From 14d8c81b0d20d03f4a6cc4bfa67850c90a13300b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 18 May 2017 22:14:37 +0200
Subject: [PATCH] missing contents for commit
3689e89d66c29253cc6cc2e3e97e486cf7f820b6
---
ippisite/db.sqlite3 | Bin 569344 -> 569344 bytes
.../management/commands/import_v1_data.py | 12 ++++++++----
ippisite/ippidb/models.py | 13 +++++++++----
3 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index e706f0b079239a64eeb573670db3d1ab0790f483..57542b95b741e72c1e7980fb7ecdb36ade6e1767 100644
GIT binary patch
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diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 4386708e..704eed48 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -2,7 +2,7 @@ from django.core.management import BaseCommand, CommandError
import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
- Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease
class Command(BaseCommand):
@@ -148,25 +148,29 @@ class Command(BaseCommand):
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
if options['ppi']:
sql_request_string = '''
-select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
union
-select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain)'''
+select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) inner join disease on (disease.IDPPI=ppi.IDPPI)'''
cursor.execute(sql_request_string)
rows = cursor.fetchall()
ProteinDomainBoundComplex.objects.all().delete()
ProteinDomainPartnerComplex.objects.all().delete()
+ Disease.objects.all().delete()
Ppi.objects.all().delete()
PpiComplex.objects.all().delete()
- self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables and Ppi'))
+ self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex, PPI, and disease tables'))
ppi_ids_mapping = {}
for row in rows:
try:
# create or retrieve Ppi object
if row[5]=='part1':
ppi = Ppi()
+ disease, created = Disease.objects.get_or_create(name=row[7])
ppi.pdb_id = row[4]
ppi.symmetry = Symmetry.objects.get(code='AS')
ppi.save()
+ ppi.diseases.add(disease)
+ ppi.save()
ppi_ids_mapping[row[6]]=ppi.id
else:
ppi = Ppi.objects.get(id=ppi_ids_mapping[row[6]])
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index f045b087..adbe32e6 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -149,9 +149,17 @@ class Symmetry(models.Model):
def __str__(self):
return '{} ({})'.format(self.code, self.description)
+
+class Disease(models.Model):
+ name = models.CharField('Disease', max_length=30, unique=True) # is there any database/nomenclature for diseases?
+
+ def __str__(self):
+ return self.name
+
class Ppi(models.Model):
pdb_id = models.CharField('PDB ID', max_length=4, null=True)
symmetry = models.ForeignKey(Symmetry)
+ diseases = models.ManyToManyField(Disease)
def __str__(self):
return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')
@@ -169,6 +177,7 @@ class Ppi(models.Model):
#this is the less efficient query ever seen, FIXME
return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
+
class PpiComplex(models.Model):
ppi = models.ForeignKey(Ppi)
complex = models.ForeignKey(ProteinDomainComplex)
@@ -180,10 +189,6 @@ class PpiComplex(models.Model):
def __str__(self):
return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
-class Disease(models.Model):
- ppi = models.ForeignKey(Ppi)
- disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
-
class Compound(models.Model):
canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=500)
--
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