forked from enviPath/enviPy
Compare commits
8 Commits
enhancemen
...
fix/missin
| Author | SHA1 | Date | |
|---|---|---|---|
| db286d14ec | |||
| d20a705011 | |||
| debbef8158 | |||
| 2799718951 | |||
| 999dc15189 | |||
| 305fdc41fb | |||
| 9deca8867e | |||
| df6056fb86 |
@ -1,15 +1,15 @@
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import csv
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import csv
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import io
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import io
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import logging
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import logging
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from datetime import datetime
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from typing import Any, Callable, List, Optional
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from typing import Any, Callable, List, Optional
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from uuid import uuid4
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from uuid import uuid4
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from celery import shared_task
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from celery import shared_task
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from celery.utils.functional import LRUCache
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from celery.utils.functional import LRUCache
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from django.utils import timezone
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from epdb.logic import SPathway
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from epdb.logic import SPathway
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from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
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from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
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logger = logging.getLogger(__name__)
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logger = logging.getLogger(__name__)
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ML_CACHE = LRUCache(3) # Cache the three most recent ML models to reduce load times.
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ML_CACHE = LRUCache(3) # Cache the three most recent ML models to reduce load times.
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@ -29,7 +29,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
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log.task_id = uuid4()
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log.task_id = uuid4()
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log.job_name = job.__name__
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log.job_name = job.__name__
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log.status = "SUCCESS"
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log.status = "SUCCESS"
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log.done_at = datetime.now()
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log.done_at = timezone.now()
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log.task_result = str(x) if x else None
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log.task_result = str(x) if x else None
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log.save()
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log.save()
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@ -142,6 +142,11 @@ urlpatterns = [
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v.package_pathway,
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v.package_pathway,
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name="package pathway detail",
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name="package pathway detail",
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),
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),
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re_path(
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rf"^package/(?P<package_uuid>{UUID})/predict$",
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v.package_predict_pathway,
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name="package predict pathway",
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),
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# Pathway Nodes
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# Pathway Nodes
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re_path(
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re_path(
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rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
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rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
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@ -374,6 +374,22 @@ def predict_pathway(request):
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return render(request, "predict_pathway.html", context)
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return render(request, "predict_pathway.html", context)
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@package_permission_required()
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def package_predict_pathway(request, package_uuid):
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"""Package-specific predict pathway view."""
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if request.method != "GET":
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return HttpResponseNotAllowed(["GET"])
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current_user = _anonymous_or_real(request)
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current_package = PackageManager.get_package_by_id(current_user, package_uuid)
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context = get_base_context(request)
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context["title"] = f"enviPath - {current_package.name} - Predict Pathway"
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context["meta"]["current_package"] = current_package
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return render(request, "predict_pathway.html", context)
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def packages(request):
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def packages(request):
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current_user = _anonymous_or_real(request)
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current_user = _anonymous_or_real(request)
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@ -955,6 +971,12 @@ def package_model(request, package_uuid, model_uuid):
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]
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]
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dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
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dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
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return redirect(current_model.url)
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elif hidden == "retrain":
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from .tasks import dispatch, retrain
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dispatch(current_user, retrain, current_model.pk)
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return redirect(current_model.url)
