def generate_and_add_tickets(self, amount=60):
name_prefix = "Example ticket number "
try:
last_example_ticket = Ticket.objects.filter(name__startswith=name_prefix).order_by('pk').reverse()[0]
except IndexError:
start_num = 1
else:
start_num = int(search(r'(\d+)$', last_example_ticket.name).group(0)) + 1
def generate_random_date():
year_today = datetime.today().year
# probably shouldn't matter, but preventing future dates.
year = randint(year_today - 3, year_today - 1)
month = randint(1, 12)
# february only has 28 days, making this harder by
# including 29-31 is unnecessary
day = randint(1, 28)
hour = randint(1, 23)
minute = randint(1, 59)
return datetime(year, month, day, hour, minute, tzinfo=UTC)
user_objects = User.objects.filter(username__startswith=USERNAME_PREFIX)
if not user_objects.exists():
raise DataError('To create example tickets, at least one example user has to be created.')
topic_objects = Topic.objects.all()
subtopic_objects = Subtopic.objects.all()
ticket_query_list = []
for n in range(start_num, start_num + amount):
created_and_updated = generate_random_date()
topic = choice(topic_objects)
try:
subtopic = choice(subtopic_objects.filter(topic=topic))
except IndexError:
# topic has no subtopics
subtopic = None
ticket_query_list.append(Ticket(
created=created_and_updated,
updated=created_and_updated,
event_date=generate_random_date(),
requested_user=choice(user_objects),
name="{}{}".format(name_prefix, n),
topic=topic,
subtopic=subtopic,
rating_percentage=randint(0, 100),
mandatory_report=choice([True, False]),
description=("Space for further notes. If you're entering a trip "
"tell us where did you go and what you did there."),
supervisor_notes=("This space is for notes of project "
"supervisors and accounting staff."),
))
Ticket.objects.bulk_create(ticket_query_list)
def create(name: str, artists: str, album: str, length: int) -> bool:
try:
new_song = Song.objects.create(name=name,
artist=artists,
album=album,
length=length)
except ValueError:
raise DataError("Song hasn't been saved")
else:
new_song.save()
return True
return False
def from_db_value(value, *_args):
"""Convert a database value to a list value."""
if not value:
return None
try:
duration, unit = value.split("|")
except ValueError as error:
raise DataError(
"Value in database should be of the form '{duration:d}|{unit:s}'"
) from error
if not duration:
return None
return int(duration), unit
def save_mutations(self, strain, var):
"""Save all the mutations in the var file"""
for snp in var.values():
#gene = snp['regionid1']
if 'varname' not in snp or len(snp['varname']) > 80:
continue
try:
(_, locus, mutation) = unpack_mutation_format(snp['varname'])
# All genes in the gene summary should be already loaded.
#locus = GeneLocus.objects.get(name=locus, genome=self.genome)
# Ignore that and ask for a new one
locus, _ = GeneLocus.objects.update_or_create(name=locus, genome=self.genome)
except ValueError:
sys.stderr.write("Failed to unpack {varname}\n".format(**snp))
continue
except GeneLocus.DoesNotExist:
raise DataError("Failed to get gene {varname}, "\
"are all genes loaded from reference?".format(**snp))
if len(mutation) > 150:
sys.stderr.write("Mutation name is too large, can not add to database.\n")
continue
try:
(mutation, _) = locus.mutations.get_or_create(name=mutation, defaults=dict(
nucleotide_position=None,
nucleotide_reference=None,
nucleotide_varient=None,
aminoacid_position=None,
aminoacid_reference=None,
aminoacid_varient=None,
codon_position=snp.get('codpos', None),
codon_varient=snp.get('altcodon', None),
codon_reference=snp.get('codon', None),
))
strain.mutations.get_or_create(mutation=mutation, defaults=dict(
quality=to_num(snp.get('qual', 0)),
mutation_reads=to_num(snp.get('hqr', 0)),
reference_reads=to_num(snp.get('hqr_ref', 0)),
mapping_quality=to_num(snp.get('fq', 0)))
)
except (ValueError, IndexError, KeyError) as err:
sys.stderr.write("Failed to add mutation: {} ({}) {}\n".format(mutation, err, snp))
continue
def to_python(self, value):
"""Convert a string value to a list value. Used for deserialization and in clean forms."""
