def do_GET(
self
): # This method is called when the client invokes the GETmethod in the HTT Protocol request
response_code = 200 # Indicates what happened with the request
json_response = False # Response only in HTML at the moment
if self.path == "/":
with open("index.html", "r") as f:
contents = f.read()
f.close()
elif "listSpecies" in self.path:
dicc = self.dictionary_split(self.path)
limit = 0
if 'limit' in dicc:
try:
limit = int(dicc['limit'])
except:
limit = 0
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request("GET", "/info/species?content-type=application/json")
r1 = conn.getresponse() # Get the response
text_json = r1.read().decode(
"utf-8"
) # Decode the response in utf-8 format (admit all characters in the response)
response = json.loads(text_json)
print(response)
species = response['species']
if 'json' in dicc and dicc['json'] == '1':
json_response = True
if limit == 0:
limit = len(species)
final_list = species[
1:
limit] # List from the first specie until the one that corresponds to the limit
contents = json.dumps(
final_list
) # json.dumps is for transforming final_list into JSON (JSON response)
else:
if limit == 0:
limit = len(species)
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Species in genome database</title>
</head>
<body style ="background-color: lightgrey;">
<h3>List with the species available in the database:</h3>
<ol> """
# List with the name of all species
cont = 0
for specie in species:
cont = cont + 1
if cont <= limit: # The loop will not concatenate more species when it reaches the limit
contents = contents + "<li>" + specie[
'display_name'] + "</li>"
contents = contents + """<ol>
<body>
<html>
"""
conn.close()
elif "karyotype" in self.path:
dicc = self.dictionary_split(self.path)
if 'specie' in dicc and dicc['specie'] != '':
specie = dicc['specie']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/info/assembly/" + specie +
"?content-type=application/json")
r1 = conn.getresponse() # Get the response
text_json = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
text_json
) # Transform JSON into a Python value (to read JSON response)
# Enter in the karyotype key
if 'karyotype' in response:
list_chromo = response['karyotype'] # List with all genes
if 'json' in dicc and dicc['json'] == '1':
json_response = True
contents = json.dumps(
list_chromo
) # Transform list_chromo into JSON (JSON response)
else:
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Information karyotype</title>
</head>
<body style ="background-color: lightblue;">
<h2>Information about the karyotype of the chosen specie:</h2>
<ul> """
for chromo in list_chromo:
new_chromo = "<li>" + chromo + "</li>"
contents = contents + new_chromo # List with elements from list_chromo
contents += """</ul>
</body>
</html>
"""
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
elif "chromosomeLength" in self.path:
dicc = self.dictionary_split(self.path)
if 'chromo' in dicc and 'specie' in dicc and dicc[
'chromo'] != '' and dicc['specie'] != '':
chromo1 = dicc['chromo']
specie = dicc['specie']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/info/assembly/" + specie +
"?content-type=application/json")
r1 = conn.getresponse() # Get the response
text_json = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
text_json
) # Transform JSON into a Python value (to read JSON response)
# Enter into the key top_level_region to obtain the length of the chromosome
info = response[
'top_level_region'] # List to save all the chromosomes
if 'json' in dicc and dicc['json'] == '1':
json_response = True
long = 0
for element in info:
if element['name'] == chromo1:
long = element['length']
dic = dict()
dic['len'] = long
contents = json.dumps(
dic) # Transform dic into JSON (JSON response)
else:
long = 0
for element in info:
if element['name'] == chromo1:
long = element['length']
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Length of the chromosome</title>
</head>
<body style ="background-color: lightyellow;">
<h3>The length of the chromosome is:</h3>
<ul> """
contents = contents + "<li>" + str(long) + "</li>"
contents = contents + """</ul>
</body>
</html>"""
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
elif "geneSeq" in self.path:
dicc = self.dictionary_split(self.path)
if 'gene' in dicc and dicc['gene'] != '':
gene = dicc['gene']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/homology/symbol/human/" + gene +
"?content-type=application/json")
r1 = conn.getresponse() # Get the response
raw_data = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
raw_data
) # Transform JSON into a Python value (to read JSON response)
try:
id = response['data'][0]['id'] # Get the id of the data
url = "/sequence/id/" + id + "?content-type=application/json"
conn.request("GET", url)
r1 = conn.getresponse()
text_json = r1.read().decode("utf-8")
response = json.loads(text_json)
cadena = response['seq']
if 'json' in dicc and dicc['json'] == '1':
json_response = True
dic = dict()
dic['seq'] = cadena
contents = json.dumps(
dic) # Transform dic into JSON (JSON response)
else:
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Sequence of the gene</title>
</head>
<body style ="background-color: lightgreen;">
<font face="garamond" color = "black"</font>
<h2>This is the sequence of the human gene requested:</h2>
<ul> """
contents += "<ul>"
contents += cadena + "<ul>"
contents += """</ul>
</body>
</html>"""
except KeyError:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
elif "geneList" in self.path:
dicc = self.dictionary_split(self.path)
if 'start' in dicc and 'chromo' in dicc and 'end' in dicc and dicc[
'start'] != '' and dicc['chromo'] != '' and dicc[
'end'] != '':
start = dicc['start']
