def sample_init_func(row):
p = Sample(code=row['code'], date=row['date'], jonc_type_id=row['jonc_type_id'],
mesure_id=row['mesure_id'], parent_id=row['parent_id'], patient_id=row['patient_id'],
sample_nature_id=row['sample_nature_id'], sample_type_id=row['sample_type_id'],
status=row['status'], technique=row['technique'], support_id=row['support_id'],
volume=row['volume'], origin_id=row['origin_id'], )
return p
def update():
content = request.get_json(silent=False)
all_feeds = content['all_feeds']
for feed in all_feeds:
feed_name = feed['feed_name']
samples = feed['samples']
feed = Feed.query.filter_by(name=feed_name).first()
if feed is None:
feed = Feed(name=feed_name)
db.session.add(feed)
db.session.commit()
for sample in samples:
new_sample = Sample(
feed_id=feed.id,
value=sample['value'],
time=datetime.fromtimestamp(
sample['time']).replace(tzinfo=timezone.utc).astimezone(
tz=local_tz).replace(tzinfo=None))
db.session.add(new_sample)
db.session.commit()
if len(Sample.query.all()) >= 9900:
Thread(target=clean_history).start()
return 'update success'
def setUp(self):
self.app = self.create_app()
self.client = self.app.test_client()
self.app_context = self.app.app_context()
self.app_context.push()
db.create_all()
# Create some data to test against, but don't commit
# Create a region
maine = Region(name='Maine', slug='maine')
db.session.add(maine)
# Create a river
andro = River(name='Androscoggin River',
slug='androscoggin')
wild = River(name='Wild River of the Androsoggin',
slug='wild-androscoggin',
parent=andro)
db.session.add(andro)
db.session.add(wild)
# Create a section
wild_section = Section(name='Wild River from Hastings',
slug='wild-river',
river=wild,
putin='SRID=4326;POINT(-71.05996191501617 44.31595096222731)',
takeout='SRID=4326;POINT(-70.97963511943817 44.390833083196924)',
path='SRID=4326;LINESTRING(-71.05997800827026 44.316024368364864,-71.05881929397583 44.31798950769032,-71.05731725692749 44.31884923545022,-71.05444192886353 44.31851148676115,-71.05298280715942 44.31943261497028,-71.05096578598022 44.322687152160796,-71.05045080184937 44.32449856163325,-71.04984998703003 44.32495908054771,-71.04761838912964 44.325849406864485,-71.04568719863892 44.32649411748597,-71.04306936264038 44.32753791965937,-71.04049444198608 44.327138821021585,-71.03847742080688 44.32664761897048,-71.03607416152954 44.32572660403795,-71.03517293930054 44.32554239931617,-71.03431463241577 44.32594150881567,-71.03341341018677 44.32805981378074,-71.03264093399048 44.329103588092785,-71.02929353713989 44.32984035877702,-71.02843523025513 44.33008594694842,-71.02757692337036 44.33137526797721,-71.02804899215698 44.33309431859246,-71.02783441543579 44.33459844654652,-71.02543115615845 44.33582627750024,-71.02311372756958 44.33714616710255,-71.0210108757019 44.33926406740166,-71.01598978042603 44.34328479806066,-71.01294279098511 44.3441441551062,-71.00916624069214 44.346752840399844,-71.0082221031189 44.34972966884455,-71.00689172744751 44.35107993293547,-71.00551843643188 44.351171995263435,-71.00393056869507 44.350374116950185,-71.00148439407349 44.35000586175751,-70.9984803199768 44.350374116950185,-70.99642038345337 44.35163230473401,-70.99328756332397 44.354117913402796,-70.9923005104065 44.3552225945275,-70.99212884902954 44.35678752380721,-70.99401712417603 44.357830786775374,-70.99517583847046 44.3607763701854,-70.99680662155151 44.36571602660432,-70.99599123001099 44.368722570068854,-70.99448919296265 44.36961223191264,-70.99242925643921 44.37123813071097,-70.99054098129272 44.371422191881805,-70.98955392837524 44.372986688478704,-70.99075555801392 44.37507261892906,-70.98963975906372 44.37691308409485,-70.98848104476929 44.37832406821415,-70.9874939918518 44.38086988832067,-70.98470449447632 44.382403461463625,-70.98273038864136 44.384059675338044,-70.9810996055603 44.38531713976433,-70.97848176956177 44.3864825704798,-70.97749471664429 44.38746396782254,-70.97903966903687 44.38970271892836)',)
db.session.add(wild_section)
# Create a gage
wild_gage = Gage(name='Wild River at Gilead',
slug='wild-river-gilead',