if isinstance(value, (list, tuple)):
return value
if not value:
return None
if isinstance(value, str):
try:
duration, unit = value.split("|")
except ValueError as error:
raise DataError(
"Value in database should be of the form '{duration:d}|{unit:s}'"
) from error
return int(duration.strip()), unit.strip()
return value
def post(self, request, *args, **kwargs):
"""
Função utilizada para realizar o login do usuário
Parameters:
request (HttpRequest): Post Request contendo email e password do usuário
Returns:
HttpResponse: Retorna o token de autenticação como dado da resposta.
"""
email = request.data['email']
password = request.data['password']
try:
user = self.queryset.get(email=email)
if not check_password(password, user.password):
raise DataError("Senha errada.")
except:
return Response(data={'error': 'Wrong email or password.'},
status=status.HTTP_403_FORBIDDEN)
token, created = Token.objects.get_or_create(user=user)
return Response({'token': f'{token}'}, status=status.HTTP_202_ACCEPTED)
def import_vcf(self, importer, vcf, var):
"""Import the VCF file and list of mutations into database"""
if 'ENRICHED' not in vcf.metadata:
raise NotEnrichedError()
if 'LOCATION' not in vcf.metadata:
raise DataError('Location is missing from metadata')
loc = vcf.metadata['LOCATION'][0]
con = loc.get('COUNTRY', None)
country = long_match(COUNTRY_MAP, self.countries, con, Country, None,\
'name', 'detail__name_short', 'detail__name_abbr', 'iso2', 'iso3')
if country is None:
raise DataError("Country not found: {}".format(con))
city = long_match(CITY_MAP, self.places, loc.get('CITY', None),\
Place, None, 'name', country=country)
pat = vcf.metadata.get('PATIENT', [{}])[0]
datum = dict(
importer=importer,
country=country, city=city,
patient_id=pat.get('ID', 'None'),
patient_sex=pat.get('SEX', None),
patient_age=(pat.get('AGE', None) or None),
patient_hiv=pat.get('HIV', None),
# TODO: Patient notes are discarded here, maybe keep them.
)
# Drug data must exist!
drugs = vcf.metadata.get('DRUG', [])
if not drugs:
raise DataError("No phenotype drug resistance data.")
# BIO SAMPLE first.
name = vcf.metadata.get('SAMPLE_ID', (None,))[0]
name = EMPTY.get(name, name)
other_name = vcf.metadata.get('STRAIN_NAME', (None,))[0]
other_name = EMPTY.get(other_name, other_name)
if name is None:
if other_name is None:
raise DataError("No valid STRAIN_NAME or bio SAMPLE_ID")
name, other_name = other_name, None
datum['old_id'] = other_name
if 'LINEAGE' in vcf.metadata:
datum['lineage'] = Lineage.objects.get_or_create(
name=vcf.metadata['LINEAGE'][0],
slug=name,
)[0]
study = None
if 'STUDY' in vcf.metadata:
name = vcf.metadata['STUDY'][0].get('NAME', None)
url = vcf.metadata['STUDY'][0].get('URL', None)
doi = vcf.metadata['STUDY'][0].get('DOI', None)
if doi:
study = Paper.objects.get_or_create(doi=doi, defaults={'name': name, 'url': url})[0]
elif name:
study = Paper.objects.get_or_create(name=name, defaults={'url': url})[0]
if study is not None:
datum['source_paper'] = study
if 'PROJECT_ID'in vcf.metadata:
datum['bioproject'] = BioProject.objects.get_or_create(
name=vcf.metadata['PROJECT_ID'][0])[0]
strain, _ = StrainSource.objects.update_or_create(name=name, defaults=datum)
for _drug in vcf.metadata.get('DRUG', []):
try:
drug = long_match({
'OFLOXACIN': 'OFLX',
}, self.drugs, _drug['NAME'], Drug, 'NOP', 'name', 'code', _match='icontains')
except Drug.DoesNotExist:
raise DataError("Can't import drug: {}".format(_drug['NAME']))
