Skip to content
Snippets Groups Projects
Commit 740d325d authored by Hervé MENAGER's avatar Hervé MENAGER
Browse files

include new parts in the application model.

parent fc462768
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
ippisite/db.sqlite3
+ 0
− 0
View file @ 740d325d
No preview for this file type
ippisite/ippidb/migrations/0005_auto_20170327_1301.py 0 → 100644
+ 54
− 0
View file @ 740d325d
# -*- coding: utf-8 -*-
# Generated by Django 1.10.5 on 2017-03-27 13:01
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('ippidb', '0004_auto_20170314_1449'),
]
operations = [
migrations.CreateModel(
name='CellLine',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('name', models.CharField(max_length=50, unique=True, verbose_name='Name')),
],
),
migrations.CreateModel(
name='TestActivityDescription',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('test_name', models.CharField(max_length=100, verbose_name='Test name')),
('test_type', models.CharField(choices=[('BIOCH', 'Biochemical assay'), ('CELL', 'Cellular assay')], max_length=5, verbose_name='Test type')),
('test_modulation_type', models.CharField(choices=[('B', 'Binding'), ('I', 'Inhibition'), ('S', 'Stabilization')], max_length=1, verbose_name='Test modulation type')),
('nb_active_compounds', models.IntegerField(verbose_name='Total number of active compounds')),
('biblio_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
('cell_line', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.CellLine')),
('complex_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex')),
('ppi_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi')),
],
),
migrations.AlterModelOptions(
name='mddrcompoundactivityclass',
options={'verbose_name_plural': 'MDDR compound activity classes'},
),
migrations.AlterModelOptions(
name='mddrcompoundimport',
options={'verbose_name_plural': 'MDDR compound imports'},
),
migrations.AlterModelOptions(
name='mddrsimilarity',
options={'verbose_name_plural': 'MDDR similarities'},
),
migrations.AlterField(
model_name='taxonomy',
name='taxonomy_id',
field=models.DecimalField(decimal_places=0, max_digits=9, unique=True, verbose_name='NCBI TaxID'),
),
]
ippisite/ippidb/migrations/0006_auto_20170327_1439.py 0 → 100644
+ 117
− 0
View file @ 740d325d
# -*- coding: utf-8 -*-
# Generated by Django 1.10.5 on 2017-03-27 14:39
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('ippidb', '0005_auto_20170327_1301'),
]
operations = [
migrations.CreateModel(
name='ActivityType',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('name', models.CharField(max_length=50, unique=True, verbose_name='Name')),
],
),
migrations.CreateModel(
name='AdministrationMode',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('name', models.CharField(blank=True, max_length=20, null=True, verbose_name='Administration mode')),
],
),
migrations.CreateModel(
name='CmpdAction',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('activation_mode', models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric'), ('U', 'Unspecified')], max_length=1, verbose_name='Activation mode')),
('modulation_type', models.CharField(choices=[('I', 'Inhibition'), ('S', 'Stabilization')], max_length=1, verbose_name='Modulation type')),
('complex_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ProteinDomainBoundComplex')),
('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
],
),
migrations.CreateModel(
name='CompoundActivityResult',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('activity', models.DecimalField(decimal_places=10, max_digits=12, verbose_name='Activity')),
('activity_type_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.ActivityType')),
('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
('test_activity_description_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestActivityDescription')),
],
),
migrations.CreateModel(
name='CompoundCytotoxicityResult',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('toxicity', models.BooleanField(default=False, verbose_name='Toxicity')),
('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
],
),
migrations.CreateModel(
name='CompoundPKResult',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('tolerated', models.NullBooleanField(verbose_name='Tolerated')),
('auc', models.IntegerField(blank=True, null=True, verbose_name='Area under curve (ng.mL-1.hr)')),
('clearance', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Clearance (mL/hr)')),
('cmax', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Maximal concentration (ng/mL)')),
('oral_bioavailability', models.IntegerField(blank=True, null=True, verbose_name='Oral Bioavailability (%F)')),
