def register():
if request.method == 'GET':
return(render_template('RegisterBioreactor.html'));
elif request.method == 'POST':
db = client[DB_NAME]
reactors = db[BIOREACTOR_COLLECTION]
global_var_collection = db[GLOBAL_VARIABLE_COLLECTION]
user_data = request.get_json()
upload_code = bigalgae.generate_digit_code(4)
experiment_validation_code = bigalgae.generate_digit_code(6)
validation_key = bigalgae.generate_validation_key(32)
utc = datetime.datetime.utcnow().isoformat()
success = False
while not success:
try:
id_str = returnNewID(global_var_collection)
reactors.insert({'_id': id_str, \
'name': user_data['name'], \
'location': user_data['location'], \
'email': user_data['email'], \
'latitude': user_data['latitude'], \
'longitude': user_data['longitude'], \
'upload_code': upload_code, \
'experiment_validation_code': experiment_validation_code, \
'validation_key': validation_key, \
'validated': False, \
'experiments': [], \
'created_datetime': utc})
success = True
except errors.DuplicateKeyError:
success = False
validation_link = url_for('validate', reactor_id=id_str, _external=True) + '?key=' + validation_key
confirmation_email = MIMEText(render_template('ConfirmationEmail', \
validation_link = validation_link, \
reactor_id = id_str))
confirmation_email['Subject'] = 'Big Algae Open Experiment Validation'
recipient = user_data['email']
try:
bigalgae.send_email(confirmation_email, recipient)
error_with_email = False
except smtplib.SMTPAuthenticationError:
error_with_email = True
return(url_for('thanks'))
def experiment(reactor_id, experiment_id):
db = client[DB_NAME]
reactors = db[BIOREACTOR_COLLECTION]
exp_search = [res for res in reactors.find({'_id': reactor_id, 'experiments': {'$elemMatch': {'id': experiment_id}}})]
if len(exp_search) == 0:
return(render_template('SorryExperiment.html', \
reactor_id=reactor_id, \
experiment_id=experiment_id))
else:
experiment_dict = exp_search[0]['experiments'][int(experiment_id)-1]
if request.method == 'GET':
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=False,
twitter_thanks=False,
incorrect_password_dry_mass=False,
analyse_image_output=[0]))
if request.method == 'POST':
if request.form['submit_button'] == 'SUBMIT DRY MASS':
file_name_to_update = request.form['file_name_input']
dry_mass_list = bigalgae.process_advanced_measurements_string(request.form['dry_mass'])
upload_code_provided = request.form['upload_validation_dry_mass']
print(dry_mass_list)
if exp_search[0]['upload_code'] == upload_code_provided:
reactor = reactors.find_and_modify({'_id': reactor_id, \
'experiments': {'$elemMatch': {'id': experiment_id}}}, \
{'$pull': {'experiments.$.measurements': \
{'file_name': file_name_to_update}
}})
for experiment in reactor['experiments']:
if experiment['id'] == experiment_id:
for measurement in experiment['measurements']:
if measurement['file_name'] == file_name_to_update:
measurement_to_update = measurement
measurement_to_update['dry_mass'] += dry_mass_list
reactor = reactors.find_and_modify({'_id': reactor_id, \
'experiments': {'$elemMatch': {'id': experiment_id}}}, \
{'$push': {'experiments.$.measurements': \
measurement_to_update
}}, new=True)
experiment_dict = reactor['experiments'][int(experiment_id)-1]
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=False,
twitter_thanks=False,
incorrect_password_dry_mass=False,
dry_mass_thanks=True,
analyse_image_output=[0]))
else:
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=False,
twitter_thanks=False,
incorrect_password_dry_mass=True,
dry_mass_thanks=False,
analyse_image_output=[0]))
elif request.form['submit_button'] == 'SUBMIT IMAGE':
upload_code_provided = request.form['upload_validation_upload']
if exp_search[0]['upload_code'] == upload_code_provided:
file_upload = request.files['upload_picture']
cell_count_list = bigalgae.process_advanced_measurements_string(request.form['cell_count'])
od680_list = bigalgae.process_advanced_measurements_string(request.form['od680'])
od750_list = bigalgae.process_advanced_measurements_string(request.form['od750'])
if file_upload and allowed_file(file_upload.filename):
original_filename = secure_filename(file_upload.filename)
utc = datetime.datetime.utcnow().isoformat()
present = True
while present:
try:
saved_filename = bigalgae.generate_validation_key(32) + '.' + original_filename.rsplit('.', 1)[1]
fd = os.open(os.path.join(app.config['UPLOAD_FOLDER'], saved_filename), os.O_WRONLY | os.O_CREAT | os.O_EXCL)
present = False
except OSError, e:
if e.errno == errno.EEXIST:
present = True
else:
raise
f = os.fdopen(fd, 'w')
file_upload.save(f)
f.close()
image_filepath = os.path.join(app.config['UPLOAD_FOLDER'], saved_filename)
exif_data = bigalgae.extract_exif_data(image_filepath)
for problem_key in ['MakerNote', 'UserComment']:
if problem_key in exif_data.keys():
try:
unicode(exif_data[problem_key], 'utf-8')
except UnicodeDecodeError:
del(exif_data[problem_key])
image_information = bigalgae.analyse_image(image_filepath)
if image_information[0] == 0:
image_binary_info = image_information[1]
elif image_information[0] == 2:
image_binary_info = {}
elif image_information[0] == 1:
global_var_collection = db[GLOBAL_VARIABLE_COLLECTION]
global_var_collection.find_and_modify({'_id': 'failed_image_analysis'},
{'$push': {'list':
{'file_name': saved_filename , \
'cell_count': cell_count_list, \
'od680': od680_list, \
'od750': od750_list, \
'upload_datetime': utc, \
'original_filename': original_filename, \
'exif': exif_data}}})
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=False,
twitter_thanks=False,
incorrect_password_dry_mass=False,
analyse_image_output=image_information))
reactor = reactors.find_and_modify({'_id': reactor_id, \
'experiments': {'$elemMatch': {'id': experiment_id}}}, \
{'$push': {'experiments.$.measurements': \
{'file_name': saved_filename , \
'cell_count': cell_count_list, \
'od680': od680_list, \
'od750': od750_list, \
'dry_mass': [], \
'cell_count_prediction_mean': None, \
'cell_count_prediction_sd': None, \
'od680_prediction_mean': None, \
'od680_prediction_sd': None, \
'od750_prediction_mean': None, \
'od750_prediction_sd': None, \
'dry_mass_prediction_mean': None, \
'dry_mass_prediction_sd': None, \
'upload_datetime': utc, \
'image_binary_info': image_binary_info, \
'original_filename': original_filename, \
'exif': exif_data}
}}, new=True)
experiment_dict = reactor['experiments'][int(experiment_id)-1]
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=False,
twitter_thanks=True,
incorrect_password_dry_mass=False,
analyse_image_output=image_information))
else:
return(render_template('ExperimentPage.html', \
reactor_id=reactor_id, \
experiment_dict=experiment_dict,
incorrect_upload_code=True,
twitter_thanks=False,
incorrect_password_dry_mass=False,
analyse_image_output=[0]))