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return redirect(current_model.url)
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else:
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else:
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return HttpResponseBadRequest()
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return HttpResponseBadRequest()
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@ -1,6 +1,9 @@
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{% if meta.can_edit %}
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{% if meta.can_edit %}
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<li>
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<li>
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<a href="{{ meta.server_url }}/predict">
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<a
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<span class="glyphicon glyphicon-plus"></span> New Pathway</a>
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href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
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</li>
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>
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<span class="glyphicon glyphicon-plus"></span> New Pathway</a
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>
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</li>
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{% endif %}
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{% endif %}
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@ -178,6 +178,23 @@
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}
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}
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});
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});
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// Open search modal function
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function openSearchModal() {
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const searchModal = document.getElementById("search_modal");
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if (searchModal) {
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searchModal.showModal();
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}
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}
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// Click handler for search badge
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const searchTrigger = document.getElementById("search-trigger");
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if (searchTrigger) {
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searchTrigger.addEventListener("click", function (event) {
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event.preventDefault();
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openSearchModal();
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});
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}
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// Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
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// Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
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document.addEventListener("keydown", function (event) {
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document.addEventListener("keydown", function (event) {
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// Check if user is typing in an input field
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// Check if user is typing in an input field
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@ -198,7 +215,7 @@
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|
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if (isCorrectModifier && event.key === "k") {
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if (isCorrectModifier && event.key === "k") {
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event.preventDefault();
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event.preventDefault();
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search_modal.showModal();
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openSearchModal();
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}
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}
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});
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});
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</script>
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</script>
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@ -1,19 +1,22 @@
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{% load static %}
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{% load static %}
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<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
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<div class="bg-base-300 text-base-content mx-auto mt-10 lg:max-w-5xl">
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<footer class="footer sm:footer-horizontal p-10">
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<footer class="footer sm:footer-horizontal p-10">
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{% if not public_mode %}
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{% if not public_mode %}
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<nav>
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<nav>
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<h6 class="footer-title">Services</h6>
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<h6 class="footer-title">Services</h6>
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<a class="link link-hover" href="/predict">Predict</a>
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<a class="link link-hover" href="/">Predict</a>
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<a class="link link-hover" href="/package">Packages</a>
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<a class="link link-hover" href="/search">Search</a>
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{% if user.is_authenticated %}
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<a class="link link-hover" href="/package">Browse</a>
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<a class="link link-hover" href="/model">Your Collections</a>
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{% if user.is_authenticated %}
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<a class="link link-hover" href="/model">Your Collections</a>
|
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{% endif %}
|
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<a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
|
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</nav>
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{% endif %}
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{% endif %}
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<a
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|
href="https://wiki.envipath.org/"
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|
target="_blank"
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|
class="link link-hover"
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|
>Documentation</a
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|
>
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|
</nav>