('t_demi', models.IntegerField(blank=True, null=True, verbose_name='t½')),
('t_max', models.IntegerField(blank=True, null=True, verbose_name='tmax')),
('voldistribution', models.DecimalField(blank=True, decimal_places=2, max_digits=5, null=True, verbose_name='Volume distribution (Vd)')),
('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
],
),
migrations.CreateModel(
name='TestCytotoxDescription',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('test_name', models.CharField(max_length=100, verbose_name='Cytotoxicity test name')),
('compound_concentration', models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Compound concentration in μM')),
('biblio_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
('cell_line', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.CellLine')),
],
),
migrations.CreateModel(
name='TestPKDescription',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('test_name', models.CharField(max_length=100, verbose_name='Pharmacokinetic test name')),
('dose', models.DecimalField(blank=True, decimal_places=4, max_digits=7, null=True, verbose_name='Dose in mg/kg')),
('dose_interval', models.IntegerField(blank=True, null=True, verbose_name='Dose interval, in hours')),
('administration_mode', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='ippidb.AdministrationMode')),
('biblio_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
('organism', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Taxonomy')),
],
),
migrations.AddField(
model_name='compoundpkresult',
name='test_pk_description_id',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestPKDescription'),
),
migrations.AddField(
model_name='compoundcytotoxicityresult',
name='test_cytotoxicity_description_id',
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.TestCytotoxDescription'),
),
migrations.AlterUniqueTogether(
name='compoundpkresult',
unique_together=set([('compound_id', 'test_pk_description_id')]),
),
migrations.AlterUniqueTogether(
name='compoundcytotoxicityresult',
unique_together=set([('compound_id', 'test_cytotoxicity_description_id')]),
),
migrations.AlterUniqueTogether(
name='compoundactivityresult',
unique_together=set([('compound_id', 'test_activity_description_id', 'activity_type_id')]),
),
]
ippisite/ippidb/models.py
+ 84
− 202
View file @ 740d325d
......@@ -245,187 +245,111 @@ class MDDRSimilarity(models.Model):
unique_together = (('canonical_smile_ippidb', 'canonical_smile_mddr'),)
verbose_name_plural = "MDDR similarities"
"""
class TestActivityDescription(models.Model):
complex_id = models.ForeignKey(Complex)
biblio_id = models.ForeignKey(Biblio)
idppi = models.ForeignKey(Ppi, models.DO_NOTHING, ='IDPPI', blank=True, null=True)
testnameactivity = models.CharField(='TestNameActivity', max_length=40)
isprimary = models.CharField(='IsPrimary', max_length=1)
protboundconstruct = models.CharField(='ProtBoundConstruct', max_length=11)
testtype = models.CharField(='TestType', max_length=5)
testmodulationtype = models.CharField(='TestModulationType', max_length=13)
nbactivescmpdstot = models.IntegerField(='NbActivesCmpdsTot')
conccmpds = models.DecimalField(='ConcCmpds', max_digits=7, decimal_places=3, blank=True, null=True)
protocol = models.TextField(='Protocol', blank=True, null=True)
concproteinbound = models.DecimalField(='ConcProteinBound', max_digits=7, decimal_places=3, blank=True, null=True)
concprotein2 = models.DecimalField(='ConcProtein2', max_digits=7, decimal_places=3, blank=True, null=True)
controlepos = models.CharField(='ControlePos', max_length=50, blank=True, null=True)
controleneg = models.CharField(='ControleNeg', max_length=50, blank=True, null=True)
cellline = models.CharField(='CellLine', max_length=50, blank=True, null=True)
pepseq = models.CharField(='PepSeq', max_length=100, blank=True, null=True)
marker = models.CharField(='Marker', max_length=35, blank=True, null=True)
class Actionevidencetest(models.Model):
idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)
class CellLine(models.Model):
name = models.CharField('Name', max_length=50, unique=True)
class Meta:
# managed = False
db_table = 'actionEvidenceTest'
unique_together = (('idcmpdaction', 'idtestactivity'),)
class Actionevidencexray(models.Model):
idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
codepdb = models.CharField(='CodePDB', max_length=4)
nbcopycompound = models.IntegerField(='NbCopyCompound')
idbindingsite = models.ForeignKey('Bindingsite', models.DO_NOTHING, ='IDBindingSite')
idbiblio = models.ForeignKey('Biblio', models.DO_NOTHING, ='IDBiblio', blank=True, null=True)
class TestActivityDescription(models.Model):
TEST_TYPES = (
('BIOCH', 'Biochemical assay'),
('CELL', 'Cellular assay')
