diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py index 40138e8542147049ca69b542cd65e345012962c7..547a4160d0803e208119b750c3a81145ea67b7a8 100644 --- a/ippisite/ippidb/forms.py +++ b/ippisite/ippidb/forms.py @@ -4,7 +4,7 @@ from django.db import models from django.core.exceptions import ValidationError from django.core.validators import RegexValidator -from .models import Bibliography, Protein, ProteinDomainComplex, Ppi, PpiComplex +from .models import Bibliography, Protein, ProteinDomainComplex, Ppi, PpiComplex, Compound, TestActivityDescription from .ws import pdb_entry_exists class IdForm(ModelForm): @@ -109,3 +109,19 @@ class PpiComplexForm(ModelForm): class Meta: model = PpiComplex fields = ['complex', 'cc_nb'] + + +class ActivityForm(ModelForm): + + class Meta: + model=TestActivityDescription + fields=['test_type','test_name','test_modulation_type'] + +class CompoundForm(ModelForm): + + class Meta: + model = Compound + fields = ['canonical_smile','common_name','is_macrocycle'] + +#CompoundFormSet = modelformset_factory( +# Compound, exclude=('mddr_compound',), extra=0) diff --git a/ippisite/ippidb/static/css/ippidb.css b/ippisite/ippidb/static/css/ippidb.css index 02add5d9edd146ac5d677460aee6c3d7d7ba25e6..98932a5cd25b5636723b58e135cd249eb6c6829f 100644 --- a/ippisite/ippidb/static/css/ippidb.css +++ b/ippisite/ippidb/static/css/ippidb.css @@ -733,11 +733,12 @@ display:block; } #Form{ - border: 1px solid; + border: 1px solid #E3E9EB; padding: 15px; min-height: 150px; text-align: center; min-height: 350px; + border-top: 1px solid #2D96FA; } .readonly { @@ -1520,7 +1521,7 @@ button, input, select, textarea { } #step li a, #step li a:hover, #step li a:focus { - width: 196.5px; + width: 146.5px; background-color: #E3E9EB; color:#8D8888; font-family: "PlayfairDisplayReg"; @@ -1532,10 +1533,16 @@ button, input, select, textarea { #step li a.active { text-decoration: none; - background-color: #000000; + background-color: #2D96FA; color:#FFFFFF; } +#step li a.validate { + text-decoration: none; + background-color: #000000; + color:#ffffff; +} + .step_desc { padding: 15px; margin-bottom: 15px; diff --git a/ippisite/ippidb/templates/ActivityForm.html b/ippisite/ippidb/templates/ActivityForm.html new file mode 100644 index 0000000000000000000000000000000000000000..fdbfd64eff2ca780652d3cd0bd346938dc3f906c --- /dev/null +++ b/ippisite/ippidb/templates/ActivityForm.html @@ -0,0 +1,43 @@ +{% extends "add.html" %} +{% load i18n %} + +{% block form %} +<div id="step"> + <ul> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> + <li><a class="validate" href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a class="validate" href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a class="active" href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> + </ul> +</div> +<div id="Form"> + <div class="step_desc"> + <p> Activity test </p> + </div> + <div class="form_div"> + <form action="" method="post"> + {% csrf_token %} + <table> + {{ wizard.management_form }} + {{ wizard.form.errors}} + {{ wizard.form.non_field_errors}} + {% block custom_form %}{% endblock %} + + {% if wizard.form.forms %} + {{ wizard.form.management_form }} + {% for form in wizard.form.forms %} + {{ form }} + {% endfor %} + {% else %} + {{ wizard.form }} + {% endif %} + </table> + <input type="submit" value="{% trans "submit" %}"/> + </form> + </div> +</div> +{% endblock %} \ No newline at end of file diff --git a/ippisite/ippidb/templates/BibliographyForm.html b/ippisite/ippidb/templates/BibliographyForm.html index 38e1c79b6f8fd8d4885a898dfdfb44564a43d5e0..5e03648279a1d694be23a6ca7185d8740dec3d26 100644 --- a/ippisite/ippidb/templates/BibliographyForm.html +++ b/ippisite/ippidb/templates/BibliographyForm.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> <li><a class="active" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> diff --git a/ippisite/ippidb/templates/CompoundForm.html b/ippisite/ippidb/templates/CompoundForm.html new file mode 100644 index 0000000000000000000000000000000000000000..2de366ec3bef4648dec796011d8abc414daaa5cd --- /dev/null +++ b/ippisite/ippidb/templates/CompoundForm.html @@ -0,0 +1,43 @@ +{% extends "add.html" %} +{% load i18n %} + +{% block form %} +<div id="step"> + <ul> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> + <li><a class="validate" href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a class="active" href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> + </ul> +</div> +<div id="Form"> + <div class="step_desc"> + <p> Activity test </p> + </div> + <div class="form_div"> + <form action="" method="post"> + {% csrf_token %} + <table> + {{ wizard.management_form }} + {{ wizard.form.errors}} + {{ wizard.form.non_field_errors}} + {% block custom_form %}{% endblock %} + + {% if wizard.form.forms %} + {{ wizard.form.management_form }} + {% for form in wizard.form.forms %} + {{ form }} + {% endfor %} + {% else %} + {{ wizard.form }} + {% endif %} + </table> + <input type="submit" value="{% trans "Next step" %}"/> + </form> + </div> +</div> +{% endblock %} \ No newline at end of file diff --git a/ippisite/ippidb/templates/IdForm.html b/ippisite/ippidb/templates/IdForm.html index ac7cc9312ec3e4ea046809874df92abe91817b36..32012a69e59436d45e286e197e94494eadcf3a7a 100644 --- a/ippisite/ippidb/templates/IdForm.html +++ b/ippisite/ippidb/templates/IdForm.html @@ -10,6 +10,8 @@ <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> diff --git a/ippisite/ippidb/templates/PDBForm.html b/ippisite/ippidb/templates/PDBForm.html index f34af0c648fde40e75f89da8968dc29d2b48188f..ca3fb8a5fbe883bedca99f4231c575652ceb4df2 100644 --- a/ippisite/ippidb/templates/PDBForm.html +++ b/ippisite/ippidb/templates/PDBForm.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> <li><a class="active" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> diff --git a/ippisite/ippidb/templates/PpiForm.html b/ippisite/ippidb/templates/PpiForm.html index 62fab54626eee2c3b1f743dfb137a21ad9191ccb..5c30ad21feb36dcd4fc82f94f0df9a080c0fa1a4 100644 --- a/ippisite/ippidb/templates/PpiForm.html +++ b/ippisite/ippidb/templates/PpiForm.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> - <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a class="active" href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> @@ -40,7 +42,7 @@ </div> {% endif %} </table> - <input type="submit" value="{% trans "submit" %}"/> + <input type="submit" value="{% trans "Next step" %}"/> </form> <div> </div> diff --git a/ippisite/ippidb/templates/ProteinDomainComplexForm.html b/ippisite/ippidb/templates/ProteinDomainComplexForm.html index 86cd603220c1b26a85f4631084bc4f2650441ed2..18853d925f9f9738ee7955b0d866bd0b3ef9e480 100644 --- a/ippisite/ippidb/templates/ProteinDomainComplexForm.html +++ b/ippisite/ippidb/templates/ProteinDomainComplexForm.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> - <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> <li><a class="active" href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> diff --git a/ippisite/ippidb/templates/ProteinDomainComplexTypeForm.html b/ippisite/ippidb/templates/ProteinDomainComplexTypeForm.html index 13b758dc3d493f7b9cdf2841427fc0ad01a01977..6fcd1e03af457d3c04d6afae020976301ad41860 100644 --- a/ippisite/ippidb/templates/ProteinDomainComplexTypeForm.html +++ b/ippisite/ippidb/templates/ProteinDomainComplexTypeForm.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> - <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> <li><a class="active" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> diff --git a/ippisite/ippidb/templates/ProteinForm.html b/ippisite/ippidb/templates/ProteinForm.html deleted file mode 100644 index 09ee2a8399bdd3ffbffb260bcee4fe0867b9dda6..0000000000000000000000000000000000000000 --- a/ippisite/ippidb/templates/ProteinForm.html +++ /dev/null @@ -1,49 +0,0 @@ -{% extends "add.html" %} -{% load i18n %} - -{% block form %} -<div id="step"> - <ul> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> - <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> - <li><a class="active" href='/admin-session/add/ProteinForm/'>{% trans "Proteins" %}</a></li> - <li><a href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> - </ul> -</div> -<div id="Form"> - <div class="step_desc"> - <p> Based on the PDB code(s) you have provided, we have identified a list of proteins and PFAM domains that may participate to the PPI. Please select ALL the proteins and PFAM domains that do participate to the formation of the full PPI complex. </p> - </div> - <form class="proteins_form" action="" method="post"> - {% csrf_token %} - {{ wizard.management_form }} - {{ wizard.form.non_field_errors}} - {% block custom_form %}{% endblock %} - - {% if wizard.form.forms %} - {{ wizard.form.management_form }} - {{ formset.management_form }} - {% for form in wizard.form.forms %} - <div class="inline_prot"> - <!