicode project names for xhtml rendering
info = [(p, len(db.get_barcodes_for_projects([p])))
for p in projects]
self.render('projects_summary.html', proj_counts=info)
def get(self):
projects = db.getProjectNames()
info = [(p, len(db.get_barcodes_for_projects([p]))) for p in projects]
self.render('projects_summary.html', proj_counts=info)
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
# 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)
def test_post(self):
self.mock_login_admin()
kits = [1, 2]
swabs = [2, 2]
tag = 'abc'
# check for correct results
projects = db.getProjectNames()
project1 = projects[0].encode('utf-8')
project2 = projects[1].encode('utf-8')
response = self.post(
'/ag_new_kit/', {
'tag': tag,
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
kitinfo = loads(response.body)
self.assertEqual(len(kitinfo['kitinfo']), sum(kits))
for k in kitinfo['kitinfo']:
self.assertIn(tag, k[0])
self.assertEqual(len(kitinfo['kitinfo'][0][-1]), swabs[0])
self.assertEqual(len(kitinfo['kitinfo'][1][-1]), swabs[1])
self.assertEqual(kitinfo['fields'],
"kit_id,password,verification_code,barcodes")
# missing argument
response = self.post('/ag_new_kit/', {
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 400)
# too long tag
response = self.post(
'/ag_new_kit/', {
'tag': 'toolongtag',
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
# TODO: we should find more speaking ways to report an error to the
# user, see issue: #113
self.assertEqual(response.code, 500)
self.assertIn("Tag must be 4 or less characters", response.body)
# test that non existing projects are recognized.
response = self.post(
'/ag_new_kit/', {
'tag': 'abc',
'projects': ['doesNotExist', 'PROJECT5'],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 500)
self.assertIn("Project(s) given don\'t exist in database:",
response.body)
# check for empty swabs list
response = self.post(
'/ag_new_kit/', {
'tag': tag,
'projects': [project1, project2],
'swabs': [],
'kits': kits,
})
self.assertEqual(response.code, 500)
self.assertIn("SET assigned_on = NOW() WHERE barcode IN ()",
response.body)
# no kits given
response = self.post(
'/ag_new_kit/', {
'tag': tag,
'projects': [project1, project2],
'swabs': swabs,
'kits': [],
})
self.assertEqual(response.code, 500)
self.assertIn("SET assigned_on = NOW() WHERE barcode IN ()",
response.body)
# what if tag is None
response = self.post(
'/ag_new_kit/', {
'tag': '',
'projects': [project1, project2],
'swabs': swabs,
'kits': kits,
})
self.assertEqual(response.code, 200)
kitinfo = loads(response.body)
self.assertNotIn('_', kitinfo['kitinfo'][0][0])
def test_post(self):
self.mock_login_admin()
action = 'unknown'
num_barcodes = 4
projects = [p.encode('utf-8') for p in db.getProjectNames()[:2]]
newProject = 'newProject' + str(os.getpid())
# check that unkown action results in a response code 400
response = self.post('/ag_new_barcode/', {'action': action,
'numbarcodes': num_barcodes})
self.assertRaises(HTTPError)
self.assertEqual(response.code, 400)
self.assertIn("HTTPError: HTTP %i: Bad Request (Unknown action: %s)"
% (400, action), response.body)
# TODO: test if exception for 0 barcodes to create is raised issue #105
# check creation of new barcodes
response = self.post('/ag_new_barcode/', {'action': 'create',
'numbarcodes': num_barcodes})
self.assertIn("%i Barcodes created! Please wait for barcode download" %
num_barcodes, response.body)
# check assignment of barcodes
# check that error is raised if project(s) cannot be found in DB
prj_nonexist = 'a non existing project name'
response = self.post('/ag_new_barcode/',
{'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects + [prj_nonexist],
'newproject': ""})
self.assertEqual(response.code, 200)
exp = xhtml_escape('ERROR! Project(s) given don\'t exist in '
'database: %s' % prj_nonexist)
self.assertIn(exp, response.body)
# check correct assignment report on HTML side
response = self.post('/ag_new_barcode/',
{'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects,
'newproject': ""})
self.assertEqual(response.code, 200)
exp = xhtml_escape(
"%i barcodes assigned to %s, please wait for download." %
(num_barcodes, ", ".join(projects)))
self.assertIn(exp, response.body)
# check if SQL error is thrown if number of barcodes is 0.
# See issue: #107
response = self.post('/ag_new_barcode/',
{'action': 'assign',
'numbarcodes': 0,
'projects': projects,
'newproject': ""})
self.assertEqual(response.code, 200)
self.assertIn("Error running SQL query: UPDATE barcodes.barcode",
response.body)
# check recognition of existing projects
response = self.post('/ag_new_barcode/',
{'action': 'assign',
'numbarcodes': num_barcodes,
'newproject': projects[0]})
self.assertEqual(response.code, 200)
self.assertIn("ERROR! Project %s already exists!" %
xhtml_escape(projects[0]),
response.body)
# check recognition of unkown action
response = self.post('/ag_new_barcode/', {'action': 'unkown'})
self.assertEqual(response.code, 400)
self.assertRaises(HTTPError)
# test that new project is appended to list of projects
response = self.post('/ag_new_barcode/',
{'action': 'assign',
'numbarcodes': num_barcodes,
'projects': projects,
'newproject': newProject})
self.assertEqual(response.code, 200)
self.assertIn("%i barcodes assigned to %s, please wait for download." %
(num_barcodes, ", ".join(map(xhtml_escape,
projects + [newProject]))),
response.body)
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)
