def get_seq_file_data():
if 'file' not in request.files:
abort(Response('No file part', 400))
file = request.files['file']
if file.filename == '':
abort(Response('No selected file', 400))
if file and allowed_file(file.filename):
secure_filename(file.filename) # TODO: secure_filename return correct filename, we should do sth with this
data = dict()
data['sequences'] = file.read().decode()
data['threshold'] = request.form['threshold']
consensus_seq = ConsensusSequence(data)
result = consensus_seq.file_seq()
add_calculation(
module_name=ModuleName.CONSENSUS_SEQUENCE_FILE_SEQ,
user_data=data,
result=result,
ip_address=request.remote_addr,
)
slack_notification.consensus_sequence_file_seq_calculation(data, result, request.remote_addr)
response = make_response(base64.b64encode(result.encode()))
response.headers['Content-Type'] = 'text/plain'
response.mimetype = 'text/plain'
return response, 200
else:
abort(Response('Illegal file extension', 400))
def get_sequences_data():
try:
data = request.get_json()
seq_tools = SequencesTools(data)
result = seq_tools.calculate()
add_calculation(
module_name=ModuleName.SEQUENCES_TOOLS, user_data=data, result=result, ip_address=request.remote_addr
)
slack_notification.sequences_tool_calculation(data, result, request.remote_addr)
return jsonify({'data': result})
except Exception as e:
abort(Response(str(e), 400))
def dot_plot_genebank_ids():
try:
data = request.get_json()
dot_plot = DotPlot(data)
result = dot_plot.genebank_seq()
add_calculation(
module_name=ModuleName.DOT_PLOT_GENEBANK_IDS, user_data=data, result=result, ip_address=request.remote_addr
)
slack_notification.dot_plot_genebank_calculation(data, result, request.remote_addr)
return jsonify(
{'data': result, 'dotplot_base64': dot_plot.get_dot_plot_image(), 'alignment': dot_plot.get_alignments()}
)
except Exception as e:
abort(Response(str(e), 400))
def get_goodness_data():
try:
data = request.get_json()
chi_goodness = ChiSquareGoodness(data["observed"], data["expected"])
result = chi_goodness.calculate()
add_calculation(
module_name=ModuleName.CHI_SQUARE_GOODNESS, user_data=data, result=result, ip_address=request.remote_addr
)
slack_notification.chi_square_goodness_calculation(data, result, request.remote_addr)
return jsonify({'data': result})
except TypeError as e:
abort(Response(f'Please check type of input data, {str(e)}', 422))
except Exception as e:
abort(Response(str(e), 400))
def get_data():
try:
data = request.get_json()
chi = ChiSquareCalculation(data)
result = chi.calculate()
add_calculation(
module_name=ModuleName.CHI_SQUARE, user_data=data, result=result, ip_address=request.remote_addr
)
slack_notification.chi_square_calculation(data, result, request.remote_addr)
return jsonify({'data': result})
except TypeError as e:
abort(Response(f'Please check type of input data, {str(e)}', 422))
except Exception as e:
abort(Response(str(e), 400))
def get_raw_seq_data():
try:
data = request.get_json()
consensus_seq = ConsensusSequence(data)
result = consensus_seq.raw_sequence()
add_calculation(
module_name=ModuleName.CONSENSUS_SEQUENCE_RAW_SEQ,
user_data=data,
result=result,
ip_address=request.remote_addr,
)
slack_notification.consensus_sequence_raw_seq_calculation(data, result, request.remote_addr)
return jsonify({'data': result})
except Exception as e:
abort(Response(str(e), 400))
def pic_dominant():
try:
data = request.get_json()
do = Dominant(data)
result = do.calculate()
add_calculation(module_name=ModuleName.PIC_DOMINANT,
user_data=data,
result=result,
ip_address=request.remote_addr)
slack_notification.pic_dominant_calculation(data, result,
request.remote_addr)
return jsonify({'data': result})
except TypeError as e:
abort(Response(f'Please check type of input data. {e}', 422))
except Exception as e:
abort(Response(str(e), 400))
def get_data():
try:
data = request.get_json()
hw = HardyWeinbergCalculation(data)
result = hw.calculate()
add_calculation(module_name=ModuleName.HARDY_WEINBERG,
user_data=data,
result=result,
ip_address=request.remote_addr)
slack_notification.hardy_weinberg_calculation(data, result,
request.remote_addr)
return jsonify({'data': result})
except TypeError:
abort(Response("Please check type of input data", 409))
except Exception as e:
abort(Response(str(e), 400))
def get_seq_genebank():
try:
data = request.get_json()
consensus_seq = ConsensusSequence(data)
result = consensus_seq.genebank_seq()
add_calculation(
module_name=ModuleName.CONSENSUS_SEQUENCE_GENE_BANK,
user_data=data,
result=result,
ip_address=request.remote_addr,
)
slack_notification.consensus_sequence_genebank_calculation(data, result, request.remote_addr)
response = make_response(base64.b64encode(result.encode()))
response.headers['Content-Type'] = 'text/plain'
response.mimetype = 'text/plain'
return response, 200
except Exception as e:
abort(Response(str(e), 400))
def get_data():
try:
data = request.get_json()
distance_choice = data.get("type_of_distance")
distance_type = {
'standard': StandardDistance(data),
'geometric': GeometricDistance(data),
'takezaki-nei': TakezakiNeiDistance(data),
}
gen_distance = distance_type[distance_choice]
gen_distance.calculate_distances()
gen_distance.build_matrix()
add_calculation(
module_name=f'{ModuleName.GENETIC_DISTANCE}_{distance_choice}',
user_data=data,
result=gen_distance.get_matrix().tolist(),
ip_address=request.remote_addr,
)
slack_notification.genetic_distance_calculation(
data, gen_distance.get_matrix(), request.remote_addr)
return jsonify({
'data': {
'dendro_base64': gen_distance.render_dendrogram(),
'matrix': gen_distance.render_matrix()
}
})
except TypeError as e:
abort(Response(f'Please check type of input data. {str(e)}', 422))
except ValueError as e:
abort(
Response(
f'The quantity or quality of the data is inappropriate! {str(e)}',
422))
except Exception as e:
abort(Response(str(e), 400))