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{% endif %}
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<nav>
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<nav>
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<h6 class="footer-title">Company</h6>
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<h6 class="footer-title">Company</h6>
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<a class="link link-hover" href="/about">About us</a>
|
<a class="link link-hover" href="/about">About us</a>
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@ -29,39 +32,61 @@
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<a class="link link-hover" href="/cite">Cite enviPath</a>
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<a class="link link-hover" href="/cite">Cite enviPath</a>
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</nav>
|
</nav>
|
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</footer>
|
</footer>
|
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<footer class="footer border-neutral-300 border-t-2 px-10 py-4">
|
<footer class="footer border-t-2 border-neutral-300 px-10 py-4">
|
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<div class="flex flex-row justify-between w-full items-start">
|
<div class="flex w-full flex-row items-start justify-between">
|
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<aside class="grid-flow-col items-center">
|
<aside class="grid-flow-col items-center">
|
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<svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
|
<svg
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<use
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class="fill-neutral-content m-2 h-14 flex-shrink-0"
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||||||
href="{% static "/images/logo-square.svg" %}#ep-logo-square"
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viewbox="0 0 65 65"
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>
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>
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</use>
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<use
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</svg>
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href="{% static "/images/logo-square.svg" %}#ep-logo-square"
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|
></use>
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|
</svg>
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|
|
||||||
enviPath Ltd.
|
enviPath Ltd.
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<br />
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<br />
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Biodegredation prediction since 2015.
|
Biodegredation prediction since 2015.
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</p>
|
</aside>
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|
<aside class="text-base-200 mt-2 text-sm">
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<span class="text-xs tracking-tight">Version</span>
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|
<span class="text-base font-bold">{{ meta.version }}</span>
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</aside>
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</aside>
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<aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
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</div>
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</div>
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<nav class="md:place-self-center md:justify-self-end">
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<nav class="md:place-self-center md:justify-self-end">
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<div class="grid grid-flow-col gap-4">
|
<div class="grid grid-flow-col gap-4">
|
||||||
<a href="https://www.youtube.com/@envipath7231" target="_blank">
|
<a href="https://www.youtube.com/@envipath7231" target="_blank">
|
||||||
<svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
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<svg
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||||||
<title>YouTube</title>
|
role="img"
|
||||||
<path d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"/>
|
viewBox="0 0 24 24"
|
||||||
</svg>
|
xmlns="http://www.w3.org/2000/svg"
|
||||||
|
class="h-6 w-6 fill-current"
|
||||||
|
>
|
||||||
|
<title>YouTube</title>
|
||||||
|
<path
|
||||||
|
d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"
|
||||||
|
/>
|
||||||
|
</svg>
|
||||||
</a>
|
</a>
|
||||||
<a href="https://community.envipath.org/" target="_blank">
|
<a href="https://community.envipath.org/" target="_blank">
|
||||||
<svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
|
<svg
|
||||||
<title>Discourse</title>
|
role="img"
|
||||||
<path d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"/>
|
viewBox="0 0 24 24"
|
||||||
</svg>
|
xmlns="http://www.w3.org/2000/svg"
|
||||||
|
class="h-6 w-6 fill-current"
|
||||||
|
>
|
||||||
|
<title>Discourse</title>
|
||||||
|
<path
|
||||||
|
d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"
|
||||||
|
/>
|
||||||
|
</svg>
|
||||||
</a>
|
</a>
|
||||||
<a href="https://www.linkedin.com/company/envipath/" target="_blank">
|
<a href="https://www.linkedin.com/company/envipath/" target="_blank">
|
||||||
<img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
|
<img
|
||||||
|
src="{% static "/images/linkedin.png" %}"
|
||||||
|
alt="LinkedIn"
|
||||||
|
class="h-6 w-6"
|
||||||
|
/>
|
||||||
</a>
|
</a>
|
||||||
</div>
|
</div>
|
||||||
</nav>
|
</nav>
|
||||||
|
|||||||
@ -1,9 +1,9 @@
|
|||||||
{% load static %}
|
{% load static %}
|
||||||
{# Modern DaisyUI Navbar #}
|
{# Modern DaisyUI Navbar #}
|
||||||
<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
|
<div class="navbar x-50 bg-neutral-50 text-neutral-950 shadow-lg">
|
||||||
<div class="navbar-start">
|
<div class="navbar-start">
|
||||||
<a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
|
<a href="{{ meta.server_url }}" class="btn btn-ghost text-xl normal-case">
|
||||||
<svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
|
<svg class="fill-base-content h-8" viewBox="0 0 104 26" role="img">
|
||||||
<use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
|
<use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
|
||||||
</svg>
|
</svg>
|
||||||
</a>
|
</a>
|
||||||
@ -26,6 +26,9 @@
|
|||||||
tabindex="-1"
|
tabindex="-1"
|
||||||
class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
|
class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
|
||||||
>
|
>
|
||||||
|
<li>
|
||||||
|
<a href="{{ meta.server_url }}/Package" id="packageLink">Package</a>
|
||||||
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
|
<a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
|
||||||
</li>
|
</li>
|
||||||
@ -57,9 +60,9 @@
|
|||||||
|
|
||||||
<div class="navbar-end">
|
<div class="navbar-end">
|
||||||
{% if not public_mode %}
|
{% if not public_mode %}
|
||||||
<a href="/search" role="button">
|
<a id="search-trigger" role="button" class="cursor-pointer">
|
||||||
<div
|
<div
|
||||||
class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
|
class="badge badge-dash bg-base-200 text-base-content/50 m-1 flex items-center space-x-1 p-2"
|
||||||
>
|
>
|
||||||
<svg
|
<svg
|
||||||
xmlns="http://www.w3.org/2000/svg"
|
xmlns="http://www.w3.org/2000/svg"
|
||||||
@ -87,7 +90,7 @@
|
|||||||
<div
|
<div
|
||||||
tabindex="0"
|
tabindex="0"
