diff --git a/Dockerfile b/Dockerfile
index 42a73544f9646b0855fcefed06b3cba280f78f7c..eb9ebfffb77c09b84161efdf55f95991221d3c07 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,8 +21,7 @@ COPY ./requirements.txt /usr/src/drugstone/requirements.txt
RUN pip install -r /usr/src/drugstone/requirements.txt
COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-COPY ./python_nedrex/ /usr/src/drugstone/python_nedrex/
-RUN pip install /usr/src/drugstone/python_nedrex/
+RUN pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple nedrex==0.1.4
COPY . /usr/src/drugstone/
diff --git a/docker-compose.yml b/docker-compose.yml
index a496008af30a3124124940bcfea3bdb01f997dd0..dff6aaa5e226eb06a2995edb7ff00decb332f7af 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -51,37 +51,37 @@ services:
- drugstone_net
# ports:
# - 6379:6379
- celery:
- command:
- - "sh"
- - "scripts/start_celery_worker.sh"
- restart: always
- image: drugstone_backend
- container_name: drugstone_celery
- hostname: drugstone_celery
- volumes:
- - drugstone_data_volume:/usr/src/drugstone/data
- env_file:
- - './docker-django.env.dev'
- depends_on:
- - redis
- - db
- networks:
- - drugstone_net
- celery-beat:
- command:
- - "sh"
- - "scripts/start_celery_beat.sh"
- image: drugstone_backend
- container_name: drugstone_celery_beat
- hostname: drugstone_celery_beat
- env_file:
- - './docker-django.env.dev'
- depends_on:
- - redis
- - db
- networks:
- - drugstone_net
+# celery:
+# command:
+# - "sh"
+# - "scripts/start_celery_worker.sh"
+# restart: always
+# image: drugstone_backend
+# container_name: drugstone_celery
+# hostname: drugstone_celery
+# volumes:
+# - drugstone_data_volume:/usr/src/drugstone/data
+# env_file:
+# - './docker-django.env.dev'
+# depends_on:
+# - redis
+# - db
+# networks:
+# - drugstone_net
+# celery-beat:
+# command:
+# - "sh"
+# - "scripts/start_celery_beat.sh"
+# image: drugstone_backend
+# container_name: drugstone_celery_beat
+# hostname: drugstone_celery_beat
+# env_file:
+# - './docker-django.env.dev'
+# depends_on:
+# - redis
+# - db
+# networks:
+# - drugstone_net
# flower:
# image: mher/flower
# container_name: drugstone_flower
diff --git a/docker-django.env b/docker-django.env
index 881fbf1d2fca2e34cd6415a75bbbe6851d597339..b4216e4c78942ead06292499cbfe65d298f1c067 100755
--- a/docker-django.env
+++ b/docker-django.env
@@ -9,4 +9,5 @@ SQL_PASSWORD=t6278yczAH7rPKVMxaDD
SQL_HOST=drugstone_postgres
SQL_PORT=5432
REDIS_HOST=redis
-REDIS_PORT=6379
\ No newline at end of file
+REDIS_PORT=6379
+GT_THREADS=16
\ No newline at end of file
diff --git a/docker-django.env.dev b/docker-django.env.dev
index 3930f4b388d33055d6bcebb8f07613f208f9f671..c0f3aa4316170325e46f3794e79220b655873414 100644
--- a/docker-django.env.dev
+++ b/docker-django.env.dev
@@ -13,4 +13,5 @@ REDIS_PORT=6379
DJANGO_SETTINGS_MODULE=drugstone.settings
CELERY_BROKER_URL=redis://redis:6379/0
FLOWER_PORT=8888
-FLOWER_BASIC_AUTH=drugstone:test
\ No newline at end of file
+FLOWER_BASIC_AUTH=drugstone:test
+GT_THREADS=1
\ No newline at end of file
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index 72a20f332b2106dce7eeec99fd2dd55103d8f63a..29c3cbb481ab72f4a2d4f94353607c81a75253ac 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -1,11 +1,12 @@
from collections import defaultdict
-import python_nedrex as nedrex
-from python_nedrex.core import get_nodes, get_edges, get_api_key
+import nedrex
+from nedrex.core import get_nodes, get_edges, get_api_key
from drugstone import models
from drugstone.management.includes.NodeCache import NodeCache
from drugstone.management.includes import DatasetLoader
+from drugstone.models import PPIDataset
def iter_node_collection(coll_name, eval):
@@ -58,16 +59,37 @@ def to_id(string):
class NedrexImporter:
cache: NodeCache = None
- url: str = ''
+ url = str = ''
+ licenced_url: str = ''
+ unlicenced_url: str = ''
+ licenced_on: bool = True
+ api_key: str = None
- def __init__(self, base_url, cache: NodeCache):
+ def __init__(self, base_url_licenced, base_url_unlicenced, cache: NodeCache):
self.cache = cache
- nedrex.config.set_url_base(base_url)
- self.url = base_url
- api_key = get_api_key(accept_eula=True)
- nedrex.config.set_api_key(api_key)
+ self.licenced_url = base_url_licenced
+ self.unlicenced_url = base_url_unlicenced
+ self.set_licenced(False)
+
+ def get_api_key(self):
+ if self.api_key is None:
+ self.api_key = get_api_key(accept_eula=True)
+ return self.api_key
+
+ def set_licenced(self, on):
+ if on == self.licenced_on:
+ return
+
+ self.url = self.licenced_url if on else self.unlicenced_url
+ nedrex.config.set_url_base(self.url)
+
+ if on:
+ nedrex.config.set_api_key(self.get_api_key())
+
+ self.licenced_on = on
def import_proteins(self, update: bool):
+ self.set_licenced(False)
proteins = dict()
gene_to_prots = defaultdict(lambda: set())
@@ -128,6 +150,7 @@ class NedrexImporter:
return len(self.cache.proteins)
def import_drugs(self, update):
+ self.set_licenced(False)
drugs = dict()
if update:
self.cache.init_drugs()
@@ -181,6 +204,9 @@ class NedrexImporter:
return len(self.cache.disorders)
def import_drug_target_interactions(self, dataset, update):
+ licenced = dataset.licenced
+ self.set_licenced(licenced)
+
self.cache.init_drugs()
self.cache.init_proteins()
@@ -190,7 +216,19 @@ class NedrexImporter:
for edge in models.ProteinDrugInteraction.objects.filter(pdi_dataset=dataset):
existing.add(edge.__hash__())
- source_datasets = DatasetLoader.get_pdr_nedrex_datasets(self.url)
+ source_datasets = dict()
+ source_is_licenced = dict()
+
+ def get_dataset(source):
+ if source not in source_datasets:
+ source_datasets[source] = DatasetLoader.get_pdi_nedrex_dataset(self.url, licenced, source)
+ return source_datasets[source]
+
+ def is_licenced(source):
+ if source not in source_is_licenced:
+ source_is_licenced[source] = DatasetLoader.is_licenced_pdi_source(source)
+ return source_is_licenced[source]
+
def add_dpi(edge):
try:
drug = self.cache.get_drug_by_drugbank(to_id(edge['sourceDomainId']))
@@ -199,7 +237,9 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- bulk.add(models.ProteinDrugInteraction(pdi_dataset=source_datasets[source], drug=drug, protein=protein))
+ if not licenced or is_licenced(source):
+ bulk.add(models.ProteinDrugInteraction(pdi_dataset=get_dataset(source), drug=drug,
+ protein=protein))
except KeyError:
pass
@@ -207,7 +247,10 @@ class NedrexImporter:
models.ProteinDrugInteraction.objects.bulk_create(bulk)
return len(bulk)
- def import_protein_protein_interactions(self, dataset, update):
+ def import_protein_protein_interactions(self, dataset: PPIDataset, update):
+ licenced = dataset.licenced
+ self.set_licenced(licenced)
+
self.cache.init_proteins()
bulk = list()
@@ -216,10 +259,21 @@ class NedrexImporter:
for edge in models.ProteinProteinInteraction.objects.filter(ppi_dataset=dataset):
existing.add(edge.__hash__())
- source_datasets = DatasetLoader.get_ppi_nedrex_datasets(self.url)
+ source_datasets = dict()
+ source_is_licenced = dict()
+
+ def get_dataset(source):
+ if source not in source_datasets:
+ source_datasets[source] = DatasetLoader.get_ppi_nedrex_dataset(self.url, licenced, source)
+ return source_datasets[source]
+
+ def is_licenced(source):
+ if source not in source_is_licenced:
+ source_is_licenced[source] = DatasetLoader.is_licenced_ppi_source(source)
+ return source_is_licenced[source]
def iter_ppi(eval):
- from python_nedrex import ppi
+ from nedrex import ppi
offset = 0
limit = 10000
while True:
@@ -238,9 +292,10 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.append(e)
for source in edge['dataSources']:
- bulk.append(
- models.ProteinProteinInteraction(ppi_dataset=source_datasets[source], from_protein=protein1,
- to_protein=protein2))
+ if not licenced or is_licenced(source):
+ bulk.append(
+ models.ProteinProteinInteraction(ppi_dataset=get_dataset(source), from_protein=protein1,
+ to_protein=protein2))
except KeyError:
pass
@@ -249,6 +304,9 @@ class NedrexImporter:
return len(bulk)
def import_protein_disorder_associations(self, dataset, update):
+ licenced = dataset.licenced
+ self.set_licenced(licenced)
+
self.cache.init_disorders()
self.cache.init_proteins()
@@ -258,7 +316,18 @@ class NedrexImporter:
for edge in models.ProteinDisorderAssociation.objects.filter(pdis_dataset=dataset):
existing.add(edge.__hash__())
- source_datasets = DatasetLoader.get_dis_prot_nedrex_datasets(self.url)
+ source_datasets = dict()
+ source_is_licenced = dict()
+
+ def get_dataset(source):
+ if source not in source_datasets:
+ source_datasets[source] = DatasetLoader.get_pdis_nedrex_dataset(self.url, licenced, source)
+ return source_datasets[source]
+
+ def is_licenced(source):
+ if source not in source_is_licenced:
+ source_is_licenced[source] = DatasetLoader.is_licenced_pdis_source(source)
+ return source_is_licenced[source]
def add_pdis(edge):
try:
@@ -269,9 +338,11 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- bulk.add(
- models.ProteinDisorderAssociation(pdis_dataset=source_datasets[source], protein=protein, disorder=disorder,
- score=edge['score']))
+ if not licenced or is_licenced(source):
+ bulk.add(
+ models.ProteinDisorderAssociation(pdis_dataset=get_dataset(source), protein=protein,
+ disorder=disorder,
+ score=edge['score']))
except KeyError:
pass
@@ -280,6 +351,9 @@ class NedrexImporter:
return len(bulk)
def import_drug_disorder_indications(self, dataset, update):
+ licenced = dataset.licenced
+ self.set_licenced(licenced)
+
self.cache.init_disorders()
self.cache.init_drugs()
@@ -289,7 +363,18 @@ class NedrexImporter:
for edge in models.DrugDisorderIndication.objects.filter(drdi_dataset=dataset):
existing.add(edge.__hash__())
- source_datasets = DatasetLoader.get_drdis_nedrex_datasets(self.url)
+ source_datasets = dict()
+ source_is_licenced = dict()
+
+ def get_dataset(source):
+ if source not in source_datasets:
+ source_datasets[source] = DatasetLoader.get_drdi_nedrex_dataset(self.url, licenced, source)
+ return source_datasets[source]
+
+ def is_licenced(source):
+ if source not in source_is_licenced:
+ source_is_licenced[source] = DatasetLoader.is_licenced_drdi_source(source)
+ return source_is_licenced[source]
def add_drdis(edge):
try:
@@ -299,12 +384,13 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- bulk.add(
- models.DrugDisorderIndication(drdi_dataset=source_datasets[source], drug=drug, disorder=disorder))
+ if not licenced or is_licenced(source):
+ bulk.add(
+ models.DrugDisorderIndication(drdi_dataset=get_dataset(source), drug=drug,
+ disorder=disorder))
except KeyError:
return
-
iter_edge_collection('drug_has_indication', add_drdis)
models.DrugDisorderIndication.objects.bulk_create(bulk)
return len(bulk)
diff --git a/drugstone/management/commands/make_graphs.py b/drugstone/management/commands/make_graphs.py
index 7759ad36f93c55325502d6888ee703968d6de1a8..98c7ce1db5a204671b48b66b7eea3787aaca4f60 100755
--- a/drugstone/management/commands/make_graphs.py
+++ b/drugstone/management/commands/make_graphs.py
@@ -1,17 +1,16 @@
from typing import List, Tuple
import graph_tool.all as gt
from drugstone import models
-from drugstone import serializers
-import json
import multiprocessing
from django import db
from django.core.management import BaseCommand
import django
+import os
django.setup()
-KERNEL = 6
+KERNEL = int(os.environ.get('GT_THREADS', 6))
def _internal_expression_scores(drugstone_id: str) -> dict:
@@ -40,7 +39,7 @@ def _internal_expression_scores(drugstone_id: str) -> dict:
return tissue_scores
-def _internal_pdis(dataset_name: str) -> List[dict]:
+def _internal_pdis(dataset) -> List[models.ProteinDrugInteraction]:
""" Fetches all internal protein-drug interactions for a given dataset.
Interactions are taken from the django database.
@@ -52,15 +51,15 @@ def _internal_pdis(dataset_name: str) -> List[dict]:
"""
# get all interactions
node_node_interaction_objects = models.ProteinDrugInteraction.objects.filter(
- pdi_dataset__name=dataset_name
+ pdi_dataset__id=dataset.id
)
- node_node_interactions = serializers.ProteinDrugInteractionSerializer(many=True) \
- .to_representation(node_node_interaction_objects)
+ # node_node_interactions = serializers.ProteinDrugInteractionSerializer(many=True) \
+ # .to_representation(node_node_interaction_objects)
- return node_node_interactions
+ return node_node_interaction_objects
-def _internal_ppis(dataset_name: str) -> List[dict]:
+def _internal_ppis(dataset) -> List[models.ProteinProteinInteraction]:
""" Fetches all internal protein-protein interactions for a given dataset.
Interactions are taken from the django database.
@@ -72,15 +71,13 @@ def _internal_ppis(dataset_name: str) -> List[dict]:
"""
# get all interactions
node_node_interaction_objects = models.ProteinProteinInteraction.objects.filter(
- ppi_dataset__name=dataset_name
+ ppi_dataset__id=dataset.id
)
- node_node_interactions = serializers.ProteinProteinInteractionSerializer(many=True) \
- .to_representation(node_node_interaction_objects)
- return node_node_interactions
+ return node_node_interaction_objects
-def create_gt(params: Tuple[str, str]) -> None:
+def create_gt(params: Tuple) -> None:
"""Fetches all required information to build a graph-tools file for given
PPI and PDI dataset names (params). Builds the graph-tools file and saves it in
the data/Networks folder.
@@ -89,23 +86,8 @@ def create_gt(params: Tuple[str, str]) -> None:
params (Tuple[str, str]): Protein-protein-dataset name, Protein-drug-dataset name
"""
ppi_dataset, pdi_dataset = params
+ licensed = ppi_dataset.licenced or pdi_dataset.licenced
# get data from api
- data = {}
-
- print(f'loading nodes')
- data['nodes'] = serializers.ProteinSerializer(many=True).to_representation(
- models.Protein.objects.all()
- )
-
- print(f'loading edges/{ppi_dataset}')
- data['edges'] = _internal_ppis(ppi_dataset)
-
- print(f'loading drugs')
- data['drugs'] = serializers.DrugSerializer(many=True).to_representation(
- models.Drug.objects.all()
- )
- print(f'loading drug_edges/{pdi_dataset}')
- data['drug_edges'] = _internal_pdis(pdi_dataset)
g = gt.Graph(directed=False)
e_type = g.new_edge_property("string")
@@ -135,59 +117,62 @@ def create_gt(params: Tuple[str, str]) -> None:
vertices = {}
drug_vertices = {}
# add vertices
- print("adding nodes")
+
+ # print("adding nodes")
+ print(f'loading nodes')
# extend node data by cancer nodes, we create a normal node for each cancer node.
# on reading the data, we decide which one to keep based on the user selected cancer types
- for node in data['nodes']:
+ for node in models.Protein.objects.all():
v = g.add_vertex()
v_type[v] = 'protein'
- v_name[v] = node['symbol']
- v_drugstone_id[v] = node['drugstone_id']
- v_entrez[v] = node['entrez']
- v_expression[v] = json.dumps(_internal_expression_scores(node['drugstone_id']))
+ v_drugstone_id[v] = f"p{node.id}"
- vertices[node['drugstone_id']] = v
+ vertices[node.id] = v
print("done with nodes")
- print(f"adding ${len(data['drugs'])} drugs")
- for node in data['drugs']:
+ print(f"adding drugs")
+ for node in models.Drug.objects.all():
v = g.add_vertex()
v_type[v] = 'drug'
- v_name[v] = node['label']
- v_status[v] = node['status']
- v_drugstone_id[v] = node['drugstone_id']
- v_drug_id[v] = node['drug_id']
+ v_status[v] = node.status
+ v_drugstone_id[v] = f'dr{node.id}'
- drug_vertices[node['drugstone_id']] = v
+ drug_vertices[node.id] = v
print("done with drugs")
# add edges
- print("adding edges")
- for edge in data['edges']:
- a = vertices[edge['protein_a']]
- b = vertices[edge['protein_b']]
- e = g.add_edge(a, b)
+ print(f'adding ppi_edges/{ppi_dataset}')
+ for edge_raw in _internal_ppis(ppi_dataset):
+ e = g.add_edge(vertices[edge_raw.from_protein_id], vertices[edge_raw.to_protein_id])
e_type[e] = 'protein-protein'
print("done with edges")
- print("adding drug edges")
- for edge in data['drug_edges']:
- protein, drug = vertices[edge['protein']], drug_vertices[edge['drug']]
- e = g.add_edge(drug, protein)
+
+ print(f'loading drug_edges/{pdi_dataset}')
+ for edge_raw in _internal_pdis(pdi_dataset):
+ e = g.add_edge(drug_vertices[edge_raw.drug_id], vertices[edge_raw.protein_id])
e_type[e] = 'drug-protein'
print("done with drug edges")
- # remove unconnected nodes
+ # remove unconnected proteins
delete_vertices = set()
- for vertex in g.iter_vertices():
+ for vertex in vertices.values():
+ if vertex.out_degree() == 0:
+ delete_vertices.add(vertex)
+
+ #remove unconnected drugs
+ for vertex in drug_vertices.values():
if vertex.out_degree() == 0:
delete_vertices.add(vertex)
g.remove_vertex(reversed(sorted(delete_vertices)), fast=True)
# save graph
- filename = f"./data/Networks/internal_{ppi_dataset}_{pdi_dataset}.gt"
+ filename = f"./data/Networks/internal_{ppi_dataset.name}_{pdi_dataset.name}"
+ if licensed:
+ filename += "_licenced"
+ filename += ".gt"
g.save(filename)
print(f"Created file {filename}")
return
@@ -199,14 +184,12 @@ class Command(BaseCommand):
def handle(self, *args, **kwargs):
ppi_datasets = models.PPIDataset.objects.all()
- ppi_datasets_names = [e.name for e in ppi_datasets]
pdi_datasets = models.PDIDataset.objects.all()
- pdi_datasets_names = [e.name for e in pdi_datasets]
parameter_combinations = []
- for protein_interaction_dataset in ppi_datasets_names:
- for pdi_dataset in pdi_datasets_names:
+ for protein_interaction_dataset in ppi_datasets:
+ for pdi_dataset in pdi_datasets:
parameter_combinations.append((protein_interaction_dataset, pdi_dataset))
# close all database connections so subprocesses will create their own connections
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index df60c8652e61bf74eac76f817f789173478361a3..429cf6fc97b2fbc0ba07ec9b1051188b227ae9c0 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -86,7 +86,9 @@ class Command(BaseCommand):
def populate(kwargs):
- nedrex_api_url = "http://82.148.225.92:8123/"
+ nedrex_api_url_unlicenced= "http://82.148.225.92:7123/"
+ nedrex_api_url_licenced = "http://82.148.225.92:8123/"
+
data_dir = kwargs['data_dir']
db_populator = DatabasePopulator(data_dir=data_dir)
@@ -100,7 +102,7 @@ def populate(kwargs):
cache = NodeCache()
update = True if kwargs['update'] else False
- importer = NedrexImporter(nedrex_api_url, cache)
+ importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_unlicenced, cache)
populator = DataPopulator(cache)
total_n = 0
@@ -147,15 +149,21 @@ def populate(kwargs):
total_n += n
print(f'Populated {n} Expressions.')
