From f209b66f24041600290a2fc45d6ccd1cfe607bc0 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 14:07:50 +0100
Subject: [PATCH] migrate TestCytotoxicityDescription (fix #28)
Former-commit-id: 67806cbeb81fdcc7428cb60b69155b7531f002e7
---
.../management/commands/import_v1_data.py | 40 +++++++++++++++++--
1 file changed, 37 insertions(+), 3 deletions(-)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 8ef965ce..c988fbe5 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -6,7 +6,8 @@ import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
- Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, CompoundAction
+ Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, \
+ CompoundAction, TestCytotoxDescription
class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -313,12 +314,14 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
else:
self.stdout.write(
self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+ CellLine.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed cell lines table'))
cursor.execute("""SELECT * FROM testActivityDescription""")
rows = cursor.fetchall()
TestActivityDescription.objects.all().delete()
- CellLine.objects.all().delete()
self.stdout.write(
- self.style.SUCCESS('Successfully flushed test activity descriptions table and cell lines table'))
+ self.style.SUCCESS('Successfully flushed test activity descriptions table'))
for row in rows:
try:
tad = TestActivityDescription()
@@ -348,6 +351,37 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
else:
self.stdout.write(
self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ cursor.execute("""SELECT * FROM testCytotoxDescription""")
+ rows = cursor.fetchall()
+ TestCytotoxDescription.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed test cytotoxicity descriptions table'))
+ for row in rows:
+ try:
+ tcd = TestCytotoxDescription()
+ cursor.execute(
+ """select IDSource from biblio where IDBiblio={}""".format(row[1]))
+ biblio_row = cursor.fetchone()
+ biblio = Bibliography.objects.get(id_source=biblio_row[0])
+ tcd.biblio = biblio
+ tcd.test_name = row[2]
+ tcd.compound_concentration = row[4]
+ if row[3] is not None:
+ tcd.cell_line, created = CellLine.objects.get_or_create(
+ name=row[3])
+ tcd.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError(
+ 'Failed inserting {} {}'.format(row[1], row[2]))
+ else:
+ self.stdout.write(
+ self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
+ else:
+ self.stdout.write(
+ self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
if options['mddr']:
from pybel import readfile
MDDRCompoundImport.objects.all().delete()
--
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