diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 5fa8acdd5362703f5fc156f3919ec608f5b424db..143dd3b480e80bbf98fce44e1a1212832f131e5c 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -122,7 +122,23 @@ class Bibliography(AutoFillableModel):
return True
class Meta:
- verbose_name_plural = "bibliographies"
+ verbose_name_plural = "Bibliographies"
+ verbose_name = "Bibliography"
+
+ def data_and_study(self):
+ ret = []
+ for f in [
+ "cytotox",
+ "xray",
+ "in_silico",
+ "in_vitro",
+ "in_cellulo",
+ "in_vivo",
+ "pharmacokinetic",
+ ]:
+ if getattr(self, f, False):
+ ret.append(self._meta.get_field(f).verbose_name.title())
+ return ", ".join(ret)
def __str__(self):
return '{}, {}'.format(self.source, self.id_source)
@@ -1204,6 +1220,8 @@ class RefCompoundBiblio(models.Model):
class Meta:
unique_together = (('compound', 'bibliography'),)
+ verbose_name_plural = "Compounds in bibliography"
+ verbose_name = "Compound in bibliography"
def __str__(self):
return 'Ref. {} on {}'.format(self.bibliography, self.compound)
diff --git a/ippisite/ippidb/templates/admin-session.html b/ippisite/ippidb/templates/admin-session.html
index 8107999b53ad09e5408e7f494acf61aeb7062589..04dbc6324f0fa0343c555ae1205e056c8fa155cb 100644
--- a/ippisite/ippidb/templates/admin-session.html
+++ b/ippisite/ippidb/templates/admin-session.html
@@ -27,7 +27,7 @@
<nav class="breadcrumb breadNav" role="navigation">
<div class="breadNav-label">You are here</div>
<div aria-labelledby="breadNav-label">
- {% block breadcrumb %}{{block.super}}{% trans 'Admin_session_title' %}{% endblock %}
+ {% block breadcrumb %}{{block.super}}<a href="{% url 'admin-session'%}" class="breadNav-link">{% trans 'Admin_session_title' %}</a>{% endblock %}
</div>
</nav>
<div id="main-wrapper" class="page">
diff --git a/ippisite/ippidb/templates/contribute-view.html b/ippisite/ippidb/templates/contribute-view.html
new file mode 100644
index 0000000000000000000000000000000000000000..2d074ca1d2d0ed62e73949d05420f4cfd870e363
--- /dev/null
+++ b/ippisite/ippidb/templates/contribute-view.html
@@ -0,0 +1,62 @@
+{% extends "admin-session.html" %}
+{% load i18n %}
+{% load static %}
+{% load customtags %}
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+
+{% block content%}
+<div class="inner-wrap">
+ <nav class="breadcrumb breadNav" role="navigation">
+ <div class="breadNav-label">You are here</div>
+ <div aria-labelledby="breadNav-label">
+ {% block breadcrumb %}{{block.super}} > View
+ contribution {% endblock %}
+ </div>
+ </nav>
+ <div id="main-wrapper" class="page">
+ <div id="main">
+ <div id="content" class="main-content">
+ <div class="section row">
+ {% include "ippidb/bibliography_card.html" with object=bibliography css_class="col-xs-12 col-md-6"%}
+ {% include "ippidb/ppi_card.html" with object=ppi css_class="col-xs-12 col-md-6" %}
+ <div class="col-12">
+ <div class="card">
+ <h5 class="card-header">{{complexes|verbose_name}}</h5>
+ <div class="card-body">
+ {%for o in complexes%}
+ {{o}}
+ {%endfor%}
+ </div>
+ </div>
+ </div>
+ <div class="col-12">
+ <div class="card">
+ <h5 class="card-header">Tests</h5>
+ <div class="card-body">
+ {%for o in testactivitydescription%}
+ {% include "ippidb/testactivitydescription_card.html" with object=o %}
+ {%endfor%}
+ {%for o in testcytotoxdescription%}
+ {% include "ippidb/testcytotoxdescription_card.html" with object=o %}
+ {%endfor%}
+ {%for o in testpkdescription%}
+ {% include "ippidb/testpkdescription_card.html" with object=o %}
+ {%endfor%}
+ </div>
+ </div>
+ </div>
+ <div class="col-12">
+ <div class="card">
+ <h5 class="card-header">{{refcompoundbiblio|verbose_name}}</h5>
+ <div class="card-body">
+ {% include "ippidb/refcompoundbiblio_table.html" with objects=refcompoundbiblio %}
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div><!-- div main -->
+ </div>
