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controller.py
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controller.py
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from flask import Flask, render_template, request
from flask_cors import CORS
from flask_caching import Cache
from sqlalchemy import select, text, insert
from sqlalchemy.orm.scoping import scoped_session
import os
import models
import services
import json
import jsonpickle
import logging
config = {
"DEBUG": True,
"CACHE_TYPE": "SimpleCache",
"CACHE_DEFAULT_TIMEOUT": 300
}
app = Flask(__name__, static_folder='public')
app.config.from_mapping(config)
cache = Cache(app)
CORS(app)
# Start with a hard-coded list of predicates to avoid having to query the evidence_score table for the list.
predicates = ['biolink:entity_negatively_regulates_entity', 'biolink:entity_positively_regulates_entity',
'biolink:gain_of_function_contributes_to', 'biolink:loss_of_function_contributes_to', 'biolink:treats',
'biolink:contributes_to']
@app.route('/')
def index():
return render_template("freetext_search.html", predicates=predicates)
@app.route('/public/', strict_slashes=False)
def public_index():
(subjects, objects) = get_options()
return render_template("mockup.html", subjects=subjects, predicates=predicates, objects=objects)
@app.route('/translator/', strict_slashes=False)
def translator_index():
(subjects_uniprot, objects_uniprot) = get_translated_options()
return render_template("mockup.html", subjects=subjects_uniprot, predicates=predicates, objects=objects_uniprot)
@app.route('/assertion/<aid>', strict_slashes=False)
@app.route('/assertions/<aid>', strict_slashes=False)
@cache.cached(timeout=30)
def assertion_page(aid):
s = Session()
assertion_query_by_id = s.query(models.Assertion).filter(models.Assertion.assertion_id == aid)
if assertion_query_by_id.count() == 0:
return "No results found"
assertion = assertion_query_by_id.one()
current_version_evidence_count = 0
for evidence in assertion.evidence_list:
if 2 in [v.version for v in evidence.version]:
current_version_evidence_count += 1
if current_version_evidence_count == 0:
return "No results found in current version"
return render_template("assertion.html", title="Assertion Display", assertion=assertion_query_by_id.one())
@app.route('/api/assertion/<aid>', strict_slashes=False)
@app.route('/api/assertions/<aid>', strict_slashes=False)
@cache.cached(timeout=30)
def assertion_lookup(aid):
s = Session()
assertion_query_by_id = s.query(models.Assertion).filter(models.Assertion.assertion_id == aid)
if assertion_query_by_id.count() == 0:
return "{}"
one = assertion_query_by_id.one()
one_data = jsonpickle.encode(one, unpicklable=False)
return json.dumps(one_data)
@app.route('/dashboard/', strict_slashes=False)
@app.route('/dashboard/<version>', strict_slashes=False)
@cache.cached(timeout=30)
def dashboard_page(version=2):
logging.info('starting')
pmc, pmid = get_documents_counts(version)
logging.info('got document counts')
assoc = get_association_counts(version)
logging.info(f'got association counts')
asser = get_assertion_counts(version)
logging.info(f'got assertion counts')
return render_template('dashboard.html',
pmc_count=pmc, pmid_count=pmid,
records_dict=assoc, assertions_dict=asser)
@app.route('/evidence/<evidence_id>', strict_slashes=False)
@cache.cached(timeout=30)
def evidence_page(evidence_id):
s = Session()
evidence_query_by_id = s.query(models.Evidence).filter(models.Evidence.evidence_id == evidence_id)
if evidence_query_by_id.count() == 0:
return "No results found"
evidence = evidence_query_by_id.one()
if 2 not in [v.version for v in evidence.version]:
return "No results found in current version"
return render_template("evidence.html", title="Evidence Display", evidence=evidence)
@app.route('/api/evidence/<evidence_id>', strict_slashes=False)
@cache.cached(timeout=30)
def evidence_lookup(evidence_id):
print(evidence_id)
s = Session()
evidence_query_by_id = s.query(models.Evidence).filter(models.Evidence.evidence_id == evidence_id)
if evidence_query_by_id.count() == 0:
return {}
one = evidence_query_by_id.one()
one.document_year_published = one.get_year()
one_data = jsonpickle.encode(one, unpicklable=False)