point='SRID=4326;POINT(-70.97963511943817 44.390833083196924)',
river=wild,
visible=True,
zipcode='04217',
local_town='Gilead, ME',
location='Wild River at Gilead above Rt 2',
key='password')
db.session.add(wild_gage)
# Create a sensor
wild_sensor = Sensor(name='Gage Height',
stype='usgs-height',
local=False, remote_type='usgs',
remote_id='01054200',
gage=wild_gage)
db.session.add(wild_sensor)
# Create a sample
wild_sample = Sample(sensor=wild_sensor,
datetime=datetime.datetime.now(),
value=5.8)
db.session.add(wild_sample)
db.session.commit()
def create(request):
if request.method == 'POST':
dataset = Dataset()
dataset.owner = request.user
dataset.name = request.POST['name']
dataset.number_of_labels = request.POST['number_of_labels']
dataset.description = request.POST['description']
if not dataset.privacy_validation(request.POST['privacy']):
return render(request, '400.html', status=400)
dataset_file = request.FILES['dataset']
reader = csv.reader(dataset_file, encoding='utf-8')
header_list = reader.next()
label_name = request.POST.get('label_name', 'CLASS')
append_label_column = request.POST.get('append_label_column', False)
if not append_label_column:
label_index = header_list.index(label_name)
header_list.pop(label_index)
header_list.append(label_name)
dataset.header = csvlist_to_string(header_list).strip()
dataset.save()
samples_count = 0
for row_list in reader:
samples_count += 1
if not append_label_column:
label_string = row_list.pop(label_index)
row = csvlist_to_string(row_list).strip()
sample = Sample(dataset=dataset,
data=row,
original_index=samples_count)
sample.save()
if not append_label_column and label_string:
label = Label(owner=request.user,
sample=sample,
label=label_string)
label.save()
sample.times_labeled = 1
sample.save()
dataset.number_of_samples = samples_count
dataset.save()
return HttpResponseRedirect(
reverse('datasets_show', args=(dataset.id, )))
def sample():
"""[summary]
Returns:
[type] -- [description]
"""
form = SampleForm()
if form.validate_on_submit():
sample = Sample(id_sample=form.id_sample.data, num_seq=form.num_seq.data, date_time=form.date_time.data, organism=form.organism.data, location=form.location.data, batch=form.batch.data, path_r1=form.path_r1.data, path_r2=form.path_r2,result1=form.result1.data,result2=form.result2.data)
#save the model to the database
db.session.add(sample)
db.session.commit()
flash('Congratulations, you are now a registered sample!')
return redirect(url_for('index'))
return render_template('sample.html', title='validate', form=form)
def create(request):
if request.method == 'POST':
dataset = Dataset()
dataset.owner = request.user
dataset.name = request.POST['name']
dataset.number_of_labels = request.POST['number_of_labels']
dataset.description = request.POST['description']
if not dataset.privacy_validation(request.POST['privacy']):
return render(request, '400.html', status=400)
dataset_file = request.FILES['dataset']
reader = csv.reader(dataset_file, encoding='utf-8')
header_list = reader.next()
label_name = request.POST.get('label_name', 'CLASS')
append_label_column = request.POST.get('append_label_column', False)
if not append_label_column:
label_index = header_list.index(label_name)
header_list.pop(label_index)
header_list.append(label_name)
dataset.header = csvlist_to_string(header_list).strip()
dataset.save()
samples_count = 0
for row_list in reader:
samples_count += 1
if not append_label_column:
label_string = row_list.pop(label_index)
row = csvlist_to_string(row_list).strip()
sample = Sample(dataset=dataset, data=row,
original_index=samples_count)
sample.save()
if not append_label_column and label_string:
label = Label(owner=request.user, sample=sample,
label=label_string)
label.save()
sample.times_labeled = 1
sample.save()
dataset.number_of_samples = samples_count
dataset.save()
return HttpResponseRedirect(
reverse('datasets_show', args=(dataset.id,)))
def add_new_sample(sensor_id, dt, svalue, deltaminutes=10):
"""
Adds a new sample with an associacted remote sensor
if there hasn't been a sample recorded within the last deltaminutes
(default is 10).
