From c4a2fb5e7c476a8361aa039cc986c3a0ddabf730 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 17 May 2017 22:26:44 +0200
Subject: [PATCH] rename foreign key fields to remove "_id" suffixes
closes #35
---
ippisite/db.sqlite3 | Bin 536576 -> 569344 bytes
ippisite/ippidb/admin.py | 8 +-
ippisite/ippidb/forms.py | 4 +-
.../migrations/0009_auto_20170517_2020.py | 196 ++++++++++++++++++
ippisite/ippidb/models.py | 60 +++---
5 files changed, 232 insertions(+), 36 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0009_auto_20170517_2020.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index 418ffe91ef59f6e2db941d723da526c109b5b5f5..d0f0db2af8cd80bce56b7148c24a74b09675dec6 100644
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diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 516d2719..dc4f162a 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -20,13 +20,13 @@ class DomainAdmin(admin.ModelAdmin):
@admin.register(ProteinDomainBoundComplex)
class ProteinDomainBoundComplexAdmin(admin.ModelAdmin):
- list_display = ('protein_id', 'domain_id', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
- list_display_links = ('protein_id', 'domain_id', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
+ list_display = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
+ list_display_links = ('protein', 'domain', 'ppc_copy_nb', 'ppp_copy_nb_per_p', 'pockets_nb')
@admin.register(ProteinDomainPartnerComplex)
class ProteinDomainPartnerComplexAdmin(admin.ModelAdmin):
- list_display = ('protein_id', 'domain_id', 'ppc_copy_nb')
- list_display_links = ('protein_id', 'domain_id', 'ppc_copy_nb')
+ list_display = ('protein', 'domain', 'ppc_copy_nb')
+ list_display_links = ('protein', 'domain', 'ppc_copy_nb')
@admin.register(Symmetry)
class Symmetry(admin.ModelAdmin):
diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index 6c83082f..d7364dac 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -22,10 +22,10 @@ class ProteinForm(ModelForm):
class ProteinDomainComplexForm(ModelForm):
class Meta:
model = ProteinDomainComplex
- fields = ['protein_id', 'domain_id', 'ppc_copy_nb']
+ fields = ['protein', 'domain', 'ppc_copy_nb']
class PpiForm(ModelForm):
class Meta:
model = Ppi
- fields = ['complex_id', 'cc_nb', 'pdb_id', 'symmetry_id']
+ fields = ['complex', 'cc_nb', 'pdb_id', 'symmetry']
diff --git a/ippisite/ippidb/migrations/0009_auto_20170517_2020.py b/ippisite/ippidb/migrations/0009_auto_20170517_2020.py
new file mode 100644
index 00000000..51fbffd8
--- /dev/null
+++ b/ippisite/ippidb/migrations/0009_auto_20170517_2020.py
@@ -0,0 +1,196 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-05-17 20:20
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0008_auto_20170329_1441'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='cmpdaction',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='compound',
+ old_name='mddr_compound_id',
+ new_name='mddr_compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='activity_type_id',
+ new_name='activity_type',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundactivityresult',
+ old_name='test_activity_description_id',
+ new_name='test_activity_description',
+ ),
+ migrations.RenameField(
+ model_name='compoundcytotoxicityresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundcytotoxicityresult',
+ old_name='test_cytotoxicity_description_id',
+ new_name='test_cytotoxicity_description',
+ ),
+ migrations.RenameField(
+ model_name='compoundpkresult',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='compoundpkresult',
+ old_name='test_pk_description_id',
+ new_name='test_pk_description',
+ ),
+ migrations.RenameField(
+ model_name='disease',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='mddrcompoundactivityclass',
+ old_name='mddr_compound_id',
+ new_name='mddr_compound',
+ ),
+ migrations.RenameField(
+ model_name='ppi',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='ppi',
+ old_name='symmetry_id',
+ new_name='symmetry',
+ ),
+ migrations.RenameField(
+ model_name='proteindomaincomplex',
+ old_name='domain_id',
+ new_name='domain',
+ ),
+ migrations.RenameField(
+ model_name='proteindomaincomplex',
+ old_name='protein_id',
+ new_name='protein',
+ ),
+ migrations.RenameField(
+ model_name='refcompoundbiblio',
+ old_name='bibliography_id',
+ new_name='bibliography',
+ ),
+ migrations.RenameField(
+ model_name='refcompoundbiblio',
+ old_name='compound_id',
+ new_name='compound',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='complex_id',
+ new_name='complex',
+ ),
+ migrations.RenameField(
+ model_name='testactivitydescription',
+ old_name='ppi_id',
+ new_name='ppi',
+ ),
+ migrations.RenameField(
+ model_name='testcytotoxdescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RenameField(
+ model_name='testpkdescription',
+ old_name='biblio_id',
+ new_name='biblio',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='dh_Petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='diam_graph_non_h_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='g_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='ig_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='radius_graph_non_h_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='surface_vdw_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='thickness_petitjean',
+ ),
+ migrations.RemoveField(
+ model_name='compound',
+ name='vol_vdw_petitjean',
+ ),
+ migrations.AlterField(
+ model_name='compound',
+ name='canonical_smile',
+ field=models.CharField(max_length=500, unique=True, verbose_name='Canonical Smile'),
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('complex', 'compound', 'pdb_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundactivityresult',
+ unique_together=set([('compound', 'test_activity_description', 'activity_type')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundcytotoxicityresult',
+ unique_together=set([('compound', 'test_cytotoxicity_description')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='compoundpkresult',
+ unique_together=set([('compound', 'test_pk_description')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='mddrcompoundactivityclass',
+ unique_together=set([('mddr_compound', 'activity_class')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound', 'bibliography')]),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index a5417a44..226227f7 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -119,8 +119,8 @@ class Domain(models.Model):
return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
class ProteinDomainComplex(models.Model):
- protein_id = models.ForeignKey('Protein')
- domain_id = models.ForeignKey('Domain')
+ protein = models.ForeignKey('Protein')
+ domain = models.ForeignKey('Domain')
ppc_copy_nb = models.IntegerField('Number of copies of the protein in the complex')
class Meta:
@@ -151,13 +151,13 @@ class Symmetry(models.Model):
class Ppi(models.Model):
ppi_id = models.IntegerField('PPI identifier')
- complex_id = models.ForeignKey(ProteinDomainComplex)
+ complex = models.ForeignKey(ProteinDomainComplex)
cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)
pdb_id = models.CharField('PDB ID', max_length=4)
- symmetry_id = models.ForeignKey(Symmetry)
+ symmetry = models.ForeignKey(Symmetry)
class Disease(models.Model):
- ppi_id = models.ForeignKey(Ppi)
+ ppi = models.ForeignKey(Ppi)
disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
@@ -212,7 +212,7 @@ class Compound(models.Model):
chemspider_id = models.CharField('Chemspider ID', unique=True, max_length=10, blank=True, null=True)
chembl_id = models.CharField('Chembl ID', unique=True, max_length=30, blank=True, null=True)
iupac_name = models.CharField('IUPAC name', unique=True, max_length=255, blank=True, null=True)
- mddr_compound_id = models.ForeignKey('MDDRCompoundImport', blank=True, null=True)
+ mddr_compound = models.ForeignKey('MDDRCompoundImport', blank=True, null=True)
class MDDRCompoundImport(models.Model):
@@ -231,11 +231,11 @@ class MDDRCompoundImport(models.Model):
class MDDRCompoundActivityClass(models.Model):
- mddr_compound_id = models.ForeignKey(MDDRCompoundImport)
+ mddr_compound = models.ForeignKey(MDDRCompoundImport)
activity_class = models.CharField('Activity Class', max_length=100)
class Meta:
- unique_together = (('mddr_compound_id', 'activity_class'),)
+ unique_together = (('mddr_compound', 'activity_class'),)
verbose_name_plural = "MDDR compound activity classes"
@@ -261,9 +261,9 @@ class TestActivityDescription(models.Model):
('I', 'Inhibition'),
('S', 'Stabilization')
)
- complex_id = models.ForeignKey(ProteinDomainBoundComplex)
- biblio_id = models.ForeignKey(Bibliography)
- ppi_id = models.ForeignKey(Ppi, blank=True, null=True)
+ complex = models.ForeignKey(ProteinDomainBoundComplex)
+ biblio = models.ForeignKey(Bibliography)
+ ppi = models.ForeignKey(Ppi, blank=True, null=True)