-
if kwargs['protein_drug']:
- print('Importing PDIs from NeDRexDB...')
+ print('Importing PDIs from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
- DatasetLoader.get_drug_target_nedrex(nedrex_api_url),
+ DatasetLoader.get_drug_target_nedrex(nedrex_api_url_unlicenced, False),
+ update)
+ total_n += n
+ print(f'Imported {n} PDIs from unlicenced NeDRexDB')
+
+ print('Importing PDIs from licenced NeDRexDB...')
+ n = NedrexImporter.import_drug_target_interactions(importer,
+ DatasetLoader.get_drug_target_nedrex(nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
- print(f'Imported {n} PDIs from NeDRexDB')
+ print(f'Imported {n} PDIs from licenced NeDRexDB')
print('Populating PDIs from Chembl...')
n = DataPopulator.populate_pdi_chembl(populator, DatasetLoader.get_drug_target_chembl(), update)
@@ -168,36 +176,59 @@ def populate(kwargs):
print(f'Populated {n} PDIs from DGIdb.')
if kwargs['protein_disorder']:
- print('Importing PDis from NeDRexDB...')
+ print('Importing PDis from unlicenced NeDRexDB...')
+ n = NedrexImporter.import_protein_disorder_associations(importer,
+ DatasetLoader.get_protein_disorder_nedrex(
+ nedrex_api_url_unlicenced, False),
+ update)
+ total_n += n
+ print(f'Imported {n} PDis from unlicenced NeDRexDB')
+
+ print('Importing PDis from licenced NeDRexDB...')
n = NedrexImporter.import_protein_disorder_associations(importer,
DatasetLoader.get_protein_disorder_nedrex(
- nedrex_api_url),
+ nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
- print(f'Imported {n} PDis from NeDRexDB')
+ print(f'Imported {n} PDis from licenced NeDRexDB')
if kwargs['drug_disorder']:
- print('Importing DrDis from NeDRexDB...')
+ print('Importing DrDis from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_disorder_indications(importer,
- DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url),
+ DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_unlicenced, False),
+ update)
+ total_n += n
+ print(f'Imported {n} DrDis from unlicenced NeDRexDB')
+
+ print('Importing DrDis from licenced NeDRexDB...')
+ n = NedrexImporter.import_drug_disorder_indications(importer,
+ DatasetLoader.get_drug_disorder_nedrex(
+ nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
- print(f'Imported {n} DrDis from NeDRexDB')
+ print(f'Imported {n} DrDis from licenced NeDRexDB')
print('Populating DrDi indications from DrugBank...')
n = DataPopulator.populate_drdis_drugbank(populator, DatasetLoader.get_drug_disorder_drugbank(), update)
total_n += n
print(f'Populated {n} DrDi associations from DrugBank.')
if kwargs['protein_protein']:
- print('Importing PPIs from NeDRexDB...')
+ print('Importing PPIs from unlicenced NeDRexDB...')
+ n = NedrexImporter.import_protein_protein_interactions(importer,
+ DatasetLoader.get_ppi_nedrex(nedrex_api_url_unlicenced, False),
+ update)
+ total_n += n
+ print(f'Imported {n} PPIs from unlicended NeDRexDB')
+ print('Importing PPIs from licenced NeDRexDB...')
n = NedrexImporter.import_protein_protein_interactions(importer,
- DatasetLoader.get_ppi_nedrex(nedrex_api_url),
+ DatasetLoader.get_ppi_nedrex(nedrex_api_url_licenced,
+ True),
update)
total_n += n
nedrex_update = True
- print(f'Imported {n} PPIs from NeDRexDB')
+ print(f'Imported {n} PPIs from licended NeDRexDB')
print('Populating PPIs from STRING...')
n = DataPopulator.populate_ppi_string(populator, DatasetLoader.get_ppi_string(), update)
total_n += n
diff --git a/drugstone/management/includes/DatasetLoader.py b/drugstone/management/includes/DatasetLoader.py
index a11e9c7e055c52fb4bcf92fae643dea6bf0d8444..e08a6fe61e6bff90ea103148900e4e689e037289 100644
--- a/drugstone/management/includes/DatasetLoader.py
+++ b/drugstone/management/includes/DatasetLoader.py
@@ -1,7 +1,7 @@
from requests.exceptions import RetryError
from drugstone import models
-from python_nedrex.static import get_metadata, get_license
+from nedrex.static import get_metadata, get_license
LICENSE_FILE = "./data/license.txt"
@@ -10,7 +10,8 @@ def get_ppi_string():
dataset, _ = models.PPIDataset.objects.get_or_create(
name='STRING',
link='https://string-db.org/',
- version='11.0'
+ version='11.0',
+ licenced=False
)
return dataset
@@ -19,106 +20,67 @@ def get_ppi_apid():
dataset, _ = models.PPIDataset.objects.get_or_create(
name='APID',
link='http://cicblade.dep.usal.es:8080/APID/',
- version='January 2019'
+ version='January 2019',
+ licenced=False
)
return dataset
-def get_ppi_nedrex_biogrid(url):
- version = get_today_version()
- try:
- version = get_metadata()['source_databases']['biogrid']['date']
- except RetryError:
- pass
-
+def get_ppi_biogrid():
dataset, _ = models.PPIDataset.objects.get_or_create(
name='BioGRID',
- link=url,
- version=version
+ link='https://thebiogrid.org/',
+ version='4.0',
+ licenced=False
)
return dataset
-def get_ppi_nedrex_iid(url):
+def get_nedrex_version():
version = get_today_version()
try:
- version = get_metadata()['source_databases']['iid']['date']
+ version = get_metadata()['version']
except RetryError:
pass
+ return version
- dataset, _ = models.PPIDataset.objects.get_or_create(
- name='IID',
- link=url,
- version=version
- )
- return dataset
-
-
-def get_ppi_nedrex_intact(url):
- version = get_today_version()
- try:
- version = get_metadata()['source_databases']['intact']['date']
- except RetryError:
- pass
- dataset, _ = models.PPIDataset.objects.get_or_create(
- name='IntAct',
+def get_drug_target_nedrex(url, licenced):
+ dataset, _ = models.PDIDataset.objects.get_or_create(
+ name='NeDRex',
link=url,
- version=version
+ version=get_nedrex_version(),
+ licenced=licenced
)
return dataset
-def get_ppi_biogrid():
+def get_ppi_nedrex(url, licenced):
dataset, _ = models.PPIDataset.objects.get_or_create(
- name='BioGRID',
- link='https://thebiogrid.org/',
- version='4.0'
- )
- return dataset
-
-
-def get_drug_target_nedrex(url):
- version = get_today_version()
- try:
- version = get_metadata()['version'],
- except RetryError:
- pass
-
- dataset, _ = models.PDIDataset.objects.get_or_create(
name='NeDRex',
link=url,
- version=version
+ version=get_nedrex_version(),
+ licenced=licenced
)
return dataset
-def get_ppi_nedrex(url):
- version = get_today_version()
- try:
- version = get_metadata()['version'],
- except RetryError:
- pass
-
- dataset, _ = models.PPIDataset.objects.get_or_create(
+def get_protein_disorder_nedrex(url,licenced):
+ dataset, _ = models.PDisDataset.objects.get_or_create(
name='NeDRex',
link=url,
- version=version
+ version=get_nedrex_version(),
+ licenced=licenced
)
return dataset
-def get_protein_disorder_nedrex(url):
- version = get_today_version()
- try:
- version = get_metadata()['version'],
- except RetryError:
- pass
-
- dataset, _ = models.PDisDataset.objects.get_or_create(
+def get_drug_disorder_nedrex(url,licenced):
+ dataset, _ = models.DrDiDataset.objects.get_or_create(
name='NeDRex',
link=url,
- version=version
+ version=get_nedrex_version(),
+ licenced=licenced
)
return dataset
@@ -150,26 +112,12 @@ def import_license():
return ""
-def get_drug_disorder_nedrex(url):
- version = get_today_version()
- try:
- version = get_metadata()['version'],
- except RetryError:
- pass
-
- dataset, _ = models.DrDiDataset.objects.get_or_create(
- name='NeDRex',
- link=url,
- version=version
- )
- return dataset
-
-
def get_drug_target_chembl():
dataset, _ = models.PDIDataset.objects.get_or_create(
name='ChEMBL',
link='https://www.ebi.ac.uk/chembl/',
version='27',
+ licenced=False
)
return dataset
@@ -178,7 +126,8 @@ def get_drug_target_dgidb():
dataset, _ = models.PDIDataset.objects.get_or_create(
name='DGIdb',
link='https://www.dgidb.org/',
- version='4.2.0'
+ version='4.2.0',
+ licenced=False
)
return dataset
@@ -187,7 +136,8 @@ def get_drug_target_drugbank():
dataset, _ = models.PDIDataset.objects.get_or_create(
name='DrugBank',
link='https://go.drugbank.com/',
- version='5.1.7'
+ version='5.1.7',
+ licenced=False
)
return dataset
@@ -197,6 +147,7 @@ def get_disorder_protein_disgenet():
name='DisGeNET',
link='https://www.disgenet.org/home/',
version='6.0',
+ licenced=False
)
return dataset
@@ -206,6 +157,7 @@ def get_drug_disorder_drugbank():
name='DrugBank',
link='https://go.drugbank.com/',
version='5.1.8',
+ licenced=False
)
return dataset
@@ -217,108 +169,115 @@ def get_today_version():
return version
-def get_dis_prot_nedrex_disgenet(url):
+def get_ppi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['disgenet']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
- dataset, _ = models.PDisDataset.objects.get_or_create(
- name='DisGeNET',
+ dataset, _ = models.PPIDataset.objects.get_or_create(
+ name=source,
link=url,
- version=version
+ version=version,
+ licenced=licenced
)
return dataset
-def get_dis_prot_nedrex_omim(url):
+def get_pdi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['omim']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
- dataset, _ = models.PDisDataset.objects.get_or_create(
- name='OMIM',
+ dataset, _ = models.PDIDataset.objects.get_or_create(
+ name=source,
link=url,
- version=version
+ version=version,
+ licenced=licenced
)
return dataset
-
-def get_drdis_nedrex_drugcentral(url):
+def get_pdis_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['drug_central']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
- dataset, _ = models.DrDiDataset.objects.get_or_create(
- name='Drug Central',
+ dataset, _ = models.PDisDataset.objects.get_or_create(
+ name=source,
link=url,
- version=version
+ version=version,
+ licenced=licenced
)
return dataset
-
-def get_drdis_nedrex_ctd(url):
+def get_drdi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['ctd']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
dataset, _ = models.DrDiDataset.objects.get_or_create(
- name='CTD',
+ name=source,
link=url,
- version=version
+ version=version,
+ licenced=licenced
)
return dataset
-
-def get_pdr_nedrex_drugcentral(url):
+def is_licenced_ppi_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['drug_central']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
- dataset, _ = models.PDIDataset.objects.get_or_create(
- name='Drug Central',
- link=url,
- version=version
- )
- return dataset
-
+ try:
+ models.PPIDataset.objects.get(name=source, version=version, licenced=False).link
+ except:
+ return True
+ return False
-def get_pdr_nedrex_drugbank(url):
+def is_licenced_pdi_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases']['drugbank']['date']
+ version = get_metadata()['source_databases'][source]['date']
except RetryError:
pass
- dataset, _ = models.PDIDataset.objects.get_or_create(
- name='DrugBank',
- link=url,
- version=version
- )
- return dataset
-
-
-def get_pdr_nedrex_datasets(url):
- return {'drugbank': get_pdr_nedrex_drugbank(url), 'drugcentral': get_pdr_nedrex_drugcentral(url)}
-
-
-def get_drdis_nedrex_datasets(url):
- return {'ctd': get_drdis_nedrex_ctd(url), 'drugcentral': get_drdis_nedrex_drugcentral(url)}
+ try:
+ models.PDIDataset.objects.get(name=source, version=version, licenced=False).link
+ except:
+ return True
+ return False
+def is_licenced_pdis_source(source):
+ version = get_today_version()
+ try:
+ version = get_metadata()['source_databases'][source]['date']
+ except RetryError:
+ pass
-def get_ppi_nedrex_datasets(url):
- return {'biogrid': get_ppi_nedrex_biogrid(url), 'iid': get_ppi_nedrex_iid(url),
- 'intact': get_ppi_nedrex_intact(url)}
+ try:
+ models.PDisDataset.objects.get(name=source, version=version, licenced=False).link
+ except:
+ return True
+ return False
+def is_licenced_drdi_source(source):
+ version = get_today_version()
+ try:
+ version = get_metadata()['source_databases'][source]['date']
+ except RetryError:
+ pass
-def get_dis_prot_nedrex_datasets(url):
- return {'disgenet': get_dis_prot_nedrex_disgenet(url), 'omim': get_dis_prot_nedrex_omim(url)}
+ try:
+ models.DrDiDataset.objects.get(name=source, version=version, licenced=False).link
+ except:
+ return True
+ return False
diff --git a/drugstone/models.py b/drugstone/models.py
index 3cc0e46cb3744b5ed28eb25b1fbce19909ada24e..ac9b14725e9cc99284f53eccac9656ddd577beeb 100755
--- a/drugstone/models.py
+++ b/drugstone/models.py
@@ -9,48 +9,52 @@ class PPIDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
+ licenced = models.BooleanField(default=True)
def __str__(self):
- return f'{self.name}-{self.version}'
+ return f'{self.name}-{self.version}_{"licenced" if self.licenced else "unlicenced"}'
class Meta:
- unique_together = ('name', 'version')
+ unique_together = ('name', 'version', 'licenced')
class PDIDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
+ licenced = models.BooleanField(default=True)
def __str__(self):
- return f'{self.name}-{self.version}'
+ return f'{self.name}-{self.version}_{"licenced" if self.licenced else "unlicenced"}'
class Meta:
- unique_together = ('name', 'version')
+ unique_together = ('name', 'version','licenced')
class PDisDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
+ licenced = models.BooleanField(default=True)
def __str__(self):
- return f'{self.name}-{self.version}'
+ return f'{self.name}-{self.version}_{"licenced" if self.licenced else "unlicenced"}'
class Meta:
- unique_together = ('name', 'version')
+ unique_together = ('name', 'version', 'licenced')
class DrDiDataset(models.Model):
name = models.CharField(max_length=128, default='', unique=False)
link = models.CharField(max_length=128, default='', unique=False)
version = models.CharField(max_length=128, default='', unique=False)
+ licenced = models.BooleanField(default=True)
def __str__(self):
- return f'{self.name}-{self.version}'
+ return f'{self.name}-{self.version}_{"licenced" if self.licenced else "unlicenced"}'
class Meta:
- unique_together = ('name', 'version')
+ unique_together = ('name', 'version', 'licenced')
class EnsemblGene(models.Model):
diff --git a/drugstone/settings/settings.py b/drugstone/settings/settings.py
index 6a56d2fadaabe96ea8a7f7db3d0ace35897ec6ff..7752e44db1d1f659bb6ee91934ba987a9fd6ddfc 100755
--- a/drugstone/settings/settings.py
+++ b/drugstone/settings/settings.py
@@ -45,7 +45,6 @@ INSTALLED_APPS = [
'django.contrib.staticfiles',
'corsheaders',
'drugstone',
- # 'python_nedrex',
'rest_framework',
]
diff --git a/python_nedrex/.editorconfig b/python_nedrex/.editorconfig
deleted file mode 100644
index d4a2c4405ec2e962c521a13af91bf5f7098a62a8..0000000000000000000000000000000000000000
--- a/python_nedrex/.editorconfig
+++ /dev/null
@@ -1,21 +0,0 @@
-# http://editorconfig.org
-
-root = true
-
-[*]
-indent_style = space
-indent_size = 4
-trim_trailing_whitespace = true
-insert_final_newline = true
-charset = utf-8
-end_of_line = lf
-
-[*.bat]
-indent_style = tab
-end_of_line = crlf
-
-[LICENSE]
-insert_final_newline = false
-
-[Makefile]
-indent_style = tab
diff --git a/python_nedrex/.travis.yml b/python_nedrex/.travis.yml
deleted file mode 100644
index aaba487b1106019a316ff25958a0f6d7ae12b5dd..0000000000000000000000000000000000000000
--- a/python_nedrex/.travis.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Config file for automatic testing at travis-ci.com
-
-language: python
-python:
- - 3.8
- - 3.7
- - 3.6
-
-# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox-travis
-
-# Command to run tests, e.g. python setup.py test
-script: tox
-
-
diff --git a/python_nedrex/AUTHORS.rst b/python_nedrex/AUTHORS.rst
deleted file mode 100644
index 1dbe264bc73d7c02d56b64482f07ca050384b9ea..0000000000000000000000000000000000000000
--- a/python_nedrex/AUTHORS.rst
+++ /dev/null
@@ -1,13 +0,0 @@
-=======
-Credits
-=======
-
-Development Lead
-----------------
-
-* David James Skelton <james.skelton@newcastle.ac.uk>
-
-Contributors
-------------
-
-None yet. Why not be the first?
diff --git a/python_nedrex/CONTRIBUTING.rst b/python_nedrex/CONTRIBUTING.rst
deleted file mode 100644
index 613ac50825a0bd720c752b727641c78a2ef2afa0..0000000000000000000000000000000000000000
--- a/python_nedrex/CONTRIBUTING.rst
+++ /dev/null
@@ -1,128 +0,0 @@
-.. highlight:: shell
-
-============
-Contributing
-============
-
-Contributions are welcome, and they are greatly appreciated! Every little bit
-helps, and credit will always be given.