Arguments:
sensor_id (int): Primary key for sensor
dt (datetime): Datetime of sample
svalue (float): Value of sample
"""
delta = datetime.datetime.now() - datetime.timedelta(minutes=deltaminutes)
sample = Sample.query.filter_by(sensor_id=sensor_id)\
.order_by(Sample.datetime.desc()).first()
if sample is None or (sample.datetime < delta and
(sample.datetime != dt.replace(tzinfo=None))):
new_sample = Sample(sensor_id=sensor_id,
value=svalue,
datetime=dt)
db.session.add(new_sample)
db.session.commit()
logger.debug('Saved sample (%s - %s - %s) for sensor %s',
new_sample.id,
svalue,
dt,
sensor_id)
else:
message = ''
if sample.datetime == dt.replace(tzinfo=None):
message = message + 'Sample times are the same. '
if sample.datetime < delta:
message = message + 'Last sample was more than {0} min ago '.format(deltaminutes)
else:
message = message + 'Last sample was less than {0} min ago '.format(deltaminutes)
logger.warning('Discarded sample (%s - %s) for sensor %s, compared to (%s - %s). %s',
svalue,
dt,
sensor_id,
sample.value,
sample.datetime,
message)
def preprocess(sample):
"""Preprocess files after upload.
:param sample: :class:`~app.models.Sample`
:return:
"""
hash_path = os.path.join(
current_app.config['APP_UPLOADS_SAMPLES'],
sample.sha256
)
if zipfile.is_zipfile(hash_path):
mt = magic.from_file(hash_path, mime=True)
if mt in skip_mimes:
return None
current_app.log.debug('Extracting {}'.format(hash_path))
zfile = zipfile.ZipFile(hash_path)
for zipfo in zfile.namelist():
cfg = current_app.config
if zfile.getinfo(zipfo).compress_type == 99: # PK compat. v5.1
pwd = '-p{}'.format(cfg['INFECTED_PASSWD'])
with popen('7z', 'e', '-so', pwd, hash_path) as zproc:
buf, stderr = zproc.communicate()
else:
buf = zfile.read(zipfo,
pwd=bytes(cfg['INFECTED_PASSWD'], 'utf-8'))
digests = get_hashes(buf)
hash_path = os.path.join(cfg['APP_UPLOADS_SAMPLES'],
digests.sha256)
if not os.path.isfile(hash_path):
with open(hash_path, 'wb') as wf:
wf.write(buf)
s = Sample(user_id=sample.user_id, filename=zipfo,
parent_id=sample.id,
md5=digests.md5, sha1=digests.sha1,
sha256=digests.sha256, sha512=digests.sha512,
ctph=digests.ctph)
db.session.add(s)
db.session.commit()
def add():
form = ProcessForm()
form.sample.choices = [(c.id, c.code)
for c in Basket.query.first().samples]
if form.validate_on_submit():
process = Aliquot(sample_id=form.sample.data, number=form.number.data)
db.session.add(process)
db.session.commit()
sample = Sample.query.get(form.sample.data)
for x in range(int(form.number.data)):
_sample = Sample()
_sample.patient_id = sample.patient_id
_sample.parent_id = sample.id
_sample.code = sample.code + "-" + str(x)
_sample.volume = int(sample.volume) / int(form.number.data)
# _sample = Sample()
# _sample.serial = get_bio_code()
# _sample.code = s.code.data
_sample.sample_type_id = sample.sample_type_id
_sample.date = sample.date
_sample.site = sample.site
_sample.tube_type_id = sample.tube_type_id
_sample.mesure_id = sample.mesure_id
_sample.status = 0
_sample.in_basket = 0
_sample.basket_id = 0
db.session.add(_sample)
sample.status = 1
db.session.commit()
flash(_('Nouveau Client ajouté avec succèss!'))
