diff --git a/epdb/urls.py b/epdb/urls.py index b4bdb9f2..151cfb51 100644 --- a/epdb/urls.py +++ b/epdb/urls.py @@ -48,6 +48,7 @@ urlpatterns = [ re_path(r"^user$", v.users, name="users"), re_path(r"^group$", v.groups, name="groups"), re_path(r"^search$", v.search, name="search"), + re_path(r"^predict$", v.predict_pathway, name="predict_pathway"), # User Detail re_path(rf"^user/(?P{UUID})", v.user, name="user"), # Group Detail diff --git a/epdb/views.py b/epdb/views.py index 5d6e0bda..e2dca3fb 100644 --- a/epdb/views.py +++ b/epdb/views.py @@ -362,6 +362,18 @@ def index(request): return render(request, "index/index.html", context) +def predict_pathway(request): + """Top-level predict pathway view using user's default package.""" + if request.method != "GET": + return HttpResponseNotAllowed(["GET"]) + + context = get_base_context(request) + context["title"] = "enviPath - Predict Pathway" + context["meta"]["current_package"] = context["meta"]["user"].default_package + + return render(request, "predict_pathway.html", context) + + def packages(request): current_user = _anonymous_or_real(request) @@ -1288,7 +1300,7 @@ def package_compound_structures(request, package_uuid, compound_uuid): elif request.method == "POST": structure_name = request.POST.get("structure-name") - structure_smiles = request.POST.get("structure-smiles").strip() + structure_smiles = request.POST.get("structure-smiles") structure_description = request.POST.get("structure-description") try: @@ -1470,11 +1482,11 @@ def package_rules(request, package_uuid): # Obtain parameters as required by rule type if rule_type == "SimpleAmbitRule": - params["smirks"] = request.POST.get("rule-smirks").strip() + params["smirks"] = request.POST.get("rule-smirks") params["reactant_filter_smarts"] = request.POST.get("rule-reactant-smarts") params["product_filter_smarts"] = request.POST.get("rule-product-smarts") elif rule_type == "SimpleRDKitRule": - params["reaction_smarts"] = request.POST.get("rule-reaction-smarts").strip() + params["reaction_smarts"] = request.POST.get("rule-reaction-smarts") elif rule_type == "ParallelRule": pass elif rule_type == "SequentialRule": @@ -1671,7 +1683,7 @@ def package_reactions(request, package_uuid): elif request.method == "POST": reaction_name = request.POST.get("reaction-name") reaction_description = request.POST.get("reaction-description") - reactions_smirks = request.POST.get("reaction-smirks").strip() + reactions_smirks = request.POST.get("reaction-smirks") educts = reactions_smirks.split(">>")[0].split(".") products = reactions_smirks.split(">>")[1].split(".") diff --git a/templates/actions/collections/pathway.html b/templates/actions/collections/pathway.html index bcfc043c..fce48c86 100644 --- a/templates/actions/collections/pathway.html +++ b/templates/actions/collections/pathway.html @@ -1,6 +1,6 @@ {% if meta.can_edit %}
  • - + New Pathway
    • -{% endif %} \ No newline at end of file +{% endif %} diff --git a/templates/framework.html b/templates/framework.html index 516d8194..ecedc8fc 100644 --- a/templates/framework.html +++ b/templates/framework.html @@ -1,11 +1,15 @@ - + -{% load static %} - + {% load static %} + {{ title }} - + {# Favicon #} - + {# Tailwind CSS disabled for legacy Bootstrap framework #} {# Pages using this framework will be migrated to framework_modern.html incrementally #} @@ -13,36 +17,45 @@ {# Legacy Bootstrap 3.3.7 - scoped to .legacy-bootstrap #} - + - - + + {# Bootstrap compatibility styles #} @@ -50,40 +63,44 @@ - {# General EP JS #} {# Modal Steps for Stepwise Modal Wizards #} {% if not debug %} - - - + + + {% endif %} - - - - -
    - -
    - + -
    - {% if breadcrumbs %} +
    + {% if breadcrumbs %}
    -
      - {% for elem in breadcrumbs %} - {% for name, url in elem.items %} - {% if forloop.parentloop.last %} -
    1. {{ name }}
      2. - {% else %} -
    2. - {{ name }} -
      3. - {% endif %} - {% endfor %} - {% endfor %} -
    +
      + {% for elem in breadcrumbs %} + {% for name, url in elem.items %} + {% if forloop.parentloop.last %} +
    1. {{ name }}
      2. + {% else %} +
    2. + {{ name }} +
      3. + {% endif %} + {% endfor %} + {% endfor %} +
    - {% endif %} - {% if message %} -
    - {{ message }} -
    - {% endif %} - {% block content %} - {% endblock content %} - {% if meta.url_contains_package and meta.current_package.license %} + {% endif %} + {% if message %} +
    {{ message }}
    + {% endif %} + {% block content %} + {% endblock content %} + {% if meta.url_contains_package and meta.current_package.license %}