-
-You can contribute in many ways:
-
-Types of Contributions
-----------------------
-
-Report Bugs
-~~~~~~~~~~~
-
-Report bugs at https://github.com/james-skelton/python_nedrex/issues.
-
-If you are reporting a bug, please include:
-
-* Your operating system name and version.
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
-
-Fix Bugs
-~~~~~~~~
-
-Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
-wanted" is open to whoever wants to implement it.
-
-Implement Features
-~~~~~~~~~~~~~~~~~~
-
-Look through the GitHub issues for features. Anything tagged with "enhancement"
-and "help wanted" is open to whoever wants to implement it.
-
-Write Documentation
-~~~~~~~~~~~~~~~~~~~
-
-python-nedrex could always use more documentation, whether as part of the
-official python-nedrex docs, in docstrings, or even on the web in blog posts,
-articles, and such.
-
-Submit Feedback
-~~~~~~~~~~~~~~~
-
-The best way to send feedback is to file an issue at https://github.com/james-skelton/python_nedrex/issues.
-
-If you are proposing a feature:
-
-* Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
- are welcome :)
-
-Get Started!
-------------
-
-Ready to contribute? Here's how to set up `python_nedrex` for local development.
-
-1. Fork the `python_nedrex` repo on GitHub.
-2. Clone your fork locally::
-
- $ git clone git@github.com:your_name_here/python_nedrex.git
-
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
-
- $ mkvirtualenv python_nedrex
- $ cd python_nedrex/
- $ python setup.py develop
-
-4. Create a branch for local development::
-
- $ git checkout -b name-of-your-bugfix-or-feature
-
- Now you can make your changes locally.
-
-5. When you're done making changes, check that your changes pass flake8 and the
- tests, including testing other Python versions with tox::
-
- $ flake8 python_nedrex tests
- $ python setup.py test or pytest
- $ tox
-
- To get flake8 and tox, just pip install them into your virtualenv.
-
-6. Commit your changes and push your branch to GitHub::
-
- $ git add .
- $ git commit -m "Your detailed description of your changes."
- $ git push origin name-of-your-bugfix-or-feature
-
-7. Submit a pull request through the GitHub website.
-
-Pull Request Guidelines
------------------------
-
-Before you submit a pull request, check that it meets these guidelines:
-
-1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
- your new functionality into a function with a docstring, and add the
- feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
- https://travis-ci.com/james-skelton/python_nedrex/pull_requests
- and make sure that the tests pass for all supported Python versions.
-
-Tips
-----
-
-To run a subset of tests::
-
-$ pytest tests.test_python_nedrex
-
-
-Deploying
----------
-
-A reminder for the maintainers on how to deploy.
-Make sure all your changes are committed (including an entry in HISTORY.rst).
-Then run::
-
-$ bump2version patch # possible: major / minor / patch
-$ git push
-$ git push --tags
-
-Travis will then deploy to PyPI if tests pass.
diff --git a/python_nedrex/HISTORY.rst b/python_nedrex/HISTORY.rst
deleted file mode 100644
index a00abfc2a76e39e812674a740560d4b9201c6ed2..0000000000000000000000000000000000000000
--- a/python_nedrex/HISTORY.rst
+++ /dev/null
@@ -1,8 +0,0 @@
-=======
-History
-=======
-
-0.1.0 (2022-02-23)
-------------------
-
-* First release on PyPI.
diff --git a/python_nedrex/LICENSE b/python_nedrex/LICENSE
deleted file mode 100644
index a5613254179213c20513fadf70bd44581641f21f..0000000000000000000000000000000000000000
--- a/python_nedrex/LICENSE
+++ /dev/null
@@ -1,22 +0,0 @@
-MIT License
-
-Copyright (c) 2022, David James Skelton
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
diff --git a/python_nedrex/MANIFEST.in b/python_nedrex/MANIFEST.in
deleted file mode 100644
index 965b2dda7db7c49f68857dc3aea9af37e30a745e..0000000000000000000000000000000000000000
--- a/python_nedrex/MANIFEST.in
+++ /dev/null
@@ -1,11 +0,0 @@
-include AUTHORS.rst
-include CONTRIBUTING.rst
-include HISTORY.rst
-include LICENSE
-include README.rst
-
-recursive-include tests *
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
diff --git a/python_nedrex/Makefile b/python_nedrex/Makefile
deleted file mode 100644
index 054489ef33bb498a7409b1df27228b0cc20dad30..0000000000000000000000000000000000000000
--- a/python_nedrex/Makefile
+++ /dev/null
@@ -1,89 +0,0 @@
-.PHONY: clean clean-build clean-pyc clean-test coverage dist docs help install lint lint/flake8 lint/black
-.DEFAULT_GOAL := help
-
-define BROWSER_PYSCRIPT
-import os, webbrowser, sys
-
-from urllib.request import pathname2url
-
-webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
-endef
-export BROWSER_PYSCRIPT
-
-define PRINT_HELP_PYSCRIPT
-import re, sys
-
-for line in sys.stdin:
- match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
- if match:
- target, help = match.groups()
- print("%-20s %s" % (target, help))
-endef
-export PRINT_HELP_PYSCRIPT
-
-BROWSER := python -c "$$BROWSER_PYSCRIPT"
-
-help:
- @python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
-
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
-
-clean-build: ## remove build artifacts
- rm -fr build/
- rm -fr dist/
- rm -fr .eggs/
- find . -name '*.egg-info' -exec rm -fr {} +
- find . -name '*.egg' -exec rm -f {} +
-
-clean-pyc: ## remove Python file artifacts
- find . -name '*.pyc' -exec rm -f {} +
- find . -name '*.pyo' -exec rm -f {} +
- find . -name '*~' -exec rm -f {} +
- find . -name '__pycache__' -exec rm -fr {} +
-
-clean-test: ## remove test and coverage artifacts
- rm -fr .tox/
- rm -f .coverage
- rm -fr htmlcov/
- rm -fr .pytest_cache
-
-lint/flake8: ## check style with flake8
- flake8 python_nedrex tests
-lint/black: ## check style with black
- black --check python_nedrex tests
-
-lint: lint/flake8 lint/black ## check style
-
-test: ## run tests quickly with the default Python
- pytest
-
-test-all: ## run tests on every Python version with tox
- tox
-
-coverage: ## check code coverage quickly with the default Python
- coverage run --source python_nedrex -m pytest
- coverage report -m
- coverage html
- $(BROWSER) htmlcov/index.html
-
-docs: ## generate Sphinx HTML documentation, including API docs
- rm -f docs/python_nedrex.rst
- rm -f docs/modules.rst
- sphinx-apidoc -o docs/ python_nedrex
- $(MAKE) -C docs clean
- $(MAKE) -C docs html
- $(BROWSER) docs/_build/html/index.html
-
-servedocs: docs ## compile the docs watching for changes
- watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
-
-release: dist ## package and upload a release
- twine upload dist/*
-
-dist: clean ## builds source and wheel package
- python setup.py sdist
- python setup.py bdist_wheel
- ls -l dist
-
-install: clean ## install the package to the active Python's site-packages
- python setup.py install
diff --git a/python_nedrex/README.rst b/python_nedrex/README.rst
deleted file mode 100644
index f7946f7194b8d94928207ab193dce4d77ca55c6d..0000000000000000000000000000000000000000
--- a/python_nedrex/README.rst
+++ /dev/null
@@ -1,39 +0,0 @@
-=============
-python-nedrex
-=============
-
-
-.. image:: https://img.shields.io/pypi/v/python_nedrex.svg
- :target: https://pypi.python.org/pypi/python_nedrex
-
-.. image:: https://img.shields.io/travis/james-skelton/python_nedrex.svg
- :target: https://travis-ci.com/james-skelton/python_nedrex
-
-.. image:: https://readthedocs.org/projects/python-nedrex/badge/?version=latest
- :target: https://python-nedrex.readthedocs.io/en/latest/?version=latest
- :alt: Documentation Status
-
-
-
-
-A Python library for interfacing with the PNeDRex API
-
-
-* Free software: MIT license
-* Documentation: https://docs.google.com/document/d/1nUngfKSXkqPi_EPaD9d1w3M0SVAuhj6PY4tRMgA8RMk/edit?usp=sharing
-..
- * Documentation: https://python-nedrex.readthedocs.io.
-
-
-Features
---------
-
-* TODO
-
-Credits
--------
-
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
-
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
diff --git a/python_nedrex/docs/Makefile b/python_nedrex/docs/Makefile
deleted file mode 100644
index a94a769f58c441889de3445fa190c4129dcf47b1..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = python -msphinx
-SPHINXPROJ = python_nedrex
-SOURCEDIR = .
-BUILDDIR = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/python_nedrex/docs/authors.rst b/python_nedrex/docs/authors.rst
deleted file mode 100644
index e122f914a87b277e565fc9567af1a7545ec9872b..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/authors.rst
+++ /dev/null
@@ -1 +0,0 @@
-.. include:: ../AUTHORS.rst
diff --git a/python_nedrex/docs/conf.py b/python_nedrex/docs/conf.py
deleted file mode 100755
index adec9e246797329e226ac345df60d2463d7cfa5e..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/conf.py
+++ /dev/null
@@ -1,160 +0,0 @@
-#!/usr/bin/env python
-#
-# python_nedrex documentation build configuration file, created by
-# sphinx-quickstart on Fri Jun 9 13:47:02 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another
-# directory, add these directories to sys.path here. If the directory is
-# relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath(".."))
-
-import python_nedrex
-
-# -- General configuration ---------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
-
-# The master toctree document.
-master_doc = "index"
-
-# General information about the project.
-project = "python-nedrex"
-copyright = "2022, David James Skelton"
-author = "David James Skelton"
-
-# The version info for the project you're documenting, acts as replacement
-# for |version| and |release|, also used in various other places throughout
-# the built documents.
-#
-# The short X.Y version.
-version = python_nedrex.__version__
-# The full version, including alpha/beta/rc tags.
-release = python_nedrex.__version__
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-
-# -- Options for HTML output -------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-#
-html_theme = "alabaster"
-
-# Theme options are theme-specific and customize the look and feel of a
-# theme further. For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
-
-
-# -- Options for HTMLHelp output ---------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = "python_nedrexdoc"
-
-
-# -- Options for LaTeX output ------------------------------------------
-
-latex_elements = {
- # The paper size ('letterpaper' or 'a4paper').
- #
- # 'papersize': 'letterpaper',
- # The font size ('10pt', '11pt' or '12pt').
- #
- # 'pointsize': '10pt',
- # Additional stuff for the LaTeX preamble.
- #
- # 'preamble': '',
- # Latex figure (float) alignment
- #
- # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass
-# [howto, manual, or own class]).
-latex_documents = [
- (
- master_doc,
- "python_nedrex.tex",
- "python-nedrex Documentation",
- "David James Skelton",
- "manual",
- ),
-]
-
-
-# -- Options for manual page output ------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "python_nedrex", "python-nedrex Documentation", [author], 1)]
-
-
-# -- Options for Texinfo output ----------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- (
- master_doc,
- "python_nedrex",
- "python-nedrex Documentation",
- author,
- "python_nedrex",
- "One line description of project.",
- "Miscellaneous",
- ),
-]
diff --git a/python_nedrex/docs/contributing.rst b/python_nedrex/docs/contributing.rst
deleted file mode 100644
index e582053ea018c369be05aae96cf730744f1dc616..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/contributing.rst
+++ /dev/null
@@ -1 +0,0 @@
-.. include:: ../CONTRIBUTING.rst
diff --git a/python_nedrex/docs/history.rst b/python_nedrex/docs/history.rst
deleted file mode 100644
index 250649964bbc36f4bec2942f69238aa6f7c02c1a..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/history.rst
+++ /dev/null
@@ -1 +0,0 @@
-.. include:: ../HISTORY.rst
diff --git a/python_nedrex/docs/index.rst b/python_nedrex/docs/index.rst
deleted file mode 100644
index af528faa0fd4fca728beed7f3686952d811d023c..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/index.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-Welcome to python-nedrex's documentation!
-======================================
-
-.. toctree::
- :maxdepth: 2
- :caption: Contents:
-
- readme
- installation
- usage
- modules
- contributing
- authors
- history
-
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/python_nedrex/docs/installation.rst b/python_nedrex/docs/installation.rst
deleted file mode 100644
index 93c04d4018d3ff7988006aaf977affd9233c20c8..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/installation.rst
+++ /dev/null
@@ -1,51 +0,0 @@
-.. highlight:: shell
-
-============
-Installation
-============
-
-
-Stable release
---------------
-
-To install python-nedrex, run this command in your terminal:
-
-.. code-block:: console
-
- $ pip install python_nedrex
-
-This is the preferred method to install python-nedrex, as it will always install the most recent stable release.
-
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
-
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
-
-
-From sources
-------------
-
-The sources for python-nedrex can be downloaded from the `Github repo`_.
-
-You can either clone the public repository:
-
-.. code-block:: console
-
- $ git clone git://github.com/james-skelton/python_nedrex
-
-Or download the `tarball`_:
-
-.. code-block:: console
-
- $ curl -OJL https://github.com/james-skelton/python_nedrex/tarball/master
-
-Once you have a copy of the source, you can install it with:
-
-.. code-block:: console
-
- $ python setup.py install
-
-
-.. _Github repo: https://github.com/james-skelton/python_nedrex
-.. _tarball: https://github.com/james-skelton/python_nedrex/tarball/master
diff --git a/python_nedrex/docs/make.bat b/python_nedrex/docs/make.bat
deleted file mode 100644
index 35b330121544f73b316d9ac94cb66c52cdacf331..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/make.bat
+++ /dev/null
@@ -1,36 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=python -msphinx
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-set SPHINXPROJ=python_nedrex
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
- echo.
- echo.The Sphinx module was not found. Make sure you have Sphinx installed,
- echo.then set the SPHINXBUILD environment variable to point to the full
- echo.path of the 'sphinx-build' executable. Alternatively you may add the
- echo.Sphinx directory to PATH.
- echo.
- echo.If you don't have Sphinx installed, grab it from
- echo.http://sphinx-doc.org/
- exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
diff --git a/python_nedrex/docs/readme.rst b/python_nedrex/docs/readme.rst
deleted file mode 100644
index 72a33558153fb57def85612b021ec596ef2a51b9..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/readme.rst
+++ /dev/null
@@ -1 +0,0 @@
-.. include:: ../README.rst
diff --git a/python_nedrex/docs/usage.rst b/python_nedrex/docs/usage.rst
deleted file mode 100644
index d6a051382e5ca140cfb74f1a28cb103d0f96ab08..0000000000000000000000000000000000000000
--- a/python_nedrex/docs/usage.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-=====
-Usage
-=====
-
-To use python-nedrex in a project::
-
- import python_nedrex
diff --git a/python_nedrex/format.sh b/python_nedrex/format.sh
deleted file mode 100755
index 5915b2fd5d360bbc452cd588700b7d19c88802ad..0000000000000000000000000000000000000000
--- a/python_nedrex/format.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-black -l 120 python_nedrex
-isort --profile black python_nedrex
-flake8 --max-line-length=120 python_nedrex
-pylint --max-line-length=120 python_nedrex
-bandit python_nedrex
-mypy --strict python_nedrex
diff --git a/python_nedrex/pylintrc b/python_nedrex/pylintrc
deleted file mode 100644
index 77a744e0a4097918044cdcb8e0b716483b13b408..0000000000000000000000000000000000000000
--- a/python_nedrex/pylintrc
+++ /dev/null
@@ -1,590 +0,0 @@
-[MASTER]
-
-# NOTE: This has been modified to disable C0114, C0115, and C0116 (docstrings)
-
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code.
-extension-pkg-allow-list=
-
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code. (This is an alternative name to extension-pkg-allow-list
-# for backward compatibility.)
-extension-pkg-whitelist=
-
-# Return non-zero exit code if any of these messages/categories are detected,
-# even if score is above --fail-under value. Syntax same as enable. Messages
-# specified are enabled, while categories only check already-enabled messages.
-fail-on=
-
-# Specify a score threshold to be exceeded before program exits with error.
-fail-under=10.0
-
-# Files or directories to be skipped. They should be base names, not paths.
-ignore=CVS
-
-# Add files or directories matching the regex patterns to the ignore-list. The
-# regex matches against paths and can be in Posix or Windows format.
