From e77216cc9520c01f9310085eb47d6c872f3b87b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 8 Mar 2018 21:07:40 +0100
Subject: [PATCH] migrate TestPKDescription (fix #29)
Former-commit-id: 1acca29b42cdc5370aeb1b0f13eb6a37f82e440f
---
.../management/commands/import_v1_data.py | 52 +++++++++++++++----
.../migrations/0029_auto_20180308_1935.py | 20 +++++++
.../0030_testpkdescription_concentration.py | 20 +++++++
ippisite/ippidb/models.py | 4 +-
4 files changed, 86 insertions(+), 10 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0029_auto_20180308_1935.py
create mode 100644 ippisite/ippidb/migrations/0030_testpkdescription_concentration.py
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index c14585e2..42c45eb7 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -7,7 +7,7 @@ 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, TestCytotoxDescription
+ CompoundAction, TestCytotoxDescription, TestPKDescription
class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -61,7 +61,7 @@ class Command(BaseCommand):
action='store_true',
dest='ppi',
default=False,
- help='Flush and migrate ppis and complexes',
+ help='Flush and migrate ppis, complexes, and tests',
)
parser.add_argument(
'--mddr',
@@ -84,13 +84,6 @@ class Command(BaseCommand):
default=False,
help='Flush and migrate compounds-bibliography',
)
- parser.add_argument(
- '--test-activity-description',
- action='store_true',
- dest='test-activity-description',
- default=False,
- help='Flush and migrate test activity descriptions',
- )
parser.add_argument(
'--stoponfail',
action='store_true',
@@ -392,6 +385,47 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
else:
self.stdout.write(
self.style.SUCCESS('Successfully inserted {}'.format(row[2])))
+ cursor.execute("""SELECT * FROM testPKDescription""")
+ rows = cursor.fetchall()
+ TestPKDescription.objects.all().delete()
+ self.stdout.write(
+ self.style.SUCCESS('Successfully flushed test PK descriptions table'))
+ for row in rows:
+ try:
+ tpd = TestPKDescription()
+ cursor.execute(
+ """select IDSource from biblio where IDBiblio={}""".format(row[1]))
+ biblio_row = cursor.fetchone()
+ biblio = Bibliography.objects.get(id_source=biblio_row[0])
+ tpd.biblio = biblio
+ tpd.test_name = row[2]
+ #tcd.compound_concentration = row[4]
+ try:
+ taxonomy = Taxonomy.objects.get(taxonomy_id=10090)
+ except Taxonomy.DoesNotExist:
+ taxonomy = Taxonomy()
+ taxonomy.taxonomy_id = 10090
+ # dirty hack: all organisms in this table are "mice",
+ # hence assuming Mus musculus
+ taxonomy.save(autofill=True)
+ tpd.organism = taxonomy
+ tpd.administration_mode = row[4]
+ tpd.concentration = row[5]
+ tpd.dose = round(row[6], 4)
+ tpd.dose_interval = row[7]
+ tpd.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()
diff --git a/ippisite/ippidb/migrations/0029_auto_20180308_1935.py b/ippisite/ippidb/migrations/0029_auto_20180308_1935.py
new file mode 100644
index 00000000..7e2c9f63
--- /dev/null
+++ b/ippisite/ippidb/migrations/0029_auto_20180308_1935.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-03-08 19:35
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0028_auto_20180307_1405'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='testpkdescription',
+ name='dose',
+ field=models.DecimalField(blank=True, decimal_places=4, max_digits=9, null=True, verbose_name='Dose in mg/kg'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py b/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py
new file mode 100644
index 00000000..3522e6e9
--- /dev/null
+++ b/ippisite/ippidb/migrations/0030_testpkdescription_concentration.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11 on 2018-03-08 19:45
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0029_auto_20180308_1935'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='testpkdescription',
+ name='concentration',
+ field=models.DecimalField(blank=True, decimal_places=3, max_digits=7, null=True, verbose_name='Concentration in mg/l'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 55e9612f..f9d77052 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -514,8 +514,10 @@ class TestPKDescription(models.Model):
organism = models.ForeignKey(Taxonomy, models.CASCADE)
administration_mode = models.CharField(
'Administration mode', max_length=2, choices=ADMINISTRATION_MODES, blank=True, null=True)
+ concentration = models.DecimalField(
+ 'Concentration in mg/l', max_digits=7, decimal_places=3, blank=True, null=True)
dose = models.DecimalField(
- 'Dose in mg/kg', max_digits=7, decimal_places=4, blank=True, null=True)
+ 'Dose in mg/kg', max_digits=9, decimal_places=4, blank=True, null=True)
dose_interval = models.IntegerField(
'Dose interval, in hours', blank=True, null=True)
--
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