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

Former-commit-id: 8c2a8fc0227d332ac9a1ec8f3a64cd16320455b6

ippisite/ippidb/forms.py

@@ -4,9 +4,11 @@ from django.db import models
 from django.core.exceptions import ValidationError
 from django.core.validators import RegexValidator
 
-from .models import Bibliography, Protein, Domain, ProteinDomainComplex, Ppi, PpiComplex, Compound, RefCompoundBiblio, Symmetry, TestActivityDescription
+from .models import *
 from .ws import pdb_entry_exists
 
+
+""" Step 1 : IdForm """
 class IdForm(ModelForm):
     class Meta:
         model = Bibliography
@@ -16,6 +18,7 @@ class IdForm(ModelForm):
             'id_source': forms.TextInput(attrs={'placeholder': 'ID'}),
         }
 
+""" Step 2 : BibliographyForm """
 class BibliographyForm(ModelForm):
     class Meta:
         model = Bibliography
@@ -29,7 +32,7 @@ class BibliographyForm(ModelForm):
         }
 
 
-
+""" Step 3 : PDBForm """
 def validate_pdb_exists(value):
     if not(pdb_entry_exists(value)):
         raise ValidationError(
@@ -58,6 +61,8 @@ class ProteinForm(ModelForm):
 ProteinFormSet = modelformset_factory(
     Protein, exclude=('recommended_name_long', 'short_name'), extra=0)
 
+
+""" Step 4 : ProteinDomainComplexTypeForm aka. Architecture """
 TYPE_COMPLEX = (
     ('inhibited', 'Inhibited'),
     ('stabilized', 'Stabilized'),
@@ -80,9 +85,11 @@ TYPE_CHOICES = (
 
 
 class ProteinDomainComplexTypeForm(forms.Form):
-	complexChoice=forms.CharField(label="PPI Complex Type", widget=forms.Select(choices=TYPE_COMPLEX))
-	complexType=forms.CharField(widget=forms.RadioSelect(choices=TYPE_CHOICES))
+    complexChoice=forms.CharField(label="PPI Complex Type", widget=forms.Select(choices=TYPE_COMPLEX))
+    complexType=forms.CharField(widget=forms.RadioSelect(choices=TYPE_CHOICES))
     
+
+""" Step 5 : ProteinDomainComplexForm aka. Composition """
 class ProteinDomainComplexForm(ModelForm):
 
     class Meta:
@@ -108,21 +115,28 @@ class ComplexCompositionForm(forms.Form):
 
 ComplexCompositionFormSet = formset_factory(ComplexCompositionForm, extra=2)
 formset= ComplexCompositionFormSet()
-print(formset.is_valid())
+#print(formset.is_valid())
 
+""" Step 6 : PpiForm """
 class PpiForm(ModelForm):
 
     class Meta:
         model = Ppi
-        fields = ['pdb_id', 'symmetry']
+        fields = ['pdb_id','symmetry','pockets_nb']
 
 class PpiComplexForm(ModelForm):
 
     class Meta:
         model = PpiComplex
-        fields = ['cc_nb',]
+        fields = ['cc_nb']
 
+class PpiAndComplexForm(forms.Form):
+    pdb_id=forms.CharField(widget=forms.TextInput())
+    symmetry=forms.ModelChoiceField(queryset=Symmetry.objects.all(), required=True)
+    pockets_nb=forms.IntegerField(initial=1,required=True)
+    cc_nb=forms.IntegerField(initial=1,required=True)
 
+""" Step 7 : CompoundForm """
 class CompoundForm(ModelForm):
 
     class Meta:
@@ -147,19 +161,25 @@ class BaseCompoundFormSet(BaseFormSet):
     def add_fields(self, form, index):
         super(BaseCompoundFormSet, self).add_fields(form, index)
         form.fields["compound_name"] = forms.CharField(widget=forms.TextInput(attrs={'placeholder':'Name in the publication','required':'required'}))
-        form.fields["molecule"] = forms.CharField(widget=forms.Select(choices=TYPE_MOLECULE))
+        form.fields["molecule"] = forms.CharField(widget=forms.RadioSelect(choices=TYPE_MOLECULE))
         form.fields["molecule_comp"] = forms.CharField(widget=forms.TextInput(attrs={'placeholder':'Molecule composition', 'required':'required'}))
 
 CompoundFormSet = formset_factory(CompoundForm, formset=BaseCompoundFormSet, max_num=500, can_delete=True)
 formset = CompoundFormSet()
 