return redirect(url_for('process.detail', id=process.id))
return render_template('process/form.html', form=form)
def validate(id):
order = Order.query.get(id)
data_xls = pd.read_excel(order.file_url)
for index, row in data_xls.iterrows():
# one patient have samples that have results
# check patient number first if exist in db per row
patient = Patient()
patient_count = Patient.query.filter_by(code=row[0]).count()
if patient_count > 0:
sample_count = Sample.query.filter_by(code=row[7]).count()
if sample_count > 0:
# add new resltuts
print(row[0] + ' ' + str(index))
else:
sample = Sample()
sample.origin_id = 1
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
print(row[14])
sample_type = SampleType.query.filter_by(name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
if jonc_type is not None:
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
order.patients.append(patient)
db.session.commit()
generateCode(sample, index + 1)
else:
# add new patient and samples and result of sample
patient.code = row[0]
patient.origin_id = 1
patient.bio_code = get_bio_code('HU')
patient.age = row[1]
patient.sexe = row[2]
patient.birthday = str(row[3])
patient.city = row[4]
patient.job = row[5]
patient.clinical_data = row[6]
# samples implementation
for r in range(int(row[15])):
sample = Sample()
sample.origin_id = 1
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature = sample_nature
sample_type = SampleType.query.filter_by(name=row[9]).first()
sample.sample_type = sample_type
support = Support.query.filter_by(name=row[13]).first()
sample.support = support
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type = jonc_type
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
sample.number = int(row[15])
patient.samples.append(sample)
generateCode(sample, r + 1)
print(str(sample.bio_code))
order.patients.append(patient)
db.session.commit()
order.status = 1
db.session.commit()
# and check sample id if already in db
flash(_('Traitement effectué avec succes!'))
return redirect(url_for('order.detail', id=order.id))
def do_import(id):
order = Order.query.get(id)
if request.method == 'POST':
file = request.files['file']
filename = documents.save(file)
data_xls = pd.read_excel(file)
for index, row in data_xls.iterrows():
# one patient have samples that have results
# check patient number first if exist in db per row
patient = Patient()
patient_count = Patient.query.filter_by(code=row[0]).count()
if patient_count > 0:
sample_count = Sample.query.filter_by(code=row[7]).count()
if sample_count > 0:
# add new resltuts
print(row[0] + ' ' + str(index))
else:
sample = Sample()
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
sample_type = SampleType.query.filter_by(
name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
order.patients.append(patient)
db.session.commit()
generateCode(sample, r + 1)
else:
# add new patient and samples and result of sample
print(row[4] + ' ' + str(index))
patient.code = row[0]
patient.origin_id = 1
patient.bio_code = get_bio_code('HU')
patient.age = row[1]
patient.sexe = row[2]
patient.birthday = str(row[3])
patient.city = row[4]
patient.job = row[5]
patient.clinical_data = row[6]
# samples implementation
for r in range(int(row[15])):
sample = Sample()
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
sample_type = SampleType.query.filter_by(
name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
generateCode(sample, r + 1)
print(str(sample.bio_code))
order.patients.append(patient)
db.session.commit()
# and check sample id if already in db
url = documents.url(filename)
document = Document(name=filename, url=url)
order.documents.append(document)
db.session.add(document)
db.session.commit()
flash(_('Fichier importé avec succes!'))
