Merge branch 'master' of https://gitlab.pasteur.fr/odoppelt/iPPIDB

Former-commit-id: 740b646d94819b249855d54c04a541f132732e0d

.gitlab-ci.yml

@@ -9,6 +9,7 @@ test-centos7:
   - yum install install -y python34-pip python34-devel
   - yum install -y gcc graphviz graphviz-devel
   - yum install -y httpd httpd-devel
+  - yum install -y gcc-c++
   - cd ippisite
   - pip3 install -r requirements.txt
   - python3 manage.py test

ippisite/db.sqlite3.REMOVED.git-id

-9a436afcb3cc2a25d2cb6b1f8cc0665b3f466d06
\ No newline at end of file
+1068c5d524bfec4a3fbb0bbd2a3b88063451db93
\ No newline at end of file

ippisite/ippidb/models.py

@@ -112,6 +112,7 @@ class Protein(AutoFillableModel):
         self.recommended_name_long = info['recommended_name']
         self.gene_name = info['gene']
         self.entry_name = info['entry_name']
+        self.short_name = info['short_name']
         try:
             taxonomy = Taxonomy.objects.get(taxonomy_id=info['organism'])
         except Taxonomy.DoesNotExist:
@@ -219,6 +220,17 @@ class Ppi(models.Model):
         # this is the less efficient query ever seen, FIXME
         return PpiComplex.objects.filter(ppi=self, complex__in=ProteinDomainBoundComplex.objects.all())
 
+    @property
+    def name(self):
+        all_protein_names = set([ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_complexes()])
+        bound_protein_names = set([ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_bound_complexes()])
+        partner_protein_names = all_protein_names - bound_protein_names
+        bound_str = ','.join(bound_protein_names)
+        partner_str = ','.join(partner_protein_names)
+        name = bound_str
+        if partner_str!='':
+            name += ' / ' + partner_str
+        return name
 
 class PpiComplex(models.Model):
     ppi = models.ForeignKey(Ppi)
@@ -308,6 +320,12 @@ class Compound(models.Model):
     mddr_compound = models.ForeignKey(
         'MDDRCompoundImport', blank=True, null=True)
 
+    @property
+    def biblio_refs(self):
+        """
+        return all RefCompoundBiblio related to this complex
+        """
+        return RefCompoundBiblio.objects.filter(compound=self)
 
 class MDDRActivityClass(models.Model):
     name = models.CharField('Activity Class', max_length=100, unique=True)

ippisite/ippidb/templates/biblio_card.html

@@ -9,6 +9,10 @@
     function display(smiles_id, viewer_id) {
       var smi = document.getElementById(smiles_id).value;
       var chemViewer = new Kekule.ChemWidget.Viewer(document.getElementById(viewer_id));
+      chemViewer.setEnableToolbar(false)
+                .setEnableDirectInteraction(false)
+                .setEnableEdit(false)
+                .setToolButtons([]);
       var mol = Kekule.IO.loadFormatData(smi, "smi"); 
       chemViewer.setChemObj(mol);
       console.log(smi);
@@ -57,7 +61,7 @@
             <div class="card">
                <div class="card-body">
                <div id="{{ compound_biblio.id }}_smilesdisplay"
-                   data-widget="Kekule.ChemWidget.Viewer2D" data-enable-toolbar="true" data-auto-size="true" data-padding="20"
+                   data-widget="Kekule.ChemWidget.Viewer2D" data-auto-size="true" data-padding="20"
                    data-toolbar-evoke-modes="[0]">
                </div>
                <textarea rows="10" cols="50" id="{{ compound_biblio.id }}_smilesvalue" style="display:none;">{{ compound_biblio.compound.canonical_smile }}</textarea>  

ippisite/ippidb/templates/biblio_citation.html

+<a target="_blank" class="card-link" href="https://www.ncbi.nlm.nih.gov/pubmed/{{ bibliography.id_source }}">{{ bibliography.authors_list }}. {{ authors.biblio_year }}. {{ bibliography.title }} {{ bibliography.journal_name }}. </a>

ippisite/ippidb/templates/biblio_list.html

@@ -12,11 +12,20 @@
 			<div id="content" class="main-content">
 					<main role="main">
 {% if bibliographies %}
-    <ul>
+<table class="table">
+  <thead class="thead-light">
+    <tr>
+      <th scope="col">Title</th>
+    </tr>
+  </thead>
+  <tbody>
     {% for biblio in bibliographies %}
-        <li><a href="/biblio/{{ biblio.source }}{{ biblio.id_source}}">{{ biblio.title }}</a></li>
+    <tr>
+        <td><a href="/biblio/{{ biblio.source }}{{ biblio.id_source}}">{{ biblio.title }}</a></td>
+    </tr>
     {% endfor %}
-    </ul>
+  </tbody>
+</table>
 {% else %}
     <p>No bibliographies available.</p>
 {% endif %}					