return one_data
@app.route('/semmed/<semmed_id>', strict_slashes=False)
@cache.cached(timeout=30)
def semmed_lookup(semmed_id):
s = Session()
semmmed_query_by_id = s.query(models.Semmed).filter(models.Semmed.sid == semmed_id)
if semmmed_query_by_id.count() == 0:
return "No results found"
return render_template("semmed.html", title="SemMedDB Display", record=semmmed_query_by_id.one())
@app.route('/semmed/predication/<pred_id>', strict_slashes=False)
@cache.cached(timeout=15)
def predication_lookup(pred_id):
s = Session()
pred_query = s.query(models.Predication).filter(models.Predication.predication_id == pred_id)
if pred_query.count() == 0:
return "No results found"
return render_template("semmed.html", title="SemMedDB Display", record=pred_query.one())
@app.route('/query/', methods=['POST'], strict_slashes=False)
def assertion_query():
s = Session()
if request.is_json:
request_dict = json.loads(request.data)
subject_curie = request_dict['subject']
predicate_curie = request_dict['predicate']
object_curie = request_dict['object']
if subject_curie.lower() == 'any':
if object_curie.lower() == 'any':
assertion_list = s.query(models.Assertion).limit(EDGE_LIMIT)
else:
if object_curie.startswith('UniProtKB'):
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.object_uniprot.has(models.PRtoUniProt.uniprot == object_curie))\
.limit(EDGE_LIMIT)
else:
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.object_curie == object_curie)\
.limit(EDGE_LIMIT)
else:
if object_curie == 'Any':
if subject_curie.startswith('UniProtKB'):
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.subject_uniprot.has(models.PRtoUniProt.uniprot == subject_curie))\
.limit(EDGE_LIMIT)
else:
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.subject_curie == subject_curie)\
.limit(EDGE_LIMIT)
else:
if object_curie.startswith('UniProtKB'):
if subject_curie.startswith('UniProtKB'):
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.object_uniprot.has(models.PRtoUniProt.uniprot == object_curie),
models.Assertion.subject_uniprot.has(models.PRtoUniProt.uniprot == subject_curie))\
.limit(EDGE_LIMIT)
else:
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.object_uniprot.has(models.PRtoUniProt.uniprot == object_curie),
models.Assertion.subject_curie == subject_curie)\
.limit(EDGE_LIMIT)
else:
if subject_curie.startswith('UniProtKB'):
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.object_curie == object_curie,
models.Assertion.subject_uniprot.has(models.PRtoUniProt.uniprot == subject_curie))\
.limit(EDGE_LIMIT)
else:
assertion_list = s.query(models.Assertion)\
.where(models.Assertion.subject_curie == subject_curie,
models.Assertion.object_curie == object_curie)\
.limit(EDGE_LIMIT)
edges = []
for edge in get_edge_list(assertion_list, use_uniprot=(subject_curie.startswith('UniProtKB') or
object_curie.startswith('UniProtKB'))):
if 2 not in edge["version"]:
continue
if edge["predicate_curie"] == predicate_curie or predicate_curie == 'Any':
edges.append(edge)
normalized_nodes = services.get_normalized_nodes([subject_curie, object_curie])
edges.sort(key=lambda x: x['confidence_score'], reverse=True)
results = {
"query": {
"subject_curie": subject_curie,
"subject_text": normalized_nodes[subject_curie] if subject_curie in normalized_nodes else subject_curie,
"predicate_curie": predicate_curie,
"object_curie": object_curie,
"object_text": normalized_nodes[object_curie] if object_curie in normalized_nodes else object_curie,
},
"results": edges
}
return json.dumps(results), 200
return 'something else', 400
@app.route('/evaluations/', methods=['POST'], strict_slashes=False)
def add_evaluation():
s = Session()
if not request.is_json:
return 'nope', 400
request_dict = json.loads(request.data)
insert_statement = insert(models.Evaluation).values(
evidence_id=request_dict['evidence_id'],
overall_correct=request_dict['overall_correct'],
subject_correct=request_dict['subject_correct'],
object_correct=request_dict['object_correct'],
predicate_correct=request_dict['predicate_correct'],
comments=request_dict['comments'] if 'comments' in request_dict else None,
source_id=TMUI_ID
)
s.execute(insert_statement)
s.commit()
return {}, 201
