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lambda.py
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lambda.py
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from __future__ import print_function
from Bio import Entrez
import xmltodict
import json
import os
import re
import collections
os.environ["HOME"] = "/tmp"
def mock_handler(event, context):
return {
"statusCode": "200",
"body": "mockReply"
}
def build_speechlet_response(title, output, reprompt_text, should_end_session):
return {
'outputSpeech': {
'type': 'PlainText',
'text': output
},
'card': {
'type': 'Simple',
'title': "SessionSpeechlet - " + title,
'content': "SessionSpeechlet - " + output
},
'reprompt': {
'outputSpeech': {
'type': 'PlainText',
'text': reprompt_text
}
},
'shouldEndSession': should_end_session
}
def build_response(session_attributes, speechlet_response):
return {
'version': '1.0',
'sessionAttributes': session_attributes,
'response': speechlet_response
}
# --------------- Functions that control the skill's behavior ------------------
def get_welcome_response():
""" If we wanted to initialize the session to have some attributes we could
add those here
"""
session_attributes = {}
card_title = "Welcome"
speech_output = "Welcome to the genome wizard by Dark Photon IT consultation for the stars, " \
" I can currently give you a summary of gene function , the location of a gene relative to our chromosomes, and the protein translations of just about any sequenced gene in the human genome , " \
" I know about a lot of genes, here is how to learn from me ," \
" You can say things like , " \
" lookup the gene labelled B R C A 2 , " \
" or, what is the location of T P 5 3 , " \
" or finally , what are the protein translations for G Y F R, " \
" Remember , you can use any official gene symbol in the human genome, which is well over 20 thousand genes available , " \
" When reciting the gene symbol , it is best to spell it out letter by letter , " \
" Finally , have fun. "
# If the user either does not reply to the welcome message or says something
# that is not understood, they will be prompted again with this text.
reprompt_text = "Please tell me what gene youre looking for by saying for example, " \
"tell me about the gene B R C A 2"
should_end_session = False
return build_response(session_attributes, build_speechlet_response(
card_title, speech_output, reprompt_text, should_end_session))
def handle_session_end_request():
card_title = "Session Ended"
speech_output = "Thank you for trying the g nome Alexa Skill. " \
"Have a nice day! "
# Setting this to true ends the session and exits the skill.
should_end_session = True
return build_response({}, build_speechlet_response(
card_title, speech_output, None, should_end_session))
def create_gene_label_attribute(gene_label):
return {"geneLabel": gene_label}
def set_gene_label_in_session(intent, session):
""" Sets the gene in the session and prepares the speech to reply to the
user.
"""
card_title = intent['name']
session_attributes = {}
should_end_session = False
if 'Gene' in intent['slots']:
geneLabel = intent['slots']['Gene']['value']
session_attributes = create_gene_label_attribute(geneLabel)
speech_output = "I now know your selected gene is " + \
geneLabel + \
". You can ask me your selected gene by saying, " \
"what's my selected gene?"
reprompt_text = ". You can ask me your selected gene by saying, " \
"what's my selected gene??"
else:
speech_output = "I'm not sure what your selected gene is. " \
"Please try again."
reprompt_text = "I'm not sure what your selected gene is. " \
"You can tell me your selected gene by saying, " \
"my selected gene is B R C A 2"
return build_response(session_attributes, build_speechlet_response(
card_title, speech_output, reprompt_text, should_end_session))
def prettify_gene_summary(gene_summary):
result = re.sub('[\[\(].*[\]\)]', '',gene_summary)
return result
def prettify_gene_location(gene_label, location):
if bool(re.match(r"(\d+)(\w{1})(.+)", location)):
rgx = re.compile('(\d+)(\w{1})(.+)')
matches = rgx.match(location)
prettyLoc = "{} is found on the {} arm of chromosome {} at position {}".format(gene_label, matches.group(2), matches.group(1), matches.group(3))
return prettyLoc
else:
prettyLoc = "{} is not on a chromosome but actually at {}".format(gene_label, location)
return prettyLoc
def get_gene_label_from_session(intent, session):
session_attributes = {}
reprompt_text = None
if session.get('attributes', {}) and "geneLabel" in session.get('attributes', {}):
selected_gene = session['attributes']['geneLabel']
speech_output = "Your selected gene is " + selected_gene + \
". Goodbye."