|
||||||
role="button"
|
role="button"
|
||||||
class="btn btn-ghost m-1 btn-circle"
|
class="btn btn-ghost btn-circle m-1"
|
||||||
id="loggedInButton"
|
id="loggedInButton"
|
||||||
>
|
>
|
||||||
<svg
|
<svg
|
||||||
|
|||||||
@ -2,74 +2,86 @@
|
|||||||
{% load static %}
|
{% load static %}
|
||||||
{% block main_content %}
|
{% block main_content %}
|
||||||
<!-- Hero Section with Logo and Search -->
|
<!-- Hero Section with Logo and Search -->
|
||||||
<section class="hero h-fit max-w-5xl w-full shadow-none mx-auto relative">
|
<section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
|
||||||
<div
|
<div
|
||||||
class="hero min-h-[calc(100vh*0.4)] bg-gradient-to-br from-primary-800 to-primary-600"
|
class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
|
||||||
style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
|
style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
|
||||||
>
|
>
|
||||||
<div class="hero-overlay"></div>
|
<div class="hero-overlay"></div>
|
||||||
<!-- Predict Pathway text over the image -->
|
<!-- Predict Pathway text over the image -->
|
||||||
<div class="absolute bottom-40 left-1/8 -translate-x-8 z-10">
|
<div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
|
||||||
<h2 class="text-3xl text-base-100 text-shadow-lg text-left">
|
<h2 class="text-base-100 text-left text-3xl text-shadow-lg">
|
||||||
Predict Your Pathway
|
Predict Your Pathway
|
||||||
</h2>
|
</h2>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
</section>
|
</section>
|
||||||
|
|
||||||
<div class="shadow-md max-w-5xl mx-auto bg-base-200">
|
<div class="bg-base-200 mx-auto max-w-5xl shadow-md">
|
||||||
<!-- Predict Pathway Section -->
|
<!-- Predict Pathway Section -->
|
||||||
<div
|
<div
|
||||||
class="flex-col lg:flex-row-reverse w-full mx-auto -mt-32 relative z-20 mb-10 "
|
class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
|
||||||
>
|
>
|
||||||
<div
|
<div
|
||||||
class="card bg-base-100 shrink-0 shadow-xl w-3/4 mx-auto transition-all duration-300 ease-in-out"
|
class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
|
||||||
>
|
>
|
||||||
<div class="card-body">
|
<div class="card-body">
|
||||||
<!-- Input Mode Toggle - Fixed position outside fieldset -->
|
<div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
|
||||||
<div class="flex flex-row justify-start items-center h-fit ml-8 my-4">
|
<div class="flex items-center gap-1">
|
||||||
<div class="flex items-center gap-2">
|
<label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
|
||||||
<!-- <span class="text-sm text-neutral-500">Input Mode:</span> -->
|
|
||||||
<label class="toggle text-base-content toggle-md">
|
|
||||||
<input type="checkbox" />
|
<input type="checkbox" />
|
||||||
<svg
|
<span class="swap-on flex items-center gap-1">
|
||||||
aria-label="smiles mode"
|
<div
|
||||||
xmlns="http://www.w3.org/2000/svg"
|
class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
|
||||||
viewBox="0 0 20 20"
|
|
||||||
class="size-5"
|
|
||||||
>
|
|
||||||
<g
|
|
||||||
stroke-linejoin="round"
|
|
||||||
stroke-linecap="round"
|
|
||||||
stroke-width="2"
|
|
||||||
fill="currentColor"
|
|
||||||
stroke="none"
|
|
||||||
>
|
>
|
||||||
<path
|
<svg
|
||||||
fill-rule="evenodd"
|
aria-label="smiles mode"
|
||||||
d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
|
xmlns="http://www.w3.org/2000/svg"
|
||||||
clip-rule="evenodd"
|
viewBox="0 0 20 20"
|
||||||
/>
|
class="size-5"
|
||||||
</g>
|
>
|
||||||
</svg>
|
<g
|
||||||
<svg
|
stroke-linejoin="round"
|
||||||
aria-label="draw mode"
|
stroke-linecap="round"
|
||||||
xmlns="http://www.w3.org/2000/svg"
|
stroke-width="2"
|
||||||
viewBox="0 0 20 20"
|
fill="currentColor"
|
||||||
fill="currentColor"
|
stroke="none"
|
||||||
stroke="none"
|
>
|
||||||
class="size-5"
|
<path
|
||||||
>
|
fill-rule="evenodd"
|
||||||
<path
|
d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
|
||||||
d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
|
clip-rule="evenodd"
|
||||||
/>
|
/>
|
||||||
</svg>
|
</g>
|
||||||
|
</svg>
|
||||||
|
</div>
|
||||||
|
<span class="ext-xs">SMILES</span>
|
||||||
|
</span>
|
||||||
|
<span class="swap-off flex items-center gap-1">
|
||||||
|
<div
|
||||||
|
class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
|
||||||
|
>
|
||||||
|
<svg
|
||||||
|
aria-label="draw mode"
|
||||||
|
xmlns="http://www.w3.org/2000/svg"
|
||||||
|
viewBox="0 0 20 20"
|
||||||
|
fill="currentColor"
|
||||||
|
stroke="none"
|
||||||
|
class="size-5"
|
||||||
|
>
|
||||||
|
<path
|
||||||
|
d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
|
||||||
|
/>
|
||||||
|
</svg>
|
||||||
|
</div>
|
||||||
|
<span class="text-base/50 text-xs">Draw</span>
|
||||||
|
</span>
|
||||||
</label>
|
</label>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<fieldset
|
<fieldset
|
||||||
class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
|
class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
|
||||||
>
|
>
|
||||||
<form
|
<form
|
||||||
id="index-form"
|
id="index-form"
|
||||||
@ -79,29 +91,29 @@
|
|||||||
{% csrf_token %}
|
{% csrf_token %}
|
||||||
<div
|
<div
|
||||||
id="text-input-container"
|
id="text-input-container"
|
||||||
class="transition-all duration-300 ease-in-out opacity-100 transform scale-100"
|
class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
|
||||||
>
|
>
|
||||||
<div class="join w-full mx-auto">
|
<div class="join mx-auto w-full">
|
||||||
<input
|
<input
|
||||||
type="text"
|
type="text"
|
||||||
id="index-form-text-input"
|
id="index-form-text-input"
|
||||||
placeholder="canonical SMILES string"
|
placeholder="canonical SMILES string"
|
||||||
class="input grow input-md join-item"
|
class="input input-md join-item grow"
|
||||||
/>
|
/>
|
||||||
<button class="btn btn-neutral join-item">Predict!</button>
|
<button class="btn btn-neutral join-item">Predict!</button>
|
||||||
</div>
|
</div>
|
||||||
<div class="label relative w-full mt-1">
|
<div class="label relative mt-1 w-full">
|
||||||
<div class="flex gap-2">
|
<div class="flex gap-2">
|
||||||
<a
|
<a
|
||||||
href="#"
|
href="#"
|
||||||
class="example-link cursor-pointer hover:text-primary"
|
class="example-link hover:text-primary cursor-pointer"
|
||||||
data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
|
data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
|
||||||
title="load example"
|
title="load example"
|
||||||
>Caffeine</a
|
>Caffeine</a
|
||||||
>
|
>
|
||||||
<a
|
<a
|
||||||
href="#"
|
href="#"
|
||||||
class="example-link cursor-pointer hover:text-primary"
|
class="example-link hover:text-primary cursor-pointer"
|
||||||
data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
|
data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
|
||||||
title="load example"
|
title="load example"
|
||||||
>Ibuprofen</a
|
>Ibuprofen</a
|
||||||
@ -114,7 +126,7 @@
|
|||||||
</div>
|
</div>
|
||||||
<div
|
<div
|
||||||
id="ketcher-container"
|
id="ketcher-container"
|
||||||
class="hidden w-full transition-all duration-300 ease-in-out opacity-0 transform scale-95"
|
class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
|
||||||
>
|
>
|
||||||
<iframe
|
<iframe
|
||||||
id="index-ketcher"
|
id="index-ketcher"
|
||||||
@ -124,11 +136,13 @@
|
|||||||
class="rounded-lg"
|
class="rounded-lg"
|
||||||
></iframe>
|
></iframe>
|
||||||
<button
|
<button
|
||||||
class="btn btn-lg bg-primary-950 text-primary-50 join-item w-full mt-2"
|
class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
|
||||||
>
|
>
|
||||||
Predict!