+</div>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/done.html b/ippisite/ippidb/templates/done.html
deleted file mode 100644
index 051fcd5b141c26e98126728c1d69c5dc13039a07..0000000000000000000000000000000000000000
--- a/ippisite/ippidb/templates/done.html
+++ /dev/null
@@ -1,15 +0,0 @@
-{% extends "add.html" %}
-{% load i18n %}
-
-{% block form %}
-<div id="Form">
- <div class="last_step">
- <div class="form_div">
- CONGRATULATIONS!!! New publication added
- </div>
- <div class="add_new">
- <a href="http://localhost:8000/admin-session/add/IdForm/">Add new content</a>
- </div>
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/templates/ippidb/bibliography_card.html b/ippisite/ippidb/templates/ippidb/bibliography_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..d3a3f07d044b5e09537cb0fc9c4d889bba3087f8
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/bibliography_card.html
@@ -0,0 +1,25 @@
+{% load customtags %}
+{%if object%}
+<div class="{{css_class}}">
+ <div class="card">
+ <h5 class="card-header">
+ {% if object.has_external_url %}
+ <a target="_blank"
+ href="{{ object.get_external_url }}">
+ {% endif %}
+ {{object.get_source_display}} <i>{{object.id_source}}</i>
+ {% if object.has_external_url %}
+ </a>
+ {% endif %}
+ <span class="float-right">{{object|verbose_name}}</span>
+ </h5>
+ <div class="card-body">
+ <b> {{object.title }}</b>
+ <br/>
+ <i>{{ object.authors_list }}</i><br/>
+ {{object.journal_name }} ({{object.biblio_year}})<br/>
+ Contains : {{object.data_and_study}}
+ </div>
+ </div>
+</div>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/ippidb/ppi_card.html b/ippisite/ippidb/templates/ippidb/ppi_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..3dac2327f876d2e88d1bacadba15cc7828e88cc7
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/ppi_card.html
@@ -0,0 +1,41 @@
+{% load customtags %}
+{%if object%}
+<div class="{{css_class}}">
+ <div class="card">
+ <h5 class="card-header">
+ {{object.pdb_id}}
+ <span class="float-right">{{object|verbose_name}}</span>
+ </h5>
+ <div class="card-body">
+ <table class="table table-sm table-striped">
+ <tbody>
+ <tr>
+ <th>{{object|verbose_name:'name'}}</th>
+ <td>{{object.name }}</td>
+ </tr>
+ <tr>
+ <th>{{object|verbose_name:'family'}}</th>
+ <td>{{object.family }}</td>
+ </tr>
+ <tr>
+ <th>{{object|verbose_name:'symmetry'}}</th>
+ <td>{{object.symmetry }}</td>
+ </tr>
+ <tr>
+ <th>{{object|verbose_name:'pockets_nb'}}</th>
+ <td>{{object.pockets_nb }}</td>
+ </tr>
+ <tr>
+ <th>{{object|verbose_name:'diseases'}}</th>
+ <td>
+ {%for d in object.diseases.all %}
+ {{d}}{%if not forloop.last%},{%endif%}
+ {%endfor %}
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </div>
+</div>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/ippidb/refcompoundbiblio_table.html b/ippisite/ippidb/templates/ippidb/refcompoundbiblio_table.html
new file mode 100644
index 0000000000000000000000000000000000000000..735153d7917cad2c64d88f2fc9fcf61f0189fba2
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/refcompoundbiblio_table.html
@@ -0,0 +1,27 @@
+{% load customtags %}
+{%if objects and objects.exists%}
+<table class="table">
+ <thead>
+ {%with sample=objects.first%}
+ <tr>
+ <th>{{sample|verbose_name:'compound_name'}}</th>
+ <th>{{sample.compound|verbose_name:'canonical_smile'}}</th>
+ <th>{{sample.compound|verbose_name:'iupac_name'}}</th>
+ <th><i class="fa fa-link"></i>
+ </tr>
+ {%endwith%}
+ </thead>
+ <tbody>
+ {%for o in objects%}
+ <tr>
+ <td>{{o.compound_name}}</td>
+ <td>{{o.compound.canonical_smile}}</td>
+ <td>{{o.compound.iupac_name}}</td>
+ <td>
+ <a target="_blank" href="{% url 'compound_card' pk=o.compound.pk %}"><i class="fa fa-link"></i></a>
+ </td>
+ </tr>
+ {%endfor%}
+ </tbody>
