Merge branch 'async-near-cavities' into 'master'

Async near cavities

See merge request !45

ippisite/ippidb/static/js/targetcentric-near-cavities-rows.js

+$(document).ready(function(){
+    $(".asnyc-construction.now[data-cavity-id]").each(function () {
+        loadNearCavityRows($(this));
+    });
+});
+
+function loadNearCavityRows($row){
+    if($row.length==0)
+        return;
+    $row.addClass("loading");
+    $.ajax({
+        url: '/cavity/'+$row.data("cavityId")+'/near-cavities',
+        data: {'chaincount':$row.data("chaincount"), 'cavcount':$row.data("cavcount")},
+        success: function(data){
+            var $data=$(data);
+            if ($row.hasClass("show"))
+                $data.addClass("show");
+            $data.insertAfter($row);
+            $row.remove();
+        }
+    });
+}
\ No newline at end of file

ippisite/ippidb/templates/targetcentric_cavity_row.html

+{% load customtags %}
+{% load humanize %}
+<tr XXXid="cavity_{{ cavity.id }}"
+    {%if near_cavity %}
+    class="collapse out collapseme{{ chaincount }}_{{ cavcount }}"
+    style="background-color:rgb({{ score|get_color }})"
+    {%else%}
+    class="table-light"
+    {%endif%}>
+    <th class="zui-sticky-col text-nowrap">
+        {%if not near_cavity %}
+        <i class="far fa-plus-square" style="cursor: pointer;" data-toggle="collapse" data-target=".collapseme{{ chaincount }}_{{ cavcount }}"
+           onclick="loadNearCavityRows($('.asnyc-construction[data-cavity-id={{ cavity.id }}]:not(loading)'));"></i>
+        {%endif%}
+        <a {%if score %} title="{{ score|floatformat:3|intcomma }}" {%endif%}
+           target="_blank"
+           rel="noopener noreferrer"
+           href="{% url 'cavities' %}?pdbsearch={{ cavity.chain.pdb.code }}">{{ cavity.chain.pdb.code }}</a>
+        /
+        <span class="dropdown">
+        <div class="dropbtn" data-toggle="dropdown" title="uniprot: {{ cavity.chain.protein.uniprot_id }}">
+            {{ cavity.chain.pdb_chain_id }} | {{ cavity.chain.protein.short_name }}
+        </div>
+        <div class="dropdown-content">
+            <a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
+            <a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ cavity.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
+        </div>
+        </span>
+        /
+        <span class="dropdown">
+            <div class="dropbtn" data-toggle="dropdown">
+                {{ cavity.cavity_number }}
+            </div>
+        <div class="dropdown-content">
+        <a target="_blank" rel="noopener noreferrer" href="{% url 'networks' %}?search={{ cavity|build_name }}"> Query pocket in pocketome</a>
+        </div>
+        </span>
+        ::
+        {% if cavity.partner.ligand %}
+        <span class="dropdown">
+        <div class="dropbtn" data-toggle="dropdown" title="smiles: {{ cavity.partner.ligand.canonical_smile }}">
+            {{ cavity.partner.ligand.pdb_ligand_id }}_{{ cavity.partner.ligand.supplementary_id }}
+        </div>
+        <div class="dropdown-content">
+            <a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?ligandcode={{ cavity.partner.ligand.pdb_ligand_id }}">Query ligand ID in pockets</a>
+            <a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?similar_to=ECFP4:{{ cavity.partner.ligand.canonical_smile|urlencode }}">Query SMILES in iPPI-DB compounds</a>
+        </div>
+        </span>
+        {% else %}
+        <span class="dropdown">
+        <div class="dropbtn" data-toggle="dropdown" title="uniprot: {{ cavity.partner.chain.protein.uniprot_id }}">
+            {{ cavity.partner.chain.pdb_chain_id }} | {{ cavity.partner.chain.protein.short_name }}
+        </div>
+        <div class="dropdown-content">
+        <a target="_blank" rel="noopener noreferrer" href="{% url 'cavities' %}?uniprotid={{ cavity.partner.chain.protein.uniprot_id }}">Query UniprotID in pockets</a>
+        <a target="_blank" rel="noopener noreferrer" href="{% url 'compound_list' %}?uniprot_id={{ cavity.partner.chain.protein.uniprot_id }}">Query UniprotID as iPPI-DB target</a>
+        </div>
+        </span>
+        {% endif %}
+    </th>
+    <td>{% if cavity.partner.ligand %}PL{% else %}HD{% endif %}</td>
+    <td>{{ cavity.volume|floatformat:0 }}</td>
+    <td>{{ cavity.npr1|floatformat:2 }}</td>
+    <td>{{ cavity.npr2|floatformat:2 }}</td>
+    <td>{{ cavity.asphericity|floatformat:2 }}</td>
+    <td>{{ cavity.eccentricity|floatformat:2 }}</td>
+    <td>{{ cavity.rgyr|floatformat:2 }}</td>
+    <td>{{ cavity.spherocityindex|floatformat:2 }}</td>
+    <td>{{ cavity.ca|floatformat:1 }}</td>
+    <td>{{ cavity.cz|floatformat:1 }}</td>
+    <td>{{ cavity.n|floatformat:1 }}</td>
+    <td>{{ cavity.o|floatformat:1 }}</td>
+    <td>{{ cavity.og|floatformat:1 }}</td>
+    <td>{{ cavity.nz|floatformat:1 }}</td>
+    <td>{{ cavity.od1|floatformat:1 }}</td>
+    <td>{{ cavity.du|floatformat:1 }}</td>
+    <td>{{ cavity.t40|floatformat:1 }}</td>
+    <td>{{ cavity.t40_50|floatformat:1 }}</td>
+    <td>{{ cavity.t50_60|floatformat:1 }}</td>
+    <td>{{ cavity.t60_70|floatformat:1 }}</td>
+    <td>{{ cavity.t70_80|floatformat:1 }}</td>
+    <td>{{ cavity.t80_90|floatformat:1 }}</td>
+    <td>{{ cavity.t90_100|floatformat:1 }}</td>
+    <td>{{ cavity.t100_110|floatformat:1 }}</td>
+    <td>{{ cavity.t110_120|floatformat:1 }}</td>
+    <td>{{ cavity.t120|floatformat:1 }}</td>
+</tr>
\ No newline at end of file