|
Predict!
|
||||||
</button>
|
</button>
|
||||||
<a class="label mx-auto w-full mt-1" href="#">Advanced</a>
|
<div class="mt-1 flex w-full justify-end">
|
||||||
|
<a class="label justify-end" href="/predict">Advanced</a>
|
||||||
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<input
|
<input
|
||||||
type="hidden"
|
type="hidden"
|
||||||
@ -150,18 +164,18 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<!-- Community News Section -->
|
<!-- Community News Section -->
|
||||||
<section class="py-16 bg-base-200 z-10 mx-8">
|
<section class="bg-base-200 z-10 mx-8 py-16">
|
||||||
<div class="max-w-7xl mx-auto px-4">
|
<div class="mx-auto max-w-7xl px-4">
|
||||||
<h2 class="h2 font-bold text-left mb-8">Community Updates</h2>
|
<h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
|
||||||
|
|
||||||
<div id="community-news-container" class="flex gap-4 justify-center">
|
<div id="community-news-container" class="flex justify-center gap-4">
|
||||||
<!-- News cards will be populated here -->
|
<!-- News cards will be populated here -->
|
||||||
<div id="loading" class="flex justify-center w-full">
|
<div id="loading" class="flex w-full justify-center">
|
||||||
<span class="loading loading-spinner loading-lg"></span>
|
<span class="loading loading-spinner loading-lg"></span>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="text-right mt-6">
|
<div class="mt-6 text-right">
|
||||||
<a
|
<a
|
||||||
href="https://community.envipath.org/c/announcements/10"
|
href="https://community.envipath.org/c/announcements/10"
|
||||||
target="_blank"
|
target="_blank"
|
||||||
@ -177,18 +191,18 @@
|
|||||||
</section>
|
</section>
|
||||||
|
|
||||||
<!-- Mission Statement Section -->
|
<!-- Mission Statement Section -->
|
||||||
<section class="py-16 from-base-200 to-base-100 bg-gradient-to-b">
|
<section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
|
||||||
<div class="mx-auto px-8 md:px-12">
|
<div class="mx-auto px-8 md:px-12">
|
||||||
<div class="flex flex-row gap-4">
|
<div class="flex flex-row gap-4">
|
||||||
<div class="w-1/3">
|
<div class="w-1/3">
|
||||||
<img
|
<img
|
||||||
src="{% static "/images/ep-rule-artwork.png" %}"
|
src="{% static "/images/ep-rule-artwork.png" %}"
|
||||||
alt="rule-based iterative tree greneration"
|
alt="rule-based iterative tree greneration"
|
||||||
class="w-full h-full object-contain"
|
class="h-full w-full object-contain"
|
||||||
/>
|
/>
|
||||||
</div>
|
</div>
|
||||||
<div class="space-y-4 text-left w-2/3 mr-8">
|
<div class="mr-8 w-2/3 space-y-4 text-left">
|
||||||
<h2 class="h2 font-bold mb-8">About enviPath</h2>
|
<h2 class="h2 mb-8 font-bold">About enviPath</h2>
|
||||||
<p class="">
|
<p class="">
|
||||||
enviPath is a database and prediction system for the microbial
|
enviPath is a database and prediction system for the microbial
|
||||||
biotransformation of organic environmental contaminants. The
|
biotransformation of organic environmental contaminants. The
|
||||||
@ -201,7 +215,7 @@
|
|||||||
products. Explore our tools and contribute to advancing
|
products. Explore our tools and contribute to advancing
|
||||||
environmental biotransformation research.
|
environmental biotransformation research.
