def karyotype(connection, ENDPOINT, PARAMS, arguments, context):
try:
specie = taking_out_space(arguments["species"][0])
except KeyError:
if len(arguments.keys()) == 0:
cont_type = 'text/html'
context["karyotype"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/karyotype.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1:
cont_type = 'application/json'
context["karyotype"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
connection.request("GET", ENDPOINT + specie + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
karyotype = response_dict["karyotype"]
# print(karyotype)
context["species"] = arguments["species"][0]
context["karyotype"] = karyotype
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/karyotype.html").render(context=context)
return contents, cont_type
def geneSeq(connection, ENDPOINT, PARAMS, arguments, context, DICT_GENES):
try:
gene = arguments["gene"][0]
except KeyError:
if len(arguments.keys()) == 0:
cont_type = 'text/html'
context["seq"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/geneSeq.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1:
cont_type = 'application/json'
context["seq"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
id = DICT_GENES[gene]
connection.request("GET", ENDPOINT + id + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
context["gene"] = arguments["gene"][0]
context["seq"] = response_dict["seq"]
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/geneSeq.html").render(context=context)
return contents, cont_type
def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
context = {}
if path_name == '/':
context["n_sequences"] = len(list_sequences)
context["list_genes"] = list_genes
contents = su.read_template_html_file('./index.html').render(
context=context)
elif path_name == "/test":
contents = su.read_template_html_file("./test.html").render()
elif path_name == "/ping":
contents = su.read_template_html_file("./ping.html").render()
elif path_name == "/get":
number_sequence = arguments["sequence"][0]
contents = su.get(list_sequences, number_sequence)
elif path_name == "/gene":
gene = arguments["gene"][0]
contents = su.gene(gene)
elif path_name == "/operation":
sequence = arguments["sequence"][0]
calculation = arguments["calculation"][0]
if calculation == "Info":
contents = su.info(sequence)
elif calculation == "Comp":
contents = su.comp(sequence)
elif calculation == "Rev":
contents = su.rev(sequence)
else:
contents = su.read_template_html_file('./Error.html').render()
else:
contents = su.read_template_html_file("./Error.html").render()
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', len(contents.encode()))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
def do_GET(self):
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
# IN this simple server version:
# We are NOT processing the client's request
# It is a happy server: It always returns a message saying
# that everything is ok
context = {}
# Message to send back to the client
if path_name == '/':
context["n_sequences"] = len(list_sequences)
context["list_genes"] = list_genes
contents = su.read_template_html_file('./html/index.html').render(
context=context)
elif path_name == "/ping":
contents = su.read_template_html_file("./html/ping.html").render()
elif path_name == "/get":
number_sequence = arguments["sequence"][0]
contents = su.get(list_sequences, number_sequence)
elif path_name == "/gene":
gene = arguments["gene"][0]
contents = su.gene(gene)
elif path_name == "/operation":
sequence = arguments['sequence'][0]
calculation = arguments['calculation'][0]
if calculation == 'Info':
contents = su.info(sequence)
elif calculation == 'Comp':
contents = su.comp(sequence)
elif calculation == 'Rev':
contents = su.rev(sequence)
else:
contents = su.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = su.read_template_html_file("./html/ERROR.html").render()
self.send_response(200)
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', len(contents.encode()))
self.end_headers()
self.wfile.write(contents.encode())
return
def list_species(connection, ENDPOINT, PARAMS, arguments, context):
connection.request("GET", ENDPOINT + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
if arguments == {}:
cont_type = 'text/html'
context["limit"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/list_species.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1 and "json" in arguments.keys():
cont_type = 'application/json'
context["limit"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
species_list = []
amount_species = len(response_dict["species"])
context["amount_species"] = amount_species
