From bd372d56f7eac22498f213e31e6c7cefa71a6c17 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 1 Jul 2022 17:37:00 +0200
Subject: [PATCH] nedrex integration mainly done
---
data/.gitignore | 1 +
docker-compose.yml | 12 +++----
drugstone/management/commands/test.py | 51 ---------------------------
drugstone/models.py | 6 ++++
drugstone/views.py | 4 +--
scripts/docker-entrypoint.sh | 3 +-
6 files changed, 16 insertions(+), 61 deletions(-)
create mode 100644 data/.gitignore
delete mode 100644 drugstone/management/commands/test.py
diff --git a/data/.gitignore b/data/.gitignore
new file mode 100644
index 0000000..6f8cd63
--- /dev/null
+++ b/data/.gitignore
@@ -0,0 +1 @@
+data.zip
diff --git a/docker-compose.yml b/docker-compose.yml
index aed9f48..05c85e6 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -15,7 +15,7 @@ services:
- drugstone_db_schema_volume:/usr/src/drugstone/drugstone/migrations
- drugstone_data_volume:/usr/src/drugstone/data
ports:
- - 8002:8000
+ - 8001:8000
networks:
- drugstone_net
depends_on:
@@ -26,8 +26,8 @@ services:
container_name: drugstone_postgres
restart: always
hostname: drugstone_postgres
-# ports:
-# - 5432:5432
+ ports:
+ - 5432:5432
networks:
- drugstone_net
volumes:
@@ -95,8 +95,8 @@ networks:
volumes:
drugstone_db_volume:
- external: true
+# external: true
drugstone_db_schema_volume:
- external: true
+# external: true
drugstone_data_volume:
- external: true
\ No newline at end of file
+# external: true
\ No newline at end of file
diff --git a/drugstone/management/commands/test.py b/drugstone/management/commands/test.py
deleted file mode 100644
index 4d01dd4..0000000
--- a/drugstone/management/commands/test.py
+++ /dev/null
@@ -1,51 +0,0 @@
-import python_nedrex as nedrex
-from python_nedrex.core import get_nodes, get_edges, get_api_key
-from python_nedrex.static import get_metadata
-
-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 iter_ppi(eval):
- from python_nedrex import ppi
- offset = 0
- limit = 1000
- while True:
- result = ppi.ppis({"exp"},skip = offset, limit=limit)
- if not result:
- return
- for edge in result:
- eval(edge)
- offset += limit
-
-base_url = "http://82.148.225.92:8123/"
-nedrex.config.set_url_base(base_url)
-api_key = get_api_key(accept_eula=True)
-nedrex.config.set_api_key(api_key)
-print(f'Nodes: {nedrex.core.get_node_types()}')
-print(f'Edges: {nedrex.core.get_edge_types()}')
-print(f'{get_metadata()}')
-
-
-iter_ppi(lambda node: print(node))
-# iter_edge_collection("gene_expressed_in_tissue", lambda node: {print(node)})
\ No newline at end of file
diff --git a/drugstone/models.py b/drugstone/models.py
index 4f160db..5391a43 100755
--- a/drugstone/models.py
+++ b/drugstone/models.py
@@ -129,6 +129,9 @@ class Disorder(models.Model):
def __ne__(self, other):
return not self.__eq__(other)
+ def __hash__(self):
+ return hash((self.mondo_id, self.label, self.icd10))
+
def update(self, other):
self.mondo_id = other.mondo_id
self.label = other.label
@@ -152,6 +155,9 @@ class Drug(models.Model):
def __ne__(self, other):
return not self.__eq__(other)
+ def __hash__(self):
+ return hash((self.drug_id, self.name, self.status))
+
def update(self, other):
self.drug_id = other.drug_id
self.name = other.name
diff --git a/drugstone/views.py b/drugstone/views.py
index 6491d09..7822f3a 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -531,7 +531,7 @@ def adjacent_disorders(request) -> Response:
data = request.data
if 'proteins' in data:
drugstone_ids = data.get('proteins', [])
- pdi_dataset = 'DisGeNET'
+ pdi_dataset = data.get('dataset','DisGeNET')
# find adjacent drugs by looking at drug-protein edges
pdis_objects = ProteinDisorderAssociation.objects.filter(protein__id__in=drugstone_ids,
pdis_dataset__name=pdi_dataset)
@@ -541,7 +541,7 @@ def adjacent_disorders(request) -> Response:
disorders = DisorderSerializer(many=True).to_representation(disorders)
elif 'drugs' in data:
drugstone_ids = data.get('drugs', [])
- drdi_dataset = 'DrugBank'
+ drdi_dataset = data.get('dataset','DrugBank')
# find adjacent drugs by looking at drug-protein edges
drdi_objects = DrugDisorderIndication.objects.filter(drug__id__in=drugstone_ids,
drdi_dataset__name=drdi_dataset)
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 6dc4cd8..c033d37 100755
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -1,6 +1,6 @@
#!/bin/bash
-file="docker-entrypoint.lock"
+file="data/docker-entrypoint.lock"
# exit if entrypoint.lock exists to prevent new import of data every time docker is restarted
@@ -13,7 +13,6 @@ if ! test -f "$file"; then
python3 manage.py cleanuptasks
python3 manage.py populate_db -u --all
python3 manage.py make_graphs
-
touch $file
fi
--
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