Merge branch 'develop' into fix/frontpage_predict

Modal now opens on badge click.
Modal now closes on random click around

Reviewed-on: enviPath/enviPy#192
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

.gitea/workflows/ci.yaml

@@ -105,7 +105,7 @@ jobs:
           until pg_isready -h postgres -U postgres; do sleep 2; done
           # until redis-cli -h redis ping; do sleep 2; done
 
-      - name: Run Django migrations
+      - name: Run Django Migrations
         run: |
           source .venv/bin/activate
           python manage.py migrate --noinput

epdb/admin.py

@@ -21,6 +21,7 @@ from .models import (
     ExternalDatabase,
     ExternalIdentifier,
     JobLog,
+    License,
 )
 
 
@@ -62,6 +63,10 @@ class EnviFormerAdmin(EPAdmin):
     pass
 
 
+class LicenseAdmin(admin.ModelAdmin):
+    list_display = ["cc_string", "link", "image_link"]
+
+
 class CompoundAdmin(EPAdmin):
     pass
 
@@ -118,6 +123,7 @@ admin.site.register(JobLog, JobLogAdmin)
 admin.site.register(Package, PackageAdmin)
 admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
 admin.site.register(EnviFormer, EnviFormerAdmin)
+admin.site.register(License, LicenseAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)

epdb/management/commands/bootstrap.py

@@ -12,10 +12,16 @@ from epdb.models import (
     Permission,
     User,
     ExternalDatabase,
+    License,
 )
 
 
 class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "-ol", "--only-licenses", action="store_true", help="Only create licenses."
+        )
+
     def create_users(self):
         # Anonymous User
         if not User.objects.filter(email="anon@envipath.com").exists():
@@ -83,6 +89,17 @@ class Command(BaseCommand):
 
         return anon, admin, g, user0
 
+    def create_licenses(self):
+        """Create the six default licenses supported by enviPath"""
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            if not License.objects.filter(cc_string=cc_string).exists():
+                new_license = License()
+                new_license.cc_string = cc_string
+                new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+                new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+                new_license.save()
+
     def import_package(self, data, owner):
         return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
@@ -157,6 +174,10 @@ class Command(BaseCommand):
 
     @transaction.atomic
     def handle(self, *args, **options):
+        # Create licenses
+        self.create_licenses()
+        if options.get("only_licenses", False):
+            return
         # Create users
         anon, admin, g, user0 = self.create_users()
 

epdb/migrations/0010_license_cc_string.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.2.7 on 2025-11-11 14:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0009_joblog"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="license",
+            name="cc_string",
+            field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
+            preserve_default=False,
+        ),
+    ]

epdb/migrations/0011_auto_20251111_1413.py

@@ -0,0 +1,59 @@
+# Generated by Django 5.2.7 on 2025-11-11 14:13
+
+import re
+
+from django.contrib.postgres.aggregates import ArrayAgg
+from django.db import migrations
+from django.db.models import Min
+
+
+def set_cc(apps, schema_editor):
+    License = apps.get_model("epdb", "License")
+
+    # For all existing licenses extract cc_string from link
+    for license in License.objects.all():
+        pattern = r"/licenses/([^/]+)/4\.0"
+        match = re.search(pattern, license.link)
+        if match:
+            license.cc_string = match.group(1)
+            license.save()
+        else:
+            raise ValueError(f"Could not find license for {license.link}")
+
+    # Ensure we have all licenses
+    cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+    for cc_string in cc_strings:
+        if not License.objects.filter(cc_string=cc_string).exists():
+            new_license = License()
+            new_license.cc_string = cc_string
+            new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+            new_license.save()
+
+    # As we might have existing Licenses representing the same License,
+    # get min pk and all pks as a list
+    license_lookup_qs = License.objects.values("cc_string").annotate(
+        lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
+    )
+
+    license_lookup = {
+        row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
+    }
+
+    Packages = apps.get_model("epdb", "Package")
+
+    for k, v in license_lookup.items():
+        # Set min pk to all packages pointing to any of the duplicates
+        Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
+        # remove the min pk from "other" pks as we use them for deletion
+        v[1].remove(v[0])
+        # Delete redundant License objects
+        License.objects.filter(pk__in=v[1]).delete()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0010_license_cc_string"),
+    ]
+
+    operations = [migrations.RunPython(set_cc)]

epdb/models.py

@@ -655,6 +655,7 @@ class ScenarioMixin(models.Model):
 