drug.strains.update_or_create(strain=strain, defaults=dict(
resistance=_drug['STATUS'].lower(),
# TODO: More drug testing information here.
))
strain.generate_resistance_group()
self.save_mutations(strain, var)
return name
def save(self, *args, **kwargs):
if self.balance < 0:
print("positive forced")
self.balance = 0
raise DataError("my exeption~~~~~~")
super().save(*args, **kwargs)
def grab_organization_posts(self, org_dict, parent=None):
url = base_url + '/organizations/'
r = requests.get(url, params=org_dict)
page_json = json.loads(r.text)
organization_ocd_id = page_json['results'][0]['id']
url = base_url + '/' + organization_ocd_id + '/'
r = requests.get(url)
page_json = json.loads(r.text)
if page_json.get('error'):
raise DataError(page_json['error'])
source_url = ''
if page_json['sources']:
source_url = page_json['sources'][0]['url']
if DEBUG: print(page_json['id'])
if parent:
if DEBUG: print('parent')
try:
org_obj, created = Organization.objects.get_or_create(
ocd_id=organization_ocd_id,
name=page_json['name'],
classification=page_json['classification'],
source_url=source_url,
slug=slugify(page_json['name']),
_parent=parent,
)
except IntegrityError:
ocd_id_part = organization_ocd_id.rsplit('-', 1)[1]
org_obj, created = Organization.objects.get_or_create(
ocd_id=organization_ocd_id,
name=page_json['name'],
classification=page_json['classification'],
source_url=source_url,
slug=slugify(page_json['name']) + ocd_id_part,
_parent=parent,
)
else:
if DEBUG: print('not parent')
try:
org_obj, created = Organization.objects.get_or_create(
ocd_id=organization_ocd_id,
name=page_json['name'],
classification=page_json['classification'],
source_url=source_url,
slug=slugify(page_json['name']),
)
except IntegrityError:
ocd_id_part = organization_ocd_id.rsplit('-', 1)[1]
org_obj, created = Organization.objects.get_or_create(
ocd_id=organization_ocd_id,
name=page_json['name'],
classification=page_json['classification'],
source_url=source_url,
slug=slugify(page_json['name']) + ocd_id_part,
)
# if created and DEBUG:
# print(' adding organization: %s' % org_obj.name )
if created and DEBUG:
print('\u263A', end=' ', flush=True)
for post_json in page_json['posts']:
try:
obj = Post.objects.get(ocd_id=post_json['id'])
obj.label = post_json['label']
obj.role = post_json['role']
obj._organization = org_obj
obj.division_ocd_id = post_json['division_id']
obj.save()
except Post.DoesNotExist:
obj, created = Post.objects.get_or_create(
ocd_id=post_json['id'],
label=post_json['label'],
role=post_json['role'],
_organization=org_obj,
division_ocd_id=post_json['division_id'],
)
for child in page_json['children']:
self.grab_organization_posts({'id': child['id']}, org_obj)
def import_vcf(self, importer, vcf, var):
"""Import the VCF file and list of mutations into database"""
if 'ENRICHED' not in vcf.metadata:
raise NotEnrichedError()
if 'LOCATION' not in vcf.metadata:
raise DataError('Location is missing from metadata')
loc = vcf.metadata['LOCATION'][0]
con = loc.get('COUNTRY', None)
country = long_match(COUNTRY_MAP, self.countries, con, Country, None,\
'name', 'detail__name_short', 'detail__name_abbr', 'iso2', 'iso3')
if country is None:
raise DataError("Country not found: {}".format(con))
city = long_match(CITY_MAP, self.places, loc.get('CITY', None),\
Place, None, 'name', country=country)
pat = vcf.metadata.get('PATIENT', [{}])[0]
datum = dict(
importer=importer,
country=country,
city=city,
patient_id=pat.get('ID', 'None'),
patient_sex=pat.get('SEX', None),
patient_age=(pat.get('AGE', None) or None),
patient_hiv=pat.get('HIV', None),
# TODO: Patient notes are discarded here, maybe keep them.
)
# Drug data must exist!
drugs = vcf.metadata.get('DRUG', [])
if not drugs:
raise DataError("No phenotype drug resistance data.")