limit = int(arguments["limit"][0])
context["limit"] = limit
if limit < amount_species:
for n in range(0, limit):
species_list.append(response_dict["species"][n]["common_name"])
context["names"] = species_list
else:
for n in range(0, amount_species):
species_list.append(response_dict["species"][n]["common_name"])
context["names"] = species_list
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/list_species.html").render(context=context)
return contents, cont_type
def geneCalc(connection, ENDPOINT, PARAMS, arguments, context, DICT_GENES):
try:
gene = arguments["gene"][0]
except KeyError:
if len(arguments.keys()) == 0:
cont_type = 'text/html'
context["bases"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/geneCalc.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1:
cont_type = 'application/json'
context["bases"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
id = DICT_GENES[gene]
connection.request("GET", ENDPOINT + id + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
sequence = Seq(response_dict["seq"])
dict_bases, percentage_list = Seq.count_base_2(sequence)
context["gene"] = gene
context["length"] = Seq.len(sequence)
context["bases"] = {
"A": str(dict_bases["A"]) + " (" + str(percentage_list[0]) + "%)",
"C": str(dict_bases["C"]) + " (" + str(percentage_list[1]) + "%)",
"T": str(dict_bases["T"]) + " (" + str(percentage_list[2]) + "%)",
"G": str(dict_bases["G"]) + " (" + str(percentage_list[3]) + "%)"
}
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/geneCalc.html").render(context=context)
return contents, cont_type
def geneInfo(connection, ENDPOINT, PARAMS, arguments, context, DICT_GENES):
try:
gene = arguments["gene"][0]
except KeyError:
if len(arguments.keys()) == 0:
cont_type = 'text/html'
context["dict_info"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/geneInfo.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1:
cont_type = 'application/json'
context["dict_info"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
id = DICT_GENES[gene]
connection.request("GET", ENDPOINT + id + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
info = response_dict["desc"].split(":")
context["gene"] = gene
context["dict_info"] = {
"Name": info[2],
"ID": id,
"Start": info[3],
"End": info[4],
"Length": (int(info[4]) - int(info[3]) + 1)
}
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/geneInfo.html").render(context=context)
return contents, cont_type
def index(arguments, context, DICT_GENES):
context["genes"] = DICT_GENES.keys()
if "json" in arguments.keys():
if arguments["json"][0] == "1":
context = {
"Basic level": [
"1) Species list (a limit is required)",
"2) Species karyotype (a species is required)",
"3) Chromosome length (a species and a chromosome are required)"
],
"Medium level": [
"4) Gene sequence (a gene is required)",
"5) Gene information (a gene is required)",
"6) Gene calculations (a gene is required)",
]
}
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/index.html").render(context=context)
return contents, cont_type
def chromosome_length(connection, ENDPOINT, PARAMS, arguments, context):
try:
specie = taking_out_space(arguments["species"][0])
except KeyError:
if len(arguments.keys()) == 0:
cont_type = 'text/html'
context["length"] = "ERROR"
contents = su.read_template_html_file("./HTML/info/chromosome_length.html").render(context=context)
return contents, cont_type
elif len(arguments.keys()) == 1:
if "chromosome" in arguments.keys():
cont_type = 'text/html'
context["length"] = "ERROR 2"
contents = su.read_template_html_file("./HTML/info/chromosome_length.html").render(context=context)
return contents, cont_type
if "json" in arguments.keys():
cont_type = 'application/json'
context["length"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
elif len(arguments.keys()) == 2:
cont_type = 'application/json'
context["length"] = "ERROR 2"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
connection.request("GET", ENDPOINT + specie + PARAMS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
try:
chromosome = arguments["chromosome"][0]
# print(json.dumps(response_dict, indent=4, sort_keys=True))
except KeyError:
if len(arguments.keys()) == 1:
if "species" in arguments.keys():
cont_type = 'text/html'
context["length"] = "ERROR 1"
contents = su.read_template_html_file("./HTML/info/chromosome_length.html").render(context=context)
return contents, cont_type
if "json" in arguments.keys():
cont_type = 'application/json'
context["length"] = "ERROR"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
elif len(arguments.keys()) == 2:
cont_type = 'application/json'