ippisite/ippidb/templates/compound_abstract.html

+<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>
+  <div class="col-sm-9">
+    <ul class="list-group">
+      {% if compound.common_name %}
+      <li class="list-group-item">Common name: {{ compound.common_name }}</li>
+      {% endif %}
+      {% if compound.canonical_smile %}
+      <li class="list-group-item">Canonical SMILES: {{ compound.canonical_smile }}</li>
+      {% endif %}
+      {% if compound.iupac_name %}
+      <li class="list-group-item">IUPAC name: {{ compound.iupac_name }}</li>
+      {% endif %}
+    </ul>
+    <p>in bibliography</p>
+    <ul class="list-group">
+      {% for biblio_ref in compound.biblio_refs %}
+      <li class="list-group-item">Mentionned in {% include "biblio_citation.html" with bibliography=biblio_ref.bibliography%} as <i>{{ biblio_ref.compound_name }}</i></li>
+      {% endfor %}
+    </ul>
+    {%if compound.pubchem_id or compound.chembl_id or compound.chemspider_id %}
+    <p>in other databases</p>
+    <ul class="list-group">
+      {% if compound.pubchem_id %}
+      <li class="list-group-item">PubChem: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank">{{ compound.pubchem_id }}</a></li>
+      {% endif %}
+      {% if compound.chembl_id %}
+      <li class="list-group-item">ChEMBL: <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id}}" target="_blank">{{ compound.chembl_id}}</a></li>
+      {% endif %}
+      {% if compound.chemspider_id %}
+      <li class="list-group-item">ChemSpider: <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank">{{ compound.chemspider_id}}</a></li>
+      {% endif %}
+    </ul>
+    {% endif %}
+  </div>
+</div>

ippisite/ippidb/templates/compound_list.html

+{% extends "base.html" %}
+
+    
+{% block title %}compound{% endblock %}
+
+{% block content %}
+
+{% 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 ppis|slice:":5"  %}
+    <div class="form-check col-12">
+      <label class="form-check-label">
+        <input class="form-check-input text-right" type="checkbox" value="{{ ppi.id }}" onchange="this.form.submit()" name="ppi" style="width: auto; margin-right: inherit!;">
+        {{ ppi.name }}
+      </label>
+    </div>
+    {% endfor %}
+  </fieldset>
+</form>
+</div>
+<main class="col-12 col-md-9 col-xl-10 pl-md-5 bd-content" role="main">
+{% if compounds %}
+    {% for compound in compounds %}
+        {% include "compound_abstract.html" with compound=compound %}
+    {% endfor %}
+{% else %}
+    <p>No bibliographies available.</p>
+{% endif %}					
+                    </main>
+</div>
+</div>
+
+<nav>
+  <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>
+    </li>
+    {% endif %}
+
+    <li class="page-item disabled">
+     <span class="page-link">Page {{ compounds.number }} of {{ compounds.paginator.num_pages }}.</span>
+    </li>
+
+    {% if compounds.has_next %}
+    <li class="page-item">
+     <a class="page-link" href="?page={{ compounds.next_page_number }}" tabindex="-1">Next</a>
+    </li>
+    {% endif %}
+  </ul>
+</nav>
+{% endblock %}

ippisite/ippidb/templates/kekule_display.html

+<script>
+    Kekule.Indigo.enable();
+    function kekule_display(smiles_id, viewer_id) {
+      var smi = document.getElementById(smiles_id).value;
+      var chemViewer = new Kekule.ChemWidget.Viewer(document.getElementById(viewer_id));
+      chemViewer.setEnableToolbar(false)
+                .setEnableDirectInteraction(false)
+                .setEnableEdit(false)
+                .setToolButtons([]);
+      var mol = Kekule.IO.loadFormatData(smi, "smi"); 
+      chemViewer.setChemObj(mol);
+    }
+</script>

ippisite/ippidb/urls.py

@@ -21,6 +21,7 @@ urlpatterns = [
     url(r'^query/chemical/$', views.chemical, name='chemical'),
     url(r'^biblio/(?P<source>\w{2})(?P<id_source>\w+)$', views.biblio_card, name='biblio_card'),
     url(r'^biblio/$', views.biblio_list, name='biblio_list'),
+    url(r'^compound/$', views.compound_list, name='compound_list'),
     url(r'^tutorials$', views.tutorials, name='tutorials'),
         url(r'^admin-session$', views.adminSession, name='admin-session'),
     url(r'^admin-session/add/(?P<step>.+)/$',

ippisite/ippidb/views.py

@@ -2,9 +2,10 @@ import ippidb
 
 from django.shortcuts import render
 from django.http import HttpResponseRedirect, Http404
+from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
 from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
 from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription
+from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi
 from .ws import get_pdb_uniprot_mapping
 
 
@@ -179,3 +180,18 @@ def biblio_card(request, source, id_source):
     return render(request, 'biblio_card.html', {'bibliography': bibliography,
                                                 'compound_biblios': refs,
                                                 'tad_ppis': tad_ppis}) 
+
+def compound_list(request):
+    compounds = Compound.objects.all()
+    paginator = Paginator(compounds, 5)
+    ppis = Ppi.objects.all()
+    page = request.GET.get('page')
+    try:
+        compounds = paginator.page(page)
+    except PageNotAnInteger:
+        # If page is not an integer, deliver first page.
+        compounds = paginator.page(1)
+    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})    

ippisite/ippidb/ws.py

@@ -49,6 +49,9 @@ def get_uniprot_info(uniprot_id):
     uniprot_client = UniProt()
     ns = {'u': 'http://uniprot.org/uniprot'}
     resp = uniprot_client.retrieve(uniprot_id)
+    f = open('/tmp/'+uniprot_id+'.xml','w')
+    f.write(str(resp))
+    f.close()
     recommended_name = resp.root.findall(
         'u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
     organism = resp.root.findall(
@@ -67,6 +70,7 @@ def get_uniprot_info(uniprot_id):
             'organism': int(organism),
             'gene': gene,
             'entry_name': entry_name,
+            'short_name': entry_name.split('_')[0],
             'molecular_functions': molecular_functions
             }