return redirect(url_for('order.detail', id=order.id))
return render_template('order/import.html', order=order)
def proceed(id):
aliquot = Aliquot.query.get(id)
for _item in range(len(aliquot.aliquot_items.all())):
num = 0
_sample = aliquot.sample
_sample.status = 3
sample = Sample()
sample.code = _sample.code
sample.parent_id = _sample.id
sample.technique = _sample.technique
sample.patient_id = _sample.patient_id
sample.sample_nature_id = _sample.sample_nature_id
sample.sample_type_id = _sample.sample_type_id
sample.support_id = _sample.support_id
sample.jonc_type_id = _sample.jonc_type_id
sample.mesure_id = _sample.mesure_id
sample.volume = aliquot.aliquot_items[num].volume
sample.site = _sample.site
sample.date = _sample.date
sample.status = 0
aliquot.aliquot_items[num].status = 1
db.session.add(sample)
db.session.commit()
num = num + 1
generateCode(sample, aliquot.nbr_aliquot(), num)
__sample = Sample.query.get(_sample.id)
__sample.volume = 0
aliquot.status = 1
db.session.commit()
flash(_('Enregistrement effectué avec succèss'))
return redirect(url_for('aliquot.index'))
def add():
form = SampleForm()
form.patient.choices = [(c.id, c.code) for c in Patient.query.all()]
form.sample_nature.choices = [(c.id, c.name) for c in SampleNature.query.all()]
form.sample_type.choices = [(c.id, c.name) for c in SampleType.query.all()]
form.support.choices = [(c.id, c.name) for c in Support.query.all()]
form.jonc_type.choices = [(c.id, c.name) for c in JoncType.query.all()]
form.mesure.choices = [(c.id, c.name) for c in Mesure.query.all()]
if form.validate_on_submit():
for r in range(int(form.number.data)):
print(form.number.data)
sample = Sample()
sample.code = form.code.data
sample.technique = form.technique.data
sample.results = form.results.data
sample.patient_id = form.patient.data
sample.sample_nature_id = form.sample_nature.data
sample.sample_type_id = form.sample_type.data
sample.support_id = form.support.data
sample.jonc_type_id = form.jonc_type.data
sample.mesure_id = form.mesure.data
sample.volume = form.volume.data
sample.site = form.site.data
sample.number = form.number.data
sample.date = form.date.data
sample.status = 0
db.session.add(sample)
db.session.commit()
generateCode(sample, r + 1)
flash(_('Nouveau prélèvement ajouté avec succèss!'))
return redirect(url_for('sample.index'))
return render_template('sample/form.html', form=form)
def setUp(self):
self.app = create_app('testing')
self.client = self.app.test_client()
self.app_context = self.app.app_context()
self.app_context.push()
db.create_all()
# Create some data to test against, but don't commit
# Create a region
maine = Region(name='Maine', slug='maine')
db.session.add(maine)
# Create a river
andro = River(name='Androscoggin River', slug='androscoggin')
wild = River(name='Wild River of the Androsoggin',
slug='wild-river',
parent=andro)
db.session.add(andro)
db.session.add(wild)
# Create a section
wild_section = Section(
name='Wild River from Hastings',
slug='hasting-to-gilead',
river=wild,
putin='SRID=4326;POINT(-71.05996191501617 44.31595096222731)',
takeout='SRID=4326;POINT(-70.97963511943817 44.390833083196924)',
path=
'SRID=4326;LINESTRING(-71.05997800827026 44.316024368364864,-71.05881929397583 44.31798950769032,-71.05731725692749 44.31884923545022,-71.05444192886353 44.31851148676115,-71.05298280715942 44.31943261497028,-71.05096578598022 44.322687152160796,-71.05045080184937 44.32449856163325,-71.04984998703003 44.32495908054771,-71.04761838912964 44.325849406864485,-71.04568719863892 44.32649411748597,-71.04306936264038 44.32753791965937,-71.04049444198608 44.327138821021585,-71.03847742080688 44.32664761897048,-71.03607416152954 44.32572660403795,-71.03517293930054 44.32554239931617,-71.03431463241577 44.32594150881567,-71.03341341018677 44.32805981378074,-71.03264093399048 44.329103588092785,-71.02929353713989 44.32984035877702,-71.02843523025513 44.33008594694842,-71.02757692337036 44.33137526797721,-71.02804899215698 44.33309431859246,-71.02783441543579 44.33459844654652,-71.02543115615845 44.33582627750024,-71.02311372756958 44.33714616710255,-71.0210108757019 44.33926406740166,-71.01598978042603 44.34328479806066,-71.01294279098511 44.3441441551062,-71.00916624069214 44.346752840399844,-71.0082221031189 44.34972966884455,-71.00689172744751 44.35107993293547,-71.00551843643188 44.351171995263435,-71.00393056869507 44.350374116950185,-71.00148439407349 44.35000586175751,-70.9984803199768 44.350374116950185,-70.99642038345337 44.35163230473401,-70.99328756332397 44.354117913402796,-70.9923005104065 44.3552225945275,-70.99212884902954 44.35678752380721,-70.99401712417603 44.357830786775374,-70.99517583847046 44.3607763701854,-70.99680662155151 44.36571602660432,-70.99599123001099 44.368722570068854,-70.99448919296265 44.36961223191264,-70.99242925643921 44.37123813071097,-70.99054098129272 44.371422191881805,-70.98955392837524 44.372986688478704,-70.99075555801392 44.37507261892906,-70.98963975906372 44.37691308409485,-70.98848104476929 44.37832406821415,-70.9874939918518 44.38086988832067,-70.98470449447632 44.382403461463625,-70.98273038864136 44.384059675338044,-70.9810996055603 44.38531713976433,-70.97848176956177 44.3864825704798,-70.97749471664429 44.38746396782254,-70.97903966903687 44.38970271892836)',