-ignore-paths=
-
-# Files or directories matching the regex patterns are skipped. The regex
-# matches against base names, not paths. The default value ignores emacs file
-# locks
-ignore-patterns=^\.#
-
-# Python code to execute, usually for sys.path manipulation such as
-# pygtk.require().
-#init-hook=
-
-# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
-# number of processors available to use.
-jobs=1
-
-# Control the amount of potential inferred values when inferring a single
-# object. This can help the performance when dealing with large functions or
-# complex, nested conditions.
-limit-inference-results=100
-
-# List of plugins (as comma separated values of python module names) to load,
-# usually to register additional checkers.
-load-plugins=
-
-# Pickle collected data for later comparisons.
-persistent=yes
-
-# Minimum Python version to use for version dependent checks. Will default to
-# the version used to run pylint.
-py-version=3.6
-
-# Discover python modules and packages in the file system subtree.
-recursive=no
-
-# When enabled, pylint would attempt to guess common misconfiguration and emit
-# user-friendly hints instead of false-positive error messages.
-suggestion-mode=yes
-
-# Allow loading of arbitrary C extensions. Extensions are imported into the
-# active Python interpreter and may run arbitrary code.
-unsafe-load-any-extension=no
-
-
-[MESSAGES CONTROL]
-
-# Only show warnings with the listed confidence levels. Leave empty to show
-# all. Valid levels: HIGH, CONTROL_FLOW, INFERENCE, INFERENCE_FAILURE,
-# UNDEFINED.
-confidence=
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once). You can also use "--disable=all" to
-# disable everything first and then re-enable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use "--disable=all --enable=classes
-# --disable=W".
-disable=raw-checker-failed,
- bad-inline-option,
- locally-disabled,
- file-ignored,
- suppressed-message,
- useless-suppression,
- deprecated-pragma,
- use-symbolic-message-instead,
- missing-module-docstring,
- missing-class-docstring,
- missing-function-docstring
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time (only on the command line, not in the configuration file where
-# it should appear only once). See also the "--disable" option for examples.
-enable=c-extension-no-member
-
-
-[REPORTS]
-
-# Python expression which should return a score less than or equal to 10. You
-# have access to the variables 'fatal', 'error', 'warning', 'refactor',
-# 'convention', and 'info' which contain the number of messages in each
-# category, as well as 'statement' which is the total number of statements
-# analyzed. This score is used by the global evaluation report (RP0004).
-evaluation=max(0, 0 if fatal else 10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10))
-
-# Template used to display messages. This is a python new-style format string
-# used to format the message information. See doc for all details.
-#msg-template=
-
-# Set the output format. Available formats are text, parseable, colorized, json
-# and msvs (visual studio). You can also give a reporter class, e.g.
-# mypackage.mymodule.MyReporterClass.
-output-format=text
-
-# Tells whether to display a full report or only the messages.
-reports=no
-
-# Activate the evaluation score.
-score=yes
-
-
-[REFACTORING]
-
-# Maximum number of nested blocks for function / method body
-max-nested-blocks=5
-
-# Complete name of functions that never returns. When checking for
-# inconsistent-return-statements if a never returning function is called then
-# it will be considered as an explicit return statement and no message will be
-# printed.
-never-returning-functions=sys.exit,argparse.parse_error
-
-
-[LOGGING]
-
-# The type of string formatting that logging methods do. `old` means using %
-# formatting, `new` is for `{}` formatting.
-logging-format-style=old
-
-# Logging modules to check that the string format arguments are in logging
-# function parameter format.
-logging-modules=logging
-
-
-[SPELLING]
-
-# Limits count of emitted suggestions for spelling mistakes.
-max-spelling-suggestions=4
-
-# Spelling dictionary name. Available dictionaries: none. To make it work,
-# install the 'python-enchant' package.
-spelling-dict=
-
-# List of comma separated words that should be considered directives if they
-# appear and the beginning of a comment and should not be checked.
-spelling-ignore-comment-directives=fmt: on,fmt: off,noqa:,noqa,nosec,isort:skip,mypy:
-
-# List of comma separated words that should not be checked.
-spelling-ignore-words=
-
-# A path to a file that contains the private dictionary; one word per line.
-spelling-private-dict-file=
-
-# Tells whether to store unknown words to the private dictionary (see the
-# --spelling-private-dict-file option) instead of raising a message.
-spelling-store-unknown-words=no
-
-
-[MISCELLANEOUS]
-
-# List of note tags to take in consideration, separated by a comma.
-notes=FIXME,
- XXX,
- TODO
-
-# Regular expression of note tags to take in consideration.
-#notes-rgx=
-
-
-[TYPECHECK]
-
-# List of decorators that produce context managers, such as
-# contextlib.contextmanager. Add to this list to register other decorators that
-# produce valid context managers.
-contextmanager-decorators=contextlib.contextmanager
-
-# List of members which are set dynamically and missed by pylint inference
-# system, and so shouldn't trigger E1101 when accessed. Python regular
-# expressions are accepted.
-generated-members=
-
-# Tells whether missing members accessed in mixin class should be ignored. A
-# class is considered mixin if its name matches the mixin-class-rgx option.
-ignore-mixin-members=yes
-
-# Tells whether to warn about missing members when the owner of the attribute
-# is inferred to be None.
-ignore-none=yes
-
-# This flag controls whether pylint should warn about no-member and similar
-# checks whenever an opaque object is returned when inferring. The inference
-# can return multiple potential results while evaluating a Python object, but
-# some branches might not be evaluated, which results in partial inference. In
-# that case, it might be useful to still emit no-member and other checks for
-# the rest of the inferred objects.
-ignore-on-opaque-inference=yes
-
-# List of class names for which member attributes should not be checked (useful
-# for classes with dynamically set attributes). This supports the use of
-# qualified names.
-ignored-classes=optparse.Values,thread._local,_thread._local
-
-# List of module names for which member attributes should not be checked
-# (useful for modules/projects where namespaces are manipulated during runtime
-# and thus existing member attributes cannot be deduced by static analysis). It
-# supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
-
-# Show a hint with possible names when a member name was not found. The aspect
-# of finding the hint is based on edit distance.
-missing-member-hint=yes
-
-# The minimum edit distance a name should have in order to be considered a
-# similar match for a missing member name.
-missing-member-hint-distance=1
-
-# The total number of similar names that should be taken in consideration when
-# showing a hint for a missing member.
-missing-member-max-choices=1
-
-# Regex pattern to define which classes are considered mixins ignore-mixin-
-# members is set to 'yes'
-mixin-class-rgx=.*[Mm]ixin
-
-# List of decorators that change the signature of a decorated function.
-signature-mutators=
-
-
-[VARIABLES]
-
-# List of additional names supposed to be defined in builtins. Remember that
-# you should avoid defining new builtins when possible.
-additional-builtins=
-
-# Tells whether unused global variables should be treated as a violation.
-allow-global-unused-variables=yes
-
-# List of names allowed to shadow builtins
-allowed-redefined-builtins=
-
-# List of strings which can identify a callback function by name. A callback
-# name must start or end with one of those strings.
-callbacks=cb_,
- _cb
-
-# A regular expression matching the name of dummy variables (i.e. expected to
-# not be used).
-dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
-
-# Argument names that match this expression will be ignored. Default to name
-# with leading underscore.
-ignored-argument-names=_.*|^ignored_|^unused_
-
-# Tells whether we should check for unused import in __init__ files.
-init-import=no
-
-# List of qualified module names which can have objects that can redefine
-# builtins.
-redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io
-
-
-[FORMAT]
-
-# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
-expected-line-ending-format=
-
-# Regexp for a line that is allowed to be longer than the limit.
-ignore-long-lines=^\s*(# )?<?https?://\S+>?$
-
-# Number of spaces of indent required inside a hanging or continued line.
-indent-after-paren=4
-
-# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
-# tab).
-indent-string=' '
-
-# Maximum number of characters on a single line.
-max-line-length=100
-
-# Maximum number of lines in a module.
-max-module-lines=1000
-
-# Allow the body of a class to be on the same line as the declaration if body
-# contains single statement.
-single-line-class-stmt=no
-
-# Allow the body of an if to be on the same line as the test if there is no
-# else.
-single-line-if-stmt=no
-
-
-[SIMILARITIES]
-
-# Comments are removed from the similarity computation
-ignore-comments=yes
-
-# Docstrings are removed from the similarity computation
-ignore-docstrings=yes
-
-# Imports are removed from the similarity computation
-ignore-imports=yes
-
-# Signatures are removed from the similarity computation
-ignore-signatures=no
-
-# Minimum lines number of a similarity.
-min-similarity-lines=4
-
-
-[STRING]
-
-# This flag controls whether inconsistent-quotes generates a warning when the
-# character used as a quote delimiter is used inconsistently within a module.
-check-quote-consistency=no
-
-# This flag controls whether the implicit-str-concat should generate a warning
-# on implicit string concatenation in sequences defined over several lines.
-check-str-concat-over-line-jumps=no
-
-
-[BASIC]
-
-# Naming style matching correct argument names.
-argument-naming-style=snake_case
-
-# Regular expression matching correct argument names. Overrides argument-
-# naming-style. If left empty, argument names will be checked with the set
-# naming style.
-#argument-rgx=
-
-# Naming style matching correct attribute names.
-attr-naming-style=snake_case
-
-# Regular expression matching correct attribute names. Overrides attr-naming-
-# style. If left empty, attribute names will be checked with the set naming
-# style.
-#attr-rgx=
-
-# Bad variable names which should always be refused, separated by a comma.
-bad-names=foo,
- bar,
- baz,
- toto,
- tutu,
- tata
-
-# Bad variable names regexes, separated by a comma. If names match any regex,
-# they will always be refused
-bad-names-rgxs=
-
-# Naming style matching correct class attribute names.
-class-attribute-naming-style=any
-
-# Regular expression matching correct class attribute names. Overrides class-
-# attribute-naming-style. If left empty, class attribute names will be checked
-# with the set naming style.
-#class-attribute-rgx=
-
-# Naming style matching correct class constant names.
-class-const-naming-style=UPPER_CASE
-
-# Regular expression matching correct class constant names. Overrides class-
-# const-naming-style. If left empty, class constant names will be checked with
-# the set naming style.
-#class-const-rgx=
-
-# Naming style matching correct class names.
-class-naming-style=PascalCase
-
-# Regular expression matching correct class names. Overrides class-naming-
-# style. If left empty, class names will be checked with the set naming style.
-#class-rgx=
-
-# Naming style matching correct constant names.
-const-naming-style=UPPER_CASE
-
-# Regular expression matching correct constant names. Overrides const-naming-
-# style. If left empty, constant names will be checked with the set naming
-# style.
-#const-rgx=
-
-# Minimum line length for functions/classes that require docstrings, shorter
-# ones are exempt.
-docstring-min-length=-1
-
-# Naming style matching correct function names.
-function-naming-style=snake_case
-
-# Regular expression matching correct function names. Overrides function-
-# naming-style. If left empty, function names will be checked with the set
-# naming style.
-#function-rgx=
-
-# Good variable names which should always be accepted, separated by a comma.
-good-names=i,
- j,
- k,
- ex,
- Run,
- _
-
-# Good variable names regexes, separated by a comma. If names match any regex,
-# they will always be accepted
-good-names-rgxs=
-
-# Include a hint for the correct naming format with invalid-name.
-include-naming-hint=no
-
-# Naming style matching correct inline iteration names.
-inlinevar-naming-style=any
-
-# Regular expression matching correct inline iteration names. Overrides
-# inlinevar-naming-style. If left empty, inline iteration names will be checked
-# with the set naming style.
-#inlinevar-rgx=
-
-# Naming style matching correct method names.
-method-naming-style=snake_case
-
-# Regular expression matching correct method names. Overrides method-naming-
-# style. If left empty, method names will be checked with the set naming style.
-#method-rgx=
-
-# Naming style matching correct module names.
-module-naming-style=snake_case
-
-# Regular expression matching correct module names. Overrides module-naming-
-# style. If left empty, module names will be checked with the set naming style.
-#module-rgx=
-
-# Colon-delimited sets of names that determine each other's naming style when
-# the name regexes allow several styles.
-name-group=
-
-# Regular expression which should only match function or class names that do
-# not require a docstring.
-no-docstring-rgx=^_
-
-# List of decorators that produce properties, such as abc.abstractproperty. Add
-# to this list to register other decorators that produce valid properties.
-# These decorators are taken in consideration only for invalid-name.
-property-classes=abc.abstractproperty
-
-# Regular expression matching correct type variable names. If left empty, type
-# variable names will be checked with the set naming style.
-#typevar-rgx=
-
-# Naming style matching correct variable names.
-variable-naming-style=snake_case
-
-# Regular expression matching correct variable names. Overrides variable-
-# naming-style. If left empty, variable names will be checked with the set
-# naming style.
-#variable-rgx=
-
-
-[CLASSES]
-
-# Warn about protected attribute access inside special methods
-check-protected-access-in-special-methods=no
-
-# List of method names used to declare (i.e. assign) instance attributes.
-defining-attr-methods=__init__,
- __new__,
- setUp,
- __post_init__
-
-# List of member names, which should be excluded from the protected access
-# warning.
-exclude-protected=_asdict,
- _fields,
- _replace,
- _source,
- _make
-
-# List of valid names for the first argument in a class method.
-valid-classmethod-first-arg=cls
-
-# List of valid names for the first argument in a metaclass class method.
-valid-metaclass-classmethod-first-arg=cls
-
-
-[IMPORTS]
-
-# List of modules that can be imported at any level, not just the top level
-# one.
-allow-any-import-level=
-
-# Allow wildcard imports from modules that define __all__.
-allow-wildcard-with-all=no
-
-# Analyse import fallback blocks. This can be used to support both Python 2 and
-# 3 compatible code, which means that the block might have code that exists
-# only in one or another interpreter, leading to false positives when analysed.
-analyse-fallback-blocks=no
-
-# Deprecated modules which should not be used, separated by a comma.
-deprecated-modules=
-
-# Output a graph (.gv or any supported image format) of external dependencies
-# to the given file (report RP0402 must not be disabled).
-ext-import-graph=
-
-# Output a graph (.gv or any supported image format) of all (i.e. internal and
-# external) dependencies to the given file (report RP0402 must not be
-# disabled).
-import-graph=
-
-# Output a graph (.gv or any supported image format) of internal dependencies
-# to the given file (report RP0402 must not be disabled).
-int-import-graph=
-
-# Force import order to recognize a module as part of the standard
-# compatibility libraries.
-known-standard-library=
-
-# Force import order to recognize a module as part of a third party library.
-known-third-party=enchant
-
-# Couples of modules and preferred modules, separated by a comma.
-preferred-modules=
-
-
-[DESIGN]
-
-# List of regular expressions of class ancestor names to ignore when counting
-# public methods (see R0903)
-exclude-too-few-public-methods=
-
-# List of qualified class names to ignore when counting class parents (see
-# R0901)
-ignored-parents=
-
-# Maximum number of arguments for function / method.
-max-args=5
-
-# Maximum number of attributes for a class (see R0902).
-max-attributes=7
-
-# Maximum number of boolean expressions in an if statement (see R0916).
-max-bool-expr=5
-
-# Maximum number of branch for function / method body.
-max-branches=12
-
-# Maximum number of locals for function / method body.
-max-locals=15
-
-# Maximum number of parents for a class (see R0901).
-max-parents=7
-
-# Maximum number of public methods for a class (see R0904).
-max-public-methods=20
-
-# Maximum number of return / yield for function / method body.
-max-returns=6
-
-# Maximum number of statements in function / method body.
-max-statements=50
-
-# Minimum number of public methods for a class (see R0903).
-min-public-methods=2
-
-
-[EXCEPTIONS]
-
-# Exceptions that will emit a warning when being caught. Defaults to
-# "BaseException, Exception".
-overgeneral-exceptions=BaseException,
- Exception
diff --git a/python_nedrex/python_nedrex/__init__.py b/python_nedrex/python_nedrex/__init__.py
deleted file mode 100644
index cc7d76faf5b55c3d3df64629e4b3760416799cb9..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/__init__.py
+++ /dev/null
@@ -1,46 +0,0 @@
-"""Top-level package for python-nedrex."""