|
||||||
</p>
|
</p>
|
||||||
<div class="flex flex-row gap-4 float-right">
|
<div class="float-right flex flex-row gap-4">
|
||||||
<a href="/about" class="btn btn-ghost-neutral">Read More</a>
|
<a href="/about" class="btn btn-ghost-neutral">Read More</a>
|
||||||
<a href="/about" class="btn btn-neutral">Publications</a>
|
<a href="/about" class="btn btn-neutral">Publications</a>
|
||||||
</div>
|
</div>
|
||||||
@ -211,7 +225,7 @@
|
|||||||
</section>
|
</section>
|
||||||
|
|
||||||
<!-- Partners Section -->
|
<!-- Partners Section -->
|
||||||
<section class="py-14 sm:py-12 bg-base-100">
|
<section class="bg-base-100 py-14 sm:py-12">
|
||||||
<div class="mx-auto px-6 lg:px-8">
|
<div class="mx-auto px-6 lg:px-8">
|
||||||
<div class="divider">
|
<div class="divider">
|
||||||
<h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
|
<h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
|
||||||
@ -222,12 +236,12 @@
|
|||||||
<img
|
<img
|
||||||
src="{% static "/images/uoa-logo-small.png" %}"
|
src="{% static "/images/uoa-logo-small.png" %}"
|
||||||
alt="The University of Auckland"
|
alt="The University of Auckland"
|
||||||
class=" max-h-20 w-full object-contain lg:col-span-1"
|
class="max-h-20 w-full object-contain lg:col-span-1"
|
||||||
/>
|
/>
|
||||||
<img
|
<img
|
||||||
src="{% static "/images/logo-eawag.svg" %}"
|
src="{% static "/images/logo-eawag.svg" %}"
|
||||||
alt="Eawag"
|
alt="Eawag"
|
||||||
class=" max-h-12 w-full object-contain lg:col-span-1"
|
class="max-h-12 w-full object-contain lg:col-span-1"
|
||||||
/>
|
/>
|
||||||
<img
|
<img
|
||||||
src="{% static "/images/uzh-logo.svg" %}"
|
src="{% static "/images/uzh-logo.svg" %}"
|
||||||
|
|||||||
@ -1,43 +1,55 @@
|
|||||||
<div class="modal fade" tabindex="-1" id="retrain_model_modal" role="dialog" aria-labelledby="retrain_model_modal"
|
<div
|
||||||
aria-hidden="true">
|
class="modal fade"
|
||||||
<div class="modal-dialog modal-lg">
|
tabindex="-1"
|
||||||
<div class="modal-content">
|
id="retrain_model_modal"
|
||||||
<div class="modal-header">
|
role="dialog"
|
||||||
<button type="button" class="close" data-dismiss="modal">
|
aria-labelledby="retrain_model_modal"
|
||||||
<span aria-hidden="true">×</span>
|
aria-hidden="true"
|
||||||
<span class="sr-only">Close</span>
|
>
|
||||||
</button>
|
<div class="modal-dialog modal-lg">
|
||||||
<h4 class="modal-title">Retrain Model</h4>
|
<div class="modal-content">
|
||||||
</div>
|
<div class="modal-header">
|
||||||
<div class="modal-body">
|
<button type="button" class="close" data-dismiss="modal">
|
||||||
<form id="retrain_model_form" accept-charset="UTF-8" action="{{ meta.current_package.url }}/model"
|
<span aria-hidden="true">×</span>
|
||||||
data-remote="true" method="post">
|
<span class="sr-only">Close</span>
|
||||||
<div class="jumbotron">
|
</button>
|
||||||
To reflect changes in the rule or data packages, you can use the "Retrain" button,
|
<h4 class="modal-title">Retrain Model</h4>
|
||||||
to let the model reflect the changes without creating a new model.
|
</div>
|
||||||
While the model is retraining, it will be unavailable for prediction.
|
<div class="modal-body">
|
||||||
</div>
|
<form
|
||||||
{% csrf_token %}
|
id="retrain_model_form"
|
||||||
<input type="hidden" name="action" value="retrain">
|
accept-charset="UTF-8"
|
||||||
</form>
|
action="{{ meta.current_object.url }}"
|
||||||
</div>
|
data-remote="true"
|
||||||
<div class="modal-footer">
|
method="post"
|
||||||
<a id="retrain_model_form_submit" class="btn btn-primary" href="#">Retrain</a>
|
>
|
||||||
<button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
|
<div class="jumbotron">
|
||||||
</div>
|
To reflect changes in the rule or data packages, you can use the
|
||||||
</div>
|
"Retrain" button, to let the model reflect the changes without
|
||||||
|
creating a new model. While the model is retraining, it will be
|
||||||
|
unavailable for prediction.
