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feat: Implement youtube, citation, and input/output data schema additions #874

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128 changes: 121 additions & 7 deletions django/library/jinja2/library/codebases/releases/retrieve.jinja
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,18 @@
<h2>Release Notes</h2>
<p>{{ release.release_notes|safe }}</p>
<h2>Associated Publications</h2>
<p>{{ markdown(codebase.associated_publication_text) }}</p>
{% if codebase.associated_publications %}
<ul>
Comment on lines 80 to +82
{% for publication in codebase.associated_publications %}
<li>
<a href="{{ publication.doi }}" target="_blank" rel="nofollow">{{ publication.doi }}</a>
{% if publication.include_in_citation %}
<span class="badge bg-info ms-1">cited</span>
{% endif %}
</li>
{% endfor %}
</ul>
{% endif %}
</div>
{% endif %}

Expand Down Expand Up @@ -134,9 +145,19 @@
{{ codebase.description|safe }}
</div>
{% with featured_image=codebase.get_featured_image() %}
{% if featured_image is not none %}
<div id="image-gallery" class="my-4" data-title="{{ codebase.title }}" data-images="{{ codebase.get_image_urls()|tojson|forceescape }}">
{{ image(featured_image, "max-900x600", class="img-fluid") }}
{% if featured_image is not none or codebase.youtube_url %}
<div
id="image-gallery"
class="my-4"
data-title="{{ codebase.title }}"
data-images="{{ codebase.get_image_urls()|tojson|forceescape }}"
{% if codebase.youtube_url %}
data-video-url="{{ codebase.youtube_url }}"
{% endif %}
>
{% if featured_image is not none %}
{{ image(featured_image, "max-900x600", class="img-fluid") }}
{% endif %}
{{ vite_asset("apps/image_gallery.ts") }}
</div>
{% endif %}
Expand All @@ -155,7 +176,23 @@
<h2 class='card-title'><u>Cite this Model</u></h2>
<div class='pb-3'>
<div id='citation-text'>
{{ markdown(release.citation_text) }}
<div class="mb-3">{{ markdown(release.citation_text) }}</div>
{% if codebase.citable_associated_publication_links %}
<p class="mb-1"><strong>Associated publications to cite</strong></p>
<div class="mb-3">
{% for publication in codebase.citable_associated_publication_links %}
<div class="mb-2">
<span
class="doi-citation"
data-doi-link="{{ publication }}"
data-fallback-text="{{ publication }}"
>
<a href="{{ publication }}" target="_blank" rel="nofollow">{{ publication }}</a>
</span>
</div>
{% endfor %}
</div>
{% endif %}
</div>
<button class='btn btn-clipboard btn-outline-info' data-clipboard-target='#citation-text'>
<i class='fas fa-copy'></i> Copy citation text to clipboard
Expand Down Expand Up @@ -186,18 +223,32 @@
<p class='card-text'>{{ markdown(codebase.replication_text) }}</p>
</div>
{% endif %}
{% if codebase.associated_publication_text %}
{% if codebase.associated_publications %}
{% set ns = namespace(has_uncited_publications=false) %}
{% for publication in codebase.associated_publications %}
{% if not publication.include_in_citation %}
{% set ns.has_uncited_publications = true %}
{% endif %}
{% endfor %}
{% if ns.has_uncited_publications %}
<div class='pt-1'>
<h2 class='card-title'><i class='fas fa-book'></i> <u>Associated Publication(s)</u></h2>
<p class='card-text'>
{% if release.live or has_change_perm %}
{{ markdown(codebase.associated_publication_text) }}
{% for publication in codebase.associated_publications %}
{% if not publication.include_in_citation %}
<div class="mb-1">
<a href="{{ publication.doi }}" target="_blank" rel="nofollow">{{ publication.doi }}</a>
</div>
{% endif %}
{% endfor %}
{% else %}
<i class='fas fa-lock'>(private)</i>
{% endif %}
</p>
</div>
{% endif %}
{% endif %}
{% if codebase.references_text %}
<div class='pt-1'>
<h2 class='card-title'><i class='fas fa-book'></i> <u>References</u></h2>
Expand Down Expand Up @@ -357,6 +408,17 @@
</a>
</div>
{% endif %}
{% if release.input_data_url %}
<b class='card-title'>Input Data</b>
<div class="card-text mb-3">
<a href="{{ release.input_data_url }}" class="d-block text-truncate">
<span class='badge bg-info'>
{{ strip_url_scheme(release.input_data_url) }}
</span>
</a>
</div>
{% endif %}

