Skip to content
Snippets Groups Projects
Commit d36f3097 authored by AndiMajore's avatar AndiMajore
Browse files

fixed automigration issue; activated nedrex based protein, disorder, drug import

parent db404c9a
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 21 additions and 163 deletions
drugstone/migrations/0054_auto_20210922_1342.py deleted 100644 → 0
+ 0
− 72
View file @ db404c9a
# 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')},
),
]
drugstone/migrations/0055_auto_20210922_1343.py deleted 100644 → 0
+ 0
− 18
View file @ db404c9a
# 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),
),
]
drugstone/migrations/0056_auto_20210922_1348.py deleted 100644 → 0
+ 0
− 18
View file @ db404c9a
# 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),
),
]
drugstone/migrations/0057_drdidataset_drugdisorderindication.py deleted 100644 → 0
+ 0
− 38
View file @ db404c9a
# 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')},
},
),
]
drugstone/migrations/__init__.py deleted 100755 → 0
+ 0
− 0
View file @ db404c9a
drugstone/models.py
+ 14
− 8
View file @ d36f3097
......@@ -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)
......
scripts/import-data.sh
+ 7
− 9
View file @ d36f3097
#!/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
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment