From 5dfd50926953e18c5137284bf5173347b2f5ad28 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Mon, 27 Jun 2022 19:42:42 +0200
Subject: [PATCH] fixed automigration issue; activated nedrex based protein,
disorder, drug import
Former-commit-id: d36f3097a091b5f3ed786351307e3bb1b72a1d1a
---
docker-compose.yml | 8 +-
docker-entrypoint.sh | 4 +
drugstone/.gitignore | 1 +
.../management/commands/import_from_nedrex.py | 26 ++---
drugstone/management/commands/populate_db.py | 62 +++++------
drugstone/management/commands/test.py | 33 ++++++
drugstone/migrations/0001_initial.py | 47 --------
drugstone/migrations/0002_organism_protein.py | 32 ------
.../migrations/0003_auto_20200329_1527.py | 24 ----
.../0004_protein_protein_description.py | 18 ---
.../migrations/0005_auto_20200329_2024.py | 24 ----
.../migrations/0006_auto_20200329_2041.py | 33 ------
.../migrations/0007_auto_20200330_1326.py | 35 ------
.../migrations/0008_auto_20200330_1748.py | 33 ------
.../migrations/0009_auto_20200330_1904.py | 18 ---
.../migrations/0010_auto_20200331_0909.py | 19 ----
.../migrations/0011_auto_20200401_1031.py | 66 -----------
.../migrations/0012_auto_20200401_1050.py | 21 ----
.../migrations/0013_auto_20200401_1124.py | 33 ------
.../migrations/0014_auto_20200401_1339.py | 28 -----
.../migrations/0015_auto_20200401_1717.py | 31 ------
drugstone/migrations/0016_task.py | 28 -----
.../migrations/0017_auto_20200402_1935.py | 23 ----
drugstone/migrations/0018_task_created_at.py | 20 ----
.../migrations/0019_auto_20200403_1234.py | 30 -----
drugstone/migrations/0019_task_status.py | 18 ---
.../migrations/0020_auto_20200403_1302.py | 18 ---
.../0021_remove_protein_proteins.py | 17 ---
.../migrations/0022_auto_20200403_1319.py | 17 ---
.../migrations/0023_auto_20200403_1400.py | 22 ----
.../migrations/0024_auto_20200403_1408.py | 38 -------
.../migrations/0025_auto_20200403_1457.py | 22 ----
.../migrations/0026_auto_20200403_1636.py | 28 -----
.../migrations/0027_merge_20200404_1240.py | 14 ---
.../migrations/0028_auto_20200404_1337.py | 31 ------
.../migrations/0029_auto_20200405_0047.py | 17 ---
.../migrations/0030_auto_20200405_0123.py | 44 --------
drugstone/migrations/0031_task_failed.py | 18 ---
drugstone/migrations/0032_task_target.py | 19 ----
.../migrations/0033_auto_20200407_1646.py | 58 ----------
.../migrations/0034_auto_20200408_0952.py | 35 ------
.../migrations/0035_auto_20200410_1107.py | 18 ---
drugstone/migrations/0036_drug_in_trial.py | 18 ---
.../migrations/0037_auto_20200417_1633.py | 58 ----------
.../migrations/0038_auto_20200417_1634.py | 18 ---
.../migrations/0039_auto_20200528_1503.py | 35 ------
.../migrations/0040_auto_20200528_1539.py | 17 ---
drugstone/migrations/0041_drug_links.py | 18 ---
.../migrations/0042_auto_20200531_1519.py | 18 ---
.../migrations/0043_auto_20210518_2120.py | 104 ------------------
.../migrations/0044_auto_20210518_2145.py | 18 ---
.../migrations/0045_auto_20210519_1401.py | 17 ---
drugstone/migrations/0046_protein_ensembl.py | 13 ---
.../migrations/0047_auto_20210615_1013.py | 33 ------
.../0048_delete_emsemblgeneproteinrelation.py | 16 ---
.../migrations/0049_auto_20210616_0932.py | 19 ----
.../migrations/0050_auto_20210722_0858.py | 27 -----
.../migrations/0051_auto_20210914_1251.py | 36 ------
.../migrations/0052_auto_20210914_1311.py | 18 ---
.../migrations/0053_auto_20210914_1314.py | 18 ---
.../migrations/0054_auto_20210922_1342.py | 72 ------------
.../migrations/0055_auto_20210922_1343.py | 18 ---
.../migrations/0056_auto_20210922_1348.py | 18 ---
...0057_drdidataset_drugdisorderindication.py | 38 -------
drugstone/migrations/__init__.py | 0
drugstone/models.py | 22 ++--
scripts/import-data.sh | 16 ++-
67 files changed, 101 insertions(+), 1715 deletions(-)
create mode 100644 drugstone/.gitignore
create mode 100644 drugstone/management/commands/test.py
delete mode 100755 drugstone/migrations/0001_initial.py
delete mode 100755 drugstone/migrations/0002_organism_protein.py
delete mode 100755 drugstone/migrations/0003_auto_20200329_1527.py
delete mode 100755 drugstone/migrations/0004_protein_protein_description.py
delete mode 100755 drugstone/migrations/0005_auto_20200329_2024.py
delete mode 100755 drugstone/migrations/0006_auto_20200329_2041.py
delete mode 100755 drugstone/migrations/0007_auto_20200330_1326.py
delete mode 100755 drugstone/migrations/0008_auto_20200330_1748.py
delete mode 100755 drugstone/migrations/0009_auto_20200330_1904.py
delete mode 100755 drugstone/migrations/0010_auto_20200331_0909.py
delete mode 100755 drugstone/migrations/0011_auto_20200401_1031.py
delete mode 100755 drugstone/migrations/0012_auto_20200401_1050.py
delete mode 100755 drugstone/migrations/0013_auto_20200401_1124.py
delete mode 100755 drugstone/migrations/0014_auto_20200401_1339.py
delete mode 100755 drugstone/migrations/0015_auto_20200401_1717.py
delete mode 100755 drugstone/migrations/0016_task.py
delete mode 100755 drugstone/migrations/0017_auto_20200402_1935.py
delete mode 100755 drugstone/migrations/0018_task_created_at.py
delete mode 100755 drugstone/migrations/0019_auto_20200403_1234.py
delete mode 100755 drugstone/migrations/0019_task_status.py
delete mode 100755 drugstone/migrations/0020_auto_20200403_1302.py
delete mode 100755 drugstone/migrations/0021_remove_protein_proteins.py
delete mode 100755 drugstone/migrations/0022_auto_20200403_1319.py
delete mode 100755 drugstone/migrations/0023_auto_20200403_1400.py
delete mode 100755 drugstone/migrations/0024_auto_20200403_1408.py
delete mode 100755 drugstone/migrations/0025_auto_20200403_1457.py
delete mode 100755 drugstone/migrations/0026_auto_20200403_1636.py
delete mode 100755 drugstone/migrations/0027_merge_20200404_1240.py
delete mode 100755 drugstone/migrations/0028_auto_20200404_1337.py
delete mode 100755 drugstone/migrations/0029_auto_20200405_0047.py
delete mode 100755 drugstone/migrations/0030_auto_20200405_0123.py
delete mode 100755 drugstone/migrations/0031_task_failed.py
delete mode 100755 drugstone/migrations/0032_task_target.py
delete mode 100755 drugstone/migrations/0033_auto_20200407_1646.py
delete mode 100755 drugstone/migrations/0034_auto_20200408_0952.py
delete mode 100755 drugstone/migrations/0035_auto_20200410_1107.py
delete mode 100755 drugstone/migrations/0036_drug_in_trial.py
delete mode 100755 drugstone/migrations/0037_auto_20200417_1633.py
delete mode 100755 drugstone/migrations/0038_auto_20200417_1634.py
delete mode 100755 drugstone/migrations/0039_auto_20200528_1503.py
delete mode 100755 drugstone/migrations/0040_auto_20200528_1539.py
delete mode 100755 drugstone/migrations/0041_drug_links.py
delete mode 100755 drugstone/migrations/0042_auto_20200531_1519.py
delete mode 100755 drugstone/migrations/0043_auto_20210518_2120.py
delete mode 100755 drugstone/migrations/0044_auto_20210518_2145.py
delete mode 100755 drugstone/migrations/0045_auto_20210519_1401.py
delete mode 100755 drugstone/migrations/0046_protein_ensembl.py
delete mode 100755 drugstone/migrations/0047_auto_20210615_1013.py
delete mode 100755 drugstone/migrations/0048_delete_emsemblgeneproteinrelation.py
delete mode 100644 drugstone/migrations/0049_auto_20210616_0932.py
delete mode 100644 drugstone/migrations/0050_auto_20210722_0858.py
delete mode 100644 drugstone/migrations/0051_auto_20210914_1251.py
delete mode 100644 drugstone/migrations/0052_auto_20210914_1311.py
delete mode 100644 drugstone/migrations/0053_auto_20210914_1314.py
delete mode 100644 drugstone/migrations/0054_auto_20210922_1342.py
delete mode 100644 drugstone/migrations/0055_auto_20210922_1343.py
delete mode 100644 drugstone/migrations/0056_auto_20210922_1348.py
delete mode 100644 drugstone/migrations/0057_drdidataset_drugdisorderindication.py
delete mode 100755 drugstone/migrations/__init__.py
diff --git a/docker-compose.yml b/docker-compose.yml
index 3912532..310e7e9 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -11,8 +11,8 @@ services:
env_file:
- 'docker-django.env.dev'
restart: always
-# volumes:
-# - drugstone_backend_volume:/usr/src/drugstone/
+ volumes:
+ - drugstone_backend_volume:/usr/src/drugstone/drugstone/migrations
ports:
- 8001:8000
networks:
@@ -55,7 +55,7 @@ services:
- "sh"
- "/usr/src/drugstone/scripts/start_celery_worker.sh"
restart: always
- build: .