ippisite/ippidb/templates/targetcentric_near_cavities.html

+{% load customtags %}
+{% for distance in object.near_cavities %}
+    {% with distance.distance|get_zscore:avg_std as score %}
+        {% if object == distance.cavity1 %}
+            {% include "targetcentric_cavity_row.html" with chaincount=chaincount cavcount=cavcount cavity=distance.cavity2 score=score near_cavity=True %}
+        {% elif object == distance.cavity2 %}
+            {% include "targetcentric_cavity_row.html" with chaincount=chaincount cavcount=cavcount cavity=distance.cavity1 score=score near_cavity=True %}
+        {% endif %}
+    {%endwith%}
+{% endfor %}
\ No newline at end of file

ippisite/ippidb/urls.py

@@ -74,6 +74,7 @@ urlpatterns = [
     ),
     re_path(r"^targetcentric/$", views.PDBView.as_view(), name="cavities"),
     re_path(r"^targetcentric/networks$", views.NetworkView.as_view(), name="networks"),
+    re_path(r"^cavity/(?P<pk>\d+)/near-cavities$", views.NearCavitiesHTMLFragmentView.as_view(), name="near_cavities"),
     re_path(r"^api/", include(ROUTER.urls)),
     re_path(r"^compounds/$", views.CompoundListView.as_view(), name="compound_list"),
     re_path(

ippisite/ippidb/views/__init__.py

@@ -11,7 +11,7 @@ iPPI-DB views
 """
 from django.contrib.auth.decorators import login_required
 from django.shortcuts import render
-from .targetcentric import PdbViewSet, DistanceViewSet, PDBView, NetworkView
+from .targetcentric import PdbViewSet, DistanceViewSet, PDBView, NetworkView, NearCavitiesHTMLFragmentView
 from .contribute import ippidb_wizard_view, ContributionDetailView
 from .compound_query import (
     CompoundListView,
@@ -111,6 +111,7 @@ __all__ = [
     PDBView,
     get_output_job,
     NetworkView,
+    NearCavitiesHTMLFragmentView,
     get_json_network,
     IppiDbCompoundSitemap,
     IppiDbContributorsSitemap,

