def send_verification_email(request):
send_email(
request.user.email, 'Eco-AlpsWater verification e-mail',
'This e-mail has been automatically sent from the Eco-AlpsWater website.'
)
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
def request_sequence(request):
samples = json.loads(request.POST['samples'])
tot_files = 0
for sample_id in samples:
sample = Sample.objects.get(id=sample_id)
tot_files += sample.sequence_set.all().count()
if tot_files == 0:
raise Exception('There are no files associated')
dirname = str(uuid.uuid1().int >> 64)
os.mkdir(os.path.join(os.environ['EAW_DOWNLOAD_DIRECTORY'], dirname))
outdir = os.environ['EAW_DOWNLOAD_DIRECTORY']
indir = os.environ['EAW_VAULT_DIRECTORY']
login = '******'
location = 'https://eco-alpswater.fmach.it/download/{dirname}/'.format(
dirname=dirname)
for sample_id in samples:
sample = Sample.objects.get(id=sample_id)
for seq in sample.sequence_set.all():
copyfile(os.path.join(indir, seq.filename),
os.path.join(outdir, dirname, seq.filename))
send_email(
request.user.email, 'Eco-AlpsWater sequence file(s) ready', '''
Dear {user},
the sequence file(s) you requested are ready to be downloaded from the Eco-AlpsWater server using your credentials.
Please note that all downloadable files get removed every day at midnight.
You can user your browser to download files from {location}.
If you prefer to use WGET you'll need to first login and save the cookie with your credentials
wget -qO- --no-check-certificate --keep-session-cookies --save-cookies cookies.txt --post-data 'username={user}&password=<password>' {login}
And then download files passing the cookie file
wget -c -r --no-check-certificate --load-cookies cookies.txt {location}
This e-mail has been automatically sent from the Eco-AlpsWater website.
'''.format(user=request.user.username,
location=location,
login=login))
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
def get_sequence(request, id, file=None):
download_dir = os.path.join(os.environ['EAW_DOWNLOAD_DIRECTORY'], id)
status_code = 401
for (dirpath, dirnames, filenames) in os.walk(download_dir):
for file in filenames:
seq = Sequence.objects.filter(filename=file).first()
if seq and (seq.sample.user.username == request.user.username
or request.user.is_superuser):
status_code = 200
try:
user = request.user.username
title = 'Eco-AlpsWater admin notification'
message = '''
Dear admin,
user {user} has just downloaded sequence files from directory {dir}.
'''.format(user=user, dir=download_dir)
for admin in User.objects.filter(is_superuser=True):
send_email(admin.email, title, message)
except Exception as e:
pass
break
return HttpResponse(json.dumps({}), status=status_code)
def update_sample(request):
sample = Sample.objects.get(id=request.POST.get('id', None))
sample.mean_river_outflow = request.POST.get('mean_river_outflow',
None) or None
sample.water_renewal_time = request.POST.get('water_renewal_time',
None) or None
sample.mixing_type_id = request.POST.get('mixing_type', None) or None
sample.catchment_area = request.POST.get('catchment_area', None) or None
sample.temperature = request.POST.get('temperature', None) or None
sample.field_ph = request.POST.get('field_ph', None) or None
sample.field_conductivity = request.POST.get('field_conductivity',
None) or None
sample.light_attenuation_coefficient = request.POST.get(
'light_attenuation_coefficient', None) or None
sample.secchi_disk_depth = request.POST.get('secchi_disk_depth',
None) or None
sample.euphotic_layer = request.POST.get('euphotic_layer', None) or None
sample.oxygen_concentration = request.POST.get('oxygen_concentration',
None) or None
sample.oxygen_percentage = request.POST.get('oxygen_percentage',
None) or None
sample.laboratory_ph = request.POST.get('laboratory_ph', None) or None
sample.laboratory_conductivity = request.POST.get(
'laboratory_conductivity', None) or None
sample.total_alkalinity = request.POST.get('total_alkalinity',
None) or None
sample.bicarbonates = request.POST.get('bicarbonates', None) or None
sample.nitrate_nitrogen = request.POST.get('nitrate_nitrogen',
None) or None
sample.sulphates = request.POST.get('sulphates', None) or None
sample.chloride = request.POST.get('chloride', None) or None
sample.calcium = request.POST.get('calcium', None) or None
sample.magnesium = request.POST.get('magnesium', None) or None