+</table>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/ippidb/testactivitydescription_card.html b/ippisite/ippidb/templates/ippidb/testactivitydescription_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..3fc3b76f2ec919109b540ac94a2401ff9562df8b
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/testactivitydescription_card.html
@@ -0,0 +1,35 @@
+{% load customtags %}
+{%if object%}
+<div class="card">
+ <h5 class="card-header">
+ {{object.test_name}}
+ <span class="float-right">{{object|verbose_name}}</span>
+ </h5>
+ <div class="card-body row">
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'protein_domain_bound_complex'}}: </b>{{object.protein_domain_bound_complex}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'protein_bound_construct'}}: </b>{{object.protein_bound_construct}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'is_primary'}}: </b>{{object.is_primary}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'test_type'}}: </b>{{object.test_type}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'test_type'}}: </b>{{object.test_type}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'test_modulation_type'}}: </b>{{object.test_modulation_type}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'nb_active_compounds'}}: </b>{{object.nb_active_compounds}}
+ </div>
+ <div class="col-xs-12 col-sm-6 col-md-4 col-lg-3 col-xl-2">
+ <b>{{object|verbose_name:'cell_line'}}: </b>{{object.cell_line}}
+ </div>
+ </div>
+</div>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/ippidb/testcytotoxdescription_card.html b/ippisite/ippidb/templates/ippidb/testcytotoxdescription_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..0ca9b239b15fb775451a42b397c21d3ff8f7f775
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/testcytotoxdescription_card.html
@@ -0,0 +1,12 @@
+{% load customtags %}
+{%if object%}
+<div class="card">
+ <h5 class="card-header">
+ {{object.test_name}}
+ <span class="float-right">{{object|verbose_name}}</span>
+ </h5>
+ <div class="card-body">
+ TODO
+ </div>
+</div>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templates/ippidb/testpkdescription_card.html b/ippisite/ippidb/templates/ippidb/testpkdescription_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..0ca9b239b15fb775451a42b397c21d3ff8f7f775
--- /dev/null
+++ b/ippisite/ippidb/templates/ippidb/testpkdescription_card.html
@@ -0,0 +1,12 @@
+{% load customtags %}
+{%if object%}
+<div class="card">
+ <h5 class="card-header">
+ {{object.test_name}}
+ <span class="float-right">{{object|verbose_name}}</span>
+ </h5>
+ <div class="card-body">
+ TODO
+ </div>
+</div>
+{%endif%}
\ No newline at end of file
diff --git a/ippisite/ippidb/templatetags/customtags.py b/ippisite/ippidb/templatetags/customtags.py
index c221019794ed09aa31e34dd5bb8c5e49cda72954..7c04040d5424d392894f40c946f7d0a0b044dd16 100644
--- a/ippisite/ippidb/templatetags/customtags.py
+++ b/ippisite/ippidb/templatetags/customtags.py
@@ -3,6 +3,7 @@ import logging
from django import forms
from django import template
from django.contrib.messages.storage.base import Message
+from django.db.models import QuerySet
from django.forms.utils import ErrorList, ErrorDict
from django.utils.safestring import mark_safe
from django.utils.translation import ugettext
@@ -143,3 +144,12 @@ def bootstrap_core(object):
@register.filter('startswith')
def startswith(text, starts):
return text.startswith(starts)
+
+
+@register.filter
+def verbose_name(obj, field_name=None):
+ if isinstance(obj, QuerySet):
+ return obj.model._meta.verbose_name_plural
+ if field_name is None:
+ return obj._meta.verbose_name
+ return obj._meta.get_field(field_name).verbose_name.title()
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index c1517c01e25dbf9198465741d380f467659aa92c..72880c1e0e1d681e9dfd35e19f8c5deca3336eab 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -22,6 +22,9 @@ urlpatterns = [
url(r'^contribute$', views.adminSession, name='admin-session'),