    -
    -
    - License -
    +
    +
    + License
    -
    -
    - - - -
    +
    +
    +
    + + +
    +
    - {% endif %} -
    - - -
    -
    -
    -
    -
    - -
    + {% endif %}
    -
    -
    -
    - +
    +
    -
    -
    - + - -{% block modals %} - {% include "modals/cite_modal.html" %} - {% include "modals/predict_modal.html" %} - {% include "modals/batch_predict_modal.html" %} -{% endblock %} - + }); + + {% block modals %} + {% include "modals/cite_modal.html" %} + {% include "modals/predict_modal.html" %} + {% include "modals/batch_predict_modal.html" %} + {% endblock %} + diff --git a/templates/framework_modern.html b/templates/framework_modern.html index bd7ffce2..b808550c 100644 --- a/templates/framework_modern.html +++ b/templates/framework_modern.html @@ -72,7 +72,7 @@ {% endif %} - + {% include "includes/navbar.html" %} {# Main Content Area #} @@ -81,7 +81,7 @@ {# Breadcrumbs - outside main content, optional #} {% if breadcrumbs %}
    -
    +
      {% for elem in breadcrumbs %} {% for name, url in elem.items %} @@ -100,7 +100,7 @@ {# Main content container - paper effect on medium+ screens #}
      {# Messages - inside paper #} {% if message %} @@ -141,7 +141,7 @@
      {% if not public_mode %} - + {% endif %} {% if meta.user.username == 'anonymous' or public_mode %} Login diff --git a/templates/index/index.html b/templates/index/index.html index 1ca5394d..b3193da6 100644 --- a/templates/index/index.html +++ b/templates/index/index.html @@ -1,190 +1,269 @@ {% extends "framework_modern.html" %} {% load static %} {% block main_content %} - - -
      - -
      -
      - -
      -

      Predict Your Pathway

      -
      -
      -
      - -
      - - -
      -
      -
      - -
      -
      - - -
      -
      - -
      -
      - {% csrf_token %} -
      -
      - - -
      -
      -
      - Caffeine - Ibuprofen -
      - Advanced -
      -
      - - - - -
      -
      -
      -
      + +
      +
      +
      + +
      +

      + Predict Your Pathway +

      +
      +
      +
      + +
      +
      +
      + +
      +
      + + +
      +
      + +
      +
      + {% csrf_token %} +
      +
      + + +
      +
      +
      + Caffeine + Ibuprofen +
      + Advanced +
      +
      + + + + +
      +
      +
      +
      +
      -
      -

      Community Updates

      +
      +

      Community Updates

      -
      - -
      - -
      -
      - -
      - - Read More Announcements - -
      - - - +
      + +
      + +
      + +
      + + Read More Announcements + +
      + + + +
      -
      -
      -
      - rule-based iterative tree greneration -
      -
      -

      About enviPath

      -

      - enviPath is a database and prediction system for the microbial - biotransformation of organic environmental contaminants. The - database provides the possibility to store and view experimentally - observed biotransformation pathways. -

      -

      - The pathway prediction system provides different relative reasoning models - to predict likely biotransformation pathways and products. Explore our tools - and contribute to advancing environmental biotransformation research. -

      -
      - Read More - Publications -
      -
      +
      +
      +
      + rule-based iterative tree greneration +
      +
      +

      About enviPath

      +

      + enviPath is a database and prediction system for the microbial + biotransformation of organic environmental contaminants. The + database provides the possibility to store and view experimentally + observed biotransformation pathways. +

      +

      + The pathway prediction system provides different relative + reasoning models to predict likely biotransformation pathways and + products. Explore our tools and contribute to advancing + environmental biotransformation research. +

      +
      + Read More + Publications
      - +
      +
      -
      -

      Backed by Science

      -
      - The University of Auckland - Eawag - University of Zurich -
      +
      +
      +

      Backed by Science

      +
      + The University of Auckland + Eawag + University of Zurich +
      +
      +
      + + // Discourse topics are now loaded automatically by discourse-api.js + }); + {% endblock main_content %} diff --git a/templates/predict_pathway.html b/templates/predict_pathway.html new file mode 100644 index 00000000..cdf8cdb1 --- /dev/null +++ b/templates/predict_pathway.html @@ -0,0 +1,188 @@ +{% extends "framework_modern.html" %} +{% load static %} +{% block content %} +
      +

      Predict a Pathway

      + +
      + {% csrf_token %} +
      +
      + + + +
      +
      + + + + +
      +
      + + + +
      OR
      + +
      + + +
      + + + +
      + Cancel + +
      +
      +
      + + +{% endblock content %} diff --git a/templates/static/login.html b/templates/static/login.html index e7525e96..2671f87e 100644 --- a/templates/static/login.html +++ b/templates/static/login.html @@ -105,7 +105,7 @@
      -
      + {% csrf_token %}