context["length"] = "ERROR 1"
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
for n in range(0, len(response_dict["top_level_region"])):
if chromosome == response_dict["top_level_region"][n]["name"]:
length = response_dict["top_level_region"][n]["length"]
# print(length)
context["species"] = arguments["species"][0]
context["chromosome"] = chromosome
context["length"] = length
if "json" in arguments.keys():
if arguments["json"][0] == "1":
cont_type = 'application/json'
contents = json.dumps(context, indent=4, sort_keys=True)
return contents, cont_type
else:
cont_type = 'text/html'
contents = su.read_template_html_file("./HTML/info/chromosome_length.html").render(context=context)
return contents, cont_type
def do_GET(self):
global contents
# colorama.init(strip="False")
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
connection = http.client.HTTPConnection(SERVER)
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
# IN this simple server version:
# We are NOT processing the client's request
# It is a happy server: It always returns a message saying
# that everything is ok
# Message to send back to the client
context = {}
try:
if path_name == "/":
contents, cont_type = su2.index(arguments, context, DICT_GENES)
elif path_name.lower() == "/listspecies":
ENDPOINT = "/info/species"
contents, cont_type = su2.list_species(connection, ENDPOINT,
PARAMS, arguments,
context)
elif path_name == "/karyotype":
ENDPOINT = "info/assembly/"
contents, cont_type = su2.karyotype(connection, ENDPOINT,
PARAMS, arguments, context)
elif path_name == "/chromosomeLength":
ENDPOINT = "info/assembly/"
contents, cont_type = su2.chromosome_length(
connection, ENDPOINT, PARAMS, arguments, context)
elif path_name == "/geneSeq":
ENDPOINT = "/sequence/id/"
contents, cont_type = su2.geneSeq(connection, ENDPOINT, PARAMS,
arguments, context,
DICT_GENES)
elif path_name == "/geneInfo":
ENDPOINT = "/sequence/id/"
contents, cont_type = su2.geneInfo(connection, ENDPOINT,
PARAMS, arguments, context,
DICT_GENES)
elif path_name == "/geneCalc":
ENDPOINT = "/sequence/id/"
contents, cont_type = su2.geneCalc(connection, ENDPOINT,
PARAMS, arguments, context,
DICT_GENES)
else:
contents = su.read_template_html_file(HTML +
"ERROR.html").render()
cont_type = 'text/html'
except KeyError:
cont_type = 'text/html'
contents = su.read_template_html_file(HTML + "ERROR.html").render()
except ValueError:
cont_type = 'text/html'
contents = su.read_template_html_file(HTML + "ERROR.html").render()
except TypeError:
cont_type = 'text/html'
contents = su.read_template_html_file(HTML + "ERROR.html").render()
except UnboundLocalError:
cont_type = 'text/html'
contents = su.read_template_html_file(HTML + "ERROR.html").render()
# Generating the response message
self.send_response(200) # -- Status line: OK!
length = len(contents.encode())
# Define the content-type header:
self.send_header('Content-Type', cont_type)
self.send_header('Content-Length', str(length))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(str.encode(contents))
return
while True:
print("Waiting for Clients to connect")
try:
(cs, client_ip_port) = ls.accept()
print("A client has connected to the server!")
count_connections += 1
client_addres_list.append((cs, client_ip_port))
print("CONNECTION " + str(count_connections) + ". Client IP, PORT: " +
str(client_ip_port))
except KeyboardInterrupt:
print("Server stopped by the user")
ls.close()
exit()
msg_raw = cs.recv(2048)
msg = msg_raw.decode()
formatted_msg = Server_utils.format_command(msg)
formatted_msg = formatted_msg.split(" ")
if len(formatted_msg) == 1:
command = formatted_msg[0]
else:
command = formatted_msg[0] + '"'
argument = '"' + formatted_msg[1]
if command == '"PING"':
Server_utils.ping(cs)
elif command == '"GET"':
Server_utils.get(list_sequences, cs, argument)
elif command == '"INFO"':
Server_utils.info(argument, cs)
def do_GET(self):
global contents
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
# IN this simple server version:
# We are NOT processing the client's request
# It is a happy server: It always returns a message saying
# that everything is ok
context = {}
# Message to send back to the client
PARAMETERS = '?content-type=application/json'
SERVER = "rest.ensembl.org"
connection = http.client.HTTPConnection(SERVER)
if path_name == '/':
contents = Path('./html/index.html').read_text()
elif path_name == "/listSpecies":
try:
ENDPOINT = '/info/species'
connection.request('GET', ENDPOINT + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
species_list = final_response['species']
names_list = []
for elem in species_list:
s1 = elem['name']
