From f79427c39f939f8f761e8231a237d78ef50fd194 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 16 May 2017 22:16:55 +0200
Subject: [PATCH] create Symmetry table initial contents
(closes #9)
---
ippisite/db.sqlite3 | Bin 536576 -> 536576 bytes
ippisite/ippidb/admin.py | 4 ++
.../management/commands/import_v1_data.py | 39 +++++++++++++++++-
3 files changed, 42 insertions(+), 1 deletion(-)
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index bb7ca110e188bf4d34171a62e5c4e6f6eda80691..418ffe91ef59f6e2db941d723da526c109b5b5f5 100644
GIT binary patch
delta 756
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delta 252
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diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 84f01827..516d2719 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -28,6 +28,10 @@ class ProteinDomainPartnerComplexAdmin(admin.ModelAdmin):
list_display = ('protein_id', 'domain_id', 'ppc_copy_nb')
list_display_links = ('protein_id', 'domain_id', 'ppc_copy_nb')
+@admin.register(Symmetry)
+class Symmetry(admin.ModelAdmin):
+ list_display = ('code', 'description')
+
for model in apps.get_app_config('ippidb').models.values():
try:
admin.site.register(model)
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 7de942bf..e2dfc077 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
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry
class Command(BaseCommand):
@@ -37,6 +37,13 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate complexes',
)
+ parser.add_argument(
+ '--symmetries',
+ action='store_true',
+ dest='symmetries',
+ default=False,
+ help='Flush and create symmetries',
+ )
parser.add_argument(
'--stoponfail',
action='store_true',
@@ -142,3 +149,33 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+ if options['symmetries']:
+ Symmetry.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed symmetries table'))
+ rows = [
+ ['AS', 'asymmetric'],
+ ['C2', 'C2 symmetry'],
+ ['D2', 'D2 symmetry'],
+ ['C3', 'C3 symmetry'],
+ ['D3', 'D3 symmetry'],
+ ['C4', 'C4 symmetry'],
+ ['D4', 'D4 symmetry'],
+ ['C5', 'C5 symmetry'],
+ ['D5', 'D5 symmetry'],
+ ]
+ for row in rows:
+ try:
+ symmetry = Symmetry()
+ symmetry.code = row[0]
+ symmetry.description = row[1]
+ symmetry.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[0], row[1]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+
--
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