 
 class License(models.Model):
+    cc_string = models.TextField(blank=False, null=False, verbose_name="CC string")
     link = models.URLField(blank=False, null=False, verbose_name="link")
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 

epdb/tasks.py

@@ -1,15 +1,15 @@
 import csv
 import io
 import logging
-from datetime import datetime
 from typing import Any, Callable, List, Optional
 from uuid import uuid4
 
 from celery import shared_task
 from celery.utils.functional import LRUCache
+from django.utils import timezone
 
 from epdb.logic import SPathway
-from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
+from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@@ -29,7 +29,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
         log.task_id = uuid4()
         log.job_name = job.__name__
         log.status = "SUCCESS"
-        log.done_at = datetime.now()
+        log.done_at = timezone.now()
         log.task_result = str(x) if x else None
         log.save()
 

epdb/views.py

@@ -955,6 +955,12 @@ def package_model(request, package_uuid, model_uuid):
                 ]
                 dispatch(current_user, evaluate_model, current_model.pk, multigen, eval_package_ids)
 
+                return redirect(current_model.url)
+            elif hidden == "retrain":
+                from .tasks import dispatch, retrain
+
+                dispatch(current_user, retrain, current_model.pk)
+
                 return redirect(current_model.url)
             else:
                 return HttpResponseBadRequest()
@@ -1084,9 +1090,7 @@ def package(request, package_uuid):
         write = request.POST.get("write") == "on"
         owner = request.POST.get("owner") == "on"
 
-        license = request.POST.get("license")
+        cc_string = request.POST.get("license")
-        license_link = request.POST.get("license-link")
-        license_image_link = request.POST.get("license-image-link")
 
         if new_package_name:
             current_package.name = new_package_name
@@ -1114,24 +1118,15 @@ def package(request, package_uuid):
 
             PackageManager.update_permissions(current_user, current_package, grantee, max_perm)
             return redirect(current_package.url)
-        elif license is not None:
-            if license == "no-license":
-                if current_package.license is not None:
-                    current_package.license.delete()
 
+        elif cc_string is not None:
+            cc_string = cc_string.strip()
+            if cc_string == "no-license":  # Reset the package's license
                 current_package.license = None
                 current_package.save()
                 return redirect(current_package.url)
-            else:
+            else:  # Get the license and assign it to the package
-                if current_package.license is not None:
+                current_package.license = License.objects.get(cc_string=cc_string)
-                    current_package.license.delete()
-
-                license = License()
-                license.link = license_link
-                license.image_link = license_image_link
-                license.save()
-
-                current_package.license = license
                 current_package.save()
 
                 return redirect(current_package.url)

templates/framework_modern.html

@@ -178,6 +178,23 @@
         }
       });
 
+      // Open search modal function
+      function openSearchModal() {
+        const searchModal = document.getElementById("search_modal");
+        if (searchModal) {
+          searchModal.showModal();
+        }
+      }
+
+      // Click handler for search badge
+      const searchTrigger = document.getElementById("search-trigger");
+      if (searchTrigger) {
+        searchTrigger.addEventListener("click", function (event) {
+          event.preventDefault();
+          openSearchModal();
+        });
+      }
+
       // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
       document.addEventListener("keydown", function (event) {
         // Check if user is typing in an input field
@@ -198,7 +215,7 @@
 
         if (isCorrectModifier && event.key === "k") {
           event.preventDefault();
-          search_modal.showModal();
+          openSearchModal();
         }
       });
     </script>

templates/includes/navbar.html

@@ -57,7 +57,7 @@
 
   <div class="navbar-end">
     {% if not public_mode %}
-      <a href="/search" role="button">
+      <a id="search-trigger" role="button" class="cursor-pointer">
         <div
           class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
         >

templates/index/index.html

@@ -2,74 +2,86 @@
 {% load static %}
 {% block main_content %}
   <!-- 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
-      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;"
     >
       <div class="hero-overlay"></div>
       <!-- 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
         </h2>
       </div>
     </div>
   </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 -->
     <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
-        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">
-          <!-- 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" />
-                <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>
             </div>
           </div>
 
           <fieldset
-            class="fieldset transition-all duration-300 ease-in-out overflow-hidden"
+            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
           >
             <form
               id="index-form"
@@ -79,29 +91,29 @@
               {% csrf_token %}
               <div
                 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
                     type="text"
                     id="index-form-text-input"
                     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>
                 </div>
-                <div class="label relative w-full mt-1">
+                <div class="label relative mt-1 w-full">
                   <div class="flex gap-2">
                     <a
                       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"
                       title="load example"
                       >Caffeine</a
                     >
                     <a
                       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"
                       title="load example"
                       >Ibuprofen</a
@@ -114,7 +126,7 @@
               </div>
               <div
                 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
                   id="index-ketcher"
@@ -124,11 +136,13 @@
                   class="rounded-lg"
                 ></iframe>
                 <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!
                 </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>
               <input
                 type="hidden"
@@ -150,18 +164,18 @@
     </div>
 