lists = [s1]
names_list = names_list + lists
if 'limit' in arguments:
limit = int(arguments['limit'][0])
final_list = names_list[:limit]
if limit <= len(final_list):
context['length'] = len(names_list)
context['final_list'] = final_list
context['limit'] = limit
contents = su.read_template_html_file(
'./html/limit_name_list.html').render(
context=context)
else:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif 'limit' not in arguments:
context['length'] = len(names_list)
context['final_list'] = names_list
contents = su.read_template_html_file(
'./html/full_name_list.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/karyotype":
try:
species_name = arguments['species_name'][0]
ENDPOINT = '/info/assembly/'
connection.request('GET', ENDPOINT + species_name + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
karyotype = final_response['karyotype']
context['karyotype'] = karyotype
contents = su.read_template_html_file(
'./html/karyotype.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/chromosomeLength":
try:
if 'species_name' not in arguments:
contents = su.read_template_html_file(
'./html basic/ERROR.html').render()
elif 'chromosome_name' not in arguments:
contents = su.read_template_html_file(
'./html basic/ERROR.html').render()
else:
global chromosome_length
species_name = arguments['species_name'][0]
chromosome_name = arguments['chromosome_name'][0]
ENDPOINT = '/info/assembly/'
connection.request('GET',
ENDPOINT + species_name + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
list_dict = final_response['top_level_region']
for elem in list_dict:
if (elem['name']
== chromosome_name) and (elem['coord_system']
== 'chromosome'):
chromosome_length = elem['length']
else:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
context['chromosome_length'] = chromosome_length
contents = su.read_template_html_file(
'./html/chromosome_length.html').render(
context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/geneSeq":
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
sequence = final_response['seq']
context['sequence'] = sequence
contents = su.read_template_html_file(
'./html/Seq.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/geneInfo":
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
info_list = final_response['desc'].split(':')
context['genname'] = gene
context['start'] = info_list[3]
context['end'] = info_list[4]
context['length'] = int(info_list[4]) - int(info_list[3])
context['id'] = GENE_ID
context['chromoname'] = info_list[1]
contents = su.read_template_html_file(
'./html/Info.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == '/geneCalc':
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
sequence = final_response['seq']
s = Seq(sequence)
context['length'] = s.len()
context['percentageA'] = s.percentage_base('A')
context['percentageC'] = s.percentage_base('C')
context['percentageG'] = s.percentage_base('G')
context['percentageT'] = s.percentage_base('T')
contents = su.read_template_html_file(
'./html/Calc.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
else:
pass
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
content_length = len(str.encode(contents))
self.send_header('Content-Length', content_length)
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
def do_GET(self):
global contents
colorama.init(strip="False")
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
# Print the request line
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
# IN this simple server version:
# We are NOT processing the client's request
# It is a happy server: It always returns a message saying
# that everything is ok
# Message to send back to the client
context = {}
if path_name == "/":
context["n_seq"] = len(LIST_SEQ)
context["list_genes"] = LIST_GENE
context["operation_list"] = OPERATION_LIST
contents = su.read_template_html_file(HTML_ASSETS + "index.html").render(context=context)
elif path_name == "/ping":
contents = su.read_template_html_file(HTML_ASSETS + "ping.html").render()
elif path_name == "/get":
number_seq = arguments["sequence"][0]
contents = su.get(LIST_SEQ, number_seq)
elif path_name == "/gene":
gene = arguments["gene"][0]
contents = su.gene(gene)
elif path_name == "/operation":
sequence = arguments["sequence"][0]
operation = arguments["calculation"][0]
if operation == "info":
contents = su.info(sequence)
elif operation == "comp":
contents = su.comp(sequence)
elif operation == "rev":
contents = su.rev(sequence)
else:
contents = su.read_template_html_file(HTML + "ERROR.html").render()
# Generating the response message
self.send_response(200) # -- Status line: OK!