)
db.session.add(wild_section)
# Create a gage
wild_gage = Gage(
name='Wild River at Gilead',
slug='wild-river-gilead',
point='SRID=4326;POINT(-70.97963511943817 44.390833083196924)',
river=wild,
visible=True,
zipcode='04217',
local_town='Gilead, ME',
location='Wild River at Gilead above Rt 2',
key='password')
db.session.add(wild_gage)
# Create a sensor
wild_sensor = Sensor(name='Gage Height',
stype='usgs-height',
local=False,
remote_type='usgs',
remote_id='01054200',
gage=wild_gage)
diamond_height = Sensor(name='Gage Height',
stype='usgs-height',
local=False,
remote_type='usgs',
remote_id='01052500')
diamond_discharge = Sensor(name='Discharge',
stype='usgs-discharge',
local=False,
remote_type='usgs',
remote_id='01052500',
remote_parameter='00060')
rapid_cfs = Sensor(name='Rapid CFS',
stype='h2oline-cfs',
local=False,
remote_type='h2oline',
remote_id='235127')
azicohos_level = Sensor(name='Aziscohol height',
stype='h2oline-height',
local=False,
remote_type='h2oline',
remote_id='235130',
remote_parameter='FT')
neilson_flow = Sensor(name='Neilson flow',
stype='cehq-flow',
local=False,
remote_type='cehq',
remote_id='050915')
skeena_level = Sensor(name='Skeena Level',
stype='cawater-level',
local=False,
remote_type='cawater',
remote_id='BC_08EB003')
humber_level = Sensor(name='Humber Level',
stype='cawater-level',
local=False,
remote_type='cawater',
remote_id='NL_02YL012')
cheakamus_discharge = Sensor(name='Cheakamus Discharge',
stype='cawater-discharge',
local=False,
remote_type='cawater',
remote_id='BC_08GA043',
remote_parameter='discharge')
canaseraga_stage = Sensor(name='Canaseraga Creek',
stype='canaseraga-stage',
local=False,
remote_type='corps',
remote_id='DSVN6')
db.session.add(wild_sensor)
db.session.add(diamond_height)
db.session.add(diamond_discharge)
db.session.add(rapid_cfs)
db.session.add(azicohos_level)
db.session.add(neilson_flow)
db.session.add(skeena_level)
db.session.add(humber_level)
db.session.add(canaseraga_stage)
# Create a sample
dt = datetime.datetime.now() - datetime.timedelta(hours=12)
wild_sample = Sample(sensor=wild_sensor, datetime=dt, value=5.8)
db.session.add(wild_sample)
wild_correlation = Correlation(sensor=wild_sensor,
section=wild_section,
minimum=3.5,
low=4.0,
medium=5.0,
high=6.0,
huge=9.0)
db.session.add(wild_correlation)
db.session.commit()
def add(order_id=0):
order = None
if order_id != 0:
order = Order.query.get(order_id)
form = PatientForm()
form.order.choices = [(c.id, c.serial) for c in Order.query.all()]
for entry in form.samples.entries:
entry.sample_type.choices = [(c.id, c.name)
for c in SampleType.query.all()]
entry.mesure.choices = [(c.id, c.name) for c in Mesure.query.all()]
entry.support.choices = [(c.id, c.name) for c in Support.query.all()]
entry.sample_nature.choices = [(c.id, c.name)
for c in SampleNature.query.all()]
entry.jonc_type.choices = [(c.id, c.name)
for c in JoncType.query.all()]
if form.validate_on_submit():
patient = Patient(bio_code=get_bio_code('HU'),
order_id=order_id,
origin_id=1,
code=form.code.data,
sexe=form.sexe.data,
birthday=form.birthday.data,
age=form.age.data,
city=form.city.data,
job=form.job.data,
clinical_data=form.clinical_data.data)
db.session.add(patient)
db.session.commit()
for s in form.samples.entries:
print(int(s.number.data))
for r in range(int(s.number.data)):
sample = Sample()
sample.origin_id = s.patient.origin_id
sample.code = s.code.data
sample.technique = s.technique.data
sample.results = s.results.data
sample.sample_nature_id = s.sample_nature.data
sample.sample_type_id = s.sample_type.data
sample.date = s.date.data
sample.site = s.site.data
sample.support_id = s.support.data
sample.jonc_type_id = s.jonc_type.data
sample.number = s.number.data
sample.mesure_id = s.mesure.data
sample.volume = s.volume.data
sample.patient_id = patient.id
sample.status = 0
db.session.add(sample)
db.session.commit()
generateCode(sample, r + 1)
flash(_('Nouveau patient ajouté avec succèss!'))
