Turn reference URLs into hyperlinks (#2234)

References in the References section should include a link, if a URL is
provided. Fixes issue #658.

I changed my mind many times about how this should be implemented. At
first, I thought that we should separately provide "description" and
"URL" fields for authors to edit.

But now I think, actually, the URL is part of the formal reference, and
should be displayed as text for transparency's sake. So I think it's
better for the URL to be extracted automatically from the description.

On the other hand, I don't want to have ad-hoc parsing rules applied at
runtime to published content. (It's possible those rules might change in
the future, which I think is okay for active but not for published
projects.) So I ended up with this approach:
- For active projects, the URL is extracted by a regular expression
whenever it's needed.
- When a project is published, the automatically-extracted URL is saved
as a model field.
- For published projects, it's possible to edit the `description` and
`url` separately via Django admin, but it will only appear as a link if
the `url` appears verbatim within the `description`.

physionet-django/project/fixtures/demo-project.json

@@ -672,6 +672,7 @@
   "pk": 1,
   "fields": {
     "description": "https://eicu-crd.mit.edu/eicutables/admissiondrug/",
+    "url": "https://eicu-crd.mit.edu/eicutables/admissiondrug/",
     "project": 1
   }
 },
@@ -680,6 +681,7 @@
   "pk": 2,
   "fields": {
     "description": "https://eicu-crd.mit.edu/eicutables/apachepatientresult/",
+    "url": "https://eicu-crd.mit.edu/eicutables/apachepatientresult/",
     "project": 1
   }
 },
@@ -688,6 +690,7 @@
   "pk": 3,
   "fields": {
     "description": "https://physionet.org/physiotools/wag/",
+    "url": "https://physionet.org/physiotools/wag/",
     "project": 2
   }
 },
@@ -696,6 +699,7 @@
   "pk": 4,
   "fields": {
     "description": "https://physionet.org/physiotools/wpg/",
+    "url": "https://physionet.org/physiotools/wpg/",
     "project": 2
   }
 },

physionet-django/project/migrations/0075_publishedreference_url.py

@@ -0,0 +1,36 @@
+# Generated by Django 4.2.11 on 2024-05-13 20:18
+
+import re
+
+from django.db import migrations, models
+
+
+def migrate_forward(apps, schema_editor):
+    pattern = re.compile(r'\bhttps?://[^\s<>"\']+', re.IGNORECASE)
+
+    PublishedReference = apps.get_model('project', 'PublishedReference')
+    for reference in PublishedReference.objects.all():
+        m = pattern.search(reference.description)
+        if m:
+            reference.url = m.group()
+            reference.save(update_fields=['url'])
+
+
+def migrate_backward(apps, schema_editor):
+    pass
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("project", "0074_migrate_archived_to_active"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="publishedreference",
+            name="url",
+            field=models.URLField(blank=True, null=True),
+        ),
+        migrations.RunPython(migrate_forward, migrate_backward),
+    ]

physionet-django/project/modelcomponents/activeproject.py

@@ -550,6 +550,7 @@ def publish(self, slug=None, make_zip=True):
                 for reference in self.references.all().order_by('order'):
                     published_reference = PublishedReference.objects.create(
                         description=reference.description,
+                        url=reference.url,
                         order=reference.order,
                         project=published_project)
 

physionet-django/project/modelcomponents/metadata.py

@@ -1,12 +1,13 @@
 import os
+import re
 import uuid
 
 from django.conf import settings
 from django.contrib.contenttypes.fields import GenericForeignKey
 from django.contrib.contenttypes.models import ContentType
 from django.db import models
 from django.utils import timezone
-from django.utils.html import format_html
+from django.utils.html import escape, format_html, mark_safe
 from html2text import html2text
 from project.modelcomponents.access import AccessPolicy, AnonymousAccess
 from project.modelcomponents.fields import SafeHTMLField
@@ -574,23 +575,50 @@ def __str__(self):
         return self.description
 
 
-class Reference(models.Model):
+class BaseReference(models.Model):
+    """
+    Abstract base class for a bibliographic reference.
+    """
+    class Meta:
+        abstract = True
+
+    order = models.PositiveIntegerField(null=True)
+    description = models.CharField(max_length=1000)
+
+    def __str__(self):
+        return self.description
+
+    @property
+    def html_description(self):
+        description = escape(self.description)
+        url = self.url
+        if url:
+            escaped_url = escape(url)
+            link = format_html('<a href="{0}">{0}</a>', url)
+            description = description.replace(escaped_url, link)
+            description = mark_safe(description)
+        return description
+
+
+class Reference(BaseReference):
     """
     Reference field for ActiveProject
     """
     content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
     object_id = models.PositiveIntegerField()
     project = GenericForeignKey('content_type', 'object_id')
-    order = models.PositiveIntegerField(null=True)
 
-    description = models.CharField(max_length=1000)
+    URL_PATTERN = re.compile(r'\bhttps?://[^\s<>"\']+', re.IGNORECASE)
 
     class Meta:
         default_permissions = ()
         unique_together = (('description', 'object_id', 'order'),)
 
-    def __str__(self):
-        return self.description
+    @property
+    def url(self):
+        m = self.URL_PATTERN.search(self.description)
+        if m:
+            return m.group()
 
     def save(self, *args, **kwargs):
         super().save(*args, **kwargs)
@@ -601,14 +629,13 @@ def delete(self, *args, **kwargs):
         self.project.content_modified()
 
 
-class PublishedReference(models.Model):
+class PublishedReference(BaseReference):
     """
     Reference field for PublishedProject
     """
-    description = models.CharField(max_length=1000)
     project = models.ForeignKey('project.PublishedProject',
         related_name='references', on_delete=models.CASCADE)
-    order = models.PositiveIntegerField(null=True)
+    url = models.URLField(blank=True, null=True)
 
     class Meta:
         default_permissions = ()

physionet-django/project/templates/project/challenge_content.html

@@ -42,10 +42,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-  {% for reference in references %}
-    <li>{{ reference.description }}</li>
-  {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/challenge_content_preview.html

@@ -68,10 +68,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-    {% for reference in references %}
-      <li>{{ reference.description }}</li>
-    {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/database_content.html

@@ -42,10 +42,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-  {% for reference in references %}
-    <li>{{ reference.description }}</li>
-  {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/database_content_preview.html

@@ -68,10 +68,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-    {% for reference in references %}
-      <li>{{ reference.description }}</li>
-    {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/model_content.html

@@ -46,10 +46,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-  {% for reference in references %}
-    <li>{{ reference.description }}</li>
-  {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/model_content_preview.html

@@ -76,10 +76,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-    {% for reference in references %}
-      <li>{{ reference.description }}</li>
-    {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/reference_list.html

@@ -0,0 +1,5 @@
+<ol>
+  {% for reference in references %}
+    <li>{{ reference.html_description }}</li>
+  {% endfor %}
+</ol>

physionet-django/project/templates/project/software_content.html

@@ -48,10 +48,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-  {% for reference in references %}
-    <li>{{ reference.description }}</li>
-  {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}

physionet-django/project/templates/project/software_content_preview.html

@@ -76,10 +76,6 @@ <h2 id="conflicts-of-interest">Conflicts of Interest</h2>
 
 {% if references %}
   <h2 id="references">References</h2>
-  <ol>
-    {% for reference in references %}
-      <li>{{ reference.description }}</li>
-    {% endfor %}
-  </ol>
+  {% include "project/reference_list.html" %}
   <hr>
 {% endif %}