chromo = dicc['chromo']
end = dicc['end']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/overlap/region/human/" + str(chromo) + ":" +
str(start) + "-" + str(end) +
"?content-type=application/json;feature=gene")
r1 = conn.getresponse() # Get the response
data1 = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
data1
) # Transform JSON into a Python value (to read JSON response)
if 'error' in response:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
else:
if 'json' in dicc and dicc['json'] == '1':
json_response = True
lista = []
for item in response:
dic = dict()
dic['external_name'] = item['external_name']
dic['start'] = str(item['start'])
dic['end'] = str(item['end'])
lista.append(
dic) # Create a list with those elements
contents = json.dumps(
lista
) # Transform lista into JSON (JSON response) (to read JSON response)
else:
print(response)
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Gene information</title>
</head>
<body style ="background-color: lightgrey;">
<font face="garamond" color = "black"</font>
<h2>Name, start and end of the genes located in the desired chromosome:</h2>
<ul> """
for item in response:
contents = contents + "<li>" + item[
'external_name'] + " Start: " + str(
item['start']) + " End: " + str(
item['end']) + "</li>"
contents = contents + """</ul>
</body>
</html>"""
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
elif "geneInfo" in self.path:
dicc = self.dictionary_split(self.path)
if 'gene' in dicc and dicc['gene'] != '':
gene = dicc['gene']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/homology/symbol/human/" + gene +
"?content-type=application/json")
r1 = conn.getresponse() # Get the response
raw_data = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
raw_data
) # Transform JSON into a Python value (to read JSON response)
try:
id = response['data'][0]['id'] # Get the id of the data
conn.request(
"GET", "/overlap/id/" + id +
"?feature=gene;content-type=application/json")
r1 = conn.getresponse()
raw_data = r1.read().decode("utf-8")
response = json.loads(raw_data)
start = response[0]['start']
end = response[0]['end']
id = response[0]['id']
lenght = end - start
chromo = response[0]['assembly_name']
if 'json' in dicc and dicc['json'] == '1':
json_response = True
dic = dict()
dic['id'] = id
dic['start'] = start
dic['end'] = end
dic['lenght'] = lenght
contents = json.dumps(dic)
else:
# HTML response
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Human gene information</title>
</head>
<body style ="background-color: lightyellow;">
<font face="garamond" size = 5 color = "black"</font>
<h3>Information about the human gene requested:</h3>
<ul> """
contents = contents + "<h4>Id: <h4>" "<li>" + id + "</li>"
contents = contents + "<h4>Start: <h4>" "<li>" + str(
start) + "</li>"
contents = contents + "<h4>End: <h4>" "<li>" + str(
end) + "</li>"
contents = contents + "<h4>Length: <h4>" "<li>" + str(
lenght) + "</li>"
contents = contents + "<h4>Chromosome: <h4>" "<li>" + chromo + "</li>"
contents = contents + """</ul>
</body>
</html>"""
except KeyError:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
else:
response_code = 404
f = open('error.html', 'r')
contents = f.read()
f.close()
elif "geneCalc" in self.path:
dicc = self.dictionary_split(self.path)
if 'gene' in dicc and dicc['gene'] != '':
gene = dicc['gene']
conn = http.client.HTTPConnection(
'rest.ensembl.org') # Connection with Enssembl
conn.request(
"GET", "/homology/symbol/human/" + gene +
"?content-type=application/json")
r1 = conn.getresponse() # Get the response
raw_data = r1.read().decode(
"utf-8") # Decode the response in utf-8 format
response = json.loads(
raw_data
) # Transform JSON into a Python value (to read JSON response)
try:
id = response['data'][0]['id'] # Get the id of the data
conn.request(
"GET", "/sequence/id/" + id +
"?content-type=application/json")
r1 = conn.getresponse()
text_json = r1.read().decode("utf-8")
response = json.loads(text_json)
cadena = response['seq']
s1 = Seq(cadena)
total = len(cadena)
percA = s1.perc('A')
percT = s1.perc('T')
percG = s1.perc('G')
percC = s1.perc('C')
if 'json' in dicc and dicc['json'] == '1':
json_response = True
dic = dict()
dic['lenght'] = total
dic['percA'] = percA
dic['percT'] = percT
dic['percG'] = percG
dic['percC'] = percC
contents = json.dumps(dic)
else:
# HTML contents
contents = """
<html>
<head>
<meta charset="utf-8">
<title>Calculations</title>
</head>
<body style ="background-color: lightgreen;">
<font face="garamond" size = 5 color = "black"</font>
<h2>Calculations about the human gene:</h2>
<ul> """
contents = contents + "<h3>Lenght: <h4>" "<li>" + str(
total) + "</li>"
contents = contents + "<h4>Percentage of A: <h4>" "<li>" + str(
percA) + "</li>"
contents = contents + "<h4>Percenatge of T: <h4>" "<li>" + str(
percT) + "</li>"
contents = contents + "<h4>Percenatge of G: <h4>" "<li>" + str(
percG) + "</li>"
contents = contents + "<h4>Percenatge of C: <h4>" "<li>" + str(
percC) + "</li>"
contents = contents + """</ul>
</body>
</html>"""
except KeyError:
response_code = 404
with open("error.html", "r") as f:
contents = f.read()
else:
response_code = 400
with open("error.html", "r") as f:
contents = f.read()
else:
response_code = 404
with open("error.html", "r") as f:
contents = f.read()
# -- Generating the response message
self.send_response(response_code)
if (json_response == True): # Define the content-type header
self.send_header('Content-Type', 'application/json')
else:
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', len(str.encode(contents)))
# -- The header is finished
self.end_headers()
# -- Send the response message
self.wfile.write(str.encode(contents))
return
