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)
# 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
try:
if path_name == "/":
contents = SU.read_template_html_file(
"./html/index.html").render()
content_type = "text/html"
elif path_name == "/listSpecies":
if "limit" in arguments.keys() and len(arguments) == 1:
limit_species = arguments["limit"][0]
if limit_species.isdigit() and int(limit_species) > 0:
contents = SU.list_species(limit_species,
json_param=False)
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
elif "limit" and "json" in arguments.keys(
) and arguments["json"][0] == "1" and len(arguments) == 2:
limit_species = arguments["limit"][0]
contents = SU.list_species(limit_species, json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
elif path_name == "/karyotype":
if "specie" in arguments.keys() and len(arguments) == 1:
specie = arguments["specie"][0]
contents = SU.information_karyotype(specie,
json_param=False)
content_type = "text/html"
elif "specie" and "json" in arguments.keys(
) and arguments["json"][0] == "1" and len(arguments) == 2:
specie = arguments["specie"][0]
contents = SU.information_karyotype(specie,
json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
elif path_name == "/chromosomeLength":
if "specie" and "chromo" in arguments.keys() and len(
arguments) == 2:
specie = arguments["specie"][0]
chromosome = arguments["chromo"][0]
contents = SU.chromosome_length(specie,
chromosome,
json_param=False)
content_type = "text/html"
elif "specie" and "chromo" and "json" in arguments.keys() and arguments["json"][0] == "1" \
and len(arguments) == 3:
specie = arguments["specie"][0]
chromosome = arguments["chromo"][0]
contents = SU.chromosome_length(specie,
chromosome,
json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
elif path_name == "/geneSeq":
if "gene" in arguments.keys() and len(arguments) == 1:
gene = arguments["gene"][0]
contents = SU.gene_seq(gene, json_param=False)
content_type = "text/html"
elif "gene" and "json" in arguments.keys(
) and arguments["json"][0] == "1" and len(arguments) == 2:
gene = arguments["gene"][0]
contents = SU.gene_seq(gene, json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
elif path_name == "/geneInfo":
if "gene" in arguments.keys() and len(arguments) == 1:
gene = arguments["gene"][0]
contents = SU.gene_info(gene, json_param=False)
content_type = "text/html"
elif "gene" and "json" in arguments.keys(
) and arguments["json"][0] == "1" and len(arguments) == 2:
gene = arguments["gene"][0]
contents = SU.gene_info(gene, json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
elif path_name == "/geneCalc":
if "gene" in arguments.keys() and len(arguments) == 1:
gene = arguments["gene"][0]
contents = SU.gene_calc(gene, json_param=False)
content_type = "text/html"
elif "gene" and "json" in arguments.keys(
) and arguments["json"][0] == "1" and len(arguments) == 2:
gene = arguments["gene"][0]
contents = SU.gene_calc(gene, json_param=True)
contents = json.dumps(contents)
content_type = "application/json"
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
print(contents)
else:
contents = SU.read_template_html_file(
"./html/Error.html").render()
content_type = "text/html"
except requests.exceptions.HTTPError:
contents = SU.read_template_html_file("./html/Error.html").render()
print(contents)
content_type = "text/html"
except KeyError:
contents = SU.read_template_html_file("./html/Error.html").render()
print(contents)
content_type = "text/html"
# Generating the response message
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', content_type)
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
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"""
# Print the request line
print(self.requestline)
print(self.path)
o = urlparse(self.path) #we create a urlparse object
path_name = o.path #create a path for the object, it will be like self.path but without the question mark
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters:", arguments)
context = {}
if path_name == "/":
contents = su.read_template_html_file("./html/index.html").render(
context=context)
elif path_name == "/geneSeq":
if 'gene_name' in arguments and not 'json' in arguments:
contents = su.gene_sequence(arguments['gene_name'][0], True)
elif 'gene_name' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.gene_sequence(arguments['gene_name'][0],
False)
else:
contents = {
'ERROR':
'json argument must be 1 to return json output'
}
else:
if not 'gene_name' in arguments and not 'json' in arguments:
contents = {'ERROR': 'You must introduce a gene name'}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint'
}
elif path_name == "/geneInfo":
if 'gene_name' in arguments and not 'json' in arguments:
contents = su.gene_info(arguments['gene_name'][0], True)
elif 'gene_name' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.gene_info(arguments['gene_name'][0], False)
else:
contents = {
'ERROR':
"json argument must be 1 to return json output"
}
else:
if not 'gene_name' in arguments and not 'json' in arguments:
contents = {'ERROR': 'You must introduce a gene name'}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint'
}
elif path_name == "/geneCalc":
if 'gene_name' in arguments and not 'json' in arguments:
contents = su.gene_calc(arguments['gene_name'][0], True)
elif 'gene_name' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.gene_calc(arguments['gene_name'][0], False)
else:
contents = {
'ERROR':
"json argument must be 1 to return json output"
}
else:
if not 'gene_name' in arguments and not 'json' in arguments:
contents = {'ERROR': 'You must introduce a gene name'}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint'
}
elif path_name == "/listSpecies":
if 'limit' in arguments and not 'json' in arguments:
contents = su.list_species(arguments['limit'][0], True)
elif 'limit' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.list_species(arguments['limit'][0], False)
else:
contents = {
'ERROR':
'json argument must be 1 to return json output'
}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint (Check you introduced a limit also!'
}
elif path_name == "/karyotype":
if 'species' in arguments and not 'json' in arguments:
contents = su.karyotype_by_specie(arguments['species'][0],
True)
elif 'species' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.karyotype_by_specie(arguments['species'][0],
False)
else:
contents = {
'ERROR':
'json argument must be 1 to return json output'
}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint. Check you have provided the name of a species'
}
elif path_name == "/chromosome_length":
if 'species' in arguments and 'length' in arguments and not 'json' in arguments:
contents = su.chromosome_length(arguments['species'][0],
arguments['length'][0], True)
elif 'species' in arguments and 'length' in arguments and 'json' in arguments:
if arguments['json'][0] == '1':
contents = su.chromosome_length(arguments['species'][0],
arguments['length'][0],
False)
else:
contents = {
'ERROR':
'json argument must be 1 to return json output'
}
else:
if 'species' in arguments and not 'length' in arguments and not 'json' in arguments:
contents = {
'ERROR':
'You missed the number of chromosome you want to check'
}
elif 'length' in arguments and not 'species' in arguments and not 'json' in arguments:
contents = {
'ERROR':
'You missed the name of the species you want to check'
}
elif not 'length' in arguments and not 'species' in arguments and not 'json' in arguments:
contents = {
'ERROR':
'You missed the name of the species and the name of the chromosome you want to check'
}
else:
contents = {
'ERROR':
'endpoint arguments are not correct for this endpoint'
}
else:
contents = su.read_template_html_file("./html/error.html").render()
# Generating the response message
if type(contents) == str:
self.send_response(200)
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())
elif type(contents) == dict:
contents_str = json.dumps(contents)
self.send_response(200)
self.send_header('Content-Type', 'text/json')
self.send_header('Content-Length', len(contents_str.encode()))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents_str.encode())
else:
pass
return