-
-__author__ = """David James Skelton"""
-__email__ = "james.skelton@newcastle.ac.uk"
-__version__ = "0.1.1"
-
-from typing import Optional
-
-from attrs import define
-
-
-@define
-class _Config:
- _url_base: Optional[str] = None
- _url_vpd: Optional[str] = None
- _api_key: Optional[str] = None
-
- @property
- def url_base(self) -> Optional[str]:
- """Returns the API URL base stored on the _Config instance"""
- return self._url_base
-
- @property
- def url_vpd(self) -> Optional[str]:
- """Returns the VPD URL base stored on the _Config instance"""
- return self._url_vpd
-
- @property
- def api_key(self) -> Optional[str]:
- """Returns the API key stored on the _Config instance"""
- return self._api_key
-
- def set_url_base(self, url_base: str) -> None:
- """Sets the URL base for the API in the configuration"""
- self._url_base = url_base.rstrip("/")
-
- def set_url_vpd(self, url_vpd: str) -> None:
- """Sets the URL base for the VPD in the configuration"""
- self._url_vpd = url_vpd.rstrip("/")
-
- def set_api_key(self, key: str) -> None:
- """Sets the API key in the configuration"""
- self._api_key = key
-
-
-config: _Config = _Config()
diff --git a/python_nedrex/python_nedrex/bicon.py b/python_nedrex/python_nedrex/bicon.py
deleted file mode 100644
index 0d2693f535c286594e59b225a849b6f91277ee53..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/bicon.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from pathlib import Path as _Path
-from typing import IO as _IO
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import download_file as _download_file
-from python_nedrex.common import http as _http
-
-
-def bicon_request(
- expression_file: _IO[str],
- lg_min: int = 10,
- lg_max: int = 15,
- network: str = "DEFAULT",
-) -> str:
- files = {"expression_file": expression_file}
- data = {"lg_min": lg_min, "lg_max": lg_max, "network": network}
-
- url = f"{_config.url_base}/bicon/submit"
- resp = _http.post(url, data=data, files=files, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-def check_bicon_status(uid: str) -> _Dict[str, _Any]:
- url = f"{_config.url_base}/bicon/status"
- resp = _http.get(url, params={"uid": uid}, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _Any] = _check_response(resp)
- return result
-
-
-def download_bicon_data(uid: str, target: _Optional[str] = None) -> None:
- if target is None:
- target = str(_Path(f"{uid}.zip").resolve())
-
- url = f"{_config.url_base}/bicon/download?uid={uid}"
-
- _download_file(url, target)
diff --git a/python_nedrex/python_nedrex/closeness.py b/python_nedrex/python_nedrex/closeness.py
deleted file mode 100644
index f75d81128138fa1895b7c55f0634496f366e3907..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/closeness.py
+++ /dev/null
@@ -1,33 +0,0 @@
-from typing import List as _List
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-def closeness_submit(
- seeds: _List[str],
- only_direct_drugs: bool = True,
- only_approved_drugs: bool = True,
- N: _Optional[int] = None, # pylint: disable=C0103
-) -> str:
- url = f"{_config.url_base}/closeness/submit"
-
- body = {"seeds": seeds, "only_direct_drugs": only_direct_drugs, "only_approved_drugs": only_approved_drugs, "N": N}
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-check_closeness_status = _check_status_factory("/closeness/status")
-
-
-def download_closeness_results(uid: str) -> str:
- url = f"{_config.url_base}/closeness/download"
- params = {"uid": uid}
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp, return_type="text")
- return result
diff --git a/python_nedrex/python_nedrex/common.py b/python_nedrex/python_nedrex/common.py
deleted file mode 100644
index 6e3fdba65da2407b45eca3696746a1ee2f8ac128..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/common.py
+++ /dev/null
@@ -1,96 +0,0 @@
-import urllib.request
-from typing import Any, Callable, Dict, Optional
-
-import cachetools
-import requests # type: ignore
-from requests.adapters import HTTPAdapter # type: ignore
-from urllib3.util.retry import Retry # type: ignore
-
-from python_nedrex import config
-from python_nedrex.exceptions import ConfigError, NeDRexError
-
-# Start - code derived from https://findwork.dev/blog/advanced-usage-python-requests-timeouts-retries-hooks/
-DEFAULT_TIMEOUT = 120
-
-
-class TimeoutHTTPAdapter(HTTPAdapter): # type: ignore
- def __init__(self, *args: Any, **kwargs: Any) -> None:
- self.timeout = DEFAULT_TIMEOUT
- if "timeout" in kwargs:
- self.timeout = kwargs["timeout"]
- del kwargs["timeout"]
- super().__init__(*args, **kwargs)
-
- # pylint: disable=arguments-differ
- def send(self, request: requests.Request, **kwargs: Any) -> requests.Response:
- timeout = kwargs.get("timeout")
- if timeout is None:
- kwargs["timeout"] = self.timeout
- return super().send(request, **kwargs)
-
-
-retry_strategy = Retry(total=3, backoff_factor=1, status_forcelist=[429, 500, 502, 503, 504])
-
-http = requests.Session()
-adapter = TimeoutHTTPAdapter(max_retries=retry_strategy)
-http.mount("https://", adapter)
-http.mount("http://", adapter)
-# End - code derived from https://findwork.dev/blog/advanced-usage-python-requests-timeouts-retries-hooks/
-
-
-def check_response(resp: requests.Response, return_type: str = "json") -> Any:
- if resp.status_code == 401:
- data = resp.json()
- if data["detail"] == "An API key is required to access the requested data":
- raise ConfigError("no API key set in the configuration")
-
- if resp.status_code in {102, 400, 422}:
- data = resp.json()
- raise NeDRexError(data["detail"])
-
- if resp.status_code == 404:
- raise NeDRexError("not found")
-
- if return_type == "json":
- data = resp.json()
- elif return_type == "text":
- data = resp.text
- else:
- raise NeDRexError(f"invalid value for return_type ({return_type!r}) in check_response")
- return data
-
-
-@cachetools.cached(cachetools.TTLCache(1, ttl=10))
-def get_pagination_limit() -> Any:
- url = f"{config.url_base}/pagination_max"
- return requests.get(url, headers={"x-api-key": config.api_key}).json()
-
-
-def check_pagination_limit(limit: Optional[int], upper_limit: int) -> None:
- if limit and upper_limit < limit:
- raise NeDRexError(f"limit={limit:,} is too great (maximum is {upper_limit:,})")
-
-
-def download_file(url: str, target: str) -> None:
- if config.api_key is not None:
- opener = urllib.request.build_opener()
- opener.addheaders = [("x-api-key", config.api_key)]
- urllib.request.install_opener(opener)
-
- try:
- urllib.request.urlretrieve(url, target)
- except urllib.error.HTTPError as err:
- if err.code == 404:
- raise NeDRexError("not found") from err
- raise NeDRexError("unexpected failure") from err
-
-
-def check_status_factory(url_suffix: str) -> Callable[[str], Dict[str, Any]]:
- def return_func(uid: str) -> Dict[str, Any]:
- url = f"{config.url_base}{url_suffix}"
- params = {"uid": uid}
- resp = http.get(url, params=params, headers={"x-api-key": config.api_key})
- result: Dict[str, Any] = check_response(resp)
- return result
-
- return return_func
diff --git a/python_nedrex/python_nedrex/core.py b/python_nedrex/python_nedrex/core.py
deleted file mode 100644
index 7e8f38c09c980ab6e6db94ce40f59860210ea4b3..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/core.py
+++ /dev/null
@@ -1,229 +0,0 @@
-"""Module containing functions relating to the general routes in the NeDRex API
-
-Additionally, this module also contains routes for obtaining API keys.
-"""
-
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Generator as _Generator
-from typing import List as _List
-from typing import Optional as _Optional
-from typing import cast as _cast
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_pagination_limit as _check_pagination_limit
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import get_pagination_limit as _get_pagination_limit
-from python_nedrex.common import http as _http
-from python_nedrex.decorators import check_url_base as _check_url_base
-from python_nedrex.exceptions import NeDRexError as _NeDRexError
-
-
-def _check_type(coll_name: str, coll_type: str) -> bool:
- if coll_type == "edge":
- if coll_name in get_edge_types():
- return True
- raise _NeDRexError(f"type={coll_name!r} not in NeDRex edge types")
-
- if coll_type == "node":
- if coll_name in get_node_types():
- return True
- raise _NeDRexError(f"type={coll_name!r} not in NeDRex node types")
-
- raise _NeDRexError(f"_check_type received invalid coll_type={coll_type!r}")
-
-
-@_check_url_base
-def api_keys_active() -> bool:
- """Checks whether API keys are active for the instance of NeDRex set in the config
-
- Returns True if the keys are active, False otherwise
- """
- url = f"{_config.url_base}/api_key_setting"
- response = _http.get(url)
- if response.status_code != 200:
- raise Exception("Unexpected non-200 status code")
- return _cast(bool, response.json())
-
-
-@_check_url_base
-def get_api_key(*, accept_eula: bool = False) -> _Any:
- """Obtains a new API key from the NeDRex API.
-
- This function will only return if accept_eula is explicitly set to True
- """
- if accept_eula is not True:
- raise _NeDRexError("an API key cannot be obtained unless accept_eula is set to True")
-
- url = f"{_config.url_base}/admin/api_key/generate"
- response = _http.post(url, json={"accept_eula": accept_eula})
- return response.json()
-
-
-@_check_url_base
-def get_node_types() -> _Any:
- """
- Returns the list of node types stored in NeDRexDB
-
- Returns:
- node_list (list[str]): List of node types in NeDRex
- """
- url: str = f"{_config.url_base}/list_node_collections"
- response = _http.get(url, headers={"x-api-key": _config.api_key})
- node_list = _check_response(response)
- return node_list
-
-
-@_check_url_base
-def get_edge_types() -> _Any:
- """
- Returns a list of edge types stored in NeDRexDB
-
- Returns:
- edge_list (list[str]): List of edge types in NeDRex
- """
- url: str = f"{_config.url_base}/list_edge_collections"
- response = _http.get(url, headers={"x-api-key": _config.api_key})
- edge_list = _check_response(response)
- return edge_list
-
-
-@_check_url_base
-def get_collection_attributes(coll_type: str, include_counts: bool = False) -> _Any:
- """
- Retrurns a list of the available attributes stored in NeDRex for the given type
-
- Parameters:
- type (str): The node or edge type to get available attributes for
-
- Returns:
- attr_list (list[str]): The list of available attributes for the specified node/edge type
- """
- url: str = f"{_config.url_base}/{coll_type}/attributes"
- response = _http.get(url, headers={"x-api-key": _config.api_key}, params={"include_counts": include_counts})
- attr_list = _check_response(response)
- return attr_list
-
-
-@_check_url_base
-def get_node_ids(coll_type: str) -> _Any:
- """
- Returns a list of node identifiers in NeDRex for the given type
-
- Parameters:
- type(str): The node type to get IDs for
- Returns:
- node_ids (list[str]): The list of available node_ids for the specified node type
- """
- _check_type(coll_type, "node")
-
- url: str = f"{_config.url_base}/{coll_type}/attributes/primaryDomainId/json"
-
- resp = _http.get(url, headers={"x-api-key": _config.api_key})
- data = _check_response(resp)
- node_ids = [i["primaryDomainId"] for i in data]
- return node_ids
-
-
-@_check_url_base
-def get_nodes(
- node_type: str,
- attributes: _Optional[_List[str]] = None,
- node_ids: _Optional[_List[str]] = None,
- limit: _Optional[int] = None,
- offset: int = 0,
-) -> _Any:
- """
- Returns nodes in NeDRex for the given type
-
- Parameters:
- node_type (str): The node type to collect
- attributes (Optional[list[str]]): A list of attributes to return for the collected nodes. The default
- (None) returns all attributes.
- node_ids (Optional[list[str]]): A list of the specific node IDs to return. The default (None) returns all
- nodes.
- limit (Optional[int]): A limit for the number of records to be returned. The maximum value for this is set
- by the API.
- offset (int): The number of records to skip before returning records. Default is 0 (no records skipped).
- Returns:
- node_ids (list[str]): The list of available node_ids for the specified node type
- """
- _check_type(node_type, "node")
-
- upper_limit = _get_pagination_limit()
- _check_pagination_limit(limit, upper_limit)
-
- params = {"node_id": node_ids, "attribute": attributes, "offset": offset, "limit": limit}
-
- resp = _http.get(
- f"{_config.url_base}/{node_type}/attributes/json", params=params, headers={"x-api-key": _config.api_key}
- )
-
- items = _check_response(resp)
- return items
-
-
-@_check_url_base
-def iter_nodes(
- node_type: str, attributes: _Optional[_List[str]] = None, node_ids: _Optional[_List[str]] = None
-) -> _Generator[_Dict[str, _Any], None, None]:
-
- _check_type(node_type, "node")
- upper_limit = _get_pagination_limit()
-
- params: _Dict[str, _Any] = {"node_id": node_ids, "attribute": attributes, "limit": upper_limit}
-
- offset = 0
- while True:
- params["offset"] = offset
- resp = _http.get(
- f"{_config.url_base}/{node_type}/attributes/json", params=params, headers={"x-api-key": _config.api_key}
- )
-
- data = _check_response(resp)
-
- for doc in data:
- yield doc
-
- if len(data) < upper_limit:
- break
- offset += upper_limit
-
-
-@_check_url_base
-def get_edges(edge_type: str, limit: _Optional[int] = None, offset: _Optional[int] = None) -> _Any:
- """
- Returns edges in NeDRex of the given type
-
- Parameters:
- edge_type (str): The node type to collect
- limit (Optional[int]): A limit for the number of records to be returned. The maximum value for this is set
- by the API.
- offset (int): The number of records to skip before returning records. Default is 0 (no records skipped).
- """
- _check_type(edge_type, "edge")
-
- params = {"limit": limit, "offset": offset, "api_key": _config.api_key}
-
- resp = _http.get(f"{_config.url_base}/{edge_type}/all", params=params, headers={"x-api-key": _config.api_key})
- items = _check_response(resp)
- return items
-
-
-@_check_url_base
-def iter_edges(edge_type: str) -> _Generator[_Dict[str, _Any], None, None]:
- _check_type(edge_type, "edge")
- upper_limit = _get_pagination_limit()
-
- offset = 0
- while True:
- params = {"offset": offset, "limit": upper_limit}
- resp = _http.get(f"{_config.url_base}/{edge_type}/all", params=params, headers={"x-api-key": _config.api_key})
- data = _check_response(resp)
-
- for doc in data:
- yield doc
-
- if len(data) < upper_limit:
- break
- offset += upper_limit
diff --git a/python_nedrex/python_nedrex/decorators.py b/python_nedrex/python_nedrex/decorators.py
deleted file mode 100644
index 29ffc65bff5852754ea062f8ab146884cd9e2391..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/decorators.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from typing import Any, Callable, TypeVar
-
-from python_nedrex import config
-from python_nedrex.exceptions import ConfigError
-
-R = TypeVar("R")
-
-
-def check_url_base(func: Callable[..., R]) -> Callable[..., R]:
- def wrapped_fx(*args: Any, **kwargs: Any) -> Any:
- if hasattr(config, "url_base") and config.url_base is not None:
- return func(*args, **kwargs)
- raise ConfigError("API URL is not set in the config")
-
- return wrapped_fx
-
-
-def check_url_vpd(func: Callable[..., R]) -> Callable[..., R]:
- def wrapped_fx(*args: Any, **kwargs: Any) -> Any:
- if hasattr(config, "url_vpd") and config.url_vpd is not None:
- return func(*args, **kwargs)
- raise ConfigError("VPD URL is not set in the config")
-
- return wrapped_fx
diff --git a/python_nedrex/python_nedrex/diamond.py b/python_nedrex/python_nedrex/diamond.py
deleted file mode 100644
index 1b5fc78f9e9a6f4b74e95f966752e093ac6c5ba1..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/diamond.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-def diamond_submit(
- seeds: _List[str],
- n: int, # pylint: disable=C0103
- alpha: int = 1,
- network: str = "DEFAULT",
- edges: str = "all",
-) -> str:
- if edges not in {"limited", "all"}:
- raise ValueError(f"invalid value for argument edges ({edges!r}), should be all|limited")
-
- url = f"{_config.url_base}/diamond/submit"
- body = {
- "seeds": seeds,
- "n": n,
- "alpha": alpha,
- "network": network,
- "edges": edges,
- }
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-check_diamond_status = _check_status_factory("/diamond/status")
-
-
-def download_diamond_results(uid: str) -> str:
- url = f"{_config.url_base}/diamond/download"
- params = {"uid": uid}
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp, return_type="text")
- return result
diff --git a/python_nedrex/python_nedrex/disorder.py b/python_nedrex/python_nedrex/disorder.py
deleted file mode 100644
index 21502be3b1dda5a92b2f787b617d615a30cac8cf..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/disorder.py
+++ /dev/null
@@ -1,31 +0,0 @@
-"""Module containing python functions to access the disorder routes in the NeDRex API"""
-
-from typing import Any as _Any
-from typing import Callable as _Callable
-from typing import List as _List
-from typing import Union as _Union
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import http as _http
-from python_nedrex.decorators import check_url_base as _check_url_base
-
-
-def _generate_route(path: str) -> _Callable[[_Union[str, _List[str]]], _Any]:
- @_check_url_base
- def new_func(codes: _Union[str, _List[str]]) -> _Any:
- if isinstance(codes, str):
- codes = [codes]
-
- url = f"{_config.url_base}/disorder/{path}"
- resp = _http.get(url, params={"q": codes}, headers={"x-api-key": _config.api_key})
- return _check_response(resp)
-
- return new_func
-
-
-search_by_icd10 = _generate_route("get_by_icd10")
-get_disorder_descendants = _generate_route("descendants")
-get_disorder_ancestors = _generate_route("ancestors")
-get_disorder_parents = _generate_route("parents")
-get_disorder_children = _generate_route("children")
diff --git a/python_nedrex/python_nedrex/domino.py b/python_nedrex/python_nedrex/domino.py
deleted file mode 100644
index b21a36fd1026ed5f43ba1c9d381fdb968f17de9c..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/domino.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-def domino_submit(seeds: _List[str], network: str = "DEFAULT") -> str:
- url = f"{_config.url_base}/domino/submit"
- body = {"seeds": seeds, "network": network}
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-check_domino_status = _check_status_factory("/domino/status")
diff --git a/python_nedrex/python_nedrex/exceptions.py b/python_nedrex/python_nedrex/exceptions.py
deleted file mode 100644
index bf9c9c6666bc30cea01a5594f09f6a22fd97ccae..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/exceptions.py
+++ /dev/null
@@ -1,6 +0,0 @@
-class NeDRexError(Exception):
- pass
-
-
-class ConfigError(NeDRexError):
- pass
diff --git a/python_nedrex/python_nedrex/graph.py b/python_nedrex/python_nedrex/graph.py
deleted file mode 100644
index fa89adb2b3c0692b485b214c4bdb466da0f44d9e..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/graph.py
+++ /dev/null
@@ -1,82 +0,0 @@
-from pathlib import Path as _Path
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import List as _List
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import download_file as _download_file
-from python_nedrex.common import http as _http
-
-
-# pylint: disable=R0913
-def build_request(
- nodes: _Optional[_List[str]] = None,
- edges: _Optional[_List[str]] = None,
- ppi_evidence: _Optional[_List[str]] = None,
- include_ppi_self_loops: bool = False,
- taxid: _Optional[_List[int]] = None,
- drug_groups: _Optional[_List[str]] = None,
- concise: bool = True,
- include_omim: bool = True,
- disgenet_threshold: float = 0.0,
- use_omim_ids: bool = False,
- split_drug_types: bool = False,
-) -> str:
-
- if nodes is None:
- nodes = ["disorder", "drug", "gene", "protein"]
- if edges is None:
- edges = [
- "disorder_is_subtype_of_disorder",
- "drug_has_indication",
- "drug_has_target",
- "gene_associated_with_disorder",
- "protein_encoded_by_gene",
- "protein_interacts_with_protein",
- ]
- if ppi_evidence is None:
- ppi_evidence = ["exp"]
- if taxid is None:
- taxid = [9606]
- if drug_groups is None:
- drug_groups = ["approved"]
-
- body = {
- "nodes": nodes,
- "edges": edges,
- "ppi_evidence": ppi_evidence,
- "ppi_self_loops": include_ppi_self_loops,
- "taxid": taxid,
- "drug_groups": drug_groups,
- "concise": concise,
- "include_omim": include_omim,
- "disgenet_threshold": disgenet_threshold,
- "use_omim_ids": use_omim_ids,
- "split_drug_types": split_drug_types,
- }
-
- url = f"{_config.url_base}/graph/builder"
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-# pylint: enable=R0913
-
-
-def check_build_status(uid: str) -> _Dict[str, _Any]:
- url = f"{_config.url_base}/graph/details/{uid}"
- resp = _http.get(url, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _Any] = _check_response(resp)
- return result
-
-
-def download_graph(uid: str, target: _Optional[str] = None) -> None:
- if target is None:
- target = str(_Path(f"{uid}.graphml").resolve())
-
- url = f"{_config.url_base}/graph/download/{uid}/{uid}.graphml"
-
- _download_file(url, target)
diff --git a/python_nedrex/python_nedrex/kpm.py b/python_nedrex/python_nedrex/kpm.py
deleted file mode 100644
index 118f53db4cb9c4ed8bef7ee25a70b13afc5edd9a..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/kpm.py
+++ /dev/null
@@ -1,27 +0,0 @@
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import http as _http
-
-
-def kpm_submit(seeds: _List[str], k: int, network: str = "DEFAULT") -> str:
-
- url = f"{_config.url_base}/kpm/submit"
- body = {"seeds": seeds, "k": k, "network": network}
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-def check_kpm_status(uid: str) -> _Dict[str, _Any]:
-
- url = f"{_config.url_base}/kpm/status"
- params = {"uid": uid}
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _Any] = _check_response(resp)
- return result
diff --git a/python_nedrex/python_nedrex/must.py b/python_nedrex/python_nedrex/must.py
deleted file mode 100644
index 8bfd1af485f74768e674ec0e76bf9fcbc27d4ec9..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/must.py
+++ /dev/null
@@ -1,36 +0,0 @@
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-# pylint: disable=R0913
-def must_request(
- seeds: _List[str],
- hubpenalty: float,
- multiple: bool,
- trees: int,
- maxit: int,
- network: str = "DEFAULT",
-) -> str:
- body = {
- "seeds": seeds,
- "network": network,
- "hubpenalty": hubpenalty,
- "multiple": multiple,
- "trees": trees,
- "maxit": maxit,
- }
-
- url = f"{_config.url_base}/must/submit"
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-# pylint: enable=R0913
-
-
-check_must_status = _check_status_factory("/must/status")
diff --git a/python_nedrex/python_nedrex/neo4j.py b/python_nedrex/python_nedrex/neo4j.py
deleted file mode 100644
index 0a1e48bb5233c2a769a778c7b60952818e89f52f..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/neo4j.py
+++ /dev/null
@@ -1,27 +0,0 @@
-import json as _json
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Generator as _Generator
-
-from requests.exceptions import ChunkedEncodingError # type: ignore
-
-from python_nedrex import config as _config
-from python_nedrex.common import http as _http
-from python_nedrex.exceptions import NeDRexError
-
-
-def neo4j_query(query: str) -> _Generator[_Dict[str, _Any], None, None]:
- url = f"{_config.url_base}/neo4j/query"
- params = {"query": query}
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key}, stream=True)
- if resp.status_code != 200:
- raise NeDRexError("Querying Neo4j returned a non-200 status code.")
