def do_GET(self):
"""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)
context = {}
if path_name == "/":
context["list_genes"] = list(HUMAN_GENES.keys())
contents = su.read_template_html_file("./html/index.html").render(
context=context)
elif path_name == "/listSpecies":
contents = su.listSpecies(arguments)
if "check" in arguments.keys():
print('The check bottom was used')
else:
print('The checkbox was not used')
elif path_name == "/karyotype":
contents = su.karyotype(arguments, path_name)
elif path_name == "/chromosomeLength":
contents = su.karyotype(arguments, path_name)
elif path_name == "/geneSeq":
contents = su.gene_seq(arguments, path_name, HUMAN_GENES)
elif path_name == "/geneInfo":
contents = su.gene_seq(arguments, path_name, HUMAN_GENES)
elif path_name == "/geneCalc":
contents = su.gene_seq(arguments, path_name, HUMAN_GENES)
else:
contents = su.read_template_html_file(
"html/errors/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') # Si no ponemos html saldrá texto!!
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")
url = urlparse(self.path)
endpoint = url.path
parameters = parse_qs(url.query)
print("Endpoint: ", endpoint)
print("Parameters: ", parameters)
has_error = False
contents = ""
status = 400 # BAD_REQUEST
if endpoint in ENDPOINTS:
if endpoint == "/":
status = 200
contents = Path("./html/index.html").read_text()
elif endpoint == "/listSpecies":
if len(parameters) == 0:
status, contents = su.list_species()
elif len(parameters) == 1:
try:
limit = int(parameters['limit'][0])
status, contents = su.list_species(limit)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
elif endpoint == "/karyotype":
if len(parameters) == 1:
try:
specie = parameters['specie'][0]
status, contents = su.karyotype(specie)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
elif endpoint == "/chromosomeLength":
if len(parameters) == 2:
try:
specie = parameters['specie'][0]
chromo = parameters['chromo'][0]
status, contents = su.chromosome_length(specie, chromo)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
elif endpoint == "/geneSeq":
if len(parameters) == 1:
try:
gene = parameters['gene'][0]
status, contents = su.gene_seq(gene)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
elif endpoint == "/geneInfo":
if len(parameters) == 1:
try:
gene = parameters['gene'][0]
status, contents = su.gene_info(gene)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
elif endpoint == "/geneCalc":
if len(parameters) == 1:
try:
gene = parameters['gene'][0]
status, contents = su.gene_calc(gene)
except (KeyError, ValueError):
has_error = True
else:
has_error = True
else:
has_error = True
if has_error:
contents = Path("./html/error.html").read_text()
self.send_response(status)
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', str(len(contents.encode())))
self.end_headers()
self.wfile.write(contents.encode())
print(contents)
def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
o = urlparse(self.path)
# get the endpoints
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
server = "https://rest.ensembl.org"
server_info = "https://grch37.rest.ensembl.org"
# main page
if path_name == "/":
contents, content_type = su.read_html("./html/form.html", "")
error_code = 200
# list species
elif path_name == "/listSpecies":
ext = "/info/species?"
html = "./html/list_of_species.html"
contents, content_type, error_code = su.listSpecies(
server, ext, arguments, html)
# karyotype
elif path_name == "/karyotype":
ext = "/info/assembly/"
html = "./html/karyotype.html"
contents, content_type, error_code = su.karyotype(
server, ext, arguments, html)
# chromosomeLength
elif path_name == "/chromosomeLength":
ext = "/info/assembly/"
html = "./html/len_chromo.html"
contents, content_type, error_code = su.chromosomeLength(
server, ext, arguments, html)
# geneSeq
elif path_name == "/geneSeq":
ext = "/sequence/id/"
html = "./html/sequence_gene.html"
contents, content_type, error_code = su.geneSeq(
server, ext, arguments, html)
# geneInfo
elif path_name == "/geneInfo":
ext = "/lookup/id/"
html = "./html/info_gene.html"
contents, content_type, error_code = su.geneInfo(
server_info, ext, arguments, html)
# geneCalc
elif path_name == "/geneCalc":
ext = "/lookup/id/"
html = "./html/calc_gene.html"
contents, content_type, error_code = su.geneCalc(
server_info, ext, arguments, html)
else:
contents, content_type = su.read_html("./html/Error.html",
"Endpoint not valid")
error_code = 404
# response message
self.send_response(error_code) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', content_type)
# print(contents) (used to print output in report-advanced)
self.send_header('Content-Length', str(len(contents.encode())))
# The header is finished
self.end_headers()
# response message
self.wfile.write(contents.encode())
return
def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
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 == "/":
contents = server_utils.read_template_html_file(
"./html/index.html").render(context=context)
elif path_name == "/listSpecies":
dict_s = server_utils.get_data("/info/species")
if len(arguments) == 1:
try:
limit = arguments["limit"][0]
except KeyError:
limit = len(dict_s["species"])
contents = server_utils.list_species(dict_s, limit)
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
elif path_name == "/karyotype":
if len(arguments) == 1:
try:
specie_name = arguments["specie"][0]
dict_k = server_utils.get_data("info/assembly" + "/" +
specie_name)
contents = server_utils.karyotype(dict_k, specie_name)
except KeyError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
except ValueError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
elif path_name == "/chromosomeLength":
if len(arguments) == 2:
try:
specie = arguments["specie"][0]
chromo = arguments["chromo"][0]
dict_c = server_utils.get_data("/info/assembly" + "/" +
specie + "/" + chromo)
contents = server_utils.length_chromosome(
dict_c, specie, chromo)
except KeyError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
except ValueError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
elif path_name == "/geneSeq":
if len(arguments) == 1:
try:
gene = arguments["gene"][0]
dict_seq = server_utils.get_data(
"/sequence/id/" + server_utils.genes_dict[gene])
contents = server_utils.sequence(dict_seq, gene)
except KeyError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
except ValueError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
elif path_name == "/geneInfo":
if len(arguments) == 1:
try:
gene = arguments["gene"][0]
dict_info = server_utils.get_data(
"/sequence/id/" + server_utils.genes_dict[gene])
contents = server_utils.infoseq(dict_info, gene)
except KeyError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
except ValueError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
elif path_name == "/geneCalc":
if len(arguments) == 1:
try:
gene = arguments["gene"][0]
dict_calc = server_utils.get_data(
"/sequence/id/" + server_utils.genes_dict[gene])
contents = server_utils.calcseq(dict_calc, gene)
except KeyError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
except ValueError:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
else:
contents = server_utils.read_template_html_file(
"./html/ERROR.html").render()
self.send_response(200)
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(str.encode(contents))
return