)
TEST_MODULATION_TYPES = (
('B', 'Binding'),
('I', 'Inhibition'),
('S', 'Stabilization')
)
complex_id = models.ForeignKey(ProteinDomainBoundComplex)
biblio_id = models.ForeignKey(Bibliography)
ppi_id = 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)
nb_active_compounds = models.IntegerField('Total number of active compounds')
cell_line = models.ForeignKey(CellLine)
class ActivityType(models.Model):
name = models.CharField('Name', max_length=50, unique=True)
class CompoundActivityResult(models.Model):
compound_id = models.ForeignKey(Compound)
test_activity_description_id = models.ForeignKey(TestActivityDescription)
activity_type_id = models.ForeignKey(ActivityType)
activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)
class Meta:
# managed = False
db_table = 'actionEvidenceXRay'
unique_together = (('idcmpdaction', 'codepdb'),)
unique_together = (('compound_id', 'test_activity_description_id', 'activity_type_id'),)
class TestCytotoxDescription(models.Model):
biblio_id = 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 Cmpdaction(models.Model):
idcmpdaction = models.AutoField(='IDCmpdAction', primary_key=True)
idcomplexebound = models.ForeignKey('Complexe', models.DO_NOTHING, ='IDComplexeBound')
idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
activationmode = models.CharField(='ActivationMode', max_length=11)
modulationtype = models.CharField(='ModulationType', max_length=10)
class CompoundCytotoxicityResult(models.Model):
compound_id = models.ForeignKey(Compound)
test_cytotoxicity_description_id = models.ForeignKey(TestCytotoxDescription)
toxicity = models.BooleanField('Toxicity', default=False)
class Meta:
# managed = False
db_table = 'cmpdAction'
class Cmpdactiveresult(models.Model):
idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
activitytype = models.CharField(='ActivityType', max_length=5)
activity = models.DecimalField(='Activity', max_digits=4, decimal_places=2)
pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)
unique_together = (('compound_id', 'test_cytotoxicity_description_id'),)
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)
test_name = models.CharField('Pharmacokinetic test name', max_length=100)
organism = models.ForeignKey(Taxonomy)
administration_mode = models.ForeignKey(AdministrationMode, blank=True, null=True)
dose = models.DecimalField('Dose in mg/kg', max_digits=7, decimal_places=4, blank=True, null=True)
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)
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)
cmax = models.DecimalField('Maximal concentration (ng/mL)', max_digits=7, decimal_places=3, blank=True, null=True)
oral_bioavailability = models.IntegerField('Oral Bioavailability (%F)', blank=True, null=True)
t_demi = models.IntegerField('t½', blank=True, null=True)
t_max = models.IntegerField('tmax', blank=True, null=True)
voldistribution = models.DecimalField('Volume distribution (Vd)', max_digits=5, decimal_places=2, blank=True, null=True)
class Meta:
# managed = False
db_table = 'cmpdActiveResult'
unique_together = (('idcompound', 'idtestactivity', 'activitytype'),)
unique_together = (('compound_id', 'test_pk_description_id'),)
class Cmpdcytotoxresult(models.Model):
idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
idtestcytotox = models.ForeignKey('Testcytotoxdescription', models.DO_NOTHING, ='IDTestCytotox')
toxicity = models.CharField(='Toxicity', max_length=1)
class Meta:
# managed = False
db_table = 'cmpdCytotoxResult'
unique_together = (('idcompound', 'idtestcytotox'),)
class CmpdAction(models.Model):
ACTIVATION_MODES = (
('O', 'Orthosteric'),
('A', 'Allosteric'),
('U', 'Unspecified')
)
MODULATION_TYPES = (
('I', 'Inhibition'),
('S', 'Stabilization')
)
complex_id = models.ForeignKey(ProteinDomainBoundComplex)
compound_id = models.ForeignKey(Compound)
activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)
modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
class Cmpdinactiveresult(models.Model):
""""
class Actionevidencetest(models.Model):
idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)
class Meta:
# managed = False
db_table = 'cmpdInactiveResult'
unique_together = (('idtestactivity', 'idcompound'),)
class Cmpdpkresult(models.Model):
idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')
idtestpk = models.ForeignKey('Testpkdescription', models.DO_NOTHING, ='IDTestPK')
tolerated = models.CharField(='Tolerated', max_length=1)
auc = models.IntegerField(='AUC', blank=True, null=True)
clearance = models.DecimalField(='Clearance', max_digits=7, decimal_places=3, blank=True, null=True)
cmax = models.DecimalField(='Cmax', max_digits=7, decimal_places=3, blank=True, null=True)