+ image: drugstone_backend
container_name: drugstone_celery
hostname: drugstone_celery
env_file:
@@ -71,7 +71,7 @@ services:
command:
- "sh"
- "/usr/src/drugstone/scripts/start_celery_beat.sh"
- build: .
+ image: drugstone_backend
container_name: drugstone_celery_beat
hostname: drugstone_celery_beat
env_file:
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index bf97629..9686a3c 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -2,6 +2,10 @@
file="docker-entrypoint.lock"
# exit if entrypoint.lock exists to prevent new import of data every time docker is restarted
+
+python3 manage.py makemigrations drugstone
+python3 manage.py migrate
+
if ! test -f "$file"; then
python3 manage.py createfixtures
python3 manage.py cleanuptasks
diff --git a/drugstone/.gitignore b/drugstone/.gitignore
new file mode 100644
index 0000000..24a8e4d
--- /dev/null
+++ b/drugstone/.gitignore
@@ -0,0 +1 @@
+migrations
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index 75b6ab2..dc3f052 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -45,7 +45,7 @@ def identify_updates(new_list, old_list):
def format_list(l):
if l is not None and len(l) > 0:
s = str(l)[1:]
- return s[:len(s) - 1]
+ return s[:len(s) - 1].replace("'","")
return ""
@@ -89,21 +89,21 @@ class nedrex_importer:
self.init_proteins()
def add_protein(node):
- print(node)
id = node['primaryDomainId'].split('.')[1]
name = node['geneName']
if len(node['synonyms']) > 0:
name = node['synonyms'][0]
- idx = name.index('{')
- if idx > 0:
- name = name[idx - 1:]
- proteins[id] = models.Protein(uniprot_code=id, name=name, gene=node['geneName'])
+ if '{' in name:
+ idx = name.index('{')
+ if idx > 0:
+ name = name[:idx - 1]
+ proteins[id] = models.Protein(uniprot_code=id, protein_name=name, gene=node['geneName'])
def add_edges(edge):
id = edge['sourceDomainId'].split('.')[1]
protein = proteins[id]
protein.entrez = edge['targetDomainId'].split('.')[1]
- gene_to_prots[edge['targetDomainId']].add(id)
+ gene_to_prots[protein.entrez].add(id)
def add_genes(node):
id = node['primaryDomainId'].split('.')[1]
@@ -125,7 +125,7 @@ class nedrex_importer:
for protein in creates:
self.proteins[protein.uniprot_code] = protein
else:
- models.Protein.objects.bulk_create(self.proteins.values())
+ models.Protein.objects.bulk_create(proteins.values())
self.proteins = proteins
return len(self.proteins)
@@ -148,10 +148,9 @@ class nedrex_importer:
for drug in creates:
self.drugs[drug.drug_id] = drug
else:
- models.Drug.objects.bulk_create(self.drugs.values())
+ models.Drug.objects.bulk_create(drugs.values())
self.drugs = drugs
- self.drugs = drugs
return len(self.drugs)
def import_disorders(self, update):
@@ -161,7 +160,7 @@ class nedrex_importer:
def add_disorder(node):
id = node['primaryDomainId'].split('.')[1]
- self.disorders[id] = models.Disorder(mondo_id=id, label=node['displayName'], icd10=format_list(node['icd10']))
+ disorders[id] = models.Disorder(mondo_id=id, label=node['displayName'], icd10=format_list(node['icd10']))
iter_node_collection('disorder', add_disorder)
@@ -173,8 +172,9 @@ class nedrex_importer:
for disorder in creates:
self.disorders[disorder.uniprot_code] = disorder
else:
- models.Disorder.objects.bulk_create(self.disorders.values())
+ models.Disorder.objects.bulk_create(disorders.values())
self.disorders = disorders
- self.disorders = disorders
return len(self.disorders)
+
+
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 3b4d1d1..00f3d7c 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -8,17 +8,18 @@ from drugstone.models import ProteinProteinInteraction, ProteinDrugInteraction
from drugstone.management.includes.DataPopulator import DataPopulator
from .import_from_nedrex import nedrex_importer
+
class DatabasePopulator:
def __init__(self, data_dir,
# protein_file,
- drug_file,
+ # drug_file,
# protein_protein_interaction_file,
# protein_drug_interaction_file,
tissue_expression_file,
):
self.data_dir = data_dir
# self.protein_file = protein_file
- self.drug_file = drug_file
+ # self.drug_file = drug_file
# self.ppi_file = protein_protein_interaction_file
# self.pdi_file = protein_drug_interaction_file
self.exp_file = tissue_expression_file
@@ -63,15 +64,14 @@ class Command(BaseCommand):
# dataset directory
parser.add_argument('-dd', '--data_dir', type=str, help='Dataset directory path')
- # parser.add_argument('-p', '--protein_file', type=str, help='Protein file')
- parser.add_argument('-dr', '--drug_file', type=str, help='Drug file name')
- # parser.add_argument('-ppi', '--ppi_file', type=str, help='Protein-Protein interaction file')
- # parser.add_argument('-pdi', '--pdi_file', type=str, help='Protein-Drug interaction file')
- parser.add_argument('-exp', '--exp_file', type=str, help='Tissue expression file (.gct without first 2 lines)')
parser.add_argument('-dm', '--delete_model', type=str, help='Delete model(s)')
- parser.add_argument('-p', '--proteins', type=str, help='Populate Proteins')
- parser.add_argument('-di', '--disorders', type=str, help='Populate Disorders')
+ parser.add_argument('-p', '--proteins', action='store_true', help='Populate Proteins')
+ parser.add_argument('-di', '--disorders', action='store_true', help='Populate Disorders')
+ parser.add_argument('-dr', '--drugs', action='store_true', help='Drug file name')
+
+ parser.add_argument('-exp', '--exp_file', type=str, help='Tissue expression file (.gct without first 2 lines)')
+
parser.add_argument('-pp', '--protein_protein', type=str, help='Populate Protein-Protein Interactions')
parser.add_argument('-pdr', '--protein_drug', type=str, help='Populate Protein-Drug Interactions')
parser.add_argument('-pdi', '--protein_disorder', type=str, help='Populate Protein-Disorder Associations')
@@ -80,20 +80,16 @@ class Command(BaseCommand):
def handle(self, *args, **kwargs):
data_dir = kwargs['data_dir']
- # protein_file = kwargs['protein_file']
- drug_file = kwargs['drug_file']
- # ppi_file = kwargs['ppi_file']
- # pdi_file = kwargs['pdi_file']
exp_file = kwargs['exp_file']
- p = kwargs['proteins']
- pp = kwargs['protein_protein']
- pd = kwargs['protein_drug']
+ # p = kwargs['proteins']
+ # pp = kwargs['protein_protein']
+ # pd = kwargs['protein_drug']
db_populator = DatabasePopulator(data_dir=data_dir,
# protein_file=protein_file,
- drug_file=drug_file,
+ # drug_file=drug_file,
# protein_protein_interaction_file=ppi_file,
# protein_drug_interaction_file=pdi_file,
tissue_expression_file=exp_file,
@@ -108,41 +104,33 @@ class Command(BaseCommand):
populator = DataPopulator()
- if kwargs['drug_file'] is not None:
+ if kwargs['drugs']:
print('Populating Drugs...')