{% if release.output_data_url %}
<b class='card-title'>Output Data</b>
<div class="card-text mb-3">
Expand Down Expand Up @@ -620,6 +682,58 @@
<script>
document.addEventListener("DOMContentLoaded", function(event) {
new ClipboardJS('.btn-clipboard');

const doiCitationElements = document.querySelectorAll(".doi-citation[data-doi-link]");

const toCanonicalDoiLink = (rawDoiLink) => {
if (!rawDoiLink) {
return null;
}
const trimmed = rawDoiLink.trim();
if (!trimmed) {
return null;
}
return trimmed.replace(/^http:\/\//i, "https://");
};

const toDoiValue = (doiLink) => {
if (!doiLink) {
return null;
}
return doiLink.replace(/^https?:\/\/(?:dx\.)?doi\.org\//i, "").trim();
};

const renderFallbackLink = (element, doiLink, fallbackText) => {
const href = doiLink || fallbackText;
if (!href) {
return;
}
element.innerHTML = `<a href="${href}" target="_blank" rel="nofollow">${fallbackText || href}</a>`;
};

doiCitationElements.forEach(async (element) => {
const doiLink = toCanonicalDoiLink(element.dataset.doiLink);
const doiValue = toDoiValue(doiLink);
const fallbackText = element.dataset.fallbackText || doiLink;

if (!doiLink || !doiValue) {
renderFallbackLink(element, doiLink, fallbackText);
return;
}

try {
const citationUrl = `https://citation.doi.org/format?doi=${encodeURIComponent(doiValue)}&style=apa&lang=en-US`;
const response = await fetch(citationUrl);
const citationText = response.ok ? (await response.text()).trim() : "";
if (citationText) {
element.textContent = citationText;
} else {
renderFallbackLink(element, doiLink, fallbackText);
}
} catch (error) {
renderFallbackLink(element, doiLink, fallbackText);
}
});
});
</script>
{% endscript %}
Expand Down
27 changes: 21 additions & 6 deletions django/library/metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,13 @@ def to_textual_creative_work(cls, text: str) -> dict:
"text": text,
}

@classmethod
def to_url_creative_work(cls, url: str) -> dict:
return {
"@type": "CreativeWork",
"url": url,
}

@classmethod
def license_to_creative_work(cls, license) -> dict:
creative_work_license = {
Expand All @@ -137,6 +144,7 @@ def url_to_datafeed(cls, url: str) -> dict:

@classmethod
def _common_codebase_fields(cls, codebase) -> dict:
associated_publication_links = codebase.associated_publication_links
return dict(
type_="SoftwareSourceCode",
name=codebase.title,
Expand All @@ -150,12 +158,16 @@ def _common_codebase_fields(cls, codebase) -> dict:
]
if text
]
+ [
cls.to_url_creative_work(doi)
for doi in codebase.citable_associated_publication_links
]
or None,
# tags are sorted so that comparisons are deterministic
keywords=[tag.name for tag in codebase.tags.all().order_by("name")] or None,
publisher=cls.COMSES_ORGANIZATION,
description=codebase.description.raw,
referencePublication=codebase.associated_publication_text or None,
referencePublication=associated_publication_links or None,
)

@classmethod
Expand Down Expand Up @@ -196,6 +208,13 @@ def _convert_release_language(cls, release_language) -> dict:
@classmethod
def _convert_release(cls, release) -> CodeMeta:
codebase = release.codebase
supporting = []
# prefer listing input data first, then output data
if getattr(release, "input_data_url", None):
supporting.append(cls.url_to_datafeed(release.input_data_url))
if release.output_data_url:
supporting.append(cls.url_to_datafeed(release.output_data_url))

return CodeMeta(
**cls._common_codebase_fields(codebase),
id_=release.permanent_url,
Expand All @@ -218,11 +237,7 @@ def _convert_release(cls, release) -> CodeMeta:
downloadUrl=f"{settings.BASE_URL}{release.get_download_url()}",
operatingSystem=release.os,
releaseNotes=release.release_notes.raw,
supportingData=(
cls.url_to_datafeed(release.output_data_url)
if release.output_data_url
else None
),
supportingData=supporting or None,
# FIXME: need better guidance on author vs contributor fields in CodeMeta
author=cls.convert_contributors(
release.author_release_contributors, "author"
Expand Down
45 changes: 45 additions & 0 deletions django/library/migrations/0038_codebase_associated_publications_and_more.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
# Generated by Django 5.2.11 on 2026-05-26 16:13

