From 276f374f817cc0c16d2065ccada11aaf00f503d2 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Tue, 6 Dec 2022 19:41:48 +0100
Subject: [PATCH] updated backend to convert compact notation; fixed issue that
only mapped main symbol nodes
Former-commit-id: b14c40ee04e4fb7100ebb049ec65c7da701e5b8b
---
drugstone/urls.py | 3 +-
drugstone/util/query_db.py | 72 ++++++++++++++++++++++++++++++++++++++
drugstone/views.py | 11 ++++--
3 files changed, 83 insertions(+), 3 deletions(-)
diff --git a/drugstone/urls.py b/drugstone/urls.py
index 7e0d16a..680f18b 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -19,12 +19,13 @@ from django.urls import path
from drugstone.views import map_nodes, tasks_view, result_view, \
graph_export, TissueView, TissueExpressionView, query_tissue_proteins, TaskView, \
adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network, get_license, get_datasets, \
- get_max_tissue_expression
+ get_max_tissue_expression, convert_compact_ids
# cache time is 6 hours
urlpatterns = [
path('get_datasets/', get_datasets),
path('map_nodes/', map_nodes),
+ path('convert_compact_node_list/', convert_compact_ids),
path('fetch_edges/', fetch_edges),
path('task/', TaskView.as_view()),
path('tasks/', tasks_view),
diff --git a/drugstone/util/query_db.py b/drugstone/util/query_db.py
index 39171f5..33584fe 100644
--- a/drugstone/util/query_db.py
+++ b/drugstone/util/query_db.py
@@ -64,6 +64,78 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
return nodes, protein_attribute
+def get_protein_ids(id_space, proteins):
+ if (id_space == 'uniprot'):
+ return [p['uniprot_ac'] for p in proteins]
+ if (id_space == 'ensg'):
+ return [p['ensg'] for p in proteins]
+ if (id_space == 'symbol'):
+ return [p['symbol'] for p in proteins]
+ if (id_space == 'entrez'):
+ return [p['entrez'] for p in proteins]
+ return set()
+
+
+def clean_proteins_from_compact_notation(node_ids: Set[str], identifier: str) -> List[str]:
+ """Queries the django database Protein table given a list of identifiers (node_ids) and a identifier name
+ (identifier).
+ The identifier name represents any protein attribute, e.g. uniprot or symbol.
+ The identifier names vary from the Protein table names since they are the strings which are set by the user
+ in the frontend, for readability they were changes from the original backend attributes.
+
+ Args:
+ node_ids (list): List of protein or gene identifiers. Note: Do not mix identifiers.
+ identifier (str): Can be one of "symbol", "ensg", "uniprot"
+
+ Returns:
+ Tuple[List[dict], str]:
+ Returns list of serialized protein entries for all matched IDs
+ Returns name of backend attribute of Protein table
+ """
+ # query protein table
+ if len(node_ids) == 0:
+ return list()
+ id_map = {
+ 'symbol:': set(),
+ 'uniprot:': set(),
+ 'ensg:': set(),
+ 'entrez:': set()
+ }
+ clean_ids = set()
+ for node_id in node_ids:
+ added = False
+ for id_space in id_map.keys():
+ if node_id.startswith(id_space):
+ id_map[id_space].add(node_id[len(id_space):].upper())
+ added = True
+ break
+ if not added:
+ clean_ids.add(node_id)
+
+ for id_space, ids in id_map.items():
+ if len(ids) == 0:
+ continue
+ if id_space == 'symbol:':
+ q_list = map(lambda n: Q(gene__iexact=n), ids)
+ elif id_space == 'uniprot:':
+ q_list = map(lambda n: Q(uniprot_code__iexact=n), ids)
+ elif id_space == 'ensg:':
+ ensembls = EnsemblGene.objects.filter(reduce(lambda a, b: a | b, map(lambda n: Q(name__iexact=n), ids)))
+ if len(ensembls) == 0:
+ continue
+ dr_ids = map(lambda n: n.protein_id, ensembls)
+ q_list = map(lambda n: Q(id=n), dr_ids)
+ elif id_space == 'entrez:':
+ q_list = map(lambda n: Q(entrez=n), ids)
+ else:
+ continue
+ q_list = reduce(lambda a, b: a | b, q_list)
+ proteins = ProteinSerializer(many=True).to_representation(Protein.objects.filter(q_list))
+ clean_ids = clean_ids.union(get_protein_ids(identifier, proteins))
+
+ return list(clean_ids)
+
+
def aggregate_nodes(nodes: List[OrderedDict]):
node = defaultdict(set)
for n in nodes:
diff --git a/drugstone/views.py b/drugstone/views.py
index d116d11..8195873 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -15,7 +15,7 @@ from django.db import IntegrityError
from rest_framework.decorators import api_view
from rest_framework.response import Response
from rest_framework.views import APIView
-from drugstone.util.query_db import query_proteins_by_identifier
+from drugstone.util.query_db import query_proteins_by_identifier, clean_proteins_from_compact_notation
from drugstone.models import *
from drugstone.serializers import *
@@ -143,6 +143,12 @@ def fetch_edges(request) -> Response:
return Response(ProteinProteinInteractionSerializer(many=True).to_representation(interaction_objects))
+@api_view(['POST'])
+def convert_compact_ids(request) -> Response:
+ nodes = request.data.get('nodes', '[]')
+ identifier = request.data.get('identifier', '')
+ cleaned = clean_proteins_from_compact_notation(nodes, identifier)
+ return Response(cleaned)
@api_view(['POST'])
def map_nodes(request) -> Response:
@@ -175,7 +181,8 @@ def map_nodes(request) -> Response:
nodes_mapped, id_key = query_proteins_by_identifier(node_ids, identifier)
# change data structure to dict in order to be quicker when merging
- nodes_mapped_dict = {node[id_key][0]: node for node in nodes_mapped}
+ nodes_mapped_dict = {id.upper(): node for node in nodes_mapped for id in node[id_key]}
+ print(nodes_mapped_dict)
# merge fetched data with given data to avoid data loss
for node in nodes:
--
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