@app.route('/api/evidence/feedback/', methods=['POST'], strict_slashes=False)
def add_evidence_feedback():
s = Session()
if not request.is_json:
return 'nope', 400
request_dict = json.loads(request.data)
if 'evidence_id' not in request_dict:
return 'no evidence id', 400
feedback_insert = insert(models.EvidenceFeedback).values(
evidence_id=request_dict['evidence_id'],
source_id = TMUI_ID,
comments=request_dict['comments'] if 'comments' in request_dict else None
)
result = s.execute(feedback_insert)
vals = []
for q, a in request_dict.items():
if q == 'evidence_id' or q == 'comments':
continue
vals.append({
'feedback_id': result.inserted_primary_key[0],
'prompt_text': q,
'response': a
})
s.execute(insert(models.EvidenceFeedbackAnswer), vals,)
s.commit()
return {}, 201
@app.route('/api/semmed/feedback/', methods=['POST'], strict_slashes=False)
def add_semmed_feedback():
s = Session()
if not request.is_json:
return 'nope', 400
request_dict = json.loads(request.data)
if 'predication_id' not in request_dict:
return 'no predication id', 400
feedback_insert = insert(models.PredicationFeedback).values(
predication_id=request_dict['predication_id'],
source_id = TMUI_ID,
comments=request_dict['comments'] if 'comments' in request_dict else None
)
result = s.execute(feedback_insert)
vals = []
for q, a in request_dict.items():
if q == 'predication_id' or q == 'comments':
continue
vals.append({
'feedback_id': result.inserted_primary_key[0],
'prompt_text': q,
'response': a
})
s.execute(insert(models.PredicationFeedbackAnswer), vals,)
s.commit()
return {}, 201
@app.route('/api/curies/subject/', strict_slashes=False)
@cache.cached(timeout=600)
def get_available_subject_curies():
s = Session()
query = select(text('DISTINCT subject_curie FROM assertion'))
results = [curie for curie, in s.execute(query)]
namespaces = set([curie.split(':')[0] for curie in results])
results.sort()
return json.dumps({
'curies': results,
'namespaces': list(namespaces)
})
@app.route('/api/curies/object/', strict_slashes=False)
@cache.cached(timeout=600)
def get_available_object_curies():
s = Session()
query = select(text('DISTINCT object_curie FROM assertion'))
results = [curie for curie, in s.execute(query)]
namespaces = set([curie.split(':')[0] for curie in results])
results.sort()
return json.dumps({
'curies': results,
'namespaces': list(namespaces)
})
@app.route('/loaderio-e04f94bd56a03c22415e96cd33e5ee90/')
def verification():
return 'loaderio-e04f94bd56a03c22415e96cd33e5ee90', 200
def get_edge_list(assertions, use_uniprot=False):
edge_list = []
for assertion in assertions:
sub = assertion.subject_curie
obj = assertion.object_curie
if use_uniprot:
if assertion.subject_uniprot:
sub = assertion.subject_uniprot.uniprot
if assertion.object_uniprot:
obj = assertion.object_uniprot.uniprot
# these are the predicates that have the high score for at least one evidence
predicate_list = assertion.get_predicates()
for predicate in predicate_list:
for ev in assertion.evidence_list:
if ev.get_top_predicate() == predicate:
edge_list.append({
"assertion_id": ev.assertion_id,
"evidence_id": ev.evidence_id,
"document_pmid": ev.document_id,
"document_zone": ev.document_zone,
"document_year": ev.document_year_published,
"predicate_curie": predicate,
"confidence_score": ev.get_score(predicate),
"sentence": ev.sentence,
"subject_span": ev.subject_entity.span if ev.subject_entity else "0|0",
"object_span": ev.object_entity.span if ev.object_entity else "0|0",
"subject_curie": sub,
"object_curie": obj,
"version": [v.version for v in ev.version]
})
return edge_list
def get_predicates() -> list:
s = Session()
return [predicate for predicate, in s.execute(select(text('DISTINCT predicate_curie FROM evidence_score')))]
def get_options() -> (list, list):
s = Session()
subject_curies = [sub[0] for sub in s.query(models.Assertion.subject_curie).distinct()]
object_curies = [obj[0] for obj in s.query(models.Assertion.object_curie).distinct()]
list_to_normalize = []
subjects = []
objects = []
list_to_normalize.extend(subject_curies)
list_to_normalize.extend(object_curies)
normalized_nodes = services.get_normalized_nodes(list_to_normalize)
for subject in subject_curies:
if subject in normalized_nodes and normalized_nodes[subject] is not None:
