From 5825febbdd9ee4a7f1fae0a50b6478ca23a50042 Mon Sep 17 00:00:00 2001
From: Rachel TORCHET <racheltorchet@users.noreply.github.com>
Date: Tue, 31 Jul 2018 10:39:07 +0200
Subject: [PATCH] Update navigation and ProteinDomainComplexForm to take
parameters from previous step into account
Former-commit-id: eb05cc7225b71022a8eea0b92aa48423faf62951
---
ippisite/ippidb/forms.py | 12 ++--
ippisite/ippidb/static/css/main.css | 5 +-
.../templates/ProteinDomainComplexForm.html | 1 +
ippisite/ippidb/templates/base.html | 3 +
ippisite/ippidb/templates/contribute.html | 64 +++++++++++++++++++
ippisite/ippidb/urls.py | 1 +
ippisite/ippidb/views.py | 33 +++++-----
ippisite/ippidb/ws.py | 2 +
8 files changed, 95 insertions(+), 26 deletions(-)
create mode 100644 ippisite/ippidb/templates/contribute.html
diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index c89307d7..830c95f0 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -109,16 +109,12 @@ class ComplexCompositionForm(forms.Form):
def __init__(self,pks=None,*args,**kwargs):
super(ComplexCompositionForm, self).__init__(*args, **kwargs)
- """ TODO : Filter based on submited PDBid"""
- #pks = kwargs.pop("prot")
- print("<<<<<<<<<<")
- print(args,kwargs)
- print(">>>>>>>>>>")
- self.fields['complex_protein'].queryset=Protein.objects.filter(pk__in=[569,570])
- self.fields['complex_domain'].queryset=Domain.objects.filter(pk__in=[73,73])
+ if pks is not None:
+ self.fields['complex_protein'].queryset = Protein.objects.filter(pk__in=pks)
+ self.fields['complex_domain'].queryset = Domain.objects.all()
-ComplexCompositionFormSet = formset_factory(ComplexCompositionForm, extra=3)
+ComplexCompositionFormSet = formset_factory(ComplexCompositionForm, extra=2)
formset= ComplexCompositionFormSet()
#print(formset.is_valid())
diff --git a/ippisite/ippidb/static/css/main.css b/ippisite/ippidb/static/css/main.css
index e4d17a2f..88b9d7a4 100644
--- a/ippisite/ippidb/static/css/main.css
+++ b/ippisite/ippidb/static/css/main.css
@@ -144,10 +144,9 @@ div.hidden {
}
.main-nav{
- margin-left: auto;
- margin-right: auto;
+ margin:0 auto;
position: relative;
- width: 600px;
+ width: max-content;
text-align: center;
height: 35px;
}
diff --git a/ippisite/ippidb/templates/ProteinDomainComplexForm.html b/ippisite/ippidb/templates/ProteinDomainComplexForm.html
index c1348605..6294d05a 100644
--- a/ippisite/ippidb/templates/ProteinDomainComplexForm.html
+++ b/ippisite/ippidb/templates/ProteinDomainComplexForm.html
@@ -52,6 +52,7 @@
</div>
</div>
{% endfor %}
+
{% endif %}
</table>
<input type="hidden" name="ippi_wizard-current_step" value="ProteinDomainComplexForm" id="id_ippi_wizard-current_step"/>
diff --git a/ippisite/ippidb/templates/base.html b/ippisite/ippidb/templates/base.html
index 30f6b5da..d44eae8b 100644
--- a/ippisite/ippidb/templates/base.html
+++ b/ippisite/ippidb/templates/base.html
@@ -199,6 +199,9 @@
<a href="/tutorials">Tutorials</a>
</li>
<li>
+ <a href="/contribute">Contribute</a>
+ </li>
+ <li>
<a href="/admin-session">Admin</a>
</li>
</ul>
diff --git a/ippisite/ippidb/templates/contribute.html b/ippisite/ippidb/templates/contribute.html
new file mode 100644
index 00000000..9d9b1248
--- /dev/null
+++ b/ippisite/ippidb/templates/contribute.html
@@ -0,0 +1,64 @@
+{% extends "index.html" %}
+
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+{% block extra_css %}
+ <link rel="stylesheet" href="/static/css/admin-session.css">
+{% endblock %}
+
+{% block content %}
+<div id="mainnav">
+ <nav class="secondary-nav">
+ <div class="inner-wrap">
+ <ul>
+ <li>
+ <a href="/queries">View Content</a>
+ </li>
+ <li>
+ <a href="/admin-session/add/IdForm">Add New Content</a>
+ </li>
+ <li>
+ <a href="/admin-session/update">Update Content</a>
+ </li>
+ </ul>
+ </div>
+ </nav>
+</div>
+<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}}Admin{% endblock %}
+ </div>
+ </nav>
+ <div id="main-wrapper" class="page">
+ <div id="main">
+ <div id="content" class="main-content">
+ <div class="section">
+ <main role="main">
+ <h1 class="page-title"> CONTRIBUTE </h1>
+ <div class="tabs"></div>
+ <div class="main__inner">
+ <div class="region region-content">
+ <div class="page-intro">
+ </div>
+ <div class="color-wrap">
+ <div class="region region-content">
+ <div class="block block-system block-system-main">
+ <div class="content">
+ <div class="view-content">
+
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </main><!-- .site-main -->
+ </div>
+ </div>
+ </div><!-- div main -->
+ </div>
+</div>
+{% endblock %}
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index 82df36de..a5554854 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -14,6 +14,7 @@ urlpatterns = [