should_end_session = True
else:
speech_output = "I'm not sure what your selected gene is, " \
"You can say, my selected gene is B.R.C.A.2."
should_end_session = False
# Setting reprompt_text to None signifies that we do not want to reprompt
# the user. If the user does not respond or says something that is not
# understood, the session will end.
return build_response(session_attributes, build_speechlet_response(
intent['name'], speech_output, reprompt_text, should_end_session))
def gene_encodes_proteins(library):
if "Entrezgene_type" in library["Entrezgene-Set"]["Entrezgene"]:
geneType = library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_type"].items()[0][1]
proteinCount = library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_type"].items()[1][1]
if geneType == 'protein-coding' and proteinCount > 0:
return True
else:
return False
def get_proteins_encoded_by_gene(library):
proteins = list()
if gene_encodes_proteins(library):
geneType = library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_type"].items()[0][1]
proteinCount = library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_type"].items()[1][1]
if "Entrezgene_prot" in library["Entrezgene-Set"]["Entrezgene"]:
if "Prot-ref" in library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_prot"]:
if "Prot-ref_name" in library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_prot"]["Prot-ref"]:
for k in library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_prot"]["Prot-ref"]["Prot-ref_name"].keys():
proteins.extend(library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_prot"]["Prot-ref"]["Prot-ref_name"][k])
return geneType, proteinCount, proteins
def prettify_protein_list(gene_label,proteins,protein_count):
speech_output = str()
protein_count = int(protein_count)
speech_output += "{} translates for {} proteins , here is a list of those proteins , ".format(gene_label, protein_count)
cnt = 0
for protein in proteins:
cnt += 1
if (cnt-1) < protein_count:
speech_output += " {} ,".format(protein)
else:
speech_output += " and finally {} .".format(protein)
return speech_output
def query_entrez_proteins(gene_label):
session_attributes = {"geneLabel": gene_label}
card_title = "ProteinsTranslatedFor"
print("Setting OS Environ Values")
Entrez.email = os.environ.get("ENTREZ_EMAIL")
Entrez.api_key = os.environ.get("ENTREZ_API_KEY")
print("Gathering records for Homo Sapiens {} gene".format(gene_label))
handle = Entrez.esearch(db="gene", term="(\"Homo Sapiens\"[orgn]) AND \"%s\"[Gene]"%(gene_label)) #pass in query terms to search.
record = Entrez.read(handle)
if int(record['Count']) == 0:
print("Query Returned No Results, Try spelling out the official HGNC gene symbol")
speech_output = "Query Returned No Results, Try spelling out the official HGNC gene symbol as your search string. Visit www.genenames.org and search by keyword or symbol for references."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) == 1:
print("Query was successful, here are the results.")
handle = Entrez.efetch(db="gene", id=record['IdList'][0], retmode="xml")
library = xmltodict.parse(handle)
handle.close()
#tmploc = str(library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_location"]["Maps"]["Maps_display-str"])
if gene_encodes_proteins(library):
geneType, proteinCount, proteinList = get_proteins_encoded_by_gene(library)
speech_output = prettify_protein_list(gene_label , proteinList, proteinCount)
else:
speech_output = "This gene does not translate to any proteins."
#speech_output = str(library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_location"]["Maps"]["Maps_display-str"])
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) > 1:
print("Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about.")
speech_output = "Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
def query_entrez_location(gene_label):
session_attributes = {"geneLabel": gene_label}
card_title = "LocateGene"
print("Setting OS Environ Values")
Entrez.email = os.environ.get("ENTREZ_EMAIL")
Entrez.api_key = os.environ.get("ENTREZ_API_KEY")
print("Gathering records for Homo Sapiens BRCA2 gene")
handle = Entrez.esearch(db="gene", term="(\"Homo Sapiens\"[orgn]) AND \"%s\"[Gene]"%(gene_label)) #pass in query terms to search.
record = Entrez.read(handle)
if int(record['Count']) == 0:
print("Query Returned No Results, Try spelling out the official HGNC gene symbol")
speech_output = "Query Returned No Results, Try spelling out the official HGNC gene symbol as your search string. Visit www.genenames.org and search by keyword or symbol for references."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) == 1:
print("Query was successful, here are the results.")