-
-class TestsForm(ModelForm):
-    
-    class Meta:
-        model=TestActivityDescription
-        fields=['test_name','test_type','test_modulation_type', 'cell_line']
-
-
-#CompoundFormSet = modelformset_factory(
-#    Compound, exclude=('mddr_compound',), extra=0)
+""" Step 8 : TestsForm """
+class TestsForm(forms.Form):
+    activityDesc_cell_line=forms.ModelChoiceField(queryset=CellLine.objects.all(), required=True)
+    activityDesc_ppi=forms.CharField(widget=forms.TextInput())
+    activityDesc_nb_active_compound=forms.IntegerField(initial=1,required=True)
+    activityDesc_test_modulation_type=forms.ModelChoiceField(queryset=TestActivityDescription.objects.all(), required=True)
+    activityDesc_test_name=forms.CharField(widget=forms.TextInput())
+    activityDesc_type=forms.ModelChoiceField(queryset=TestActivityDescription.objects.all(), required=True)
+    cytotoxDesc_cell_line=forms.ModelChoiceField(queryset=CellLine.objects.all(), required=True)
+    cytotoxDesc_compound_concentration=forms.CharField(widget=forms.TextInput())
+    cytotoxDesc_test_name=forms.CharField(widget=forms.TextInput())
+    pkDesc_organism=forms.ModelChoiceField(queryset=Taxonomy.objects.all(), required=True)
+    pkDesc_administration_mode=forms.CharField(widget=forms.TextInput())
+    pkDesc_dose=forms.IntegerField(initial=1,required=True)
+    pkDesc_dose_interval=forms.IntegerField(initial=1,required=True)
+    pkDesc_test_name=forms.CharField(widget=forms.TextInput())

ippisite/ippidb/static/css/admin-session.css

@@ -176,6 +176,11 @@ Description: IPPI-DB Theme
     margin-bottom: 5px;
 }
 
+.compound_input input{
+    width: 100%;
+    padding: 5px;
+}
+
 #compound_mol {
     overflow: hidden;
     display: flex;

ippisite/ippidb/templates/CompoundForm.html

@@ -52,12 +52,14 @@
 								</div>
 								{% endfor %}
 							</div>
-							<div id="molecule_comp_{{ form.molecule.id_for_label }}">
+							<div class="compound_input" id="molecule_comp_{{ form.molecule.id_for_label }}">
 								{{form.molecule_comp}}
 							</div>
 							<div id="ck-button-long" class="compound_input">
 								<label>{{ form.is_macrocycle}}<span>{{ form.is_macrocycle.label }}</span></label>
 							</div>
+							<div id="ck-button-long" class="submit_button"> Add compound
+							</div>
 						</div>
 				{% endfor %}
 				</div>
@@ -67,7 +69,7 @@
 			{% endif %}
 			<input type="hidden" name="ippi_wizard-current_step" value="CompoundForm" id="id_ippi_wizard-current_step"/>
 			</table>
-				<input type="submit" value="{% trans "Next step" %}"/>
+				<input class="submit_button" type="submit" value="{% trans "Next step" %}"/>
 		</form>
 	</div>
 </div>

ippisite/ippidb/templates/PpiForm.html

@@ -34,12 +34,14 @@
 		
 			{% if wizard.form.forms %}
 				{% for form in wizard.form.forms %}
+				Test
 				    {{ form }}
 				{% endfor %}
 			{% else %}
 			<div class="inline_box_complex">
 				<div class="inline_label"> PPI: </div>
 				<div class="input_field">{{ wizard.form.pdb_id }}</div>
+				<div class="input_field">{{ wizard.form.pockets_nb}}</div>
 				<div class="inline_field">{{ wizard.form.cc_nb }}</div>
 				<div class="inline_field">{{ wizard.form.symmetry }}</div>
 			</div>

ippisite/ippidb/views.py

@@ -4,7 +4,7 @@ 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, ComplexCompositionForm, ComplexCompositionFormSet, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, ProteinFormSet,TestsForm, CompoundForm, CompoundFormSet
+from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ComplexCompositionForm, ComplexCompositionFormSet, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, PpiAndComplexForm, ProteinFormSet,TestsForm, CompoundForm, CompoundFormSet
 from .models import Protein, Bibliography, ProteinDomainComplex, ProteinDomainBoundComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy, LeLleBiplotData
 from .ws import get_pdb_uniprot_mapping
 
@@ -60,7 +60,7 @@ FORMS = [("IdForm", ippidb.forms.IdForm),
          ("ProteinDomainComplexTypeForm",
           ippidb.forms.ProteinDomainComplexTypeForm),
          ("ProteinDomainComplexForm", ippidb.forms.ComplexCompositionFormSet),
-         ("PpiForm", ippidb.forms.PpiForm),
+         ("PpiForm", ippidb.forms.PpiAndComplexForm),
          ("CompoundForm", ippidb.forms.CompoundFormSet),
          ("TestsForm", ippidb.forms.TestsForm),]
 
@@ -90,7 +90,7 @@ class IppiWizard(NamedUrlSessionWizardView):
         if self.steps.current == 'PpiForm':
             context['complex_choice']=self.storage.get_step_data('ProteinDomainComplexTypeForm').get('ProteinDomainComplexTypeForm-complexChoice')
             context['complex_type']=self.storage.get_step_data('ProteinDomainComplexTypeForm').get('ProteinDomainComplexTypeForm-complexType')
-            context['pdb']=self.storage.get_step_data('PDBForm').get('PDBForm-pdb_id')
+            context['pdb_id']=self.storage.get_step_data('PDBForm').get('PDBForm-pdb_id')
         return context 
 
     def get_form_initial(self, step):