-
- try:
- for line in resp.iter_lines():
- data = _json.loads(line.decode())
- for item in data:
- yield item
- except ChunkedEncodingError as exc:
- raise NeDRexError("cypher query could not be executed") from exc
diff --git a/python_nedrex/python_nedrex/ppi.py b/python_nedrex/python_nedrex/ppi.py
deleted file mode 100644
index 1fe05527932cebebc7bc59b8ffb98284dd05c5ff..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/ppi.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Iterable as _Iterable
-from typing import List as _List
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_pagination_limit as _check_pagination_limit
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import get_pagination_limit as _get_pagination_limit
-from python_nedrex.common import http as _http
-from python_nedrex.exceptions import NeDRexError
-
-
-def ppis(evidence: _Iterable[str], skip: int = 0, limit: _Optional[int] = None) -> _List[_Dict[str, _Any]]:
- evidence_set = set(evidence)
- extra_evidence = evidence_set - {"exp", "pred", "ortho"}
- if extra_evidence:
- raise NeDRexError(f"unexpected evidence types: {extra_evidence}")
-
- maximum_limit = _get_pagination_limit()
- _check_pagination_limit(limit, maximum_limit)
-
- params = {"iid_evidence": list(evidence_set), "skip": skip, "limit": limit}
-
- resp = _http.get(f"{_config.url_base}/ppi", params=params, headers={"x-api-key": _config.api_key})
- result: _List[_Dict[str, _Any]] = _check_response(resp)
- return result
diff --git a/python_nedrex/python_nedrex/relations.py b/python_nedrex/python_nedrex/relations.py
deleted file mode 100644
index d5b7e5cfc6102439576c2501cef83c5645cd997d..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/relations.py
+++ /dev/null
@@ -1,87 +0,0 @@
-from typing import Dict as _Dict
-from typing import Iterable as _Iterable
-from typing import List as _List
-from typing import Union as _Union
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import http as _http
-
-
-def get_encoded_proteins(gene_list: _Iterable[_Union[int, str]]) -> _Dict[str, _List[str]]:
- """
- Genes the proteins encoded by genes in a supplied gene list.
-
- The genes can be submitted either as a list of strings or integers.
- """
- genes = []
- for gene in gene_list:
- if isinstance(gene, int):
- gene = str(gene)
- if not isinstance(gene, str):
- raise ValueError("items in gene_list must be int or str")
-
- gene = gene.lower()
- if not gene.startswith("entrez."):
- genes.append(f"entrez.{gene}")
- else:
- genes.append(gene)
-
- url = f"{_config.url_base}/relations/get_encoded_proteins"
- resp = _http.get(url, params={"gene": genes}, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _List[str]] = _check_response(resp)
- return result
-
-
-def get_drugs_indicated_for_disorders(disorder_list: _Iterable[str]) -> _Dict[str, _List[str]]:
- disorders = []
- for disorder in disorder_list:
- if not isinstance(disorder, str):
- raise ValueError("items in disorder_list must be str")
-
- if disorder.startswith("mondo."):
- disorders.append(disorder)
- else:
- disorders.append(f"mondo.{disorder}")
-
- url = f"{_config.url_base}/relations/get_drugs_indicated_for_disorders"
- resp = _http.get(url, params={"disorder": disorders}, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _List[str]] = _check_response(resp)
- return result
-
-
-def get_drugs_targetting_proteins(protein_list: _Iterable[str]) -> _Dict[str, _List[str]]:
- proteins = []
- for protein in protein_list:
- if not isinstance(protein, str):
- raise ValueError("items in protein_list must be str")
-
- if protein.startswith("uniprot."):
- proteins.append(protein)
- else:
- proteins.append(f"uniprot.{protein}")
-
- url = f"{_config.url_base}/relations/get_drugs_targetting_proteins"
- resp = _http.get(url, params={"protein": proteins}, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _List[str]] = _check_response(resp)
- return result
-
-
-def get_drugs_targetting_gene_products(gene_list: _Iterable[str]) -> _Dict[str, _List[str]]:
- genes = []
- for gene in gene_list:
- if isinstance(gene, int):
- gene = str(gene)
- if not isinstance(gene, str):
- raise ValueError("items in gene_list must be int or str")
-
- gene = gene.lower()
- if not gene.startswith("entrez."):
- genes.append(f"entrez.{gene}")
- else:
- genes.append(gene)
-
- url = f"{_config.url_base}/relations/get_drugs_targetting_gene_products"
- resp = _http.get(url, params={"gene": genes}, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _List[str]] = _check_response(resp)
- return result
diff --git a/python_nedrex/python_nedrex/robust.py b/python_nedrex/python_nedrex/robust.py
deleted file mode 100644
index 57c5455c22ec9abc1711c12b0f4fbc86f09bb44b..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/robust.py
+++ /dev/null
@@ -1,45 +0,0 @@
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-# pylint: disable=R0913
-def robust_submit(
- seeds: _List[str],
- network: str = "DEFAULT",
- initial_fraction: float = 0.25,
- reduction_factor: float = 0.9,
- num_trees: int = 30,
- threshold: float = 0.1,
-) -> str:
-
- body = {
- "seeds": seeds,
- "network": network,
- "initial_fraction": initial_fraction,
- "reduction_factor": reduction_factor,
- "num_trees": num_trees,
- "threshold": threshold,
- }
- url = f"{_config.url_base}/robust/submit"
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-# pylint: enable=R0913
-
-check_robust_status = _check_status_factory("/robust/status")
-
-
-def download_robust_results(uid: str) -> str:
- url = f"{_config.url_base}/robust/results"
- params = {"uid": uid}
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp, return_type="text")
- return result
diff --git a/python_nedrex/python_nedrex/static.py b/python_nedrex/python_nedrex/static.py
deleted file mode 100644
index 00bf86c94a48c7b67b4987a429ddea0fe6d8226a..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/static.py
+++ /dev/null
@@ -1,31 +0,0 @@
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import download_file as _download_file
-from python_nedrex.common import http as _http
-
-
-def get_metadata() -> _Dict[str, _Any]:
- url = f"{_config.url_base}/static/metadata"
- resp = _http.get(url, headers={"x-api-key": _config.api_key})
- result: _Dict[str, _Any] = _check_response(resp)
- return result
-
-
-def get_license() -> str:
- url = f"{_config.url_base}/static/licence"
- resp = _http.get(url)
- result: str = _check_response(resp=resp, return_type='text')
- return result
-
-
-def download_lengths_map(target: _Optional[str] = None) -> None:
- if target is None:
- target = "lengths.map"
-
- url = f"{_config.url_base}/static/lengths.map"
-
- _download_file(url, target)
diff --git a/python_nedrex/python_nedrex/trustrank.py b/python_nedrex/python_nedrex/trustrank.py
deleted file mode 100644
index 36812c405ad98fd0c2c59e08aeafa84bc460cfc0..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/trustrank.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from typing import List as _List
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-
-def trustrank_submit(
- seeds: _List[str],
- damping_factor: float = 0.85,
- only_direct_drugs: bool = True,
- only_approved_drugs: bool = True,
- n: _Optional[int] = None, # pylint: disable=C0103
-) -> str:
- url = f"{_config.url_base}/trustrank/submit"
-
- body = {
- "seeds": seeds,
- "damping_factor": damping_factor,
- "only_direct_drugs": only_direct_drugs,
- "only_approved_drugs": only_approved_drugs,
- "N": n,
- }
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-check_trustrank_status = _check_status_factory("/trustrank/status")
-
-
-def download_trustrank_results(uid: str) -> str:
- url = f"{_config.url_base}/trustrank/download"
- params = {"uid": uid}
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp, return_type="text")
- return result
diff --git a/python_nedrex/python_nedrex/validation.py b/python_nedrex/python_nedrex/validation.py
deleted file mode 100644
index 599793b35bb8373001949c413e63aaf99c8d62a4..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/validation.py
+++ /dev/null
@@ -1,80 +0,0 @@
-from typing import List as _List
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import check_status_factory as _check_status_factory
-from python_nedrex.common import http as _http
-
-check_validation_status = _check_status_factory("/validation/status")
-
-
-def check_module_member_type(mmt: str) -> None:
- if mmt not in {"gene", "protein"}:
- raise ValueError(f"module_member_type {mmt!r} is invalid (should be 'gene' or 'protein'")
-
-
-# pylint: disable=R0913
-def joint_validation_submit(
- module_members: _List[str],
- module_member_type: str,
- test_drugs: _List[str],
- true_drugs: _List[str],
- permutations: int,
- only_approved_drugs: bool = True,
-) -> str:
- check_module_member_type(module_member_type)
-
- url = f"{_config.url_base}/validation/joint"
- body = {
- "module_members": module_members,
- "module_member_type": module_member_type,
- "test_drugs": test_drugs,
- "true_drugs": true_drugs,
- "permutations": permutations,
- "only_approved_drugs": only_approved_drugs,
- }
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-# pylint: enable=R0913
-
-
-def module_validation_submit(
- module_members: _List[str],
- module_member_type: str,
- true_drugs: _List[str],
- permutations: int,
- only_approved_drugs: bool = True,
-) -> str:
- check_module_member_type(module_member_type)
-
- url = f"{_config.url_base}/validation/module"
- body = {
- "module_members": module_members,
- "module_member_type": module_member_type,
- "true_drugs": true_drugs,
- "permutations": permutations,
- "only_approved_drugs": only_approved_drugs,
- }
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
-
-
-def drug_validation_submit(
- test_drugs: _List[str], true_drugs: _List[str], permutations: int, only_approved_drugs: bool = True
-) -> str:
-
- url = f"{_config.url_base}/validation/drug"
- body = {
- "test_drugs": test_drugs,
- "true_drugs": true_drugs,
- "permutations": permutations,
- "only_approved_drugs": only_approved_drugs,
- }
-
- resp = _http.post(url, json=body, headers={"x-api-key": _config.api_key})
- result: str = _check_response(resp)
- return result
diff --git a/python_nedrex/python_nedrex/variants.py b/python_nedrex/python_nedrex/variants.py
deleted file mode 100644
index d6e47a68cb3a3b64b2b56386d05115d7053a4d2d..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/variants.py
+++ /dev/null
@@ -1,160 +0,0 @@
-from typing import Any as _Any
-from typing import Dict as _Dict
-from typing import Generator as _Generator
-from typing import List as _List
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import check_pagination_limit as _check_pagination_limit
-from python_nedrex.common import check_response as _check_response
-from python_nedrex.common import get_pagination_limit as _get_pagination_limit
-from python_nedrex.common import http as _http
-
-
-def get_effect_choices() -> _List[str]:
- url = f"{_config.url_base}/variants/get_effect_choices"
- resp = _http.get(url, headers={"x-api-key": _config.api_key})
- result: _List[str] = _check_response(resp)
- return result
-
-
-def get_review_status_choices() -> _List[str]:
- url = f"{_config.url_base}/variants/get_review_choices"
- resp = _http.get(url, headers={"x-api-key": _config.api_key})
- result: _List[str] = _check_response(resp)
- return result
-
-
-# pylint: disable=R0913
-def get_variant_disorder_associations(
- variant_ids: _Optional[_List[str]] = None,
- disorder_ids: _Optional[_List[str]] = None,
- review_status: _Optional[_List[str]] = None,
- effect: _Optional[_List[str]] = None,
- limit: _Optional[int] = None,
- offset: int = 0,
-) -> _List[_Dict[str, _Any]]:
- max_limit = _get_pagination_limit()
- if isinstance(limit, int):
- _check_pagination_limit(limit, max_limit)
- else:
- limit = max_limit
-
- params = {
- "variant_id": variant_ids,
- "disorder_id": disorder_ids,
- "review_status": review_status,
- "effect": effect,
- "limit": limit,
- "offset": offset,
- }
-
- url = f"{_config.url_base}/variants/get_variant_disorder_associations"
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: _List[_Dict[str, _Any]] = _check_response(resp)
- return result
-
-
-# pylint: enable=R0913
-
-
-def iter_variant_disorder_associations(
- variant_ids: _Optional[_List[str]] = None,
- disorder_ids: _Optional[_List[str]] = None,
- review_status: _Optional[_List[str]] = None,
- effect: _Optional[_List[str]] = None,
-) -> _Generator[_Dict[str, _Any], None, None]:
- max_limit = _get_pagination_limit()
- offset = 0
-
- kwargs = {
- "variant_ids": variant_ids,
- "disorder_ids": disorder_ids,
- "review_status": review_status,
- "effect": effect,
- "limit": max_limit,
- "offset": offset,
- }
-
- while True:
- results = get_variant_disorder_associations(**kwargs)
- if len(results) == 0:
- return
- yield from results
-
- offset += max_limit
- kwargs["offset"] = offset
-
-
-def get_variant_gene_associations(
- variant_ids: _Optional[_List[str]] = None,
- gene_ids: _Optional[_List[str]] = None,
- limit: _Optional[int] = None,
- offset: int = 0,
-) -> _List[_Dict[str, _Any]]:
-
- max_limit = _get_pagination_limit()
- if isinstance(limit, int):
- _check_pagination_limit(limit, max_limit)
- else:
- limit = max_limit
-
- params = {
- "variant_id": variant_ids,
- "gene_id": gene_ids,
- "offset": offset,
- "limit": limit,
- }
-
- url = f"{_config.url_base}/variants/get_variant_gene_associations"
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: _List[_Dict[str, _Any]] = _check_response(resp)
- return result
-
-
-def iter_variant_gene_associations(
- variant_ids: _Optional[_List[str]] = None,
- gene_ids: _Optional[_List[str]] = None,
-) -> _Generator[_Dict[str, _Any], None, None]:
- max_limit = _get_pagination_limit()
- offset = 0
-
- kwargs = {
- "variant_ids": variant_ids,
- "gene_ids": gene_ids,
- "limit": max_limit,
- "offset": offset,
- }
-
- while True:
- results = get_variant_gene_associations(**kwargs)
- if len(results) == 0:
- return
- yield from results
-
- offset += max_limit
- kwargs["offset"] = offset
-
-
-def get_variant_based_disorder_associated_genes(
- disorder_id: str, review_status: _Optional[_List[str]] = None, effect: _Optional[_List[str]] = None
-) -> _List[_Dict[str, _Any]]:
- params = {"disorder_id": disorder_id, "review_status": review_status, "effect": effect}
-
- url = f"{_config.url_base}/variants/variant_based_disorder_associated_genes"
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: _List[_Dict[str, _Any]] = _check_response(resp)
- return result
-
-
-def get_variant_based_gene_associated_disorders(
- gene_id: str, review_status: _Optional[_List[str]] = None, effect: _Optional[_List[str]] = None
-) -> _List[_Dict[str, _Any]]:
- params = {"gene_id": gene_id, "review_status": review_status, "effect": effect}
-
- url = f"{_config.url_base}/variants/variant_based_gene_associated_disorders"
-
- resp = _http.get(url, params=params, headers={"x-api-key": _config.api_key})
- result: _List[_Dict[str, _Any]] = _check_response(resp)
- return result
diff --git a/python_nedrex/python_nedrex/vpd.py b/python_nedrex/python_nedrex/vpd.py
deleted file mode 100644
index 11689d8a2c50a30c99b70b4be1a80ba5d6b466c0..0000000000000000000000000000000000000000
--- a/python_nedrex/python_nedrex/vpd.py
+++ /dev/null
@@ -1,32 +0,0 @@
-import os as _os
-from typing import Optional as _Optional
-
-from python_nedrex import config as _config
-from python_nedrex.common import http as _http
-from python_nedrex.decorators import check_url_vpd as _check_url_vpd
-
-
-@_check_url_vpd
-def get_vpd(disorder: str, number_of_patients: int, out_dir: str) -> _Optional[str]:
- """
- Downloads a .zip archive with the requested virtual patient data to the given directory.