handle = Entrez.efetch(db="gene", id=record['IdList'][0], retmode="xml")
library = xmltodict.parse(handle)
handle.close()
tmploc = str(library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_location"]["Maps"]["Maps_display-str"])
speech_output = prettify_gene_location(gene_label, tmploc)
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) > 1:
print("Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about.")
speech_output = "Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
def query_entrez_summary(gene_label):
session_attributes = {"geneLabel": gene_label}
card_title = "DescribeGene"
print("Setting OS Environ Values")
Entrez.email = os.environ.get("ENTREZ_EMAIL")
Entrez.api_key = os.environ.get("ENTREZ_API_KEY")
print("Gathering records for the HomoSapiens {} gene".format(gene_label))
handle = Entrez.esearch(db="gene", term="(\"Homo Sapiens\"[orgn]) AND \"%s\"[Gene]"%(gene_label)) #pass in query terms to search.
record = Entrez.read(handle)
if int(record['Count']) == 0:
print("Query Returned No Results, Try spelling out the official HGNC gene symbol")
speech_output = "Query Returned No Results, Try spelling out the official HGNC gene symbol as your search string. Visit www.genenames.org and search by keyword or symbol for references."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) == 1:
print("Query was successful, here are the results.")
handle = Entrez.efetch(db="gene", id=record['IdList'][0], retmode="xml")
library = xmltodict.parse(handle)
handle.close()
speech_output = prettify_gene_summary(library["Entrezgene-Set"]["Entrezgene"]["Entrezgene_summary"])
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
elif int(record['Count']) > 1:
print("Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about.")
speech_output = "Query Returned Multiple Results, Try spelling out the gene symbol as officially defined by HGNC, or be more specific about which gene you would like to know about."
reprompt_text = None
should_end_session = False
print(build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session)))
return build_response(session_attributes, build_speechlet_response(card_title, speech_output, reprompt_text, should_end_session))
# --------------- Events ------------------
def on_session_started(session_started_request, session):
""" Called when the session starts """
print("on_session_started requestId=" + session_started_request['requestId']
+ ", sessionId=" + session['sessionId'])
def on_launch(launch_request, session):
""" Called when the user launches the skill without specifying what they
want
"""
print("on_launch requestId=" + launch_request['requestId'] +
", sessionId=" + session['sessionId'])
# Dispatch to your skill's launch
return get_welcome_response()
def on_intent(intent_request, session):
""" Called when the user specifies an intent for this skill """
print("on_intent requestId=" + intent_request['requestId'] +
", sessionId=" + session['sessionId'], ", intentName=" + intent_request['intent']['name'])
intent = intent_request['intent']
intent_name = intent_request['intent']['name']
#print("Gene Selected: %s"%(intent['slots']['Gene']['value']))
# Dispatch to your skill's intent handlers
if intent_name == "DescribeGene":
return query_entrez_summary(str(intent['slots']['Gene']['value']))
elif intent_name == "LocateGene":
return query_entrez_location(str(intent['slots']['Gene']['value']))
elif intent_name == "ProteinsTranslatedFor":
return query_entrez_proteins(str(intent['slots']['Gene']['value']))
elif intent_name == "AMAZON.HelpIntent":
return get_welcome_response()
elif intent_name == "AMAZON.CancelIntent" or intent_name == "AMAZON.StopIntent":
return handle_session_end_request()
else:
raise ValueError("Invalid intent")
def on_session_ended(session_ended_request, session):
""" Called when the user ends the session.
Is not called when the skill returns should_end_session=true
"""
print("on_session_ended requestId=" + session_ended_request['requestId'] +
", sessionId=" + session['sessionId'])
# add cleanup logic here
# --------------- Main handler ------------------
def lambda_handler(event, context):
#print(event.keys())
if event['session']['new']:
on_session_started({'requestId': event['request']['requestId']},event['session'])
if event['request']['type'] == "LaunchRequest":
return on_launch(event['request'], event['session'])
elif event['request']['type'] == "IntentRequest":
return on_intent(event['request'], event['session'])
elif event['request']['type'] == "SessionEndedRequest":
return on_session_ended(event['request'], event['session'])