- n = DataPopulator.populate_drugs(populator)
- # n = nedrex_importer.import_drugs(importer,False)
+ # n = DataPopulator.populate_drugs(populator)
+ n = nedrex_importer.import_drugs(importer,False)
print(f'Populated {n} Drugs.')
- # if kwargs['protein_file'] is not None:
- # db_poulator.populate_protein_model()
-
- # if kwargs['pdi_file'] is not None:
- # db_poulator.populate_pdi_model()
-
- # if kwargs['ppi_file'] is not None:
- # db_poulator.populate_ppi_model()
if kwargs['exp_file'] is not None:
print('Populating Expressions...')
n = DataPopulator.populate_expessions(populator)
print(f'Populated {n} Expressions.')
- if kwargs['proteins'] is not None:
+ if kwargs['proteins']:
print('Populating Proteins...')
- # n = nedrex_importer.import_proteins(importer, False)
- n = DataPopulator.populate_proteins(populator)
+ n = nedrex_importer.import_proteins(importer, False)
+ # n = DataPopulator.populate_proteins(populator)
print(f'Populated {n} Proteins.')
- print('Populating ENSG IDs...')
- n = DataPopulator.populate_ensg(populator)
- print(f'Populated {n} ENSG IDs.')
+ # print('Populating ENSG IDs...')
+ # n = DataPopulator.populate_ensg(populator)
+ # print(f'Populated {n} ENSG IDs.')
- if kwargs['disorders'] is not None:
+ if kwargs['disorders']:
print('Populating Disorders...')
- # n = nedrex_importer.import_disorders(importer, False)
- n = DataPopulator.populate_disorders(populator)
+ n = nedrex_importer.import_disorders(importer, False)
+ # n = DataPopulator.populate_disorders(populator)
print(f'Populated {n} Disorders.')
if kwargs['protein_protein'] is not None:
diff --git a/drugstone/management/commands/test.py b/drugstone/management/commands/test.py
new file mode 100644
index 0000000..5afbea2
--- /dev/null
+++ b/drugstone/management/commands/test.py
@@ -0,0 +1,33 @@
+import python_nedrex as nedrex
+from python_nedrex.core import get_nodes, get_edges, get_api_key
+
+def iter_node_collection(coll_name, eval):
+ offset = 0
+ limit = 10000
+ while True:
+ result = get_nodes(coll_name, offset=offset, limit=limit)
+ if not result:
+ return
+ for node in result:
+ eval(node)
+ offset += limit
+
+
+def iter_edge_collection(coll_name, eval):
+ offset = 0
+ limit = 10000
+ while True:
+ result = get_edges(coll_name, offset=offset, limit=limit)
+ if not result:
+ return
+ for edge in result:
+ eval(edge)
+ offset += limit
+
+
+base_url = "http://82.148.225.92:8123/"
+nedrex.config.set_url_base(base_url)
+api_key = get_api_key(accept_eula=True)
+nedrex.config.set_api_key(api_key)
+
+iter_edge_collection("gene_expressed_in_tissue", lambda node: {print(node)})
\ No newline at end of file
diff --git a/drugstone/migrations/0001_initial.py b/drugstone/migrations/0001_initial.py
deleted file mode 100755
index 61778c5..0000000
--- a/drugstone/migrations/0001_initial.py
+++ /dev/null
@@ -1,47 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-27 17:36
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- initial = True
-
- dependencies = [
- ]
-
- operations = [
- migrations.CreateModel(
- name='Edge',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='Effect',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='ProteinGroup',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ('effects', models.ManyToManyField(through='drugstone.Edge', to='drugstone.Effect')),
- ],
- ),
- migrations.AddField(
- model_name='edge',
- name='effect',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Effect'),
- ),
- migrations.AddField(
- model_name='edge',
- name='protein_group',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.ProteinGroup'),
- ),
- ]
diff --git a/drugstone/migrations/0002_organism_protein.py b/drugstone/migrations/0002_organism_protein.py
deleted file mode 100755
index 9344741..0000000
--- a/drugstone/migrations/0002_organism_protein.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-28 13:41
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0001_initial'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Organism',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='Protein',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('uniprot_code', models.CharField(max_length=10)),
- ('protein_name', models.CharField(max_length=128)),
- ('gene_name', models.CharField(max_length=128)),
- ('organism', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Organism')),
- ('protein_group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.ProteinGroup')),
- ],
- ),
- ]
diff --git a/drugstone/migrations/0003_auto_20200329_1527.py b/drugstone/migrations/0003_auto_20200329_1527.py
deleted file mode 100755
index e17ef5d..0000000
--- a/drugstone/migrations/0003_auto_20200329_1527.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-29 15:27
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0002_organism_protein'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='protein',
- name='organism',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Organism'),
- ),
- migrations.AlterField(
- model_name='protein',
- name='protein_group',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.ProteinGroup'),
- ),
- ]
diff --git a/drugstone/migrations/0004_protein_protein_description.py b/drugstone/migrations/0004_protein_protein_description.py
deleted file mode 100755
index 37fb632..0000000
--- a/drugstone/migrations/0004_protein_protein_description.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-29 15:49
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0003_auto_20200329_1527'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='protein',
- name='protein_description',
- field=models.CharField(default='No Description', max_length=512),
- ),
- ]
diff --git a/drugstone/migrations/0005_auto_20200329_2024.py b/drugstone/migrations/0005_auto_20200329_2024.py
deleted file mode 100755
index 901aa64..0000000
--- a/drugstone/migrations/0005_auto_20200329_2024.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-29 20:24
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0004_protein_protein_description'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='edge',
- name='effect',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Effect'),
- ),
- migrations.AlterField(
- model_name='edge',
- name='protein_group',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.ProteinGroup'),
- ),
- ]
diff --git a/drugstone/migrations/0006_auto_20200329_2041.py b/drugstone/migrations/0006_auto_20200329_2041.py
deleted file mode 100755
index 93f451c..0000000
--- a/drugstone/migrations/0006_auto_20200329_2041.py
+++ /dev/null
@@ -1,33 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-29 20:41
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0005_auto_20200329_2024'),
- ]
-
- operations = [
- migrations.RenameField(
- model_name='protein',
- old_name='protein_description',
- new_name='description',
- ),
- migrations.RenameField(
- model_name='protein',
- old_name='gene_name',
- new_name='gene',
- ),
- migrations.RenameField(
- model_name='protein',
- old_name='protein_name',
- new_name='name',
- ),
- migrations.AddField(
- model_name='proteingroup',
- name='group_id',
- field=models.IntegerField(default=-1),
- ),
- ]
diff --git a/drugstone/migrations/0007_auto_20200330_1326.py b/drugstone/migrations/0007_auto_20200330_1326.py
deleted file mode 100755
index b7e6500..0000000
--- a/drugstone/migrations/0007_auto_20200330_1326.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-30 13:26
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0006_auto_20200329_2041'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Virus',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='VirusEffect',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=128)),
- ('effect', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Effect')),
- ('virus', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Virus')),
- ],
- ),
- migrations.AddField(
- model_name='virus',
- name='effects',
- field=models.ManyToManyField(through='drugstone.VirusEffect', to='drugstone.Effect'),
- ),
- ]
diff --git a/drugstone/migrations/0008_auto_20200330_1748.py b/drugstone/migrations/0008_auto_20200330_1748.py
deleted file mode 100755
index fa2d0bd..0000000
--- a/drugstone/migrations/0008_auto_20200330_1748.py
+++ /dev/null
@@ -1,33 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-30 17:48
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0007_auto_20200330_1326'),
- ]
-
- operations = [
- migrations.RemoveField(
- model_name='viruseffect',
- name='effect',
- ),
- migrations.RemoveField(
- model_name='viruseffect',
- name='virus',
- ),
- migrations.AddField(
- model_name='effect',
- name='organism',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Organism'),
- ),
- migrations.DeleteModel(
- name='Virus',
- ),
- migrations.DeleteModel(
- name='VirusEffect',
- ),
- ]
diff --git a/drugstone/migrations/0009_auto_20200330_1904.py b/drugstone/migrations/0009_auto_20200330_1904.py