sample.sodium = request.POST.get('sodium', None) or None
sample.potassium = request.POST.get('potassium', None) or None
sample.ammonium = request.POST.get('ammonium', None) or None
sample.total_nitrogen = request.POST.get('total_nitrogen', None) or None
sample.soluble_reactive_phosphorus = request.POST.get(
'soluble_reactive_phosphorus', None) or None
sample.total_phosphorus = request.POST.get('total_phosphorus',
None) or None
sample.reactive_silica = request.POST.get('reactive_silica', None) or None
sample.dry_weight = request.POST.get('dry_weight', None) or None
sample.chlorophyll_a = request.POST.get('chlorophyll_a', None) or None
sample.dna_extraction_kit_id = request.POST.get('dna_extraction_kit',
None) or None
sample.dna_extraction_date = request.POST.get('dna_extraction_date',
None) or None
sample.dna_quantity = request.POST.get('dna_quantity', None) or None
sample.dna_quantification_method_id = request.POST.get(
'dna_quantification_method', None) or None
sample.dna_quality_a260_280 = request.POST.get('dna_quality_a260_280',
None) or None
sample.dna_quality_a260_230 = request.POST.get('dna_quality_a260_230',
None) or None
if sample.dna_extraction_date:
dt = datetime.datetime.strptime(sample.dna_extraction_date, '%m/%d/%Y')
sample.dna_extraction_date = datetime.datetime(dt.year,
dt.month,
dt.day,
tzinfo=pytz.UTC)
full_dir = os.path.join('/tmp/', sample.sample_code)
files = [
'vertical_temperature_profiles', 'phytoplankton_countings',
'cyanotoxin_samples'
]
for f in files:
full_path = os.path.join(full_dir, f + '.xlsx')
if os.path.exists(full_path):
with open(full_path, 'rb') as fi:
setattr(sample, f, fi.read())
os.remove(full_path)
sample.save()
for k, v in request.POST.items():
if k.endswith('_comment') and v:
field_name = k.replace('_comment', '')
value = v
comment = Comment.objects.filter(
Q(sample=sample) & Q(field_name=field_name)).first()
if not comment:
comment = Comment(sample=sample, field_name=field_name)
comment.comment = value
comment.save()
barcode_buffer = __create_barcode_file([sample.id])
excel_buffer = __create_env_metadata([sample.id])
send_email(
request.user.email,
'Eco-AlpsWater sample updated: ' + sample.sample_code, '''
Dear {user},
sample with code {sample_code} has just been successfully updated to the Eco-AlpsWater database.
Please find attached to this e-mail a PNG file with the sample barcode and an Excel file with all the sample information.
Both files are ZIP-compressed.
This e-mail has been automatically sent from the Eco-AlpsWater website.
'''.format(user=request.user.username,
sample_code=sample.sample_code),
[(sample.sample_code + '_barcode.zip', barcode_buffer.getvalue(),
'application/zip'),
(sample.sample_code + '_sample.zip', excel_buffer.getvalue(),
'application/zip')])
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
def upload_complete(request):
sample = Sample.objects.get(id=request.POST.get('sample_id', None))
be = BiologicalElement.objects.get(
id=request.POST.get('biological_element', None))
edna = EDNAMarker.objects.get(id=request.POST.get('edna_marker', None))
hash_md5 = hashlib.md5()
with open(request.POST['sequence_file.path'], "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
hash_md5.update(chunk)
md5 = hash_md5.hexdigest()
file_md5 = False
with open(request.POST['md5_checksum_file.path']) as f:
for l in f:
if l.startswith('#'):
continue
for s in l.strip().split():
if s == md5:
file_md5 = True
break
if not file_md5:
raise Exception(
'MD5SUM mismatch, sequence file corrupted or wrong MD5')
file_unique_id = uuid.uuid4()
new_file_name = '{sample_code}_{be}_{edna}_{file_unique_id}_{org_name}'.format(
sample_code=sample.sample_code,
be=be.code,
edna=edna.name,
file_unique_id=file_unique_id,
org_name=request.POST['sequence_file.name'])
# move file
full_name = os.path.join(os.environ['EAW_VAULT_DIRECTORY'], new_file_name)
shutil.move(request.POST['sequence_file.path'], full_name)
os.chmod(full_name, S_IREAD | S_IRGRP | S_IROTH)
# add entry in db
Sequence.objects.create(
sample=sample,
filename=new_file_name,
original_filename=request.POST['sequence_file.name'],
md5sum=md5)
try:
user = request.user.username
title = 'Eco-AlpsWater admin notification'
message = '''
Dear admin,
user {user} has just uploaded the sequence file {file} for sample {sample}.