return redirect(url_for('patient.add', order_id=order_id))
form.order.data = order_id
return render_template('patient/form.html', form=form, order=order)
def add_sample():
"""Upload untrusted files, E.i. malware samples, files for analysis.
Uploaded files are save in :attr:`config.Config.APP_UPLOADS_SAMPLES` using
the SHA-256 of the content as file name. Existing files are not
overwritten. After upload MD5, SHA1, SHA256, SHA512 and CTPH hashes
are calculated.
**Example request**:
.. sourcecode:: http
POST /api/1.0/samples HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Length: 317825
Content-Type: multipart/form-data; boundary=-----------3fa8efc8eb2a42e7
Content-Disposition: form-data; name="files[0]"; filename="zepto.exe"
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"files": [
{
"created": "2016-08-02T14:26:15",
"ctph": "6144:dOWrXkMZWMKsLXiyLgDf1tedfmqmqeGGAV//CNGa1FPi:d3rV",
"filename": "zepto.exe",
"id": 32,
"md5": "a8188e964bc1f9cb1e905ce8f309e086",
"sha1": "c3db12e0ffc4b4b090e32679c95aaa76e07150f7",
"sha256": "7768d4e54b066a567bed1456077025ba7eb56a88aed1bc8cb207",
"sha512": "1fa1ea4a72be8adc9257185a9d71d889fbea2360cee3f6102302e"
}
],
"message": "Files uploaded"
}
:reqheader Accept: Content type(s) accepted by the client
:reqheader Content-Type: multipart/form-data required
:resheader Content-Type: this depends on `Accept` header or request
:form files: Files to be uploaded
:>json array files: List of files saved to disk
:>jsonarr integer id: Sample unique ID
:>jsonarr string created: Time of upload
:>jsonarr string sha256: SHA256 of file
:>jsonarr string ctph: CTPH (a.k.a. fuzzy hash) of file
:>jsonarr string filename: Filename (as provided by the client)
:>json string message: Status message
:statuscode 201: Files successfully saved
"""
uploaded_samples = []
for idx, file in request.files.items():
buf = file.stream.read()
digests = get_hashes(buf)
hash_path = os.path.join(current_app.config['APP_UPLOADS_SAMPLES'],
digests.sha256)
if not os.path.isfile(hash_path):
file.stream.seek(0)
file.save(hash_path)
s = Sample(user_id=g.user.id,
filename=file.filename,
md5=digests.md5,
sha1=digests.sha1,
sha256=digests.sha256,
sha512=digests.sha512,
ctph=digests.ctph)
db.session.add(s)
try:
db.session.commit()
analysis.preprocess(s)
except Exception as e:
db.session.rollback()
db.session.flush()
current_app.log.error(e.args[0])
uploaded_samples.append(s.serialize())
return ApiResponse({
'message': 'Files uploaded',
'files': uploaded_samples
}, 201)
def add_fireeye_url_analysis():
"""Submit URLs to the FireEye Sandbox. Also accepts :http:method:`put`.
.. warning::
Not Implemented
**Example request**:
.. sourcecode:: http
POST /api/1.0/analysis/fireeye-url HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"urls": ["http://cert.europa.eu"],
"dyn_analysis": {
"fireeye": [5, 6]
}
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Your URLs have been submitted for dynamic analysis",
"statuses": [
{
"sha256": "33a53e3b28ee41c29afe79f49ecc53b34ac125e5e15f9e7c..."