deleted file mode 100755
index 5ceb36b..0000000
--- a/drugstone/migrations/0009_auto_20200330_1904.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-30 19:04
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0008_auto_20200330_1748'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='protein',
- name='gene',
- field=models.CharField(default='', max_length=128),
- ),
- ]
diff --git a/drugstone/migrations/0010_auto_20200331_0909.py b/drugstone/migrations/0010_auto_20200331_0909.py
deleted file mode 100755
index f6c45d2..0000000
--- a/drugstone/migrations/0010_auto_20200331_0909.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Generated by Django 3.0.4 on 2020-03-31 07:09
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0009_auto_20200330_1904'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='effect',
- name='organism',
- field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Organism'),
- ),
- ]
diff --git a/drugstone/migrations/0011_auto_20200401_1031.py b/drugstone/migrations/0011_auto_20200401_1031.py
deleted file mode 100755
index 9910c86..0000000
--- a/drugstone/migrations/0011_auto_20200401_1031.py
+++ /dev/null
@@ -1,66 +0,0 @@
-# Generated by Django 3.0.4 on 2020-04-01 10:31
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0010_auto_20200331_0909'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='DatasetVirus',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('dataset', models.CharField(max_length=128)),
- ('virus', models.CharField(max_length=128)),
- ],
- options={
- 'unique_together': {('dataset', 'virus')},
- },
- ),
- migrations.RemoveField(
- model_name='proteingroup',
- name='effects',
- ),
- migrations.RemoveField(
- model_name='edge',
- name='protein_group',
- ),
- migrations.RemoveField(
- model_name='effect',
- name='organism',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='organism',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='protein_group',
- ),
- migrations.AddField(
- model_name='edge',
- name='protein',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Protein'),
- ),
- migrations.AddField(
- model_name='protein',
- name='effects',
- field=models.ManyToManyField(through='drugstone.Edge', to='drugstone.Effect'),
- ),
- migrations.DeleteModel(
- name='Organism',
- ),
- migrations.DeleteModel(
- name='ProteinGroup',
- ),
- migrations.AddField(
- model_name='effect',
- name='dataset_virus',
- field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.DatasetVirus'),
- ),
- ]
diff --git a/drugstone/migrations/0012_auto_20200401_1050.py b/drugstone/migrations/0012_auto_20200401_1050.py
deleted file mode 100755
index ffd68ab..0000000
--- a/drugstone/migrations/0012_auto_20200401_1050.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# Generated by Django 3.0.4 on 2020-04-01 10:50
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0011_auto_20200401_1031'),
- ]
-
- operations = [
- migrations.RemoveField(
- model_name='protein',
- name='description',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='name',
- ),
- ]
diff --git a/drugstone/migrations/0013_auto_20200401_1124.py b/drugstone/migrations/0013_auto_20200401_1124.py
deleted file mode 100755
index 2a51246..0000000
--- a/drugstone/migrations/0013_auto_20200401_1124.py
+++ /dev/null
@@ -1,33 +0,0 @@
-# Generated by Django 3.0.4 on 2020-04-01 11:24
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0012_auto_20200401_1050'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='protein',
- name='description',
- field=models.CharField(default='No description', max_length=512),
- ),
- migrations.AddField(
- model_name='protein',
- name='name',
- field=models.CharField(default='No name', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='gene',
- field=models.CharField(default='No gene', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='uniprot_code',
- field=models.CharField(default='No code', max_length=10),
- ),
- ]
diff --git a/drugstone/migrations/0014_auto_20200401_1339.py b/drugstone/migrations/0014_auto_20200401_1339.py
deleted file mode 100755
index 05e02b1..0000000
--- a/drugstone/migrations/0014_auto_20200401_1339.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# Generated by Django 3.0.4 on 2020-04-01 13:39
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0013_auto_20200401_1124'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='effect',
- name='effect_id',
- field=models.CharField(default='No id', max_length=128),
- ),
- migrations.AlterField(
- model_name='effect',
- name='name',
- field=models.CharField(default='No name', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='uniprot_code',
- field=models.CharField(default='No accession number', max_length=10),
- ),
- ]
diff --git a/drugstone/migrations/0015_auto_20200401_1717.py b/drugstone/migrations/0015_auto_20200401_1717.py
deleted file mode 100755
index 7bbc438..0000000
--- a/drugstone/migrations/0015_auto_20200401_1717.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# Generated by Django 3.0.4 on 2020-04-01 15:17
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0014_auto_20200401_1339'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='effect',
- name='effect_id',
- field=models.CharField(default='No id', max_length=128, unique=True),
- ),
- migrations.AlterField(
- model_name='protein',
- name='uniprot_code',
- field=models.CharField(default='No accession number', max_length=10, unique=True),
- ),
- migrations.AlterUniqueTogether(
- name='edge',
- unique_together={('effect', 'protein')},
- ),
- migrations.AlterUniqueTogether(
- name='effect',
- unique_together={('name', 'dataset_virus')},
- ),
- ]
diff --git a/drugstone/migrations/0016_task.py b/drugstone/migrations/0016_task.py
deleted file mode 100755
index 347abda..0000000
--- a/drugstone/migrations/0016_task.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-02 16:54
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0015_auto_20200401_1717'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Task',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('token', models.CharField(max_length=32, unique=True)),
- ('algorithm', models.CharField(max_length=128)),
- ('parameters', models.TextField()),
- ('progress', models.FloatField(default=0.0)),
- ('started_at', models.DateTimeField(null=True)),
- ('finished_at', models.DateTimeField(null=True)),
- ('worker_id', models.IntegerField(null=True)),
- ('done', models.BooleanField(default=False)),
- ('result', models.TextField(null=True)),
- ],
- ),
- ]
diff --git a/drugstone/migrations/0017_auto_20200402_1935.py b/drugstone/migrations/0017_auto_20200402_1935.py
deleted file mode 100755
index cc3ac2c..0000000
--- a/drugstone/migrations/0017_auto_20200402_1935.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-02 17:35
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0016_task'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='task',
- name='job_id',
- field=models.CharField(max_length=128, null=True),
- ),
- migrations.AlterField(
- model_name='task',
- name='worker_id',
- field=models.CharField(max_length=128, null=True),
- ),
- ]
diff --git a/drugstone/migrations/0018_task_created_at.py b/drugstone/migrations/0018_task_created_at.py
deleted file mode 100755
index 018ad15..0000000
--- a/drugstone/migrations/0018_task_created_at.py
+++ /dev/null
@@ -1,20 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-02 21:50
-
-from django.db import migrations, models
-import django.utils.timezone
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0017_auto_20200402_1935'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='task',
- name='created_at',
- field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
- preserve_default=False,
- ),
- ]
diff --git a/drugstone/migrations/0019_auto_20200403_1234.py b/drugstone/migrations/0019_auto_20200403_1234.py
deleted file mode 100755
index 5312dca..0000000
--- a/drugstone/migrations/0019_auto_20200403_1234.py
+++ /dev/null
@@ -1,30 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 12:34
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0018_task_created_at'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='PPI',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('from_protein', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='from_protein', to='drugstone.Protein')),
- ('to_protein', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='to_protein', to='drugstone.Protein')),
- ],
- options={
- 'unique_together': {('from_protein', 'to_protein')},
- },
- ),
- migrations.AddField(
- model_name='protein',
- name='proteins',
- field=models.ManyToManyField(related_name='_protein_proteins_+', through='drugstone.PPI', to='drugstone.Protein'),
- ),
- ]
diff --git a/drugstone/migrations/0019_task_status.py b/drugstone/migrations/0019_task_status.py
deleted file mode 100755
