diff --git a/ippisite/db.sqlite3.REMOVED.git-id b/ippisite/db.sqlite3.REMOVED.git-id
index 1e8b356813e3c25ccb49abc3c792bf6064131654..76a796217b3f4cfbd42d7bb04dbe57bd088b3bbc 100644
--- a/ippisite/db.sqlite3.REMOVED.git-id
+++ b/ippisite/db.sqlite3.REMOVED.git-id
@@ -1 +1 @@
-1068c5d524bfec4a3fbb0bbd2a3b88063451db93
\ No newline at end of file
+996a2c5897e7d16bd61e296b0099825e1e96e664
\ No newline at end of file
diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 259d17564fc5a3625e9d12c220cfaa82513fd62d..e8213ad744af2cf2ab5f962948011f0f1bc0a2bd 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -6,7 +6,7 @@ import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex, Disease, \
- Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio
+ Compound, MDDRCompoundImport, MDDRActivityClass, TestActivityDescription, CellLine, RefCompoundBiblio, CompoundAction
class MyConverter(mysql.connector.conversion.MySQLConverter):
@@ -102,6 +102,8 @@ class Command(BaseCommand):
conn = mysql.connector.connect(
converter_class=MyConverter, host="localhost", user="root", password="ippidb", database="ippidb")
cursor = conn.cursor()
+ cursor_aux = conn.cursor(buffered=True)
+ cursor_aux2 = conn.cursor(buffered=True)
if options['bibliographies']:
cursor.execute("""SELECT * FROM biblio""")
rows = cursor.fetchall()
@@ -234,8 +236,9 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
Disease.objects.all().delete()
Ppi.objects.all().delete()
PpiComplex.objects.all().delete()
+ CompoundAction.objects.all().delete()
self.stdout.write(
- self.style.SUCCESS('Successfully flushed protein domain complex, PPI, and disease tables'))
+ self.style.SUCCESS('Successfully flushed protein domain complex, PPI, compound actions, and disease tables'))
ppi_ids_mapping = {}
for row in rows:
try:
@@ -272,6 +275,32 @@ select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy,
ppi_complex.complex = c
ppi_complex.cc_nb = 1
ppi_complex.save()
+ if row[3] is not None:
+ sql_ca_string = '''select distinct c.CanonicalSmile from cmpdAction as ca
+ inner join compound as c on ca.IDCompound=c.IDCompound where ca.IDComplexeBound='''\
+ + str(row[3])
+ cursor_aux.execute(sql_ca_string)
+ rows_aux = cursor_aux.fetchall()
+ for row_aux in rows_aux:
+ if row_aux is None:
+ self.stdout.write(sql_ca_string)
+ continue
+ canonical_smile = row_aux[0]
+ sql_bse_string = '''select CodePDB from bindingSiteEvidence where IDPPI=''' + str(ppi.id)
+ cursor_aux.execute(sql_bse_string)
+ row_aux2 = cursor_aux2.fetchone()
+ if row_aux2 is None:
+ pdb_id_ca = None
+ else:
+ pdb_id_ca = row_aux2[0]
+ c = Compound.objects.get(canonical_smile=canonical_smile)
+ ca = CompoundAction()
+ ca.compound = c
+ ca.ppi = ppi
+ ca.activation_mode = 'U'
+ ca.nb_copy_compounds = 1
+ ca.pdb_id = pdb_id_ca
+ ca.save()
except Exception as e:
if options['stoponfail']:
import traceback
diff --git a/ippisite/ippidb/migrations/0025_auto_20171110_1046.py b/ippisite/ippidb/migrations/0025_auto_20171110_1046.py
new file mode 100644
index 0000000000000000000000000000000000000000..a8726087da8c0b36c5b71e72f6f95bdd2dbe1089
--- /dev/null
+++ b/ippisite/ippidb/migrations/0025_auto_20171110_1046.py
@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2017-11-10 10:46
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0024_auto_20170523_2000'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_cellulo',
+ field=models.BooleanField(default=False, verbose_name='in cellulo study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_silico',
+ field=models.BooleanField(default=False, verbose_name='in silico study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_vitro',