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json array files: List of URLs to scan
:<jsonarr string sha256: SHA256 of the shortcut file created
:<json object dyn_analysis: Sandbox configuration
:<jsonarr array fireeye: List of FireEye environments to submit to
Get the list from :http:get:`/api/1.0/analysis/fireeye/environments`
:>json array statuses: List of statuses returned by upstream APIs
:>jsonarr string error: Error message from upstream API
:>jsonarr string sha256: SHA256 calculated by upstream API
:>json string message: Status message
:status 202: The URLs have been accepted for scanning
:status 400: Bad request
"""
raise ApiException({}, 501)
statuses = []
samples = {}
for env in request.json['dyn_analysis']['fireeye']:
for url in request.json['urls']:
sdata = {'environmentId': env, 'analyzeurl': url}
headers = {
'User-Agent': 'FireEye Sandbox API Client',
'Accept': 'application/json'
}
resp = fireeye.submiturl(sdata, headers=headers)
samples[resp['response']['sha256']] = url
statuses.append(resp['response'])
if resp['response_code'] != 0:
current_app.log.debug(resp)
for sha256, url in samples.items():
surl = Sample(filename=url,
sha256=sha256,
user_id=g.user.id,
md5='N/A',
sha1='N/A',
sha512='N/A',
ctph='N/A')
db.session.add(surl)
db.session.commit()
return {
'statuses': statuses,
'message': 'Your URLs have been submitted for dynamic analysis'
}, 202
def add_cp_sample():
"""Upload untrusted files, E.i. malware samples, files for analysis.
After upload MD5, SHA1, SHA256, SHA512 and CTPH hashes are calculated.
**Example request**:
.. sourcecode:: http
POST /api/1.0/samples HTTP/1.1
Host: cp.cert.europa.eu
Accept: application/json
Content-Type: multipart/form-data; boundary=----FormBoundaryrflTTZA0oE
------FormBoundaryrflTTZA0oE
Content-Disposition: form-data; name="files[0]"; filename="stux.zip"
Content-Type: application/zip
------FormBoundaryrflTTZA0oE--
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"files": [
{
"created": "2016-03-21T16:09:47",
"ctph": "49152:77qzLl6EKvwkdB7qzLl6EKvwkTY40GfAHw7qzLl6EKvwk...",
"filename": "stux.zip",
"id": 2,
"sha256": "1eedab2b09a4bf6c87b273305c096fa2f597ff9e4bdd39bc4..."
}
],
"message": "Files uploaded"
}
:reqheader Accept: Content type(s) accepted by the client
:reqheader Content-Type: multipart/form-data required
:resheader Content-Type: this depends on `Accept` header or request
:form files: Files to be uploaded
:>json array files: List of files saved to disk
:>jsonarr integer id: Sample unique ID
:>jsonarr string created: Time of upload
:>jsonarr string sha256: SHA256 of file
:>jsonarr string ctph: CTPH (a.k.a. fuzzy hash) of file
:>jsonarr string filename: Filename (as provided by the client)
:>json string message: Status message
:statuscode 201: Files successfully saved
"""
uploaded_samples = []
for idx, file_ in request.files.items():
buf = file_.stream.read()
hashes = get_hashes(buf)
hash_path = os.path.join(current_app.config['APP_UPLOADS_SAMPLES'],
hashes.sha256)
if not os.path.isfile(hash_path):
file_.stream.seek(0)
file_.save(hash_path)
s = Sample(user_id=g.user.id,
filename=file_.filename,
md5=hashes.md5,
sha1=hashes.sha1,
sha256=hashes.sha256,
sha512=hashes.sha512,
ctph=hashes.ctph)
db.session.add(s)
try:
db.session.commit()
analysis.preprocess(s)
except Exception as e:
db.session.rollback()
db.session.flush()
current_app.log.error(e.args[0])
uploaded_samples.append(s.serialize())
return ApiResponse({
'message': 'Files uploaded',
'files': uploaded_samples
}, 201)
def get_pending_samples():
return Sample.get_pending_data()
def _create_url_sample(url):
sha256 = hashlib.sha256(url.encode('utf-8')).hexdigest()
return Sample(filename=url, sha256=sha256, user_id=g.user.id, md5='N/A', sha1='N/A', sha512='N/A', ctph='N/A')