index 261f7f5..0000000
--- a/drugstone/migrations/0019_task_status.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 13:28
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0018_task_created_at'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='task',
- name='status',
- field=models.CharField(max_length=255, null=True),
- ),
- ]
diff --git a/drugstone/migrations/0020_auto_20200403_1302.py b/drugstone/migrations/0020_auto_20200403_1302.py
deleted file mode 100755
index 607a81e..0000000
--- a/drugstone/migrations/0020_auto_20200403_1302.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 13:02
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0019_auto_20200403_1234'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='protein',
- name='proteins',
- field=models.ManyToManyField(through='drugstone.PPI', to='drugstone.Protein'),
- ),
- ]
diff --git a/drugstone/migrations/0021_remove_protein_proteins.py b/drugstone/migrations/0021_remove_protein_proteins.py
deleted file mode 100755
index fa7b145..0000000
--- a/drugstone/migrations/0021_remove_protein_proteins.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 13:08
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0020_auto_20200403_1302'),
- ]
-
- operations = [
- migrations.RemoveField(
- model_name='protein',
- name='proteins',
- ),
- ]
diff --git a/drugstone/migrations/0022_auto_20200403_1319.py b/drugstone/migrations/0022_auto_20200403_1319.py
deleted file mode 100755
index 9fb6784..0000000
--- a/drugstone/migrations/0022_auto_20200403_1319.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 13:19
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0021_remove_protein_proteins'),
- ]
-
- operations = [
- migrations.AlterUniqueTogether(
- name='ppi',
- unique_together=set(),
- ),
- ]
diff --git a/drugstone/migrations/0023_auto_20200403_1400.py b/drugstone/migrations/0023_auto_20200403_1400.py
deleted file mode 100755
index 5733623..0000000
--- a/drugstone/migrations/0023_auto_20200403_1400.py
+++ /dev/null
@@ -1,22 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 14:00
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0022_auto_20200403_1319'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='protein',
- name='proteins',
- field=models.ManyToManyField(related_name='_protein_proteins_+', through='drugstone.PPI', to='drugstone.Protein'),
- ),
- migrations.AlterUniqueTogether(
- name='ppi',
- unique_together={('from_protein', 'to_protein')},
- ),
- ]
diff --git a/drugstone/migrations/0024_auto_20200403_1408.py b/drugstone/migrations/0024_auto_20200403_1408.py
deleted file mode 100755
index 316fbf5..0000000
--- a/drugstone/migrations/0024_auto_20200403_1408.py
+++ /dev/null
@@ -1,38 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 14:08
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0023_auto_20200403_1400'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Drug',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('status', models.CharField(max_length=32, null=True)),
- ],
- ),
- migrations.RemoveField(
- model_name='protein',
- name='proteins',
- ),
- migrations.CreateModel(
- name='PDI',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('drug', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Drug')),
- ('protein', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='drugstone.Protein')),
- ],
- ),
- migrations.AddField(
- model_name='protein',
- name='drugs',
- field=models.ManyToManyField(through='drugstone.PDI', to='drugstone.Drug'),
- ),
- ]
diff --git a/drugstone/migrations/0025_auto_20200403_1457.py b/drugstone/migrations/0025_auto_20200403_1457.py
deleted file mode 100755
index 83a800a..0000000
--- a/drugstone/migrations/0025_auto_20200403_1457.py
+++ /dev/null
@@ -1,22 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 14:57
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0024_auto_20200403_1408'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='drug',
- name='name',
- field=models.CharField(max_length=128, null=True),
- ),
- migrations.AlterUniqueTogether(
- name='pdi',
- unique_together={('protein', 'drug')},
- ),
- ]
diff --git a/drugstone/migrations/0026_auto_20200403_1636.py b/drugstone/migrations/0026_auto_20200403_1636.py
deleted file mode 100755
index ca1e2d7..0000000
--- a/drugstone/migrations/0026_auto_20200403_1636.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-03 16:36
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0025_auto_20200403_1457'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='drug',
- name='drug_id',
- field=models.CharField(default='No id', max_length=10, unique=True),
- ),
- migrations.AlterField(
- model_name='drug',
- name='name',
- field=models.CharField(default='No name', max_length=128),
- ),
- migrations.AlterField(
- model_name='drug',
- name='status',
- field=models.CharField(default='No status', max_length=32),
- ),
- ]
diff --git a/drugstone/migrations/0027_merge_20200404_1240.py b/drugstone/migrations/0027_merge_20200404_1240.py
deleted file mode 100755
index 4541a15..0000000
--- a/drugstone/migrations/0027_merge_20200404_1240.py
+++ /dev/null
@@ -1,14 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-04 10:40
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0019_task_status'),
- ('drugstone', '0026_auto_20200403_1636'),
- ]
-
- operations = [
- ]
diff --git a/drugstone/migrations/0028_auto_20200404_1337.py b/drugstone/migrations/0028_auto_20200404_1337.py
deleted file mode 100755
index ef478be..0000000
--- a/drugstone/migrations/0028_auto_20200404_1337.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-04 11:37
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- atomic = False
-
- dependencies = [
- ('drugstone', '0027_merge_20200404_1240'),
- ]
-
- operations = [
- migrations.RenameModel(
- old_name='PDI',
- new_name='ProteinDrugInteraction',
- ),
- migrations.RenameModel(
- old_name='PPI',
- new_name='ProteinProteinInteraction',
- ),
- migrations.RenameModel(
- old_name='Edge',
- new_name='ProteinViralInteraction',
- ),
- migrations.RenameModel(
- old_name='Effect',
- new_name='ViralProtein',
- ),
- ]
diff --git a/drugstone/migrations/0029_auto_20200405_0047.py b/drugstone/migrations/0029_auto_20200405_0047.py
deleted file mode 100755
index 2a37368..0000000
--- a/drugstone/migrations/0029_auto_20200405_0047.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-04 22:47
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0028_auto_20200404_1337'),
- ]
-
- operations = [
- migrations.AlterUniqueTogether(
- name='proteinproteininteraction',
- unique_together=set(),
- ),
- ]
diff --git a/drugstone/migrations/0030_auto_20200405_0123.py b/drugstone/migrations/0030_auto_20200405_0123.py
deleted file mode 100755
index 535ea2e..0000000
--- a/drugstone/migrations/0030_auto_20200405_0123.py
+++ /dev/null
@@ -1,44 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-04 23:23
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0029_auto_20200405_0047'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='proteindruginteraction',
- name='drug',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Drug'),
- ),
- migrations.AlterField(
- model_name='proteindruginteraction',
- name='protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein'),
- ),
- migrations.AlterField(
- model_name='proteinproteininteraction',
- name='from_protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='from_protein', to='drugstone.Protein'),
- ),
- migrations.AlterField(
- model_name='proteinproteininteraction',
- name='to_protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='to_protein', to='drugstone.Protein'),
- ),
- migrations.AlterField(
- model_name='proteinviralinteraction',
- name='effect',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.ViralProtein'),
- ),
- migrations.AlterField(
- model_name='proteinviralinteraction',
- name='protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein'),
- ),
- ]
diff --git a/drugstone/migrations/0031_task_failed.py b/drugstone/migrations/0031_task_failed.py
deleted file mode 100755
index f87dcea..0000000
--- a/drugstone/migrations/0031_task_failed.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-05 15:03
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0030_auto_20200405_0123'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='task',
- name='failed',
- field=models.BooleanField(default=False),
- ),
- ]
diff --git a/drugstone/migrations/0032_task_target.py b/drugstone/migrations/0032_task_target.py
deleted file mode 100755
index 6c3e71c..0000000
--- a/drugstone/migrations/0032_task_target.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-07 09:54
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0031_task_failed'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='task',
- name='target',
- field=models.CharField(choices=[('drug', 'Drug'), ('drug-target', 'Drug Target')], default='drug-target', max_length=32),
