diff --git a/data/.gitignore b/data/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..6f8cd6338cce6b214cdbe5a3677699e24a5707cf
--- /dev/null
+++ b/data/.gitignore
@@ -0,0 +1 @@
+data.zip
diff --git a/data/Networks/internal_APID_ChEMBL.gt b/data/Networks/internal_APID_ChEMBL.gt
index 2acaf64a4ad93bc4816d75d1a482780b50e5722e..dbf194d7be8fcd0cf29ee2cfdb9a1d68ff34a928 100755
Binary files a/data/Networks/internal_APID_ChEMBL.gt and b/data/Networks/internal_APID_ChEMBL.gt differ
diff --git a/data/Networks/internal_APID_DGIdb.gt b/data/Networks/internal_APID_DGIdb.gt
index 9845e5839168745be7f046ebf35ba37193e1c157..c02f8cccfef229ff647b5064e4daa455102ae30f 100755
Binary files a/data/Networks/internal_APID_DGIdb.gt and b/data/Networks/internal_APID_DGIdb.gt differ
diff --git a/data/Networks/internal_APID_DrugBank.gt b/data/Networks/internal_APID_DrugBank.gt
index c1334ded9beba26f68b1629a9a75d512eb71fc3c..eaf6c74bc9d3a9f96ee070cd41af80e21453517b 100755
Binary files a/data/Networks/internal_APID_DrugBank.gt and b/data/Networks/internal_APID_DrugBank.gt differ
diff --git a/data/Networks/internal_APID_NeDRex.gt b/data/Networks/internal_APID_NeDRex.gt
new file mode 100644
index 0000000000000000000000000000000000000000..6ea92296d61f4175a0fa306de92dc8e1cb0b7660
Binary files /dev/null and b/data/Networks/internal_APID_NeDRex.gt differ
diff --git a/data/Networks/internal_BioGRID_ChEMBL.gt b/data/Networks/internal_BioGRID_ChEMBL.gt
index 6bc34f74ab07b62127479f4bcee14eb264598d4c..850d5bbc44324dda6e2b97a1b3ab2d3585f188a6 100755
Binary files a/data/Networks/internal_BioGRID_ChEMBL.gt and b/data/Networks/internal_BioGRID_ChEMBL.gt differ
diff --git a/data/Networks/internal_BioGRID_DGIdb.gt b/data/Networks/internal_BioGRID_DGIdb.gt
index c92ed09666e21ab9f42bfe50467659154bb6795d..1bcbf3bce6853078089263e80495a370939fb6cd 100755
Binary files a/data/Networks/internal_BioGRID_DGIdb.gt and b/data/Networks/internal_BioGRID_DGIdb.gt differ
diff --git a/data/Networks/internal_BioGRID_DrugBank.gt b/data/Networks/internal_BioGRID_DrugBank.gt
index de11a0a60ba4e5c235a91cef7610b67229f81e47..5c118ec5a15deef860878e4c71e8df4d15157bcf 100755
Binary files a/data/Networks/internal_BioGRID_DrugBank.gt and b/data/Networks/internal_BioGRID_DrugBank.gt differ
diff --git a/data/Networks/internal_BioGRID_NeDRex.gt b/data/Networks/internal_BioGRID_NeDRex.gt
new file mode 100644
index 0000000000000000000000000000000000000000..f4646e18f8d08d46a50a04ffc95c958295ab7fd7
Binary files /dev/null and b/data/Networks/internal_BioGRID_NeDRex.gt differ
diff --git a/data/Networks/internal_NeDRex_ChEMBL.gt b/data/Networks/internal_NeDRex_ChEMBL.gt
new file mode 100644
index 0000000000000000000000000000000000000000..443d881091b3d8be0e8baa6d367810090d94bbb3
Binary files /dev/null and b/data/Networks/internal_NeDRex_ChEMBL.gt differ
diff --git a/data/Networks/internal_NeDRex_DGIdb.gt b/data/Networks/internal_NeDRex_DGIdb.gt
new file mode 100644
index 0000000000000000000000000000000000000000..0c14421eecddbce924e80a55cc9bbc832fff46b1
Binary files /dev/null and b/data/Networks/internal_NeDRex_DGIdb.gt differ
diff --git a/data/Networks/internal_NeDRex_DrugBank.gt b/data/Networks/internal_NeDRex_DrugBank.gt
new file mode 100644
index 0000000000000000000000000000000000000000..e00195ba3ac70dc33f314a20e9bff1795f56f92f
Binary files /dev/null and b/data/Networks/internal_NeDRex_DrugBank.gt differ
diff --git a/data/Networks/internal_NeDRex_NeDRex.gt b/data/Networks/internal_NeDRex_NeDRex.gt
new file mode 100644
index 0000000000000000000000000000000000000000..5c11434ef5cb2a13cb802982e1cd2914b22170a3
Binary files /dev/null and b/data/Networks/internal_NeDRex_NeDRex.gt differ
diff --git a/data/Networks/internal_STRING_ChEMBL.gt b/data/Networks/internal_STRING_ChEMBL.gt
index 3c7989751227d48ef98929d97b97c905b102ce3a..8764ba363c3266bd1d17c350e2aa1219f1d4dc24 100755
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diff --git a/data/Networks/internal_STRING_DGIdb.gt b/data/Networks/internal_STRING_DGIdb.gt
index dc0879f419e34e5f1365e27fc0e9f04aba3f4b73..defa5a420e0650eb7ebedc3484f94923d48c33c1 100755
Binary files a/data/Networks/internal_STRING_DGIdb.gt and b/data/Networks/internal_STRING_DGIdb.gt differ
diff --git a/data/Networks/internal_STRING_DrugBank.gt b/data/Networks/internal_STRING_DrugBank.gt
index 46bfa9110298057abd266c9f2f087c8eb8d1ec1b..bb58c6a793bcfa05a41c9b327bff95bf86f7d1a1 100755
Binary files a/data/Networks/internal_STRING_DrugBank.gt and b/data/Networks/internal_STRING_DrugBank.gt differ
diff --git a/data/Networks/internal_STRING_NeDRex.gt b/data/Networks/internal_STRING_NeDRex.gt
new file mode 100644
index 0000000000000000000000000000000000000000..2da41415db9c7a8abf82cec3c04cff031e01f703
Binary files /dev/null and b/data/Networks/internal_STRING_NeDRex.gt differ
diff --git a/docker-compose.yml b/docker-compose.yml
index aed9f483dedaf6cd6d3d2f181b4dc69d5214382e..05c85e64064e9b7d8b020a912b9355190bbfef6d 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 4d01dd45c09e844124c1d244516d543bda8d9c58..0000000000000000000000000000000000000000
--- 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 4f160dbe5101281d53520f54a353835cf9c10570..5391a43d5383bf0ca5c3c5fbabe248714fada698 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 6491d095b57ff99685997c02b63e6a61510e1b43..7822f3ab63e84c4c813a2d569fd290b8d3c0f207 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 6dc4cd8b33ca3885b1507ec6296168651dcde399..c033d37ff042ec5966a07a83d151d164ae58caf5 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