+ field=models.BooleanField(default=False, verbose_name='in vitro study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='in_vivo',
+ field=models.BooleanField(default=False, verbose_name='in vivo study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='pharmacokinetic',
+ field=models.BooleanField(default=False, verbose_name='pharmacokinetic study'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='source',
+ field=models.CharField(choices=[('PM', 'PubMed ID'), ('PT', 'Patent'), ('DO', 'DOI ID')], default='PM', max_length=2, verbose_name='Bibliographic type'),
+ ),
+ migrations.AlterField(
+ model_name='bibliography',
+ name='xray',
+ field=models.BooleanField(default=False, verbose_name='X-Ray data'),
+ ),
+ migrations.AlterField(
+ model_name='compoundaction',
+ name='activation_mode',
+ field=models.CharField(choices=[('O', 'Orthosteric'), ('A', 'Allosteric'), ('U', 'Unspecified')], max_length=1, verbose_name='Activation mode'),
+ ),
+ migrations.AlterField(
+ model_name='protein',
+ name='organism',
+ field=models.ForeignKey(default='Homo sapiens', on_delete=django.db.models.deletion.CASCADE, to='ippidb.Taxonomy'),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0026_auto_20171110_1426.py b/ippisite/ippidb/migrations/0026_auto_20171110_1426.py
new file mode 100644
index 0000000000000000000000000000000000000000..0dca58c57af03dd6d5061ddcfb8a7b7443cb686c
--- /dev/null
+++ b/ippisite/ippidb/migrations/0026_auto_20171110_1426.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2017-11-10 14:26
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0025_auto_20171110_1046'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compoundaction',
+ name='pdb_id',
+ field=models.CharField(blank=True, max_length=4, null=True, verbose_name='PDB ID'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 232e595e92ef3807ff99b21fa2cabed997f7de95..5e4c3d225e8da27831ddd30b070c7103291ec8f8 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -513,13 +513,14 @@ class CompoundPKResult(models.Model):
class CompoundAction(models.Model):
ACTIVATION_MODES = (
('O', 'Orthosteric'),
- ('A', 'Allosteric')
+ ('A', 'Allosteric'),
+ ('U', 'Unspecified')
)
compound = models.ForeignKey(Compound)
activation_mode = models.CharField(
'Activation mode', max_length=1, choices=ACTIVATION_MODES)
ppi = models.ForeignKey(Ppi)
- pdb_id = models.CharField('PDB ID', max_length=4)
+ pdb_id = models.CharField('PDB ID', max_length=4, blank=True, null=True)
nb_copy_compounds = models.IntegerField(
'Number of copies for the compound')
diff --git a/ippisite/ippidb/templates/compound_abstract.html b/ippisite/ippidb/templates/compound_abstract.html
index a8094c2741faac61dc5108baf4e510c57c1eb6fb..82110001a00658878fafadbe3f30d18222c1425d 100644
--- a/ippisite/ippidb/templates/compound_abstract.html
+++ b/ippisite/ippidb/templates/compound_abstract.html
@@ -1,15 +1,6 @@
<div class="row m-2 border border-info bg-light">
- <div class="col-sm-3 bg-info">
- <div id="{{ compound.id }}_smilesdisplay"
- data-widget="Kekule.ChemWidget.Viewer2D" data-auto-fit="true"
- data-toolbar-evoke-modes="[0]" style="width: 200px; height: 200px;">
- </div>
- <textarea rows="10" cols="50" id="{{ compound.id }}_smilesvalue" style="display:none;">{{ compound.canonical_smile }}</textarea>
- <script>
- $(window).on('load', function(){
- kekule_display('{{ compound.id }}_smilesvalue','{{ compound.id }}_smilesdisplay')
- });
- </script>
+ <div class="col-sm-3 border-info d-flex justify-content-center align-content-center">
+ <img src="https://pubchem.ncbi.nlm.nih.gov/image/imagefly.cgi?cid={{ compound.pubchem_id }}&width=300&height=300" style="width:300px;height:300px;"/>
</div>
<div class="col-sm-9">
<ul class="list-group">