     <!-- 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 -->
-          <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>
           </div>
         </div>
 
-        <div class="text-right mt-6">
+        <div class="mt-6 text-right">
           <a
             href="https://community.envipath.org/c/announcements/10"
             target="_blank"
@@ -177,18 +191,18 @@
     </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="flex flex-row gap-4">
           <div class="w-1/3">
             <img
               src="{% static "/images/ep-rule-artwork.png" %}"
               alt="rule-based iterative tree greneration"
-              class="w-full h-full object-contain"
+              class="h-full w-full object-contain"
             />
           </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="">
               enviPath is a database and prediction system for the microbial
               biotransformation of organic environmental contaminants. The
@@ -201,7 +215,7 @@
               products. Explore our tools and contribute to advancing
               environmental biotransformation research.
             </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-neutral">Publications</a>
             </div>
@@ -211,7 +225,7 @@
     </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="divider">
           <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
@@ -222,12 +236,12 @@
           <img
             src="{% static "/images/uoa-logo-small.png" %}"
             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
             src="{% static "/images/logo-eawag.svg" %}"
             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
             src="{% static "/images/uzh-logo.svg" %}"

templates/modals/objects/retrain_model_modal.html

@@ -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">&times;</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">&times;</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>
 
 <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>

templates/modals/objects/set_license_modal.html

@@ -52,8 +52,6 @@
                         </div>
                     </div>
                     <input type="hidden" id="license" name="license">
-                    <input type="hidden" id="license-link" name="license-link">
-                    <input type="hidden" id="license-image-link" name="license-image-link">
                 </form>
             </div>
             <div class="modal-footer">
@@ -128,8 +126,6 @@ function cc() {
 
         $('#ccfig').append(img_tpl);
         $('#license').val(ccstr);
-        $('#license-link').val(link);
-        $('#license-image-link').val(imageLink);
     } else {
         $('#ccfig').empty();
         $('#set_license_form_submit').prop('disabled', true);

templates/search.html

@@ -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 %}

tests/views/test_package_views.py

@@ -4,7 +4,14 @@ from django.test import TestCase, tag
 from django.urls import reverse
 
 from epdb.logic import UserManager
-from epdb.models import Package, UserPackagePermission, Permission, GroupPackagePermission, Group
+from epdb.models import (
+    Package,
+    UserPackagePermission,
+    Permission,
+    GroupPackagePermission,
+    Group,
+    License,
+)
 
 
 class PackageViewTest(TestCase):
@@ -29,6 +36,15 @@ class PackageViewTest(TestCase):
             add_to_group=True,
             is_active=True,
         )
+        # Create the default license set.
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            if not License.objects.filter(cc_string=cc_string).exists():
+                new_license = License()
+                new_license.cc_string = cc_string
+                new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+                new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+                new_license.save()
 
     def setUp(self):
         self.client.force_login(self.user1)
@@ -188,7 +204,28 @@ class PackageViewTest(TestCase):
         self.client.post(package_url, {"license": "no-license"})
 
         self.assertIsNone(p.license)
-        # TODO test others
+
+        # Test other possible licenses
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            self.client.post(package_url, {"license": cc_string})
+            # Without this, the instance of p doesn't have the license. However, the one retrieved with get does
+            p = Package.objects.get(url=package_url)
+            self.assertEqual(
+                p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            )
+
+        # Test again to ensure that Licenses are reused
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            self.client.post(package_url, {"license": cc_string})
+            # Without this, the instance of p doesn't have the license. However, the one retrieved with get does
+            p = Package.objects.get(url=package_url)
+            self.assertEqual(
+                p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+            )
+
+        self.assertEqual(License.objects.count(), len(cc_strings))
 
     def test_delete_package(self):
         response = self.client.post(

utilities/misc.py

@@ -714,6 +714,7 @@ class PackageImporter:
             license_obj, _ = License.objects.get_or_create(
                 name=license_data["name"],
                 defaults={
+                    "cc_string": license_data.get("cc_string", ""),
                     "link": license_data.get("link", ""),
                     "image_link": license_data.get("image_link", ""),
                 },