--{{form.id}}--> - <div class="inline_label">Protein</div> - <div class="inline_field"> {{ form.uniprot_id }}</div> - <div class="inline_field">{{ form.gene_name }}</div> - <div class="inline_field">{{ form.entry_name }}</div> - <div class="inline_field">{{ form.organism }}</div> - </div> - {% endfor %} - {% else %} - <div class="readonlyfields"> - {{ wizard.form.uniprot_id }}<br/> - {{ wizard.form.gene_name }}<br/> - {{ wizard.form.entry_name}}<br/> - {{ wizard.form.organism }}<br/> - {{ wizard.form.molecular_functions }}<br/> - </div> - {% endif %} - <input type="submit" value="{% trans "Next step" %}"/> - </form> -</div> -{% endblock %} diff --git a/ippisite/ippidb/templates/admin-session.html b/ippisite/ippidb/templates/admin-session.html index 0521f88a6632ea55f9d8dd69631da9de7b8c1c5a..5a96ed40529e78e867fdb80db1219a5cc8cc91a3 100644 --- a/ippisite/ippidb/templates/admin-session.html +++ b/ippisite/ippidb/templates/admin-session.html @@ -9,7 +9,7 @@ <div class="inner-wrap"> <ul> <li> - <a href="/admin-session/view">View Content</a> + <a href="/compound/">View Content</a> </li> <li> <a href="/admin-session/add/IdForm">Add New Content</a> diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html index 92cec141dc5deee1bc98f556dad7eae55839c60a..df4b25038688bd84b582e681a043fd9da40af30a 100644 --- a/ippisite/ippidb/templates/compound_list.html +++ b/ippisite/ippidb/templates/compound_list.html @@ -1,10 +1,34 @@ -{% extends "base.html" %} +{% extends "admin-session.html" %} {% block title %}compound{% endblock %} {% block content %} - +<div id="mainnav"> + <nav class="secondary-nav"> + <div class="inner-wrap"> + <ul> + <li> + <a href="/admin-session/view">View Content</a> + </li> + <li> + <a href="/admin-session/add">Add New Content</a> + </li> + <li> + <a hfref="/admin-session/update">Update Content</a> + </li> + </ul> + </div> + </nav> +</div> +<div class="inner-wrap"> + <nav class="breadcrumb" role="navigation"> + <div id="breadcrumb-label" class="breadcrumb-label">You are here</div> + <div aria-labelledby="breadcrumb-label"> + {% block breadcrumb %} {{block.super}}> <a href="/compound/">View content</a>{% endblock %} + </div> + </nav> +</div> {% include "kekule_display.html" %} <div class="container-fluid"> <div class="row flex-xl-nowrap"> diff --git a/ippisite/ippidb/templates/done.html b/ippisite/ippidb/templates/done.html index 8bdd5fe769724813001ce94e7aa90692c0f0d65b..6cda4306df16b11567729c1fba0c65682a9668fd 100644 --- a/ippisite/ippidb/templates/done.html +++ b/ippisite/ippidb/templates/done.html @@ -4,12 +4,14 @@ {% block form %} <div id="step"> <ul> - <li><a href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> - <li><a href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> - <li><a href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> - <li><a href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> - <li><a class="active" href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a class="validate" href='/admin-session/add/IdForm/'>{% trans "ID" %}</a></li> + <li><a class="validate" href='/admin-session/add/BibliographyForm/'>{% trans "Bibliography" %}</a></li> + <li><a class="validate" href='/admin-session/add/PDBForm/'>{% trans "PDB id" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexTypeForm/'>{% trans "Architecture" %}</a></li> + <li><a class="validate" href='/admin-session/add/ProteinDomainComplexForm/'>{% trans "Composition" %}</a></li> + <li><a class="validate" href='/admin-session/add/PPIForm/'>{% trans "PPI" %}</a></li> + <li><a class="validate" href='/admin-session/add/CompoundForm/'>{% trans "Compounds" %}</a></li> + <li><a class="validate" href='/admin-session/add/ActivityForm/'>{% trans "Activity" %}</a></li> </ul> </div> <div id="Form"> diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py index bc416a80a5d21f24cb3eff70ff9aabcd89443598..785b3ac9b6725bb7669ff739ec3a47adf469fbb3 100644 --- a/ippisite/ippidb/views.py +++ b/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, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet +from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, ProteinFormSet,ActivityForm, CompoundForm from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi from .ws import get_pdb_uniprot_mapping @@ -57,14 +57,18 @@ FORMS = [("IdForm", ippidb.forms.IdForm), ("ProteinDomainComplexTypeForm", ippidb.forms.ProteinDomainComplexTypeForm), ("ProteinDomainComplexForm", ippidb.forms.ProteinDomainComplexForm), - ("PpiForm", ippidb.forms.PpiForm),] + ("PpiForm", ippidb.forms.PpiForm), + ("CompoundForm", ippidb.forms.CompoundForm), + ("ActivityForm", ippidb.forms.ActivityForm),] TEMPLATES = {"IdForm": "IdForm.html", "BibliographyForm": "BibliographyForm.html", "PDBForm": "PDBForm.html", "ProteinDomainComplexTypeForm": "ProteinDomainComplexTypeForm.html", "ProteinDomainComplexForm": "ProteinDomainComplexForm.html", - "PpiForm": "PpiForm.html", + "PpiForm": "PpiForm.html", + "CompoundForm":"CompoundForm.html", + "ActivityForm":"ActivityForm.html", }