diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6df7ed09a088452955ac736d2f21729ad6810fb3
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,9 @@
+test-centos7:
+ image: centos:centos7
+ stage: test
+ script:
+ - yum install -y epel-release
+ - yum install install -y python34-pip python34-devel
+ - cd ippisite
+ - pip3 install -r requirements.txt
+ - python3 manage.py test
\ No newline at end of file
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index 89d5cf044b79d1546780d04ccc912a4742b52c8c..47ec17349e4b67ca860f635c93619456554a9e2f 100644
Binary files a/ippisite/db.sqlite3 and b/ippisite/db.sqlite3 differ
diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 29b059b53b45ac71042ed0257ab091187cf3c2a9..da7c16f971962cd68c714bfdd3cbfff2d9088f3f 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -14,6 +14,10 @@ class ProteinAdmin(admin.ModelAdmin):
class TaxonomyAdmin(admin.ModelAdmin):
list_display = ('taxonomy_id', 'name')
+@admin.register(Domain)
+class DomainAdmin(admin.ModelAdmin):
+ list_display = ('pfam_acc', 'pfam_id', 'pfam_description', 'domain_family')
+
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 5d6592cc642cec1bcbbe1e0e411930ac3fec7eed..11861016c345b4d89e79b9960b7ddb8fce10db9e 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 0000000000000000000000000000000000000000..47a59cc6b02bd96637dc325113682f9f3a82d2fc
--- /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/migrations/0008_auto_20170329_1441.py b/ippisite/ippidb/migrations/0008_auto_20170329_1441.py
new file mode 100644
index 0000000000000000000000000000000000000000..a4226179155219adea04ba3b82a39d7d71e0d581
--- /dev/null
+++ b/ippisite/ippidb/migrations/0008_auto_20170329_1441.py
@@ -0,0 +1,66 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-03-29 14:41
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0007_auto_20170328_2045'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='RefCompoundBiblio',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('compound_name', models.CharField(max_length=50, verbose_name='Compound name in the publication')),
+ ('bibliography_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Bibliography')),
+ ('compound_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='ippidb.Compound')),
+ ],
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='nb_copy_compounds',
+ field=models.IntegerField(default=1, verbose_name='Number of copies for the compound'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='pdb_id',
+ field=models.CharField(default='NA', max_length=4, verbose_name='PDB ID'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='cmpdaction',
+ name='ppi_id',
+ field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, to='ippidb.Ppi'),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='compoundactivityresult',
+ name='modulation_type',
+ field=models.CharField(choices=[('B', 'Binding'), ('I', 'Inhibition'), ('S', 'Stabilization')], default='B', max_length=1, verbose_name='Modulation type'),
+ preserve_default=False,
+ ),
+ migrations.AlterField(
+ model_name='cmpdaction',
+ name='activation_mode',
+ field=models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric')], max_length=1, verbose_name='Activation mode'),
+ ),
+ migrations.RemoveField(
+ model_name='cmpdaction',
+ name='modulation_type',
+ ),
+ migrations.AlterUniqueTogether(
+ name='cmpdaction',
+ unique_together=set([('complex_id', 'compound_id', 'pdb_id')]),
+ ),
+ migrations.AlterUniqueTogether(
+ name='refcompoundbiblio',
+ unique_together=set([('compound_id', 'bibliography_id')]),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 4ce93714c4252e463804ef049342e5a135f2f92d..73de8458539437385dce0540cea8f25e73073cf9 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 +111,16 @@ 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)
+
+ def __str__(self):
+ return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)
class ProteinDomainComplex(models.Model):
protein_id = models.ForeignKey('Protein')
@@ -271,10 +280,16 @@ class ActivityType(models.Model):
name = models.CharField('Name', max_length=50, unique=True)
class CompoundActivityResult(models.Model):
+ MODULATION_TYPES = (
+ ('B', 'Binding'),
+ ('I', 'Inhibition'),
+ ('S', 'Stabilization')
+ )
compound_id = models.ForeignKey(Compound)
test_activity_description_id = models.ForeignKey(TestActivityDescription)
activity_type_id = models.ForeignKey(ActivityType)
activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)
+ modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
class Meta:
unique_together = (('compound_id', 'test_activity_description_id', 'activity_type_id'),)
@@ -323,43 +338,22 @@ class CompoundPKResult(models.Model):
class CmpdAction(models.Model):
ACTIVATION_MODES = (
('O', 'Orthosteric'),
- ('A', 'Allosteric'),
- ('U', 'Unspecified')
- )
- MODULATION_TYPES = (
- ('I', 'Inhibition'),
- ('S', 'Stabilization')
+ ('A', 'Allosteric')
)
complex_id = models.ForeignKey(ProteinDomainBoundComplex)
compound_id = models.ForeignKey(Compound)
activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)
- modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)
-
-""""
-class Actionevidencetest(models.Model):
- idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')
- idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')
- nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)
+ ppi_id = models.ForeignKey(Ppi)
+ pdb_id = models.CharField('PDB ID', max_length=4)
+ nb_copy_compounds = models.IntegerField('Number of copies for the compound')
class Meta:
-# managed = False
- db_table = 'actionEvidenceTest'
- unique_together = (('idcmpdaction', 'idtestactivity'),)
-
-
+ unique_together = (('complex_id', 'compound_id', 'pdb_id'),)
-
-
-
-
-class Refcmpdbiblio(models.Model):
- idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')
- idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')
- cmpdnameinbiblio = models.CharField(='CmpdNameInBiblio', max_length=20, blank=True, null=True)
+class RefCompoundBiblio(models.Model):
+ compound_id = models.ForeignKey(Compound)
+ bibliography_id = models.ForeignKey(Bibliography)
+ compound_name = models.CharField('Compound name in the publication', max_length=50)
class Meta:
-# managed = False
- db_table = 'refCmpdBiblio'
- unique_together = (('idcompound', 'idbiblio'),)
-
-"""
+ unique_together = (('compound_id', 'bibliography_id'),)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 768d0afb7775f26deba7d7a32b0da3231a776ee3..2c178fc1e80ca0bdb39e41d30571bde6756a9797 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -1,6 +1,6 @@
from bioservices.eutils import EUtils
from bioservices.uniprot import UniProt
-from xml.etree.ElementTree import register_namespace
+import xml.etree.ElementTree as ET
import requests
def get_pubmed_info(pmid):
@@ -66,4 +66,15 @@ def get_taxonomy_info(taxonomy_id):
eu = EUtils()
r = eu.EFetch('taxonomy', taxonomy_id, retmode='dict')
scientific_name = r['TaxaSet']['Taxon']['ScientificName']
- return {'scientific_name': scientific_name}
+ return {'scientific_name': scientific_name}
+
+def get_pfam_info(pfam_acc):
+ resp = requests.get('http://pfam.xfam.org/family/{}?output=xml'.format(pfam_acc))
+ root = ET.fromstring(resp.text)
+ ns = {'pfam': 'http://pfam.xfam.org/'}
+ entry = root.findall('pfam:entry', ns)[0]
+ pfam_id = entry.attrib['id']
+ description = entry.findall('pfam:description', ns)[0].text.strip()
+ domain_family = ''
+ return {'id': pfam_id,
+ 'description': description}
diff --git a/ippisite/requirements.txt b/ippisite/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd634ed6600b9499d62c890ffe7005b60be0c12b
--- /dev/null
+++ b/ippisite/requirements.txt
@@ -0,0 +1,3 @@
+Django
+django-bootstrap3
+bioservices
\ No newline at end of file