From a0f5ef19b0f9325e48cc1e78788b4e928ac5c3c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 28 Mar 2017 22:47:44 +0200
Subject: [PATCH] Domain corrections and migration
correct Domain model, use PFAM service, add migration command
and update database.
---
ippisite/db.sqlite3 | Bin 512000 -> 520192 bytes
.../management/commands/import_v1_data.py | 29 +++++++++++++++++-
.../migrations/0007_auto_20170328_2045.py | 20 ++++++++++++
ippisite/ippidb/models.py | 10 ++++--
4 files changed, 56 insertions(+), 3 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0007_auto_20170328_2045.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index 89d5cf044b79d1546780d04ccc912a4742b52c8c..4322d387f7390adb118f06d2b776199986ca1340 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 5d6592cc..11861016 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -1,7 +1,7 @@
from django.core.management import BaseCommand, CommandError
import mysql.connector
-from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction
+from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, Domain
class Command(BaseCommand):
@@ -22,6 +22,13 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate proteins',
)
+ parser.add_argument(
+ '--domains',
+ action='store_true',
+ dest='domains',
+ default=False,
+ help='Flush and migrate domains',
+ )
parser.add_argument(
'--stoponfail',
action='store_true',
@@ -75,4 +82,24 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
+ if options['domains']:
+ cursor.execute("""SELECT * FROM domain""")
+ rows = cursor.fetchall()
+ Domain.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed domain table'))
+ for row in rows:
+ try:
+ p = Domain()
+ p.pfam_acc = row[2]
+ p.domain_family = row[4]
+ p.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[1], row[2])))
diff --git a/ippisite/ippidb/migrations/0007_auto_20170328_2045.py b/ippisite/ippidb/migrations/0007_auto_20170328_2045.py
new file mode 100644
index 00000000..47a59cc6
--- /dev/null
+++ b/ippisite/ippidb/migrations/0007_auto_20170328_2045.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-03-28 20:45
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0006_auto_20170327_1439'),
+ ]
+
+ operations = [
+ migrations.RenameField(
+ model_name='domain',
+ old_name='domainfamily',
+ new_name='domain_family',
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 4ce93714..325a849e 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -3,7 +3,7 @@ from __future__ import unicode_literals
from django.db import models
from django.forms import ModelForm
-from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info, get_go_info
+from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info, get_go_info, get_pfam_info
class Bibliography(models.Model):
"""
@@ -111,7 +111,13 @@ class Domain(models.Model):
pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
pfam_description = models.CharField('Pfam Description', max_length=100)
- domainfamily = models.CharField('Domain family', max_length=25) #TODO: what is this field? check database contents
+ domain_family = models.CharField('Domain family', max_length=25) #TODO: what is this field? check database contents
+
+ def save(self, *args, **kwargs):
+ info = get_pfam_info(self.pfam_acc)
+ self.pfam_id = info['id']
+ self.pfam_description = info['description']
+ super(Domain, self).save(*args, **kwargs)
class ProteinDomainComplex(models.Model):
protein_id = models.ForeignKey('Protein')
--
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