|
||||||
|
</div>
|
||||||
|
{% csrf_token %}
|
||||||
|
<input type="hidden" name="hidden" value="retrain" />
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
<div class="modal-footer">
|
||||||
|
<a id="retrain_model_form_submit" class="btn btn-primary" href="#"
|
||||||
|
>Retrain</a
|
||||||
|
>
|
||||||
|
<button type="button" class="btn btn-default" data-dismiss="modal">
|
||||||
|
Cancel
|
||||||
|
</button>
|
||||||
|
</div>
|
||||||
</div>
|
</div>
|
||||||
|
</div>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<script>
|
<script>
|
||||||
|
$(function () {
|
||||||
$(function () {
|
$("#retrain_model_form_submit").on("click", function (e) {
|
||||||
|
e.preventDefault();
|
||||||
$('#retrain_model_form_submit').on('click', function (e) {
|
$("#retrain_model_form").submit();
|
||||||
e.preventDefault();
|
|
||||||
$('#retrain_model_form').submit();
|
|
||||||
});
|
|
||||||
|
|
||||||
});
|
});
|
||||||
|
});
|
||||||
</script>
|
</script>
|
||||||
|
|||||||
File diff suppressed because it is too large
Load Diff
@ -2,7 +2,13 @@
|
|||||||
{% load static %}
|
{% load static %}
|
||||||
{% block content %}
|
{% block content %}
|
||||||
<div class="mx-auto w-full p-8">
|
<div class="mx-auto w-full p-8">
|
||||||
<h1 class="h1 mb-4 text-3xl font-bold">Predict a Pathway</h1>
|
<h1 class="h1 mb-4 text-3xl font-bold">
|
||||||
|
Predict a Pathway
|
||||||
|
|
||||||
|
<span class="text-base-content/50 text-xs"
|
||||||
|
>in <strong>{{ meta.current_package.name|safe }}</strong>
|
||||||
|
</span>
|
||||||
|
</h1>
|
||||||
|
|
||||||
<form
|
<form
|
||||||
id="predict_form"
|
id="predict_form"
|
||||||
|
|||||||
@ -1,197 +0,0 @@
|
|||||||
{% extends "framework.html" %}
|
|
||||||
{% load static %}
|
|
||||||
{% block content %}
|
|
||||||
|
|
||||||
<div id=searchContent>
|
|
||||||
<div id="packSelector">
|
|
||||||
<label>Select Packages</label><br>
|
|
||||||
<select id="selPackages" name="selPackages" data-actions-box='true' class="selPackages" multiple
|
|
||||||
data-width='100%'>
|
|
||||||
{% if unreviewed_objects %}
|
|
||||||
<option disabled>Reviewed Packages</option>
|
|
||||||
{% endif %}
|
|
||||||
{% for obj in reviewed_objects %}
|
|
||||||
<option value="{{ obj.url }}" selected>{{ obj.name|safe }}</option>
|
|
||||||
{% endfor %}
|
|
||||||
{% if unreviewed_objects %}
|
|
||||||
<option disabled>Unreviewed Packages</option>
|
|
||||||
{% endif %}
|
|
||||||
{% for obj in unreviewed_objects %}
|
|
||||||
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
|
|
||||||
{% endfor %}
|
|
||||||
</select>
|
|
||||||
</div>
|
|
||||||
<p></p>
|
|
||||||
<div>
|
|
||||||
<label>Search Term</label><br>
|
|
||||||
<div class="input-group" id="index-form-bar">
|
|
||||||
<input type="text" class="form-control" id='searchbar' placeholder="Benfuracarb">
|
|
||||||
<div class="input-group-btn">
|
|
||||||
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
|
|
||||||
id="mode-button"
|
|
||||||
aria-haspopup="true" aria-expanded="false">Text <span class="caret"></span></button>
|
|
||||||
<ul class="dropdown-menu">
|
|
||||||
<li class="dropdown-header">Text</li>
|
|
||||||
<li><a id="dropdown-predict-text-text">Text</a></li>
|
|
||||||
<li class="dropdown-header">SMILES</li>
|
|
||||||
<li><a id="dropdown-search-smiles-default" data-toggle="tooltip">Default</a></li>
|
|
||||||
<li><a id="dropdown-search-smiles-canonical">Canonical</a></li>
|
|
||||||
<li><a id="dropdown-search-smiles-exact">Exact</a></li>
|
|
||||||
<li class="dropdown-header">InChI</li>
|
|
||||||
<li><a id="dropdown-search-inchi-inchikey">InChIKey</a></li>
|
|
||||||
</ul>
|
|
||||||
<button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="search-button">
|
|
||||||
Go!