oralbioavailability = models.IntegerField(='OralBioavailability', blank=True, null=True)
tdemi = models.IntegerField(='Tdemi', blank=True, null=True)
tmax = models.IntegerField(='Tmax', blank=True, null=True)
voldistribution = models.DecimalField(='VolDistribution', max_digits=5, decimal_places=2, blank=True, null=True)
class Meta:
# managed = False
db_table = 'cmpdPKResult'
unique_together = (('idcompound', 'idtestpk'),)
class Meta:
# managed = False
db_table = 'disease'
unique_together = (('idppi', 'disease'),)
class DjangoMigrations(models.Model):
app = models.CharField(max_length=255)
name = models.CharField(max_length=255)
applied = models.DateTimeField()
class Meta:
# managed = False
db_table = 'django_migrations'
class Domain(models.Model):
iddomain = models.AutoField(='IDDomain', primary_key=True)
pfamid = models.CharField(='PfamID', max_length=20)
pfamnumaccession = models.CharField(='PfamNumAccession', unique=True, max_length=10)
domaindescription = models.CharField(='DomainDescription', max_length=100)
domainfamily = models.CharField(='DomainFamily', max_length=25)
class Meta:
# managed = False
db_table = 'domain'
class Mddrsimilarity(models.Model):
idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')
idmddrcompound = models.ForeignKey(Mddrcompound, models.DO_NOTHING, ='IDMDDRCompound')
versionmddr = models.CharField(='VersionMDDR', max_length=7)
tanimoto = models.DecimalField(='Tanimoto', max_digits=6, decimal_places=5)
nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)
class Meta:
# managed = False
db_table = 'mDDRSimilarity'
unique_together = (('idcompound', 'idmddrcompound', 'versionmddr'),)
db_table = 'actionEvidenceTest'
unique_together = (('idcmpdaction', 'idtestactivity'),)
class Ppi(models.Model):
idppi = models.AutoField(='IDPPI', primary_key=True)
idcomplexe1 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe1', related_name='cplx_id_1')
idcomplexe2 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe2', related_name='cplx_id_2')
idbindingsite1 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite1', related_name='bs_id_1')
idbindingsite2 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite2', related_name='bs_id_2')
family = models.CharField(='Family', max_length=25)
class Meta:
# managed = False
db_table = 'ppi'
unique_together = (('idcomplexe1', 'idcomplexe2', 'idbindingsite1', 'idbindingsite2'),)
class Protein(models.Model):
idprotein = models.AutoField(='IDProtein', primary_key=True)
numuniprot = models.CharField(='NumUniprot', unique=True, max_length=10)
protnamelg = models.CharField(='ProtNameLg', max_length=75)
protnamesh = models.CharField(='ProtNameSh', max_length=50)
protalias = models.CharField(='ProtAlias', unique=True, max_length=30)
protnamesp = models.CharField(='ProtNameSp', max_length=30)
organism = models.CharField(='Organism', max_length=80)
class Meta:
# managed = False
db_table = 'protein'
class Refcmpdbiblio(models.Model):
......@@ -438,46 +362,4 @@ class Refcmpdbiblio(models.Model):
db_table = 'refCmpdBiblio'
unique_together = (('idcompound', 'idbiblio'),)
class Refproteinfonction(models.Model):
idprotein = models.ForeignKey(Protein, models.DO_NOTHING, ='IDProtein')
protfonctionsp = models.CharField(='ProtFonctionSP', max_length=200)
class Meta:
# managed = False
db_table = 'refProteinFonction'
unique_together = (('protfonctionsp', 'idprotein'),)
class Meta:
# managed = False
db_table = 'testActivityDescription'
class Testcytotoxdescription(models.Model):
idtestcytotox = models.AutoField(='IDTestCytotox', primary_key=True)
idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
testnamecytotox = models.CharField(='TestNameCytotox', max_length=40)
cellline = models.CharField(='CellLine', max_length=50)
conccmpd = models.DecimalField(='ConcCmpd', max_digits=7, decimal_places=3, blank=True, null=True)
class Meta:
# managed = False
db_table = 'testCytotoxDescription'
class Testpkdescription(models.Model):
idtestpk = models.AutoField(='IDTestPK', primary_key=True)
idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
testnamepk = models.CharField(='TestNamePK', max_length=40)
animal = models.CharField(='Animal', max_length=100)
administrationmode = models.CharField(='AdministrationMode', max_length=2, blank=True, null=True)
concentration = models.DecimalField(='Concentration', max_digits=7, decimal_places=3, blank=True, null=True)
dose = models.DecimalField(='Dose', max_digits=7, decimal_places=2, blank=True, null=True)
doseinterval = models.IntegerField(='DoseInterval', blank=True, null=True)
class Meta:
# managed = False
db_table = 'testPKDescription'
"""
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