- preserve_default=False,
- ),
- ]
diff --git a/drugstone/migrations/0033_auto_20200407_1646.py b/drugstone/migrations/0033_auto_20200407_1646.py
deleted file mode 100755
index d5e89f0..0000000
--- a/drugstone/migrations/0033_auto_20200407_1646.py
+++ /dev/null
@@ -1,58 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-07 14:46
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0032_task_target'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='drug',
- name='drug_id',
- field=models.CharField(max_length=10, unique=True),
- ),
- migrations.AlterField(
- model_name='drug',
- name='name',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='drug',
- name='status',
- field=models.CharField(default='', max_length=32),
- ),
- migrations.AlterField(
- model_name='protein',
- name='description',
- field=models.CharField(default='', max_length=512),
- ),
- migrations.AlterField(
- model_name='protein',
- name='gene',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='name',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='uniprot_code',
- field=models.CharField(max_length=10, unique=True),
- ),
- migrations.AlterField(
- model_name='viralprotein',
- name='effect_id',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='viralprotein',
- name='name',
- field=models.CharField(default='', max_length=128),
- ),
- ]
diff --git a/drugstone/migrations/0034_auto_20200408_0952.py b/drugstone/migrations/0034_auto_20200408_0952.py
deleted file mode 100755
index 24b9322..0000000
--- a/drugstone/migrations/0034_auto_20200408_0952.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-08 09:52
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0033_auto_20200407_1646'),
- ]
-
- operations = [
- migrations.RemoveField(
- model_name='protein',
- name='description',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='name',
- ),
- migrations.RemoveField(
- model_name='proteinviralinteraction',
- name='name',
- ),
- migrations.AddField(
- model_name='proteinviralinteraction',
- name='is_AP_MS',
- field=models.BooleanField(default=False),
- ),
- migrations.AddField(
- model_name='proteinviralinteraction',
- name='is_overexpression',
- field=models.BooleanField(default=False),
- ),
- ]
diff --git a/drugstone/migrations/0035_auto_20200410_1107.py b/drugstone/migrations/0035_auto_20200410_1107.py
deleted file mode 100755
index c7a9dff..0000000
--- a/drugstone/migrations/0035_auto_20200410_1107.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-10 11:07
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0034_auto_20200408_0952'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='drug',
- name='name',
- field=models.CharField(default='', max_length=256),
- ),
- ]
diff --git a/drugstone/migrations/0036_drug_in_trial.py b/drugstone/migrations/0036_drug_in_trial.py
deleted file mode 100755
index 79d44d2..0000000
--- a/drugstone/migrations/0036_drug_in_trial.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-11 12:05
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0035_auto_20200410_1107'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='drug',
- name='in_trial',
- field=models.BooleanField(default=False),
- ),
- ]
diff --git a/drugstone/migrations/0037_auto_20200417_1633.py b/drugstone/migrations/0037_auto_20200417_1633.py
deleted file mode 100755
index 96bf52c..0000000
--- a/drugstone/migrations/0037_auto_20200417_1633.py
+++ /dev/null
@@ -1,58 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-17 14:33
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0036_drug_in_trial'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='drug',
- name='in_literature',
- field=models.BooleanField(default=False),
- ),
- migrations.AddField(
- model_name='protein',
- name='protein_name',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='drugs',
- field=models.ManyToManyField(related_name='interacting_proteins', through='drugstone.ProteinDrugInteraction', to='drugstone.Drug'),
- ),
- migrations.AlterField(
- model_name='protein',
- name='effects',
- field=models.ManyToManyField(related_name='interacting_proteins', through='drugstone.ProteinViralInteraction', to='drugstone.ViralProtein'),
- ),
- migrations.AlterField(
- model_name='proteinproteininteraction',
- name='from_protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='interacting_proteins_out', to='drugstone.Protein'),
- ),
- migrations.AlterField(
- model_name='proteinproteininteraction',
- name='to_protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='interacting_proteins_in', to='drugstone.Protein'),
- ),
- migrations.CreateModel(
- name='ClosestViralProtein',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('distance', models.PositiveIntegerField()),
- ('protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein')),
- ('viral_protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.ViralProtein')),
- ],
- ),
- migrations.AddField(
- model_name='protein',
- name='closest_effects',
- field=models.ManyToManyField(related_name='closest_proteins', through='drugstone.ClosestViralProtein', to='drugstone.ViralProtein'),
- ),
- ]
diff --git a/drugstone/migrations/0038_auto_20200417_1634.py b/drugstone/migrations/0038_auto_20200417_1634.py
deleted file mode 100755
index c22cd22..0000000
--- a/drugstone/migrations/0038_auto_20200417_1634.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-04-17 14:34
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0037_auto_20200417_1633'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='protein',
- name='drugs',
- field=models.ManyToManyField(related_name='interacting_drugs', through='drugstone.ProteinDrugInteraction', to='drugstone.Drug'),
- ),
- ]
diff --git a/drugstone/migrations/0039_auto_20200528_1503.py b/drugstone/migrations/0039_auto_20200528_1503.py
deleted file mode 100755
index ff67d56..0000000
--- a/drugstone/migrations/0039_auto_20200528_1503.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# Generated by Django 3.0.5 on 2020-05-28 13:03
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0038_auto_20200417_1634'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Tissue',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(default='', max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='ExpressionLevel',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('expression_level', models.FloatField()),
- ('protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein')),
- ('tissue', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Tissue')),
- ],
- ),
- migrations.AddField(
- model_name='protein',
- name='tissue_expression',
- field=models.ManyToManyField(related_name='interacting_drugs', through='drugstone.ExpressionLevel', to='drugstone.Tissue'),
- ),
- ]
diff --git a/drugstone/migrations/0040_auto_20200528_1539.py b/drugstone/migrations/0040_auto_20200528_1539.py
deleted file mode 100755
index b51aaf2..0000000
--- a/drugstone/migrations/0040_auto_20200528_1539.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Generated by Django 3.0.5 on 2020-05-28 13:39
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0039_auto_20200528_1503'),
- ]
-
- operations = [
- migrations.AlterUniqueTogether(
- name='expressionlevel',
- unique_together={('tissue', 'protein')},
- ),
- ]
diff --git a/drugstone/migrations/0041_drug_links.py b/drugstone/migrations/0041_drug_links.py
deleted file mode 100755
index 5e20cc9..0000000
--- a/drugstone/migrations/0041_drug_links.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-05-31 13:00
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0040_auto_20200528_1539'),
- ]
-
- operations = [
- migrations.AddField(
- model_name='drug',
- name='links',
- field=models.CharField(default='', max_length=1024),
- ),
- ]
diff --git a/drugstone/migrations/0042_auto_20200531_1519.py b/drugstone/migrations/0042_auto_20200531_1519.py
deleted file mode 100755
index 2700351..0000000
--- a/drugstone/migrations/0042_auto_20200531_1519.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2020-05-31 13:19
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0041_drug_links'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='drug',
- name='links',
- field=models.CharField(default='', max_length=16384),
- ),
- ]
diff --git a/drugstone/migrations/0043_auto_20210518_2120.py b/drugstone/migrations/0043_auto_20210518_2120.py
deleted file mode 100755
index 97154ba..0000000
--- a/drugstone/migrations/0043_auto_20210518_2120.py
+++ /dev/null
@@ -1,104 +0,0 @@
-# Generated by Django 3.0.5 on 2021-05-18 19:20
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0042_auto_20200531_1519'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='PDIDataset',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(default='', max_length=128, unique=True)),
- ('link', models.CharField(default='', max_length=128)),