|
|
||||||
</button>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
<p></p>
|
|
||||||
<div id="results"></div>
|
|
||||||
<p></p>
|
|
||||||
<div id="loading"></div>
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
<script>
|
|
||||||
function modeDropdownClicked() {
|
|
||||||
var suffix = ' <span class="caret"></span>';
|
|
||||||
var dropdownVal = $(this).text();
|
|
||||||
$('#mode-button').html(dropdownVal + suffix);
|
|
||||||
}
|
|
||||||
|
|
||||||
function handleSearchResponse(id, data) {
|
|
||||||
content = `
|
|
||||||
<div class='panel-group' id='search-accordion'>
|
|
||||||
<div class='panel panel-default'>
|
|
||||||
<div class='panel-heading' id='headingPanel' style='font-size:2rem;height: 46px'>
|
|
||||||
Results
|
|
||||||
</div>
|
|
||||||
<div id='descDiv'></div>
|
|
||||||
</div>`;
|
|
||||||
|
|
||||||
function makeContent(objs) {
|
|
||||||
links = "";
|
|
||||||
for (idx in objs) {
|
|
||||||
obj = objs[idx];
|
|
||||||
links += `<a class='list-group-item' href='${obj.url}'>${obj.name}</a>`
|
|
||||||
}
|
|
||||||
return links;
|
|
||||||
}
|
|
||||||
|
|
||||||
allEmpty = true;
|
|
||||||
for (key in data) {
|
|
||||||
if (key === 'searchterm') {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (data[key].length < 1) {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
allEmpty = false;
|
|
||||||
content += `
|
|
||||||
<div class='panel panel-default panel-heading list-group-item' style='background-color:silver'>
|
|
||||||
<h4 class='panel-title'>
|
|
||||||
<a id='${key}_link' data-toggle='collapse' data-parent='#search-accordion' href='#${key}_panel'>
|
|
||||||
${key}
|
|
||||||
</a>
|
|
||||||
</h4>
|
|
||||||
</div>
|
|
||||||
<div id='${key}_panel' class='panel-collapse collapse in'>
|
|
||||||
<div class='panel-body list-group-item'>
|
|
||||||
${makeContent(data[key])}
|
|
||||||
</div>
|
|
||||||
</div>
|
|
||||||
|
|
||||||
`;
|
|
||||||
}
|
|
||||||
if (allEmpty) {
|
|
||||||
$('#' + id).append('<div class="alert alert-danger" role="alert"><p>' + "No results..." + '</p></div>');
|
|
||||||
} else {
|
|
||||||
$('#' + id).append(content);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
function search(e) {
|
|
||||||
e.preventDefault();
|
|
||||||
|
|
||||||
query = $("#searchbar").val()
|
|
||||||
|
|
||||||
if (!query) {
|
|
||||||
// Nothing to search...
|
|
||||||
console.log("Search phrase empty, won't do search")
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
var selPacks = [];
|
|
||||||
$("#selPackages :selected").each(function () {
|
|
||||||
var id = this.value;
|
|
||||||
selPacks.push(id);
|
|
||||||
});
|
|
||||||
|
|
||||||
if (selPacks.length < 1) {
|
|
||||||
console.log("No package selected, won't do search")
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
|
|
||||||
var mode = $('#mode-button').text().trim().toLowerCase();
|
|
||||||
|
|
||||||
var par = {};
|
|
||||||
par['packages'] = selPacks;
|
|
||||||
par['search'] = query;
|
|
||||||
par['mode'] = mode;
|
|
||||||
|
|
||||||
console.log(par);
|
|
||||||
|
|
||||||
var queryString = $.param(par, true);
|
|
||||||
|
|
||||||
makeLoadingGif("#loading", "{% static '/images/wait.gif' %}");
|
|
||||||
|
|
||||||
$("#results").empty();
|
|
||||||
|
|
||||||
$.getJSON("{{ SERVER_BASE }}/search?" + queryString, function (result) {
|
|
||||||
handleSearchResponse("results", result);
|
|
||||||
$("#loading").empty();
|
|
||||||
}).fail(function (d) {
|
|
||||||
$("#loading").empty();
|
|
||||||
console.log(d.responseText);
|
|
||||||
handleError(JSON.parse(d.responseText));
|
|
||||||
});
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
$(function () {
|
|
||||||
|
|
||||||
tooltips = {
|
|
||||||
'dropdown-predict-text-text': 'The inserted pattern will be searched on all enviPath object names and descriptions',
|
|
||||||
'dropdown-search-smiles-default': 'Search by SMILES, stereochemistry and charge are ignored',
|
|
||||||
'dropdown-search-smiles-canonical': 'Search by SMILES, stereochemistry is ignored but charge is preserved',
|
|
||||||
'dropdown-search-smiles-exact': 'Search by SMILES, exact match for stereochemistry and charge',
|
|
||||||
'dropdown-search-inchi-inchikey': 'Search by InChIKey',
|
|
||||||
}
|
|
||||||
|
|
||||||
Object.keys(tooltips).forEach(key => {
|
|
||||||
$('#' + key).tooltip({
|
|
||||||
placement: "top",
|
|
||||||
title: tooltips[key]
|
|
||||||
});
|
|
||||||
|
|
||||||
$('#' + key).on('click', modeDropdownClicked);
|
|
||||||
});
|
|
||||||
|
|
||||||
$("#selPackages").selectpicker();
|
|
||||||
$("#search-button").on("click", search);
|
|
||||||
|
|
||||||
$("#searchbar").on("keydown", function (e) {
|
|
||||||
if (e.key === "Enter") {
|
|
||||||
e.preventDefault();
|
|
||||||
search(e);
|
|
||||||
}
|
|
||||||
});
|
|
||||||
|
|
||||||
});
|
|
||||||
{% if search_result %}
|
|
||||||
$('#searchbar').val('{{ search_result.searchterm }}')
|
|
||||||
handleSearchResponse("results", {{ search_result|safe }});
|
|
||||||
{% endif %}
|
|
||||||
</script>
|
|
||||||
|
|
||||||
{% endblock content %}
|
|
||||||
Reference in New Issue
Block a user