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index df4b25038688bd84b582e681a043fd9da40af30a..26917de79bec1069bb2351429d6fe2ba440ff4f3 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -1,5 +1,5 @@
{% extends "admin-session.html" %}
-
+{% load customtags %}
{% block title %}compound{% endblock %}
@@ -30,12 +30,22 @@
</nav>
</div>
{% include "kekule_display.html" %}
+=======
+
<div class="container-fluid">
<div class="row flex-xl-nowrap">
<div class="col-12 col-md-3 col-xl-2 bd-sidebar">
<form>
<fieldset class="form-group row border border-info m-2">
<div class="bg-info col-12"><legend>PPI</legend></div>
+ {% for ppi in selected_ppis %}
+ <div class="form-check col-12">
+ <label class="form-check-label">
+ <input class="form-check-input text-right" type="checkbox" checked value="{{ ppi.id }}" onchange="this.form.submit()" name="ppi" style="width: auto; margin-right: inherit!;">
+ {{ ppi.name }}
+ </label>
+ </div>
+ {% endfor %}
{% for ppi in ppis|slice:":5" %}
<div class="form-check col-12">
<label class="form-check-label">
@@ -53,7 +63,7 @@
{% include "compound_abstract.html" with compound=compound %}
{% endfor %}
{% else %}
- <p>No bibliographies available.</p>
+ <p>Nothing found there!</p>
{% endif %}
</main>
</div>
@@ -63,7 +73,7 @@
<ul class="pagination justify-content-end">
{% if compounds.has_previous %}
<li class="page-item">
- <a class="page-link" href="?page={{ compounds.previous_page_number }}" tabindex="-1">Previous</a>
+ <a class="page-link" href="?{% url_replace request 'page' compounds.previous_page_number %}" tabindex="-1">Previous</a>
</li>
{% endif %}
@@ -73,7 +83,7 @@
{% if compounds.has_next %}
<li class="page-item">
- <a class="page-link" href="?page={{ compounds.next_page_number }}" tabindex="-1">Next</a>
+ <a class="page-link" href="?{% url_replace request 'page' compounds.next_page_number %}" tabindex="-1">Next</a>
</li>
{% endif %}
</ul>
diff --git a/ippisite/ippidb/templatetags/__init__.py b/ippisite/ippidb/templatetags/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/ippisite/ippidb/templatetags/customtags.py b/ippisite/ippidb/templatetags/customtags.py
new file mode 100644
index 0000000000000000000000000000000000000000..c01874f816c8d9e59c10eb2558494886a46063c4
--- /dev/null
+++ b/ippisite/ippidb/templatetags/customtags.py
@@ -0,0 +1,9 @@
+from django import template
+
+register = template.Library()
+
+@register.simple_tag
+def url_replace(request, field, value):
+ dict_ = request.GET.copy()
+ dict_[field] = value
+ return dict_.urlencode()
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index 785b3ac9b6725bb7669ff739ec3a47adf469fbb3..2866d6ea3248514bc5e35032c96c446800e4940b 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -186,9 +186,17 @@ def biblio_card(request, source, id_source):
'tad_ppis': tad_ppis})
def compound_list(request):
+ """
+ Display the list of compounds
+ """
compounds = Compound.objects.all()
+ # if filtering on "action on PPI"
+ if request.GET.get('ppi'):
+ compounds = compounds.filter(compoundaction__ppi__id__in=request.GET.getlist('ppi'))
+ selected_ppis = Ppi.objects.filter(id__in=request.GET.getlist('ppi'))
+ ppis = Ppi.objects.exclude(id__in=request.GET.getlist('ppi'))
+ # handle pagination in compounds list
paginator = Paginator(compounds, 5)
- ppis = Ppi.objects.all()
page = request.GET.get('page')
try:
compounds = paginator.page(page)
@@ -198,4 +206,4 @@ def compound_list(request):
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
compounds = paginator.page(paginator.num_pages)
- return render(request, 'compound_list.html', {'compounds': compounds, 'ppis': ppis})
+ return render(request, 'compound_list.html', {'compounds': compounds, 'selected_ppis': selected_ppis, 'ppis': ppis})