url(r'^compounds/$', views.compound_list, name='compound_list'),
url(r'^compounds/(?P<compound_id>\w+)$', views.compound_card, name='compound_card'),
url(r'^tutorials$', views.tutorials, name='tutorials'),
+ url(r'^contribute$', views.contribute, name='contribute'),
url(r'^admin-session$', views.adminSession, name='admin-session'),
url(r'^admin-session/add/(?P<step>.+)/$',
ippidb_wizard, name='ippidb_step'),
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index e4f6363b..f59bdf31 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -10,7 +10,7 @@ from django.contrib.auth.mixins import LoginRequiredMixin
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
import ippidb
-from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ComplexCompositionForm, ComplexCompositionFormSet, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, PpiAndComplexForm, ProteinFormSet,TestsForm, CompoundForm, CompoundFormSet
+from .forms import *
from .models import Protein, Bibliography, ProteinDomainComplex, ProteinDomainBoundComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy, LeLleBiplotData, PcaBiplotData, PpiFamily
from .ws import get_pdb_uniprot_mapping
@@ -30,6 +30,8 @@ def general(request):
def tutorials(request):
return render(request, 'tutorials.html')
+def contribute(request):
+ return render(request, 'contribute.html')
def adminSession(request):
return render(request, 'admin-session.html')
@@ -37,6 +39,8 @@ def adminSession(request):
def update (request):
return render(request, 'update.html')
+#---------------------------------------------- CONTRIBUTE SESSION - WIZARD -------------------------------------------#
+
FORMS = [("IdForm", ippidb.forms.IdForm),
("BibliographyForm", ippidb.forms.BibliographyForm),
("PDBForm", ippidb.forms.PDBForm),
@@ -76,19 +80,22 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
context['pdb_id']=self.storage.get_step_data('PDBForm').get('PDBForm-pdb_id')
return context
- def get_form_initial(self, step):
- # Works for form.forms
- initial = {}
- # Pre-fill fields with data from a previous form
+ def get_form_kwargs(self, step):
+ # change args pass to a form
+ kwargs = super().get_form_kwargs()
if step == 'ProteinDomainComplexForm':
pks = self.storage.get_step_data('PDBForm').get('pks')
- #initial['pks']=pks
- #return {'pks':pks}
- #form = ComplexCompositionForm(prot=pks)
+ # print("test pks: ",pks)
+ kwargs['form_kwargs']={'pks':pks}
+ return kwargs
+
+ def get_form_initial(self, step):
+ # Works for form.forms
+ # change value pass to a form
+ initial = super().get_form_initial(step)
if step == 'PpiForm':
initial['pdb_id'] = self.storage.get_step_data('PDBForm').get('PDBForm-pdb_id')
- print(self.initial_dict)
- return self.initial_dict.get(step, initial)
+ return initial
def process_step(self, form):
"""
@@ -124,11 +131,6 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
if self.steps.current == 'BibliographyForm':
pk = self.storage.get_step_data('IdForm').get('pk')
return Bibliography.objects.get(pk=pk)
- if self.steps.current == 'ProteinDomainComplexForm':
- print("blablabla", self.storage.get_step_data('PDBForm').get('pks'))
- pks = self.storage.get_step_data('PDBForm').get('pks')
- print("blablabla", self.storage.get_step_data('PDBForm').get('pks'))
- return Protein.objects.filter(id__in=pks)
if self.steps.current == 'ProteinDomainComplexTypeForm':
print("blablabla", self.storage.get_step_data('PDBForm').get('pks'))
pks = self.storage.get_step_data('PDBForm').get('pks')
@@ -143,6 +145,7 @@ class IppiWizard(LoginRequiredMixin, NamedUrlSessionWizardView):
'form_data': [form.cleaned_data for form in form_list],
})
+#----------------------------------------------------------------------------------------------------------------------#
def process_cutoff_value(name, context, request, cutoff_dir='l'):
c = context['compounds']
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 03fc0ff1..2676c12c 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -122,6 +122,7 @@ def get_pfam_info(pfam_acc):
def get_pdb_uniprot_mapping(pdb_id):
+ pdb_id = pdb_id.lower()
resp = requests.get(
'https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}'.format(pdb_id.lower()))
uniprot_ids = list(resp.json()[pdb_id]['UniProt'].keys())
@@ -133,6 +134,7 @@ def pdb_entry_exists(pdb_id):
resp = requests.get(
'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{}'.format(pdb_id.lower()))
# EBI sends back either a 404 or an empty json if the PDB does not exist
+ print("PDB id:", pdb_id)
if not(resp.ok):
return False
else:
--
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