# BIO SAMPLE first.
name = vcf.metadata.get('SAMPLE_ID', (None, ))[0]
name = EMPTY.get(name, name)
other_name = vcf.metadata.get('STRAIN_NAME', (None, ))[0]
other_name = EMPTY.get(other_name, other_name)
if name is None:
if other_name is None:
raise DataError("No valid STRAIN_NAME or bio SAMPLE_ID")
name, other_name = other_name, None
datum['old_id'] = other_name
if 'LINEAGE' in vcf.metadata:
datum['lineage'] = Lineage.objects.get_or_create(
name=vcf.metadata['LINEAGE'][0], slug=name)[0]
study = None
if 'STUDY' in vcf.metadata:
name = vcf.metadata['STUDY'][0].get('NAME', None)
url = vcf.metadata['STUDY'][0].get('URL', None)
doi = vcf.metadata['STUDY'][0].get('DOI', None)
if doi:
study = Paper.objects.get_or_create(doi=doi,
defaults={
'name': name,
'url': url
})[0]
elif name:
study = Paper.objects.get_or_create(name=name,
defaults={'url': url})[0]
if study is not None:
datum['source_paper'] = study
if 'PROJECT_ID' in vcf.metadata:
datum['bioproject'] = BioProject.objects.get_or_create(
name=vcf.metadata['PROJECT_ID'][0])[0]
strain, _ = StrainSource.objects.update_or_create(name=name,
defaults=datum)
for _drug in vcf.metadata.get('DRUG', []):
try:
drug = long_match({
'OFLOXACIN': 'OFLX',
},
self.drugs,
_drug['NAME'],
Drug,
'NOP',
'name',
'code',
_match='icontains')
except Drug.DoesNotExist:
raise DataError("Can't import drug: {}".format(_drug['NAME']))
drug.strains.update_or_create(
strain=strain,
defaults=dict(resistance=_drug['STATUS'].lower(),
# TODO: More drug testing information here.
))
strain.generate_resistance_group()
for snp in var.values():
#gene = snp['regionid1']
if 'varname' not in snp or len(snp['varname']) > 80:
continue
try:
(_, locus, mutation) = unpack_mutation_format(snp['varname'])
# All genes in the gene summary should be already loaded.
#locus = GeneLocus.objects.get(name=locus, genome=self.genome)
# Ignore that and ask for a new one
locus, _ = GeneLocus.objects.update_or_create(
name=locus, genome=self.genome)
except ValueError:
#raise DataError("Failed to unpack {varname}".format(**snp))
sys.stderr.write("Failed to unpack {varname}\n".format(**snp))
continue
except GeneLocus.DoesNotExist:
raise DataError("Failed to get gene {varname}, "\
"are all genes loaded from reference?".format(**snp))
if len(mutation) > 150:
sys.stderr.write(
"Mutation name is too large, can not add to database.\n")
continue
try:
locus.mutations.get_or_create(
name=mutation,
defaults=dict(
nucleotide_position=None,
nucleotide_reference=None,
nucleotide_varient=None,
aminoacid_position=None,
aminoacid_reference=None,
aminoacid_varient=None,
codon_position=snp.get('codpos', None),
codon_varient=snp.get('altcodon', None),
codon_reference=snp.get('codon', None),
))
except Exception as err:
sys.stderr.write("Failed to add mutation: {} ({}) {}\n".format(
mutation, err, snp))
continue
return name