- ('version', models.CharField(default='', max_length=128)),
- ],
- ),
- migrations.CreateModel(
- name='PPIDataset',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(default='', max_length=128)),
- ('link', models.CharField(default='', max_length=128)),
- ('version', models.CharField(default='', max_length=128)),
- ],
- ),
- migrations.AlterUniqueTogether(
- name='datasetvirus',
- unique_together=None,
- ),
- migrations.AlterUniqueTogether(
- name='proteinviralinteraction',
- unique_together=None,
- ),
- migrations.RemoveField(
- model_name='proteinviralinteraction',
- name='effect',
- ),
- migrations.RemoveField(
- model_name='proteinviralinteraction',
- name='protein',
- ),
- migrations.AlterUniqueTogether(
- name='viralprotein',
- unique_together=None,
- ),
- migrations.RemoveField(
- model_name='viralprotein',
- name='dataset_virus',
- ),
- migrations.RemoveField(
- model_name='drug',
- name='in_literature',
- ),
- migrations.RemoveField(
- model_name='drug',
- name='in_trial',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='closest_effects',
- ),
- migrations.RemoveField(
- model_name='protein',
- name='effects',
- ),
- migrations.AddField(
- model_name='protein',
- name='entrez',
- field=models.CharField(default='', max_length=128, unique=True),
- ),
- migrations.AlterField(
- model_name='tissue',
- name='name',
- field=models.CharField(default='', max_length=128, unique=True),
- ),
- migrations.DeleteModel(
- name='ClosestViralProtein',
- ),
- migrations.DeleteModel(
- name='DatasetVirus',
- ),
- migrations.DeleteModel(
- name='ProteinViralInteraction',
- ),
- migrations.DeleteModel(
- name='ViralProtein',
- ),
- migrations.AddField(
- model_name='proteindruginteraction',
- name='pdi_dataset',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='pdi_dataset_relation', to='drugstone.PDIDataset'),
- ),
- migrations.AddField(
- model_name='proteinproteininteraction',
- name='ppi_dataset',
- field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='ppi_dataset_relation', to='drugstone.PPIDataset'),
- ),
- ]
diff --git a/drugstone/migrations/0044_auto_20210518_2145.py b/drugstone/migrations/0044_auto_20210518_2145.py
deleted file mode 100755
index e409609..0000000
--- a/drugstone/migrations/0044_auto_20210518_2145.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2021-05-18 19:45
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0043_auto_20210518_2120'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='drug',
- name='status',
- field=models.CharField(default='', max_length=128),
- ),
- ]
diff --git a/drugstone/migrations/0045_auto_20210519_1401.py b/drugstone/migrations/0045_auto_20210519_1401.py
deleted file mode 100755
index cc9a872..0000000
--- a/drugstone/migrations/0045_auto_20210519_1401.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Generated by Django 3.0.5 on 2021-05-19 12:01
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0044_auto_20210518_2145'),
- ]
-
- operations = [
- migrations.AlterUniqueTogether(
- name='proteindruginteraction',
- unique_together={('pdi_dataset', 'protein', 'drug')},
- ),
- ]
diff --git a/drugstone/migrations/0046_protein_ensembl.py b/drugstone/migrations/0046_protein_ensembl.py
deleted file mode 100755
index 3f70faa..0000000
--- a/drugstone/migrations/0046_protein_ensembl.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# Generated by Django 3.0.5 on 2021-06-11 18:50
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0045_auto_20210519_1401'),
- ]
-
- operations = [
- ]
diff --git a/drugstone/migrations/0047_auto_20210615_1013.py b/drugstone/migrations/0047_auto_20210615_1013.py
deleted file mode 100755
index 4e216fd..0000000
--- a/drugstone/migrations/0047_auto_20210615_1013.py
+++ /dev/null
@@ -1,33 +0,0 @@
-# Generated by Django 3.0.5 on 2021-06-15 10:13
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0046_protein_ensembl'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='EnsemblGene',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(max_length=15, unique=True)),
- ('protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein')),
- ],
- ),
- migrations.CreateModel(
- name='EmsemblGeneProteinRelation',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('ensembl_gene', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.EnsemblGene', unique=True)),
- ('protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein')),
- ],
- options={
- 'unique_together': {('ensembl_gene', 'protein')},
- },
- ),
- ]
diff --git a/drugstone/migrations/0048_delete_emsemblgeneproteinrelation.py b/drugstone/migrations/0048_delete_emsemblgeneproteinrelation.py
deleted file mode 100755
index d48c7a2..0000000
--- a/drugstone/migrations/0048_delete_emsemblgeneproteinrelation.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# Generated by Django 3.0.5 on 2021-06-15 15:01
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0047_auto_20210615_1013'),
- ]
-
- operations = [
- migrations.DeleteModel(
- name='EmsemblGeneProteinRelation',
- ),
- ]
diff --git a/drugstone/migrations/0049_auto_20210616_0932.py b/drugstone/migrations/0049_auto_20210616_0932.py
deleted file mode 100644
index bc2c32a..0000000
--- a/drugstone/migrations/0049_auto_20210616_0932.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Generated by Django 3.0.5 on 2021-06-16 09:32
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0048_delete_emsemblgeneproteinrelation'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='ensemblgene',
- name='protein',
- field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='ensg', to='drugstone.Protein'),
- ),
- ]
diff --git a/drugstone/migrations/0050_auto_20210722_0858.py b/drugstone/migrations/0050_auto_20210722_0858.py
deleted file mode 100644
index 88d434e..0000000
--- a/drugstone/migrations/0050_auto_20210722_0858.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Generated by Django 3.0.5 on 2021-07-22 08:58
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0049_auto_20210616_0932'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='protein',
- name='entrez',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterField(
- model_name='protein',
- name='uniprot_code',
- field=models.CharField(max_length=10),
- ),
- migrations.AlterUniqueTogether(
- name='protein',
- unique_together={('uniprot_code', 'gene', 'entrez')},
- ),
- ]
diff --git a/drugstone/migrations/0051_auto_20210914_1251.py b/drugstone/migrations/0051_auto_20210914_1251.py
deleted file mode 100644
index 3bc30ce..0000000
--- a/drugstone/migrations/0051_auto_20210914_1251.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-14 12:51
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0050_auto_20210722_0858'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Network',
- fields=[
- ('id', models.AutoField(primary_key=True, serialize=False)),
- ('created_at', models.DateTimeField(auto_now_add=True)),
- ('nodes', models.TextField(null=True)),
- ('edges', models.TextField(null=True)),
- ('config', models.TextField(null=True)),
- ],
- ),
- migrations.AlterField(
- model_name='pdidataset',
- name='name',
- field=models.CharField(default='', max_length=128),
- ),
- migrations.AlterUniqueTogether(
- name='pdidataset',
- unique_together={('name', 'version')},
- ),
- migrations.AlterUniqueTogether(
- name='ppidataset',
- unique_together={('name', 'version')},
- ),
- ]
diff --git a/drugstone/migrations/0052_auto_20210914_1311.py b/drugstone/migrations/0052_auto_20210914_1311.py
deleted file mode 100644
index a791314..0000000
--- a/drugstone/migrations/0052_auto_20210914_1311.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-14 13:11
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0051_auto_20210914_1251'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='network',
- name='id',
- field=models.CharField(max_length=28, primary_key=True, serialize=False, unique=True),
- ),
- ]
diff --git a/drugstone/migrations/0053_auto_20210914_1314.py b/drugstone/migrations/0053_auto_20210914_1314.py
deleted file mode 100644
index 93986cb..0000000
--- a/drugstone/migrations/0053_auto_20210914_1314.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-14 13:14
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0052_auto_20210914_1311'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='network',
- name='id',
- field=models.CharField(max_length=32, primary_key=True, serialize=False, unique=True),
- ),
- ]
diff --git a/drugstone/migrations/0054_auto_20210922_1342.py b/drugstone/migrations/0054_auto_20210922_1342.py
deleted file mode 100644
index 3f1f8a5..0000000
--- a/drugstone/migrations/0054_auto_20210922_1342.py
+++ /dev/null
@@ -1,72 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-22 13:42
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0053_auto_20210914_1314'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='Disorder',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('mondo_id', models.CharField(max_length=7)),