url(r'^contribute/add/(?P<step>.+)/$', ippidb_wizard, name='ippidb_step'),
url(r'^contribute/add/$', ippidb_wizard, name='admin-session-add'),
+ url(r'^contribute/view/(?P<bibli_pk>\d+)-(?P<ppi_pk>\d+)/$', views.admin_session_view, name='admin-session-view'),
+ url(r'^contribute/view/(?P<bibli_pk>\d+)-/$', views.admin_session_view, {'ppi_pk': None}),
+ url(r'^contribute/view/-(?P<ppi_pk>\d+)/$', views.admin_session_view, {'bibli_pk': None}),
url(r'^contribute/update/$', views.update, name='admin-session-update'),
url(r'^utils/mol2smi$', views.convert_mol2smi, name='mol2smi'),
url(r'^utils/smi2mol$', views.convert_smi2mol, name='smi2mol'),
diff --git a/ippisite/ippidb/views/contribute.py b/ippisite/ippidb/views/contribute.py
index 7d91ae87f7e0ca9ba6e726a241cf227417873c64..0b2a786c6f8f31295d4d59b19ba4994de3682926 100644
--- a/ippisite/ippidb/views/contribute.py
+++ b/ippisite/ippidb/views/contribute.py
@@ -114,7 +114,11 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
protein_subset_ids.append(complex_json["protein"].pk)
form.set_protein_subset_ids(protein_subset_ids)
- if current_step in ["TestActivityDescriptionFormSet", "TestCytotoxDescriptionFormSet", "TestPKDescriptionFormSet"]:
+ if current_step in [
+ "TestActivityDescriptionFormSet",
+ "TestCytotoxDescriptionFormSet",
+ "TestPKDescriptionFormSet",
+ ]:
compound_form = super().get_form(
'CompoundForm',
data=self.storage.get_step_data('CompoundForm')
@@ -234,7 +238,7 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
# Step 7 Compounds
compounds = dict()
- created_compounds=0
+ created_compounds = 0
for f in form_dict["CompoundForm"]:
if not f.is_valid():
continue
@@ -283,7 +287,7 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
# We set the dicts to translates attributes into model
form_dict["TestCytotoxDescriptionFormSet"].set_compounds(compounds)
# We set the constants attributes among the instances to be created by the modelformset
- form_dict["TestCytotoxDescriptionFormSet"].instance=bibliography
+ form_dict["TestCytotoxDescriptionFormSet"].instance = bibliography
form_dict["TestCytotoxDescriptionFormSet"].is_valid()
cytotox_tests = form_dict["TestCytotoxDescriptionFormSet"].save()
print("Step 8.2: %i cytotox tests and %i results" % (
@@ -295,7 +299,7 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
# We set the dicts to translates attributes into model
form_dict["TestPKDescriptionFormSet"].set_compounds(compounds)
# We set the constants attributes among the instances to be created by the modelformset
- form_dict["TestPKDescriptionFormSet"].instance=bibliography
+ form_dict["TestPKDescriptionFormSet"].instance = bibliography
form_dict["TestPKDescriptionFormSet"].is_valid()
pk_tests = form_dict["TestPKDescriptionFormSet"].save()
print("Step 8.3: %i PK tests and %i results" % (
@@ -306,6 +310,22 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
# re-save the ppi to update its name
ppi.save()
super().done(form_list=form_list, **kwargs)
- return render(self.request, 'done.html', {
- 'form_data': [form.cleaned_data for form in form_list],
- })
+ return admin_session_view(self.request, bibliography.pk, ppi.pk)
+
+
+def admin_session_view(request, bibli_pk, ppi_pk):
+ context = {}
+ if bibli_pk:
+ bibliography = models.Bibliography.objects.get(pk=bibli_pk)
+ context["bibliography"] = bibliography
+ context["testactivitydescription"] = bibliography.testactivitydescription_set.all()
+ context["testcytotoxdescription"] = bibliography.testcytotoxdescription_set.all()
+ context["testpkdescription"] = bibliography.testpkdescription_set.all()
+ context["refcompoundbiblio"] = bibliography.refcompoundbiblio_set.all()
+
+ if ppi_pk:
+ ppi = models.Ppi.objects.get(pk=ppi_pk)
+ context["ppi"] = ppi
+ context["complexes"] = ppi.ppicomplex_set.all()
+
+ return render(request, 'contribute-view.html', context=context)