ippisite/ippidb/views/targetcentric.py

@@ -4,7 +4,7 @@ iPPI-DB targetcentric views and related classes
 from itertools import product
 from functools import reduce
 from operator import add
-from django.views.generic import ListView
+from django.views.generic import ListView, DetailView
 from django.contrib import messages
 from django.db.models import Case, When, Value, IntegerField, F, Q
 from rest_framework import viewsets
@@ -308,3 +308,16 @@ class NetworkView(ListView):
     def get_queryset(self):
         queryset = self.model.objects.all()
         return queryset.order_by("number")
+
+
+class NearCavitiesHTMLFragmentView(DetailView):
+    model = Cavity
+    template_name = "targetcentric_near_cavities.html"
+
+    def get_context_data(self, *, object_list=None, **kwargs):
+        return dict(
+            **super().get_context_data(**kwargs),
+            chaincount=self.request.GET.get('chaincount', '0'),
+            cavcount=self.request.GET.get('cavcount', '0'),
+            avg_std=MetaInformation.objects.first(),
+        )

ippisite/ippisite/db_finder.py

+import os
+import subprocess
+
+
+def get_db_ip():
+    result = subprocess.run(
+        [
+            "docker",
+            "ps",
+            "-f",
+            "name=%s" % get_guessed_container_name(),
+            "-q",
+        ],
+        stdout=subprocess.PIPE,
+    )
+    ids = result.stdout.decode("utf-8").strip().split("\n")
+    if len(ids) > 1:
+        raise Exception("Can't find the DB, too much match")
+    if len(ids) == 0 or len(ids[0]) == 0:
+        result = subprocess.run(
+            [
+                "docker",
+                "ps",
+                "-f",
+                "name=_db",
+                "-q",
+            ],
+            stdout=subprocess.PIPE,
+        )
+        ids = result.stdout.decode("utf-8").strip().split("\n")
+        if len(ids) > 1:
+            raise Exception(
+                "Can't find the DB, couldn't guess container name (tried '%s'), "
+                "and too much match with '_db'" % get_guessed_container_name()
+            )
+        if len(ids) == 0 or len(ids[0]) == 0:
+            raise Exception("Can't find the DB")
+    result = subprocess.run(
+        [
+            "docker",
+            "inspect",
+            "-f",
+            "'{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}'",
+            ids[0],
+        ],
+        stdout=subprocess.PIPE,
+    )
+    return result.stdout.decode("utf-8").strip().replace("'", "")
+
+
+def get_guessed_container_name():
+    return (
+        str(os.path.dirname(__file__).split(os.path.sep)[-2]).lower().replace("-", "")
+        + "_db"
+    )
+
+
+if __name__ == "__main__":
+    print(get_db_ip())

ippisite/ippisite/settings.py

@@ -17,6 +17,8 @@ from decouple import config
 from django.utils.translation import gettext_lazy
 from socket import gethostname, gethostbyname
 
+from ippisite import db_finder
+
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 PERSISTENT_DIR = os.path.join(BASE_DIR, 'persistent')
 
@@ -122,13 +124,16 @@ if config("USE_SQLITE_AS_DB", default="False").upper() == "TRUE":
         }
     }
 else:
+    POSTGRES_HOST = config("POSTGRES_HOST", '')
+    if not POSTGRES_HOST:
+        POSTGRES_HOST = db_finder.get_db_ip()
     DATABASES = {
         "default": {
             "ENGINE": "django.db.backends.postgresql",
             "NAME": config("POSTGRES_DB"),
             "USER": config("POSTGRES_USER"),
             "PASSWORD": config("POSTGRES_PASSWORD"),
-            "HOST": config("POSTGRES_HOST"),
+            "HOST": POSTGRES_HOST,
             "PORT": 5432,
         }
     }