length = len(contents.encode())
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', str(length))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
while True:
print("Waiting for Clients to connect")
try:
(cs, client_ip_port) = ls.accept()
client_address_list.append(client_ip_port)
count_connections += 1
print('Connection: ' + str(count_connections) + '. Client ip, port: ' +
str(client_ip_port))
except KeyboardInterrupt:
print("Server stopped by the user")
ls.close()
exit()
msg_raw = cs.recv(2048)
msg = msg_raw.decode()
formatted_msg = su.format_command(msg)
#print(formatted_msg)
formatted_msg = formatted_msg.split(' ')
if len(formatted_msg) == 1:
command = formatted_msg[0]
else:
command = formatted_msg[0]
argument = formatted_msg[1]
if command == 'PING':
su.ping(cs)
elif command == 'GET':
su.get(cs, list_sequences, argument)
elif command == 'INFO':
su.info(cs, argument)
def do_GET(self):
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, "blue")
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resoruce requested: ", path_name)
print("Parameters: ", arguments)
if 'json' in arguments.keys() and arguments["json"][0] == "1":
if path_name == "/listSpecies":
ENDPOINT = "/info/species"
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
try:
if type(arguments["limit"][0]) == str:
contents = json.dumps(au.json_species(
response, int(arguments["limit"][0])),
indent=4,
sort_keys=True)
except KeyError:
contents = json.dumps(au.json_species(response),
indent=4,
sort_keys=True)
except ValueError:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
elif path_name == "/Karyotype":
try:
ENDPOINT = "/info/assembly/"
specie = arguments["specie"][0]
for element in specie:
if element == " ":
specie = specie.replace(element, "_")
ENDPOINT = ENDPOINT + specie
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
context = {
"specie": specie,
"karyotype": response["karyotype"]
}
contents = json.dumps(context, indent=4, sort_keys=True)
except KeyError:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
elif path_name == "/chromosomeLength":
try:
ENDPOINT = "/info/assembly/"
specie = arguments["specie"][0]
for element in specie:
if element == " ":
specie = specie.replace(element, "_")
print(specie)
chromo = arguments["chromo"][0]
ENDPOINT = ENDPOINT + specie
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = json.dumps(au.json_chromosome_length(
response, specie, chromo),
indent=4,
sort_keys=True)
except KeyError:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
elif path_name == "/geneSeq":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
if ID in gene_dict:
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
context = {
"Sequence": response["seq"],
"name": ID,
"id": response["id"]
}
contents = json.dumps(context, indent=4, sort_keys=True)
else:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
elif path_name == "/geneInfo":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
if ID in gene_dict:
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = json.dumps(au.json_calculations(response, ID),
indent=4,
sort_keys=True)
else:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
elif path_name == "/geneCalc":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
if ID in gene_dict:
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = json.dumps(au.json_second_calculations(
response, ID),
indent=4,
sort_keys=True)
else:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
else:
contents = json.dumps("Sorry, the data introduced is bad",
indent=4,
sort_keys=True)
else:
if path_name == "/":
context = {"gene_list": gene_dict}
contents = su.read_template_html_file(
ROOT + "/Basic_level.html").render(context=context)
elif path_name == "/listSpecies":
ENDPOINT = "/info/species"
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
if "check" in arguments.keys():
termcolor.cprint("The checkbox was checked", "red")
else:
termcolor.cprint("The checkbox was unchecked", "red")
try:
if type(arguments["limit"][0]) == str:
contents = su.species_list(response,
int(arguments["limit"][0]))
except KeyError:
contents = su.species_list(response)
except ValueError:
contents = su.read_template_html_file(
ROOT + "/ERROR.html").render()
elif path_name == "/Karyotype":
try:
ENDPOINT = "/info/assembly/"
specie = arguments["specie"][0]
for element in specie:
if element == " ":
specie = specie.replace(element, "_")
ENDPOINT = ENDPOINT + specie
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
context = {
"specie": specie,
"karyotype": response["karyotype"]
}
contents = su.read_template_html_file(
ROOT + "/karyotype.html").render(context=context)
except KeyError:
contents = su.read_template_html_file(
ROOT + "/ERROR.html").render()
elif path_name == "/chromosomeLength":
try:
ENDPOINT = "/info/assembly/"
specie = arguments["specie"][0]
for element in specie:
if element == " ":
specie = specie.replace(element, "_")
chromo = arguments["chromo"][0]
ENDPOINT = ENDPOINT + specie
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = su.chromosome_length(response, specie, chromo)
except KeyError:
contents = su.read_template_html_file(
ROOT + "/ERROR.html").render()
elif path_name == "/geneSeq":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
context = {
"Sequence": response["seq"],
"name": ID,
"id": response["id"]
}
contents = su.read_template_html_file(ROOT +
"/GENE.html").render(
context=context)
elif path_name == "/geneInfo":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = su.calculations(response, ID)
elif path_name == "/geneCalc":
ENDPOINT = "/sequence/id/"
ID = arguments["gene"][0]
ENDPOINT = ENDPOINT + gene_dict[ID]
response = su.api_connection(ENDPOINT, PARAMS, SERVER)
contents = su.second_calculations(response, ID)
else:
contents = su.read_template_html_file(ROOT +
"/ERROR.html").render()
# Generating the response message
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', str(len(contents.encode())))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return