subjects.append((
subject,
normalized_nodes[subject]['id']['label'] if 'label' in normalized_nodes[subject]['id'] else subject))
else:
subjects.append((subject, subject))
for obj in object_curies:
if obj in normalized_nodes and normalized_nodes[obj] is not None:
objects.append((
obj,
normalized_nodes[obj]['id']['label'] if 'label' in normalized_nodes[obj]['id'] else obj))
else:
objects.append((obj, obj))
subjects.sort(key=lambda x: x[1].upper())
objects.sort(key=lambda x: x[1].upper())
return subjects, objects
def get_translated_options() -> (list, list):
s = Session()
subject_subquery = s.query(models.Assertion.subject_curie.distinct())
object_subquery = s.query(models.Assertion.object_curie.distinct())
subject_curies = [sub[0] for sub in s.query(models.PRtoUniProt.uniprot.distinct()).filter(models.PRtoUniProt.pr.in_(subject_subquery))]
object_curies = [obj[0] for obj in s.query(models.PRtoUniProt.uniprot.distinct()).filter(models.PRtoUniProt.pr.in_(object_subquery))]
subject_curies.extend(sub[0] for sub in s.query(models.Assertion.subject_curie.distinct()).filter(models.Assertion.subject_curie.notilike('PR'), models.Assertion.subject_curie.notilike('UniProt')))
subject_curies.extend(sub[0] for sub in s.query(models.Assertion.object_curie.distinct()).filter(models.Assertion.object_curie.notilike('PR'), models.Assertion.object_curie.notilike('UniProt')))
list_to_normalize = []
subjects = []
objects = []
list_to_normalize.extend(subject_curies)
list_to_normalize.extend(object_curies)
normalized_nodes = services.get_normalized_nodes(list_to_normalize)
for subject in subject_curies:
if subject in normalized_nodes and normalized_nodes[subject] is not None:
subjects.append((subject, normalized_nodes[subject]['id']['label'] if 'label' in normalized_nodes[subject]['id'] else subject))
else:
subjects.append((subject, subject))
for obj in object_curies:
if obj in normalized_nodes and normalized_nodes[obj] is not None:
objects.append((obj, normalized_nodes[obj]['id']['label'] if 'label' in normalized_nodes[obj]['id'] else obj))
else:
objects.append((obj, obj))
subjects.sort(key=lambda x: x[1].upper())
objects.sort(key=lambda x: x[1].upper())
return subjects, objects
def get_documents_counts(version=1) -> tuple[int, int]:
pmc_query = text("SELECT document_type, count FROM document_counts WHERE version = :v")
s = Session()
logging.info('starting query')
pmc_count = 0
pmid_count = 0
for row in s.execute(pmc_query, {'v': version}):
if row['document_type'] == 'PMC':
pmc_count = row['count']
elif row['document_type'] == 'PMID':
pmid_count = row['count']
logging.info('data retrieved')
return pmc_count, pmid_count
def get_association_counts(version=1) -> dict[str, dict[str, int]]:
association_query = text("SELECT association_curie, predicate_curie, count FROM evidence_counts WHERE version = :v")
s = Session()
association_count_dict = {}
for row in s.execute(association_query, {'v': version}):
key = row['association_curie']
if key in association_count_dict:
association_count_dict[key][row['predicate_curie']] = row['count']
else:
association_count_dict[key] = {row['predicate_curie']: row['count']}
return association_count_dict
def get_assertion_counts(version=1) -> dict[str, int]:
assertion_count_query = text("SELECT association_curie, count FROM assertion_counts WHERE version = :v")
s = Session()
assertion_count_dict = {}
for row in s.execute(assertion_count_query, {'v': version}):
key = row['association_curie']
value = row['count']
assertion_count_dict[key] = value
return assertion_count_dict
@app.teardown_appcontext
def shutdown_session(response_or_exc):
Session.remove()
username = os.getenv('MYSQL_DATABASE_USER', None)
secret_password = os.getenv('MYSQL_DATABASE_PASSWORD', None)
EDGE_LIMIT = int(os.getenv('EDGE_LIMIT', '500'))
TMUI_ID = 0
assert username
assert secret_password
models.init_db(username=username, password=secret_password)
Session = scoped_session(models.Session)
logging.basicConfig(format='%(asctime)s %(module)s:%(funcName)s:%(levelname)s: %(message)s', level=logging.INFO)
logging.info('Starting Main')
if __name__ == "__main__":
app.run(debug=True, host="0.0.0.0", port=int(os.environ.get("PORT", 8080)))