from django.db import migrations, models


class Migration(migrations.Migration):

dependencies = [
("library", "0037_initial_github_integration_overview_content"),
]

operations = [
migrations.AddField(
model_name="codebase",
name="associated_publications",
field=models.JSONField(
blank=True,
Comment on lines +13 to +17
default=list,
help_text="List of DOI links associated with this codebase. Each item should include a DOI link and whether it should appear in the citation area.",
),
),
migrations.AddField(
model_name="codebase",
name="preferred_citation",
field=models.TextField(
blank=True,
help_text="Legacy preferred citation text. Use associated_publications to control what appears in the citation area.",
),
),
migrations.AddField(
model_name="codebase",
name="youtube_url",
field=models.URLField(
blank=True,
help_text="Optional YouTube URL showcasing this codebase (e.g., a demo or tutorial video).",
),
),
migrations.AddField(
model_name="codebaserelease",
name="input_data_url",
field=models.URLField(
blank=True, help_text="Permanent URL to input data used by this model."
),
),
]
49 changes: 45 additions & 4 deletions django/library/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1089,6 +1089,12 @@ class Codebase(index.Indexed, ModeratedContent, ClusterableModel):
"URL to code repository, e.g., https://github.com/comses/wolf-sheep"
),
)
youtube_url = models.URLField(
blank=True,
help_text=_(
"Optional YouTube URL showcasing this codebase (e.g., a demo or tutorial video)."
),
)
replication_text = models.TextField(
blank=True,
help_text=_("URL / DOI / citation for the original model being replicated"),
Expand All @@ -1106,6 +1112,19 @@ class Codebase(index.Indexed, ModeratedContent, ClusterableModel):
"DOI, Permanent URL, or citation to a publication associated with this codebase."
),
)
preferred_citation = models.TextField(
blank=True,
help_text=_(
"Legacy preferred citation text. Use associated_publications to control what appears in the citation area."
),
)
associated_publications = models.JSONField(
default=list,
blank=True,
help_text=_(
"List of DOI links associated with this codebase. Each item should include a DOI link and whether it should appear in the citation area."
),
)
tags = ClusterTaggableManager(through=CodebaseTag)
# evaluate this JSONField as an add-anything way to record relationships between this Codebase and other entities
# with URLs / resolvable identifiers
Expand Down Expand Up @@ -1317,6 +1336,27 @@ def publication_year(self):
self.last_published_on.year if self.last_published_on else date.today().year
)

@staticmethod
def _publication_doi(publication: dict) -> str:
return (publication.get("doi") or "").strip()

@property
def associated_publication_links(self):
return [
doi
for publication in self.associated_publications
if (doi := self._publication_doi(publication))
]

@property
def citable_associated_publication_links(self):
return [
doi
for publication in self.associated_publications
if publication.get("include_in_citation")
and (doi := self._publication_doi(publication))
]

@property
def all_contributors(self):
"""
Expand Down Expand Up @@ -1529,7 +1569,6 @@ def get_or_create_draft(self, initial_version: str | None = None):
# reset fields that should not be copied over to a new draft
draft_release.doi = None
draft_release.release_notes = ""
draft_release.output_data_url = ""
draft_release.save()
return draft_release

Expand Down Expand Up @@ -1856,6 +1895,9 @@ class Status(models.TextChoices):
output_data_url = models.URLField(
blank=True, help_text=_("Permanent URL to output data from this model.")
)
input_data_url = models.URLField(
blank=True, help_text=_("Permanent URL to input data used by this model.")
)
version_number = models.CharField(
max_length=32, help_text=_("semver string, e.g., 1.0.5, see semver.org")
)
Expand Down Expand Up @@ -3378,10 +3420,9 @@ def __init__(self, release: CodebaseRelease):
release.citation_text,
codebase.references_text,
codebase.replication_text,
codebase.associated_publication_text,
]
if text
]
] + codebase.citable_associated_publication_links

if release.live:
self.first_published = release.first_published_at.date()
Expand Down Expand Up @@ -3737,7 +3778,7 @@ def convert(cls, codebase: Codebase):
```
"""
# FIXME: establish CommonMetadata for Codebases as well and change signature to operate on CommonMetadata
# add references_text and associated_publication_text fields when better structured metadata for those fields are available
# add references_text and associated_publications fields when better structured metadata for those fields are available
metadata = {
"creators": cls.to_citable_authors(codebase.all_author_contributors),
"titles": [{"title": codebase.title}],
Expand Down
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