'''.format(user=user,
file=request.POST['sequence_file.name'],
sample=sample.sample_code)
for admin in User.objects.filter(is_superuser=True):
send_email(admin.email, title, message)
send_email(
request.user.email, 'Eco-AlpsWater sequence uploaded', '''
Dear {user},
sequence file named {file} has been successfully uploaded for sample with code {sample_code}.
This e-mail has been automatically sent from the Eco-AlpsWater website.
'''.format(user=request.user.username,
file=request.POST['sequence_file.name'],
sample_code=sample.sample_code))
except Exception as e:
pass
return HttpResponse(json.dumps({'success': True}),
content_type="application/json")
def wrapped_f(*args):
request = args[0]
title = 'Eco-AlpsWater admin notification'
message = ''
if self.operation == 'update_sample':
user = request.user.username
sample = Sample.objects.get(id=request.POST.get('id', None))
message = '''
Dear admin,
user {user} has just performed an update operation on sample {sample_code}.
'''.format(user=user, sample_code=sample.sample_code)
elif self.operation == 'save_sample':
user = request.user.username
sample_code = request.POST.get('sample_code', None)
message = '''
Dear admin,
user {user} has just performed a create new sample operation with code {sample_code}.
'''.format(user=user, sample_code=sample_code)
elif self.operation == 'request_sequence':
user = request.user.username
samples = json.loads(request.POST['samples'])
message = '''
Dear admin,
user {user} has just request to download sequence files for samples {samples}.
'''.format(user=user,
samples=', '.join([
Sample.objects.get(id=sample_id).sample_code
for sample_id in samples
]))
elif self.operation == 'get_env_metadata':
user = request.user.username
samples = json.loads(request.POST['samples'])
message = '''
Dear admin,
user {user} has just request to download environmental metadata for samples {samples}.
'''.format(user=user,
samples=', '.join([
Sample.objects.get(id=sample_id).sample_code
for sample_id in samples
]))
elif self.operation == 'get_barcode':
user = request.user.username
samples = json.loads(request.POST['samples'])
message = '''
Dear admin,
user {user} has just request to download barcode for samples {samples}.
'''.format(user=user,
samples=', '.join([
Sample.objects.get(id=sample_id).sample_code
for sample_id in samples
]))
elif self.operation == 'save_station':
user = request.user.username
values = json.loads(request.POST['values'])
message = '''
Dear admin,
user {user} has just request to create a new station with name {station}.
'''.format(user=user, station=values['station'])
elif self.operation == 'ftp_file_received':
ftp_obj = request
user = ftp_obj.username
file = args[1]
message = '''
Dear admin,
user {user} has just sent a file named {file_name} to the FTP server.
'''.format(user=user, file_name=os.path.basename(file))
elif self.operation == 'add_tracking_comment':
user = request.user.username
params = json.loads(request.POST.get('params', None))
sample = Sample.objects.get(id=params['id'])
message = '''
Dear admin,
user {user} has just added a tracking comment for sample {sample}. The comment is: {comment}.
'''.format(user=user,
sample=sample.sample_code,
comment=params['comment'])
for admin in User.objects.filter(is_superuser=True):
try:
send_email(admin.email, title, message)
except Exception as e:
pass
return f(*args)