- ('label', models.CharField(default='', max_length=256)),
- ('icd10', models.CharField(default='', max_length=32)),
- ],
- ),
- migrations.CreateModel(
- name='PDisDataset',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(default='', max_length=128)),
- ('link', models.CharField(default='', max_length=128)),
- ('version', models.CharField(default='', max_length=128)),
- ],
- options={
- 'unique_together': {('name', 'version')},
- },
- ),
- migrations.AlterField(
- model_name='network',
- name='config',
- field=models.TextField(default='', null=True),
- ),
- migrations.AlterField(
- model_name='network',
- name='edges',
- field=models.TextField(default='', null=True),
- ),
- migrations.AlterField(
- model_name='network',
- name='nodes',
- field=models.TextField(default='', null=True),
- ),
- migrations.CreateModel(
- name='ProteinDisorderAssociation',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('score', models.FloatField()),
- ('disorder', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Disorder')),
- ('pdis_dataset', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='pdis_dataset_relation', to='drugstone.PDisDataset')),
- ('protein', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Protein')),
- ],
- options={
- 'unique_together': {('pdis_dataset', 'protein', 'disorder')},
- },
- ),
- migrations.AddField(
- model_name='disorder',
- name='proteins',
- field=models.ManyToManyField(related_name='associated_proteins', through='drugstone.ProteinDisorderAssociation', to='drugstone.Protein'),
- ),
- migrations.AlterUniqueTogether(
- name='disorder',
- unique_together={('mondo_id', 'label', 'icd10')},
- ),
- ]
diff --git a/drugstone/migrations/0055_auto_20210922_1343.py b/drugstone/migrations/0055_auto_20210922_1343.py
deleted file mode 100644
index 32d88d8..0000000
--- a/drugstone/migrations/0055_auto_20210922_1343.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-22 13:43
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0054_auto_20210922_1342'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='disorder',
- name='icd10',
- field=models.CharField(default='', max_length=64),
- ),
- ]
diff --git a/drugstone/migrations/0056_auto_20210922_1348.py b/drugstone/migrations/0056_auto_20210922_1348.py
deleted file mode 100644
index 8481e96..0000000
--- a/drugstone/migrations/0056_auto_20210922_1348.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-22 13:48
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0055_auto_20210922_1343'),
- ]
-
- operations = [
- migrations.AlterField(
- model_name='disorder',
- name='icd10',
- field=models.CharField(default='', max_length=128),
- ),
- ]
diff --git a/drugstone/migrations/0057_drdidataset_drugdisorderindication.py b/drugstone/migrations/0057_drdidataset_drugdisorderindication.py
deleted file mode 100644
index 881827c..0000000
--- a/drugstone/migrations/0057_drdidataset_drugdisorderindication.py
+++ /dev/null
@@ -1,38 +0,0 @@
-# Generated by Django 3.0.5 on 2021-09-23 15:47
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
- dependencies = [
- ('drugstone', '0056_auto_20210922_1348'),
- ]
-
- operations = [
- migrations.CreateModel(
- name='DrDiDataset',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('name', models.CharField(default='', max_length=128)),
- ('link', models.CharField(default='', max_length=128)),
- ('version', models.CharField(default='', max_length=128)),
- ],
- options={
- 'unique_together': {('name', 'version')},
- },
- ),
- migrations.CreateModel(
- name='DrugDisorderIndication',
- fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('disorder', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Disorder')),
- ('drdi_dataset', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='drdi_dataset_relation', to='drugstone.DrDiDataset')),
- ('drug', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drugstone.Drug')),
- ],
- options={
- 'unique_together': {('drdi_dataset', 'drug', 'disorder')},
- },
- ),
- ]
diff --git a/drugstone/migrations/__init__.py b/drugstone/migrations/__init__.py
deleted file mode 100755
index e69de29..0000000
diff --git a/drugstone/models.py b/drugstone/models.py
index 0d38f46..9299122 100755
--- a/drugstone/models.py
+++ b/drugstone/models.py
@@ -69,9 +69,9 @@ class ExpressionLevel(models.Model):
unique_together = ('tissue', 'protein')
-class EnsemblGene(models.Model):
- name = models.CharField(max_length=15, unique=True) # starts with ENSG...
- protein = models.ForeignKey('Protein', on_delete=models.CASCADE, related_name='ensg')
+# class EnsemblGene(models.Model):
+# name = models.CharField(max_length=15, unique=True) # starts with ENSG...
+# protein = models.ForeignKey('Protein', on_delete=models.CASCADE, related_name='ensg')
class Protein(models.Model):
@@ -79,9 +79,9 @@ class Protein(models.Model):
# are either 6 or 10 characters long
uniprot_code = models.CharField(max_length=10)
- gene = models.CharField(max_length=128, default='') # symbol
- protein_name = models.CharField(max_length=128, default='')
- entrez = models.CharField(max_length=128, default='')
+ gene = models.CharField(max_length=127, default='') # symbol
+ protein_name = models.CharField(max_length=255, default='')
+ entrez = models.CharField(max_length=15, default='')
drugs = models.ManyToManyField('Drug', through='ProteinDrugInteraction',
related_name='interacting_drugs')
tissue_expression = models.ManyToManyField('Tissue', through='ExpressionLevel',
@@ -105,6 +105,7 @@ class Protein(models.Model):
self.protein_name = other.protein_name
self.entrez = other.entrez
+
class Disorder(models.Model):
mondo_id = models.CharField(max_length=7)
label = models.CharField(max_length=256, default='') # symbol
@@ -124,7 +125,7 @@ class Disorder(models.Model):
def __ne__(self, other):
return not self.__eq__(other)
- def update(self,other):
+ def update(self, other):
self.mondo_id = other.mondo_id
self.label = other.label
self.icd10 = other.icd10
@@ -144,7 +145,7 @@ class Drug(models.Model):
def __eq__(self, other):
return self.drug_id == other.uniprot_code and self.name == other.name and self.status == other.status
- def __ne__(self,other):
+ def __ne__(self, other):
return not self.__eq__(other)
def update(self, other):
@@ -153,6 +154,7 @@ class Drug(models.Model):
self.status = other.status
self.links = other.links
+
class ProteinDisorderAssociation(models.Model):
pdis_dataset = models.ForeignKey(
'PDisDataset', null=True, on_delete=models.CASCADE, related_name='pdis_dataset_relation')
@@ -166,6 +168,7 @@ class ProteinDisorderAssociation(models.Model):
def __str__(self):
return f'{self.pdis_dataset}-{self.protein}-{self.disorder}'
+
class DrugDisorderIndication(models.Model):
drdi_dataset = models.ForeignKey(
'DrDiDataset', null=True, on_delete=models.CASCADE, related_name='drdi_dataset_relation')
@@ -207,6 +210,7 @@ class ProteinProteinInteraction(models.Model):
def __str__(self):
return f'{self.ppi_dataset}-{self.from_protein}-{self.to_protein}'
+
class ProteinDrugInteraction(models.Model):
pdi_dataset = models.ForeignKey(
'PDIDataset', null=True, on_delete=models.CASCADE, related_name='pdi_dataset_relation')
@@ -219,6 +223,7 @@ class ProteinDrugInteraction(models.Model):
def __str__(self):
return f'{self.pdi_dataset}-{self.protein}-{self.drug}'
+
class Task(models.Model):
token = models.CharField(max_length=32, unique=True)
created_at = models.DateTimeField(auto_now_add=True)
@@ -238,6 +243,7 @@ class Task(models.Model):
result = models.TextField(null=True)
+
class Network(models.Model):
id = models.CharField(primary_key=True, max_length=32, unique=True)
created_at = models.DateTimeField(auto_now_add=True)
diff --git a/scripts/import-data.sh b/scripts/import-data.sh
index 8da89e5..de1c938 100755
--- a/scripts/import-data.sh
+++ b/scripts/import-data.sh
@@ -1,13 +1,11 @@
-#!/bin/bash
-python3 manage.py migrate --run-syncdb
-
+ #!/bin/bash
python3 manage.py populate_db --delete_model PPI,PDI,Drug,Protein,Tissue,Disorder,PDiAssociations
-python3 manage.py populate_db --data_dir . -p protein-file.txt
+python3 manage.py populate_db --data_dir . -p
python3 manage.py populate_db --data_dir . -exp gene_tissue_expression.gct
-python3 manage.py populate_db --data_dir . -dr drug-file.txt
-python3 manage.py populate_db --data_dir . -pdr drug-protein-interaction.txt
-python3 manage.py populate_db -di ""
-python3 manage.py populate_db --data_dir . -pdi "" -ddi ""
-python3 manage.py populate_db -pp protein_protein_interaction_file.txt
\ No newline at end of file
+python3 manage.py populate_db --data_dir . -dr
+#python3 manage.py populate_db --data_dir . -pdr drug-protein-interaction.txt
+python3 manage.py populate_db -di
+#python3 manage.py populate_db --data_dir . -pdi "" -ddi ""
+#python3 manage.py populate_db -pp protein_protein_interaction_file.txt
\ No newline at end of file
--
GitLab