From 5c324c85e0643663e1b44625a3af660ad17a55e3 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Thu, 23 Jun 2022 18:40:01 +0200
Subject: [PATCH] added nedrex_python support and import for protein table
---
Dockerfile | 3 +
.../management/commands/import_from_nedrex.py | 137 +++++++++---------
drugstone/management/commands/populate_db.py | 8 +-
python_nedrex | 1 +
4 files changed, 79 insertions(+), 70 deletions(-)
create mode 160000 python_nedrex
diff --git a/Dockerfile b/Dockerfile
index 9f236cf..aec4578 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -24,9 +24,12 @@ RUN pip install gunicorn
COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
COPY ./docker-entrypoint.sh /usr/src/drugstone/docker-entrypoint.sh
# COPY ./scripts/ /usr/src/drugstone/scripts/
+COPY ./python_nedrex/ /usr/src/drugstone/python_nedrex/
+RUN pip install /usr/src/drugstone/python_nedrex/
COPY . /usr/src/drugstone/
+
#EXPOSE 8000
# ENTRYPOINT ["sh", "/entrypoint.sh"]
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index 39d0001..cc6a26b 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -1,68 +1,69 @@
-# from collections import defaultdict
-#
-#
-# def import_proteins():
-# import python_nedrex as nedrex
-# from python_nedrex.core import get_nodes, get_api_key, get_edges
-# from models import Protein
-#
-# def iter_node_collection(coll_name, eval):
-# offset = 0
-# limit = 10000
-# while True:
-# result = get_nodes(coll_name, offset=offset, limit=limit)
-# if not result:
-# return
-# for node in result:
-# eval(node)
-# offset += limit
-#
-# def iter_edge_collection(coll_name, eval):
-# offset = 0
-# limit = 10000
-# while True:
-# result = get_edges(coll_name, offset=offset, limit=limit)
-# if not result:
-# return
-# for edge in result:
-# eval(edge)
-# offset += limit
-#
-# def add_protein(node):
-# global proteins
-# id = node['primaryDomainId']
-# proteins[id] = Protein(uniprot_code=id.split('.')[1], gene=node['geneName'])
-#
-# def add_edges(edge):
-# global proteins
-# id = edge['sourceDomainId']
-# protein = proteins[id]
-# protein.entrez = edge['targetDomainId'].split('.')[1]
-# global gene_to_prots
-# gene_to_prots[edge['targetDomainId']].add(id)
-#
-# def add_genes(node):
-# global proteins
-# global gene_to_prots
-# id = node['primaryDomainId']
-# for prot_id in gene_to_prots[id]:
-# protein = proteins[prot_id]
-# try:
-# protein.protein_name = node['synonyms'][0]
-# except:
-# pass
-#
-# nedrex.config.set_url_base("http://82.148.225.92:8123/")
-# api_key = get_api_key(accept_eula=True)
-# nedrex.config.set_api_key(api_key)
-#
-# proteins = dict()
-# gene_to_prots = defaultdict(lambda: set())
-#
-# print('Importing Proteins')
-# iter_node_collection('protein', add_protein)
-# print('Importing Protein-Gene mapping')
-# iter_edge_collection('protein_encoded_by_gene', add_edges)
-# print('Mapping Gene information')
-# iter_node_collection('gene', add_genes)
-# Protein.objects.bulk_create(proteins.values())
+from collections import defaultdict
+
+
+class nedrex_importer:
+
+ proteins = dict()
+
+ def import_proteins(self):
+ import python_nedrex as nedrex
+ from python_nedrex.core import get_nodes, get_api_key, get_edges
+ from drugstone.models import Protein
+
+ gene_to_prots = defaultdict(lambda: set())
+
+ def iter_node_collection(coll_name, eval):
+ offset = 0
+ limit = 10000
+ while True:
+ result = get_nodes(coll_name, offset=offset, limit=limit)
+ if not result:
+ return
+ for node in result:
+ eval(node)
+ offset += limit
+
+ def iter_edge_collection(coll_name, eval):
+ offset = 0
+ limit = 10000
+ while True:
+ result = get_edges(coll_name, offset=offset, limit=limit)
+ if not result:
+ return
+ for edge in result:
+ eval(edge)
+ offset += limit
+
+ def add_protein(node):
+ id = node['primaryDomainId']
+ self.proteins[id] = Protein(uniprot_code=id.split('.')[1], gene=node['geneName'])
+
+ def add_edges(edge):
+ id = edge['sourceDomainId']
+ protein = self.proteins[id]
+ protein.entrez = edge['targetDomainId'].split('.')[1]
+ gene_to_prots[edge['targetDomainId']].add(id)
+
+ def add_genes(node):
+ id = node['primaryDomainId']
+ for prot_id in gene_to_prots[id]:
+ protein = self.proteins[prot_id]
+ try:
+ protein.protein_name = node['synonyms'][0]
+ except:
+ pass
+
+ nedrex.config.set_url_base("http://82.148.225.92:8123/")
+ api_key = get_api_key(accept_eula=True)
+ nedrex.config.set_api_key(api_key)
+
+
+
+ print('Importing Proteins')
+ iter_node_collection('protein', add_protein)
+ print('Importing Protein-Gene mapping')
+ iter_edge_collection('protein_encoded_by_gene', add_edges)
+ print('Mapping Gene information')
+ iter_node_collection('gene', add_genes)
+ Protein.objects.bulk_create(self.proteins.values())
+ return len(self.proteins)
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 2408eb3..a0f7693 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -6,7 +6,7 @@ from drugstone.models import Protein, Drug, Tissue, ExpressionLevel, PPIDataset,
from drugstone.models import ProteinProteinInteraction, ProteinDrugInteraction
from drugstone.management.includes.DataPopulator import DataPopulator
-
+from .import_from_nedrex import nedrex_importer
class DatabasePopulator:
def __init__(self, data_dir,
@@ -99,6 +99,8 @@ class Command(BaseCommand):
tissue_expression_file=exp_file,
)
+ importer = nedrex_importer()
+
if kwargs['delete_model'] is not None:
model_list = kwargs['delete_model'].split(',')
db_populator.delete_models(model_list)
@@ -127,7 +129,9 @@ class Command(BaseCommand):
if kwargs['proteins'] is not None:
print('Populating Proteins...')
- n = DataPopulator.populate_proteins(populator)
+
+ n = nedrex_importer.import_proteins(nedrex_importer)
+ # n = DataPopulator.populate_proteins(populator)
print(f'Populated {n} Proteins.')
print('Populating ENSG IDs...')
diff --git a/python_nedrex b/python_nedrex
new file mode 160000
index 0000000..ee1cd32
--- /dev/null
+++ b/python_nedrex
@@ -0,0 +1 @@
+Subproject commit ee1cd32fd15f6b73647df70bacb9d0ebd7858236
--
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