test_name = models.CharField('Test name', max_length=100)
test_type = models.CharField('Test type', max_length=5, choices=TEST_TYPES)
test_modulation_type = models.CharField('Test modulation type', max_length=1, choices=TEST_MODULATION_TYPES)
@@ -279,34 +279,34 @@ class CompoundActivityResult(models.Model):
('I', 'Inhibition'),
('S', 'Stabilization')
)
- compound_id = models.ForeignKey(Compound)
- test_activity_description_id = models.ForeignKey(TestActivityDescription)
- activity_type_id = models.ForeignKey(ActivityType)
+ compound = models.ForeignKey(Compound)
+ test_activity_description = models.ForeignKey(TestActivityDescription)
+ activity_type = models.ForeignKey(ActivityType)
activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)
modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
class Meta:
- unique_together = (('compound_id', 'test_activity_description_id', 'activity_type_id'),)
+ unique_together = (('compound', 'test_activity_description', 'activity_type'),)
class TestCytotoxDescription(models.Model):
- biblio_id = models.ForeignKey(Bibliography)
+ biblio = models.ForeignKey(Bibliography)
test_name = models.CharField('Cytotoxicity test name', max_length=100)
cell_line = models.ForeignKey(CellLine)
compound_concentration = models.DecimalField('Compound concentration in μM', max_digits=7, decimal_places=3, blank=True, null=True)
class CompoundCytotoxicityResult(models.Model):
- compound_id = models.ForeignKey(Compound)
- test_cytotoxicity_description_id = models.ForeignKey(TestCytotoxDescription)
+ compound = models.ForeignKey(Compound)
+ test_cytotoxicity_description = models.ForeignKey(TestCytotoxDescription)
toxicity = models.BooleanField('Toxicity', default=False)
class Meta:
- unique_together = (('compound_id', 'test_cytotoxicity_description_id'),)
+ unique_together = (('compound', 'test_cytotoxicity_description'),)
class AdministrationMode(models.Model):
name = models.CharField('Administration mode', max_length=20, blank=True, null=True)
class TestPKDescription(models.Model):
- biblio_id = models.ForeignKey(Bibliography)
+ biblio = models.ForeignKey(Bibliography)
test_name = models.CharField('Pharmacokinetic test name', max_length=100)
organism = models.ForeignKey(Taxonomy)
administration_mode = models.ForeignKey(AdministrationMode, blank=True, null=True)
@@ -314,8 +314,8 @@ class TestPKDescription(models.Model):
dose_interval = models.IntegerField('Dose interval, in hours', blank=True, null=True)
class CompoundPKResult(models.Model):
- compound_id = models.ForeignKey(Compound)
- test_pk_description_id = models.ForeignKey(TestPKDescription)
+ compound = models.ForeignKey(Compound)
+ test_pk_description = models.ForeignKey(TestPKDescription)
tolerated = models.NullBooleanField('Tolerated', null=True)
auc = models.IntegerField('Area under curve (ng.mL-1.hr)', blank=True, null=True)
clearance = models.DecimalField('Clearance (mL/hr)', max_digits=7, decimal_places=3, blank=True, null=True)
@@ -326,7 +326,7 @@ class CompoundPKResult(models.Model):
voldistribution = models.DecimalField('Volume distribution (Vd)', max_digits=5, decimal_places=2, blank=True, null=True)
class Meta:
- unique_together = (('compound_id', 'test_pk_description_id'),)
+ unique_together = (('compound', 'test_pk_description'),)
class CmpdAction(models.Model):
@@ -334,20 +334,20 @@ class CmpdAction(models.Model):
('O', 'Orthosteric'),
('A', 'Allosteric')
)
- complex_id = models.ForeignKey(ProteinDomainBoundComplex)
- compound_id = models.ForeignKey(Compound)
+ complex = models.ForeignKey(ProteinDomainBoundComplex)
+ compound = models.ForeignKey(Compound)
activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)
- ppi_id = models.ForeignKey(Ppi)
+ ppi = models.ForeignKey(Ppi)
pdb_id = models.CharField('PDB ID', max_length=4)
nb_copy_compounds = models.IntegerField('Number of copies for the compound')
class Meta:
- unique_together = (('complex_id', 'compound_id', 'pdb_id'),)
+ unique_together = (('complex', 'compound', 'pdb_id'),)
class RefCompoundBiblio(models.Model):
- compound_id = models.ForeignKey(Compound)
- bibliography_id = models.ForeignKey(Bibliography)
+ compound = models.ForeignKey(Compound)
+ bibliography = models.ForeignKey(Bibliography)
compound_name = models.CharField('Compound name in the publication', max_length=50)
class Meta:
- unique_together = (('compound_id', 'bibliography_id'),)
+ unique_together = (('compound', 'bibliography'),)
--
GitLab