-
- Parameters:
- disorder (str): The disorder mondoID (e.g mondo.0000090) for which the virtual patient should be retrieved.
- number_of_patients (int): The number of simulated patients in the dataset. Can be 1, 10 or 100.
- out_dir (str): The absolute path of a directory where the virtual patient data should be stored.
-
- Returns:
- archive (str): Absolute path of the downloaded zip archive or None if the requested resource does not exist.
- """
- archive_name: str = f"{disorder}_1000GP_{number_of_patients}VPSim.zip"
- url: str = f"{_config.url_vpd}/vpd/{disorder}/{archive_name}"
- archive: str = _os.path.join(out_dir, archive_name)
-
- data = _http.get(url)
- if data.status_code != 200:
- return None
-
- with open(archive, "wb") as arch:
- arch.write(data.content)
- return archive
diff --git a/python_nedrex/requirements.txt b/python_nedrex/requirements.txt
deleted file mode 100644
index 0e892733197052aa14d4c16d7e1c0358f5b08907..0000000000000000000000000000000000000000
--- a/python_nedrex/requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-attrs==21.4.0
-cachetools==4.2.4
-more-itertools==8.13.0
-pytest==7.0.1
-pytest-xdist==2.5.0
-requests==2.27.1
diff --git a/python_nedrex/requirements_dev.txt b/python_nedrex/requirements_dev.txt
deleted file mode 100644
index ebb3f1d1574b67f08c0fa8073ce6234d9ac46989..0000000000000000000000000000000000000000
--- a/python_nedrex/requirements_dev.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-pip==19.2.3
-bump2version==0.5.11
-wheel==0.33.6
-watchdog==0.9.0
-flake8==3.7.8
-tox==3.14.0
-coverage==4.5.4
-Sphinx==1.8.5
-twine==1.14.0
-
-pytest==6.2.4
-black==21.7b0
diff --git a/python_nedrex/setup.cfg b/python_nedrex/setup.cfg
deleted file mode 100644
index 249095598218cc569f99d18343afbeb95b47bfea..0000000000000000000000000000000000000000
--- a/python_nedrex/setup.cfg
+++ /dev/null
@@ -1,20 +0,0 @@
-[bumpversion]
-current_version = 0.1.1
-commit = True
-tag = True
-
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
-
-[bumpversion:file:python_nedrex/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
-
-[bdist_wheel]
-universal = 1
-
-[flake8]
-exclude = docs
-[tool:pytest]
-
diff --git a/python_nedrex/setup.py b/python_nedrex/setup.py
deleted file mode 100644
index 81d119071d4e633408e4ab6e72bc9937428074e8..0000000000000000000000000000000000000000
--- a/python_nedrex/setup.py
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env python
-
-"""The setup script."""
-
-from setuptools import setup, find_packages
-
-with open("README.rst") as readme_file:
- readme = readme_file.read()
-
-with open("HISTORY.rst") as history_file:
- history = history_file.read()
-
-requirements = [
- "attrs",
- "requests",
- "cachetools",
-]
-
-test_requirements = [
- "pytest>=3",
-]
-
-setup(
- author="David James Skelton",
- author_email="james.skelton@newcastle.ac.uk",
- python_requires=">=3.6",
- classifiers=[
- "Development Status :: 2 - Pre-Alpha",
- "Intended Audience :: Developers",
- "License :: OSI Approved :: MIT License",
- "Natural Language :: English",
- "Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.6",
- "Programming Language :: Python :: 3.7",
- "Programming Language :: Python :: 3.8",
- ],
- description="A Python library for interfacing with the PNeDRex API",
- install_requires=requirements,
- license="MIT license",
- long_description=readme + "\n\n" + history,
- include_package_data=True,
- keywords="python_nedrex",
- name="python_nedrex",
- packages=find_packages(include=["python_nedrex", "python_nedrex.*"]),
- test_suite="tests",
- tests_require=test_requirements,
- url="https://github.com/james-skelton/python_nedrex",
- version="0.1.1",
- zip_safe=False,
-)
diff --git a/python_nedrex/tests/__init__.py b/python_nedrex/tests/__init__.py
deleted file mode 100644
index 6aa35229e03913395096d31118ae720a840f6899..0000000000000000000000000000000000000000
--- a/python_nedrex/tests/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Unit test package for python_nedrex."""
diff --git a/python_nedrex/tests/test_python_nedrex.py b/python_nedrex/tests/test_python_nedrex.py
deleted file mode 100644
index e86cb19f4067673e9f7b99b2f400ed2bbf3c3451..0000000000000000000000000000000000000000
--- a/python_nedrex/tests/test_python_nedrex.py
+++ /dev/null
@@ -1,730 +0,0 @@
-#!/usr/bin/env python
-
-"""Tests for `python_nedrex` package."""
-
-from email import quoprimime
-import os
-import re
-from pathlib import Path
-import random
-import tempfile
-import time
-from contextlib import contextmanager
-from functools import lru_cache
-
-from more_itertools import take
-
-import pytest
-import requests
-
-import python_nedrex
-from python_nedrex.common import get_pagination_limit
-from python_nedrex.core import (
- get_edges,
- iter_edges,
- iter_nodes,
- get_node_types,
- get_edge_types,
- get_collection_attributes,
- get_node_ids,
- get_nodes,
- api_keys_active,
-)
-from python_nedrex.diamond import diamond_submit, check_diamond_status, download_diamond_results
-from python_nedrex.disorder import (
- get_disorder_ancestors,
- get_disorder_children,
- get_disorder_descendants,
- get_disorder_parents,
- search_by_icd10,
-)
-from python_nedrex.domino import (
- domino_submit,
- check_domino_status
-)
-from python_nedrex.exceptions import ConfigError, NeDRexError
-from python_nedrex.graph import (
- build_request,
- check_build_status,
- download_graph,
-)
-from python_nedrex.must import must_request, check_must_status
-from python_nedrex.neo4j import neo4j_query
-from python_nedrex.ppi import ppis
-from python_nedrex.relations import (
- get_encoded_proteins,
- get_drugs_indicated_for_disorders,
- get_drugs_targetting_proteins,
- get_drugs_targetting_gene_products,
-)
-
-
-API_URL = "http://82.148.225.92:8123/"
-API_KEY = requests.post(f"{API_URL}admin/api_key/generate", json={"accept_eula": True}).json()
-
-
-SEEDS = [
- "P43121",
- "P01589",
- "P30203",
- "P21554",
- "P01579",
- "O43557",
- "Q99572",
- "P01920",
- "P25942",
- "P01189",
- "P21580",
- "Q02556",
- "P01584",
- "P01574",
- "P02649",
- "P29466",
- "P22301",
- "P16581",
- "P06276",
- "P11473",
- "O60333",
- "P19256",
- "Q96P20",
- "P01911",
- "Q2KHT3",
- "P18510",
- "P05362",
- "P01903",
- "P29597",
- "P13232",
- "Q13191",
- "Q06330",
- "P04440",
- "P78508",
- "P19320",
- "P19438",
- "P02774",
- "O75508",
- "P29459",
- "P16871",
- "Q14765",
- "Q16552",
-]
-
-UID_REGEX = re.compile(r"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}")
-
-
-@contextmanager
-def url_base():
- python_nedrex.config.set_url_base(API_URL)
- yield
- python_nedrex.config._url_base = None
-
-
-@contextmanager
-def api_key():
- python_nedrex.config.set_api_key(API_KEY)
- yield
- python_nedrex.config._api_key = None
-
-
-@lru_cache(maxsize=10)
-def get_node_collections():
- with api_key(), url_base():
- collections = get_node_types()
- return collections
-
-
-@lru_cache(maxsize=10)
-def get_edge_collections():
- with api_key(), url_base():
- collections = get_edge_types()
- return collections
-
-
-def get_random_disorder_selection(n, skip_root=True):
- random.seed(20220621)
- with api_key(), url_base():
- disorder_ids = set(get_node_ids("disorder"))
- disorder_ids.remove("mondo.0000001")
- return random.sample(sorted(disorder_ids), n)
-
-
-@pytest.fixture
-def config():
- return {"api_url": API_URL, "api_key": API_KEY}
-
-
-@pytest.fixture
-def set_api_key(config):
- with api_key():
- yield
-
-
-@pytest.fixture
-def set_base_url(config):
- with url_base():
- yield
-
-
-def test_set_api_base(set_base_url):
- assert python_nedrex.config._url_base == API_URL.rstrip("/")
-
-
-class TestGetNodeTypes:
- @pytest.fixture
- def result(self, set_base_url, set_api_key):
- result = get_node_types()
- return result
-
- def test_return_type(self, result):
- assert isinstance(result, list)
- assert all(isinstance(item, str) for item in result)
-
- def test_ordering(self, result):
- assert result == sorted(result)
-
- def test_content(self, result):
- assert "protein" in result
-
-
-class TestGetEdgeTypes:
- @pytest.fixture
- def result(self, set_base_url, set_api_key):
- result = get_edge_types()
- return result
-
- def test_return_type(self, result):
- assert isinstance(result, list)
- assert all(isinstance(item, str) for item in result)
-
- def test_ordering(self, result):
- assert result == sorted(result)
-
- def test_content(self, result):
- assert "protein_encoded_by_gene" in result
-
-
-class TestGetCollectionAttributes:
- @pytest.mark.parametrize("collection", get_node_collections())
- def test_get_node_collection_attributes(self, set_base_url, set_api_key, collection):
- expected_attributes = ("primaryDomainId", "domainIds", "type")
- coll_attributes = get_collection_attributes(collection)
- assert all(attr in coll_attributes for attr in expected_attributes)
-
- @pytest.mark.parametrize("collection", get_edge_collections())
- def test_get_edge_collection_attributes(self, set_base_url, set_api_key, collection):
- # NOTE: Exclude the protein_interacts_with_protein collection because of its size.
- coll_attributes = get_collection_attributes(collection)
- assert "type" in coll_attributes
-
- assert all(attr in coll_attributes for attr in ("memberOne", "memberTwo")) or all(
- attr in coll_attributes for attr in ("sourceDomainId", "targetDomainId")
- )
-
-
-class TestGetNodeIds:
- @pytest.mark.parametrize("collection", get_node_collections())
- def test_get_node_ids(self, set_base_url, set_api_key, collection):
- assert get_node_ids(collection)
-
- @pytest.mark.parametrize("collection", get_edge_collections())
- def test_get_node_ids_fails_for_edges(self, set_base_url, set_api_key, collection):
- with pytest.raises(NeDRexError):
- get_node_ids(collection)
-
-
-class TestGetEdgeRoutes:
- @pytest.mark.parametrize("collection", get_edge_collections())
- def test_return_type_get_edges(self, set_base_url, set_api_key, collection):
- edges = get_edges(collection, limit=1_000)
- assert isinstance(edges, list)
-
- @pytest.mark.parametrize("collection", get_edge_collections())
- def test_edge_attributes(self, set_base_url, set_api_key, collection):
- result = get_collection_attributes(collection, include_counts=True)
- total = result["document_count"]
- attr_counts = result["attribute_counts"]
-
- assert attr_counts["type"] == total
- assert (
- attr_counts.get("memberOne", 0) == attr_counts.get("memberTwo", 0) == total
- and attr_counts.get("sourceDomainId", 0) == attr_counts.get("targetDomainId", 0) == 0
- ) ^ (
- attr_counts.get("memberOne", 0) == attr_counts.get("memberTwo", 0) == 0
- and attr_counts.get("sourceDomainId", 0) == attr_counts.get("targetDomainId", 0) == total
- )
-
-
-class TestGetNodeRoutes:
- @pytest.mark.parametrize("collection", get_node_collections())
- def test_get_all_nodes(self, set_base_url, set_api_key, collection):
- assert isinstance(get_nodes(collection), list)
-
- def test_get_specific_nodes(self, set_base_url, set_api_key):
- nodes = get_nodes("disorder", node_ids=["mondo.0000001"])
- assert isinstance(nodes, list)
- assert len(nodes) == 1
- assert nodes[0]["primaryDomainId"] == "mondo.0000001"
-
- def test_get_drugs_with_api_key(self, set_base_url, set_api_key):
- nodes = get_nodes("drug")
- assert isinstance(nodes, list)
-
- def test_get_specific_attributes(self, set_base_url, set_api_key):
- nodes = get_nodes("disorder", attributes=["displayName"])
- assert isinstance(nodes, list)
- assert [set(i.keys()) == {"primaryDomainId", "displayName"} for i in nodes]
-
- def test_get_specific_attribute_and_nodes(self, set_base_url, set_api_key):
- nodes = get_nodes("disorder", attributes=["displayName"], node_ids=["mondo.0000001"])
- assert isinstance(nodes, list)
- assert len(nodes) == 1
- assert nodes[0] == {
- "displayName": "disease or disorder",
- "primaryDomainId": "mondo.0000001",
- }
-
- def test_pagination(self, set_base_url, set_api_key):
- nodes = get_nodes("genomic_variant", limit=1000, offset=1000)
- assert isinstance(nodes, list)
- assert len(nodes) == 1000
-
- def test_consistent_pagination(self, set_base_url, set_api_key):
- offset = 1234
- limit = 69
-
- nodes = get_nodes("genomic_variant", limit=limit, offset=offset)
-
- for _ in range(10):
- nodes_repeat = get_nodes("genomic_variant", limit=limit, offset=offset)
- assert nodes_repeat == nodes
-
-
-class TestDisorderRoutes:
- def test_search_by_icd10(self, set_base_url, set_api_key):
- # NOTE: There is currently an ICD-10 mapping issue due to MONDO
- search_by_icd10("I52")
-
- def test_get_disorder_ancestors(self, set_base_url, set_api_key):
- # Check that `disease or disorder`is an ancestor of `lupus nephritis`
- # `disease or disorder` is not a parent of `lupus neprhitis`
- lupus_nephritis = "mondo.0005556"
- disease_or_disorder = "mondo.0000001"
-
- result = get_disorder_ancestors(lupus_nephritis)
- assert disease_or_disorder in result[lupus_nephritis]
-
- def test_get_disorder_descendants(self, set_base_url, set_api_key):
- # Check that `lupus nephritis` is a descendant of `inflammatory disease`
- # `lupus nephritis` is not a child of `inflammatory disease`
- inflam_disease = "mondo.0021166"
- lupus_nephritis = "mondo.0005556"
-
- result = get_disorder_descendants(inflam_disease)
- assert lupus_nephritis in result[inflam_disease]
-
- def test_get_disorder_parents(self, set_base_url, set_api_key):
- # Check that `glomerulonephritis` is a parent of `lupus nephritis`
- lupus_nephritis = "mondo.0005556"
- glomerulonephritis = "mondo.0002462"
-
- result = get_disorder_parents("mondo.0005556")
- assert glomerulonephritis in result[lupus_nephritis]
-
- def test_get_disorder_children(self, set_base_url, set_api_key):
- # Check that `lupus nephritis` is a child of `glomerulonephritis`
- glomerulonephritis = "mondo.0002462"
- lupus_nephritis = "mondo.0005556"
-
- result = get_disorder_children(glomerulonephritis)
- assert lupus_nephritis in result[glomerulonephritis]
-
- @pytest.mark.parametrize("chosen_id", get_random_disorder_selection(20))
- def test_parent_child_reciprocity(self, set_base_url, set_api_key, chosen_id):
- parents = get_disorder_parents(chosen_id)
- children_of_parents = get_disorder_children(parents[chosen_id])
- assert all(chosen_id in value for value in children_of_parents.values())
-
- @pytest.mark.parametrize("chosen_id", get_random_disorder_selection(20))
- def test_ancestor_descendant_reciprocity(self, set_base_url, set_api_key, chosen_id):
- parents = get_disorder_ancestors(chosen_id)
- descendants_of_parents = get_disorder_descendants(parents[chosen_id])
- assert all(chosen_id in value for value in descendants_of_parents.values())
-
-
-class TestRoutesFailWithoutAPIUrl:
- def test_get_node_type(self, set_api_key):
- with pytest.raises(ConfigError) as excinfo:
- get_node_types()
- assert "API URL is not set in the config" == str(excinfo.value)
-
- def test_get_edge_type(self, set_api_key):
- with pytest.raises(ConfigError) as excinfo:
- get_edge_types()
- assert "API URL is not set in the config" == str(excinfo.value)
-
-
-class TestRoutesFailWithoutAPIKey:
- def test_get_node_type(self, set_base_url):
- if not api_keys_active():
- return
-
- with pytest.raises(ConfigError) as excinfo:
- get_node_types()
- assert "no API key set in the configuration" == str(excinfo.value)
-
- if not api_keys_active():
- return
-
- with pytest.raises(ConfigError) as excinfo:
- get_edge_types()
- assert "no API key set in the configuration" == str(excinfo.value)
-
- @pytest.mark.parametrize("collection", get_node_collections())
- def test_node_routes_fail(self, set_base_url, collection):
- if not api_keys_active():
- return
-
- with pytest.raises(ConfigError) as excinfo:
- get_collection_attributes(collection)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_node_ids(collection)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_nodes(collection)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- for _ in take(1, iter_nodes(collection)):
- pass
- assert "no API key set in the configuration" == str(excinfo.value)
-
- @pytest.mark.parametrize("collection", get_edge_collections())
- def test_edge_routes_fail(self, set_base_url, collection):
- if not api_keys_active():
- return
-
- with pytest.raises(ConfigError) as excinfo:
- get_collection_attributes(collection)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_edges(collection)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- for _ in take(1, iter_edges(collection)):
- pass
- assert "no API key set in the configuration" == str(excinfo.value)
-
- def test_disorder_routes_fail(self, set_base_url):
- disorder_id = "mondo.0000001" # root of the MONDO tree
- icd10_id = "I59.1" # Heart disease, unspecified
-
- with pytest.raises(ConfigError) as excinfo:
- get_disorder_children(disorder_id)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_disorder_parents(disorder_id)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_disorder_ancestors(disorder_id)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- get_disorder_descendants(disorder_id)
- assert "no API key set in the configuration" == str(excinfo.value)
-
- with pytest.raises(ConfigError) as excinfo:
- search_by_icd10(icd10_id)
- assert "no API key set in the configuration" == str(excinfo.value)
-
-
-class TestPPIRoute:
- def test_ppi_route(self, set_base_url, set_api_key):
- ppis(["exp"], 0, get_pagination_limit())
-
- def test_overlap_with_pagination(self, set_base_url, set_api_key):
- page_limit = 1_000
- delta = page_limit // 2
- skip = delta
-
- previous = ppis(["exp"], 0, page_limit)
-
- for _ in range(100):
- current = ppis(["exp"], skip, page_limit)
- assert previous[-delta:] == current[:delta]
- previous = current
- skip += delta
-
- def test_each_evidence_type_works(self, set_base_url, set_api_key):
- for evidence_type in ["exp", "pred", "ortho"]:
- results = ppis([evidence_type], 0, get_pagination_limit())
- assert all(evidence_type in doc["evidenceTypes"] for doc in results)
-
- def test_fails_with_invalid_type(self, set_base_url, set_api_key):
- for evidence_type in ["exps", "pr3d", "orth"]:
- with pytest.raises(NeDRexError) as excinfo:
- ppis([evidence_type])
- err_val = {evidence_type}
- assert str(excinfo.value) == f"unexpected evidence types: {err_val}"
-
- def test_fails_with_large_limit(self, set_base_url, set_api_key):
- page_limit = get_pagination_limit()
- with pytest.raises(NeDRexError) as excinfo:
- ppis(["exp"], limit=page_limit + 1)
-
- assert str(excinfo.value) == f"limit={page_limit + 1:,} is too great (maximum is {page_limit:,})"
-
-
-class TestRelationshipRoutes:
- def test_get_encoded_proteins(self, set_base_url, set_api_key):
- # NOTE: If result changes, check these examples are still accurate.
-
- histamine_receptor_genes = ["3269", 3274, "entrez.11255"] # HRH1, as str # HRH2, as int # HRH3, as prefix
-
- results = get_encoded_proteins(histamine_receptor_genes)
-
- assert "P35367" in results["3269"]
- assert "P25021" in results["3274"]
- assert "Q9Y5N1" in results["11255"]
-
- def test_get_drugs_indicated_for_disorders(self, set_base_url, set_api_key):
- # NOTE: If result changes, check these examples are still accurate.
-
- disorders = [
- "mondo.0005393", # Gout
- "0005362", # ED
- ]
-
- results = get_drugs_indicated_for_disorders(disorders)
-
- assert "DB00437" in results["0005393"] # Allopurinol for gout
- assert "DB00203" in results["0005362"] # Sildenafil for ED
-
- def test_get_drugs_targetting_proteins(self, set_base_url, set_api_key):
- # NOTE: If result changes, check these examples are still accurate.
-
- proteins = [
- "P35367", # Histamine H1 receptor, targetted by antihistamines
- "uniprot.P03372", # Estrogen receptor α, targetted by ethinylestradiol
- ]
-
- results = get_drugs_targetting_proteins(proteins)
-
- assert "DB00341" in results["P35367"]
- assert "DB00977" in results["P03372"]
-
- def test_get_drugs_targetting_gene_products(self, set_base_url, set_api_key):
- genes = [
- "entrez.3269", # HRH1 gene (product targetted by antihistamines)
- 2099, # Estrogen receptor α gene (product targetted by ethinylestradiol)
- "6532", # SLC6A4, encodes Sodium-dependent serotonin transporter, targetted by SSRIs
- ]
-
- results = get_drugs_targetting_gene_products(genes)
-
- assert "DB00341" in results["3269"]
- assert "DB00977" in results["2099"]
- assert "DB00215" in results["6532"]
-
-
-class TestGraphRoutes:
- def test_default_build(self, set_base_url, set_api_key):
- build_request()
-
- @pytest.mark.parametrize(
- "kwargs",
- [
- {"nodes": ["this_is_not_a_node"]},
- {"edges": ["this_is_not_an_edge"]},
- {"ppi_evidence": ["made_up"]},
- {"taxid": ["human"]},
- ],
- )
- def test_build_fails_with_invalid_params(self, kwargs, set_base_url, set_api_key):
- with pytest.raises(NeDRexError):
- build_request(**kwargs)
-
- def test_get_uid(self, set_base_url, set_api_key):
- uid = build_request()
- assert UID_REGEX.match(uid)
- check_build_status(uid)
-
- def test_fails_with_invalid_uid(self, set_base_url, set_api_key):
- uid = "this-is-not-a-valid-uid!"
- with pytest.raises(NeDRexError):
- check_build_status(uid)
-
- def test_download_graph(self, set_base_url, set_api_key):
- uid = build_request()
- while True:
- status = check_build_status(uid)
- if status["status"] == "completed":
- break
- time.sleep(10)
-
- download_graph(uid)
- p = Path(f"{uid}.graphml")
- assert p.exists()
- p.unlink()
-
- def test_download_graph_different_dir(self, set_base_url, set_api_key):
- with tempfile.TemporaryDirectory() as tmpdir:
-
- uid = build_request()
- while True:
- status = check_build_status(uid)
- if status["status"] == "completed":
- break
- time.sleep(10)
-
- target = os.path.join(tmpdir, "mygraph.graphml")
-
- download_graph(uid, target)
- p = Path(target)
- assert p.exists()
- p.unlink()
-
- def test_download_fails_with_invalid_uid(self, set_base_url, set_api_key):
- uid = "this-is-not-a-valid-uid!"
- with pytest.raises(NeDRexError):
- download_graph(uid)
-
-
-class TestMustRoutes:
- def test_simple_request(self, set_base_url, set_api_key):
- uid = must_request(SEEDS, 0.5, True, 10, 2)
- assert UID_REGEX.match(uid)
-
- def test_must_status(self, set_base_url, set_api_key):
- uid = must_request(SEEDS, 0.5, True, 10, 2)
- status = check_must_status(uid)
- assert isinstance(status, dict)
- assert "status" in status.keys()
-
- @pytest.mark.parametrize(
- "update",
- [
- {"hubpenalty": 1.01},
- {"hubpenalty": -0.01},
- {"hubpenalty": None},
- {"multiple": None},
- {"trees": -1},
- {"trees": None},
- {"maxit": -1},
- {"maxit": None},
- ],
- )
- def test_must_fails_with_invalid_arguments(self, set_base_url, set_api_key, update):
- kwargs = {"seeds": SEEDS, "hubpenalty": 0.5, "multiple": True, "trees": 10, "maxit": 2, "network": "DEFAULT"}
-
- with pytest.raises(NeDRexError):
- kwargs = {**kwargs, **update}
- must_request(**kwargs)
-
-
-class TestDiamondRoutes:
- def test_simple_request(self, set_base_url, set_api_key):
- uid = diamond_submit(SEEDS, 10)
- assert UID_REGEX.match(uid)
-
- def test_diamond_status(self, set_base_url, set_api_key):
- uid = diamond_submit(SEEDS, 10)
- status = check_diamond_status(uid)
- assert isinstance(status, dict)
- assert "status" in status.keys()
-
- def test_diamond_download(self, set_base_url, set_api_key):
- uid = diamond_submit(SEEDS, 10)
-
- while True:
- status = check_diamond_status(uid)
- if status["status"] == "completed":
- break
- time.sleep(10)
-
- download_diamond_results(uid)
-
- def test_diamond_fails_with_invalid_arguments(self, set_base_url, set_api_key):
- with pytest.raises(ValueError):
- diamond_submit(SEEDS, n=10, edges="some")
-
-
-class TestDominoRoutes:
- def test_simple_request(self, set_base_url, set_api_key):
- uid = domino_submit(SEEDS)
- assert UID_REGEX.match(uid)
-
- def test_check_domino_status(self, set_base_url, set_api_key):
- uid = domino_submit(SEEDS)
- status = check_domino_status(uid)
- assert isinstance(status, dict)
- assert "status" in status.keys()
-
-
-class TestNeo4j:
- def test_general_node_query(self, set_base_url, set_api_key):
- query = """
- MATCH (n: Gene)
- RETURN n
- LIMIT 25
- """
-
- assert all(i[0]["type"] == "Gene" for i in neo4j_query(query))
-
- def test_general_edge_query(self, set_base_url, set_api_key):
- query = """
- MATCH ()-[n:GeneAssociatedWithDisorder]-()
- RETURN n
- LIMIT 25
- """
-
- assert all(i[0]["type"] == "GeneAssociatedWithDisorder" for i in neo4j_query(query))
-
- def test_general_node_query_with_attributes(self, set_base_url, set_api_key):
- query = """
- MATCH (n: Gene {approvedSymbol: 'A1BG'})
- RETURN n
- """
-
- x = list(neo4j_query(query))
- assert len(x) == 1
- assert x[0][0]['chromosome'] == '19'
-
-
- def test_general_edge_query_with_attributes(self, set_base_url, set_api_key):
- query = """
- MATCH ()-[n: GeneAssociatedWithDisorder {score: 1.0}]-()
- RETURN n
- LIMIT 1000
- """
-
- results = list(neo4j_query(query))
- assert len(results) != 0
- assert all(i[0]['score'] == 1.0 for i in results)
-
-
- def test_gene_associated_with_disorder(self, set_base_url, set_api_key):
- query = """
- MATCH (g: Gene)-[gawd: GeneAssociatedWithDisorder]-(d: Disorder)
- RETURN g, d, gawd
- LIMIT 50
- """
-
- for gene, disorder, assoc in neo4j_query(query):
- assert gene['type'] == 'Gene'
- assert disorder['type'] == "Disorder"
- assert assoc['type'] == "GeneAssociatedWithDisorder"
-
- def test_write_fails(self, set_base_url, set_api_key):
- query = """
- CREATE (n: SomeRandomNode)
- """
-
- with pytest.raises(NeDRexError):
- for _ in neo4j_query(query):
- pass
\ No newline at end of file
diff --git a/python_nedrex/tox.ini b/python_nedrex/tox.ini
deleted file mode 100644
index 57d5be83ec43e13626112cdd3592297e4d5cef90..0000000000000000000000000000000000000000
--- a/python_nedrex/tox.ini
+++ /dev/null
@@ -1,26 +0,0 @@
-[tox]
-envlist = py36, py37, py38, flake8
-
-[travis]
-python =
- 3.8: py38
- 3.7: py37
- 3.6: py36
-
-[testenv:flake8]
-basepython = python
-deps = flake8
-commands = flake8 python_nedrex tests
-
-[testenv]
-setenv =
- PYTHONPATH = {toxinidir}
-deps =
- -r{toxinidir}/requirements_dev.txt
-; If you want to make tox run the tests with the same versions, create a
-; requirements.txt with the pinned versions and uncomment the following line:
-; -r{toxinidir}/requirements.txt
-commands =
- pip install -U pip
- pytest --basetemp={envtmpdir}
-
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index db7a2d39ad5d4040b6dd34294c675ea20ae7b9bf..43bf32df3da5898d25d96f8abd734edf4872ea3c 100755
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
python3 manage.py migrate
python3 manage.py createfixtures
python3 manage.py cleanuptasks
-#python3 manage.py populate_db --update -a
-#python3 manage.py make_graphs
+python3 manage.py populate_db --update -a
+python3 manage.py make_graphs
/usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"
diff --git a/tasks/multi_steiner.py b/tasks/multi_steiner.py
index 30a8adb887a4814d98a3b0363ad758be61d8a818..fa0912e89ca810eab55b9308ec4b749ab336a009 100755
--- a/tasks/multi_steiner.py
+++ b/tasks/multi_steiner.py
@@ -114,6 +114,9 @@ def multi_steiner(task_hook: TaskHook):
weights = edge_weights(g, hub_penalty)
# Find first steiner trees
+ seeds = list(filter(lambda s: s in seed_map, seeds))
+ print(seeds)
+ print(seed_ids)
task_hook.set_progress(2 / (float(num_trees + 3)), "Computing Steiner tree 1 of {}.".format(num_trees))
first_tree = steiner_tree(g, seeds, seed_map, weights, hub_penalty > 0)
num_found_trees = 1
diff --git a/tasks/trust_rank.py b/tasks/trust_rank.py
index 42950ec1b0821e46c749033796757a07222ef547..a01fbe412b3266863b8d1df0f9bd3cced74481e2 100755
--- a/tasks/trust_rank.py
+++ b/tasks/trust_rank.py
@@ -210,6 +210,7 @@ def trust_rank(task_hook: TaskHook):
# Call graph-tool to compute TrustRank.
task_hook.set_progress(2 / 4.0, "Computing TrustRank.")
trust = g.new_vertex_property("double")
+ print(seed_ids)
trust.a[seed_ids] = 1.0 / len(seed_ids)
scores = gtc.pagerank(g, damping=damping_factor, pers=trust, weight=weights)
diff --git a/tasks/util/read_graph_tool_graph.py b/tasks/util/read_graph_tool_graph.py
index fb5b3aad20bd2dafde7a268a847cce601d5d4596..4e7c9fe2212435152dd973ebb63f2b22ac1a12b9 100755
--- a/tasks/util/read_graph_tool_graph.py
+++ b/tasks/util/read_graph_tool_graph.py
@@ -1,8 +1,10 @@
import graph_tool as gt
import graph_tool.topology as gtt
+
# def read_graph_tool_graph(file_path, seeds, datasets, ignored_edge_types, max_deg, ignore_non_seed_baits=False, include_indirect_drugs=False, include_non_approved_drugs=False):
-def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=False, include_non_approved_drugs=False, target='drug'):
+def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=False, include_non_approved_drugs=False,
+ target='drug'):
r"""Reads a graph-tool graph from file.
Reads a graph-tool graph from graphml or gt file and returns is along
@@ -47,11 +49,12 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
# Delete all nodes that are not contained in the selected datasets and have degrees higher than max_deg
deleted_nodes = []
for node in range(g.num_vertices()):
- #Remove all unconnected nodes TODO probably already skip when creating .gt files
+ # Remove all unconnected nodes TODO probably already skip when creating .gt files
if g.vertex(node).out_degree() == 0 and target == 'drug':
deleted_nodes.append(node)
# if not g.vertex_properties["name"][node] in set(seeds) and g.vertex(node).out_degree() > max_deg:
- elif not g.vertex_properties[node_name_attribute][node] in set(seeds) and (g.vertex(node).out_degree() > max_deg):
+ elif not g.vertex_properties[node_name_attribute][node] in set(seeds) and (
+ g.vertex(node).out_degree() > max_deg):
deleted_nodes.append(node)
# remove all drugs from graph if we are not looking for drugs
elif target != 'drug' and g.vertex_properties["type"][node] == d_type:
@@ -61,14 +64,15 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
# Retrieve internal IDs of seed_ids
seeds = set(seeds)
print(seeds)
- seed_ids = []
+ seed_ids = {}
drug_ids = []
- is_matched = {protein: False for protein in seeds}
+ # is_matched = {protein: False for protein in seeds}
for node in range(g.num_vertices()):
node_type = g.vertex_properties["type"][node]
- if g.vertex_properties[node_name_attribute][node] in seeds:
- seed_ids.append(node)
- is_matched[g.vertex_properties[node_name_attribute][node]] = node
+ seed_id = g.vertex_properties[node_name_attribute][node]
+ if seed_id in seeds:
+ seed_ids[node] = seed_id
+ # is_matched[seed_id] = node
if node_type == d_type:
if include_non_approved_drugs:
drug_ids.append(node)
@@ -80,6 +84,9 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
# Check that all seed seeds have been matched and throw error, otherwise.
# print(deleted_nodes)
# print(seed_ids)
+ # seeds = set(seed_ids.values())
+ # for (node, seed_id) in seed_ids.items():
+ # if is_matched[node]
# for protein, found in is_matched.items():
# if not found:
# raise ValueError("Invalid seed protein {}. No node named {} in {}.".format(protein, protein, file_path))
@@ -98,7 +105,8 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
deleted_edges = []
- if (drug_ids and not include_indirect_drugs): # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of any seeds
+ if (
+ drug_ids and not include_indirect_drugs): # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of any seeds
direct_drugs = set()
for edge in g.edges():
if g.vertex_properties["type"][edge.target()] == d_type and edge.source() in seed_ids:
@@ -115,7 +123,8 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
if indir_drug and int(edge.target()) in drug_ids:
drug_ids.remove(int(edge.target()))
- elif g.vertex_properties["type"][edge.source()] == d_type and edge.source() not in direct_drugs or edge.target() not in seed_ids:
+ elif g.vertex_properties["type"][
+ edge.source()] == d_type and edge.source() not in direct_drugs or edge.target() not in seed_ids:
indir_drug = edge.source() not in direct_drugs
not_seed = edge.target() not in seed_ids
if indir_drug or not_seed:
@@ -139,7 +148,7 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
print("Edges")
edges = 0
for _ in g.edges():
- edges+=1
+ edges += 1
print(f'\t{edges}')
# Return the graph and the indices of the seed_ids and the seeds.
- return g, seed_ids, drug_ids
+ return g, list(seed_ids.keys()), drug_ids