Domain corrections and migration

correct Domain model, use PFAM service, add migration command
and update database.

ippisite/ippidb/management/commands/import_v1_data.py

 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])))
             

ippisite/ippidb/migrations/0007_auto_20170328_2045.py

+# -*- 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',
+        ),
+    ]

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')