From a7e1e68e059d0cde3907ce32cd28fb96e12f65f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Wed, 7 Mar 2018 15:16:40 +0100
Subject: [PATCH] add new fields in migration of TestActivityDescription
fix #27
Former-commit-id: c85e9128b02978d2510d64a04393529fa81ee39e
---
.../ippidb/management/commands/import_v1_data.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index c988fbe5..c14585e2 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -227,9 +227,9 @@ class Command(BaseCommand):
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, 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)
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI, disease.Disease, complexe.IDComplexe 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, 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)'''
+select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI, disease.Disease, complexe.IDComplexe 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()
@@ -241,6 +241,7 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
self.stdout.write(
self.style.SUCCESS('Successfully flushed protein domain complex, PPI, compound actions, and disease tables'))
ppi_ids_mapping = {}
+ protein_domain_bound_complexes_mapping = {}
for row in rows:
try:
# create or retrieve Ppi object
@@ -270,6 +271,9 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
if isinstance(c, ProteinDomainBoundComplex):
c.ppp_copy_nb_per_p = 1
c.save()
+ # save ProteinDomainBoundComplex/source ID in 'complexe' table
+ if row[3] is not None:
+ protein_domain_bound_complexes_mapping[row[8]] = c
# create the PpiComplex object
ppi_complex = PpiComplex()
ppi_complex.ppi = ppi
@@ -330,8 +334,14 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
biblio_row = cursor.fetchone()
biblio = Bibliography.objects.get(id_source=biblio_row[0])
tad.biblio = biblio
+ tad.protein_domain_bound_complex = protein_domain_bound_complexes_mapping[row[1]]
tad.ppi = Ppi.objects.get(id=ppi_ids_mapping[row[3]])
tad.test_name = row[4]
+ tad.is_primary = row[5]=='Y'
+ if row[6]=='Unspecified':
+ tad.protein_bound_construct = 'U'
+ elif row[6]=='Full length':
+ tad.protein_bound_construct = 'F'
tad.test_type = row[7].upper()
tad.test_modulation_type = row[8][0]
tad.nb_active_compounds = row[9]
--
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