From 8da607b713b34b28b39f286a1132b8d760465cc8 Mon Sep 17 00:00:00 2001
From: George Katsikas <giorgakis.katsikas@gmail.com>
Date: Mon, 5 Aug 2024 17:33:10 +0200
Subject: [PATCH] add supplemental information publication resources
fixes #316
---
scipost_django/journals/forms.py | 16 ++++
scipost_django/journals/managers.py | 3 +
.../0135_alter_publicationresource__type.py | 25 ++++++
scipost_django/journals/models/resource.py | 2 +
.../manage_publication_resources.html | 8 +-
.../journals/publication_detail.html | 78 ++++++++++++-------
scipost_django/journals/urls/general.py | 5 ++
scipost_django/journals/views.py | 48 ++++++++++++
8 files changed, 153 insertions(+), 32 deletions(-)
create mode 100644 scipost_django/journals/migrations/0135_alter_publicationresource__type.py
diff --git a/scipost_django/journals/forms.py b/scipost_django/journals/forms.py
index 4c22f8114..c956f800e 100644
--- a/scipost_django/journals/forms.py
+++ b/scipost_django/journals/forms.py
@@ -693,6 +693,22 @@ class DraftPublicationForm(forms.ModelForm):
)
self.instance.topics.add(*self.submission.topics.all())
+ # Create supplementary information for any provided external links
+ if self.submission.code_repository_url:
+ PublicationResource.objects.get_or_create(
+ publication=self.instance,
+ _type=PublicationResource.TYPE_SUP_INFO,
+ url=self.submission.code_repository_url,
+ comments="Code repository",
+ )
+ if self.submission.data_repository_url:
+ PublicationResource.objects.get_or_create(
+ publication=self.instance,
+ _type=PublicationResource.TYPE_SUP_INFO,
+ url=self.submission.data_repository_url,
+ comments="Data repository",
+ )
+
def prefill_fields(self):
if self.submission:
self.fields["title"].initial = self.submission.title
diff --git a/scipost_django/journals/managers.py b/scipost_django/journals/managers.py
index c2bce4fdc..4d73e6848 100644
--- a/scipost_django/journals/managers.py
+++ b/scipost_django/journals/managers.py
@@ -96,3 +96,6 @@ class PublicationResourceQuerySet(models.QuerySet):
def live(self):
return self.filter(_type=self.model.TYPE_LIVE_REPO)
+
+ def sup_info(self):
+ return self.filter(_type=self.model.TYPE_SUP_INFO)
diff --git a/scipost_django/journals/migrations/0135_alter_publicationresource__type.py b/scipost_django/journals/migrations/0135_alter_publicationresource__type.py
new file mode 100644
index 000000000..93516ca8c
--- /dev/null
+++ b/scipost_django/journals/migrations/0135_alter_publicationresource__type.py
@@ -0,0 +1,25 @@
+# Generated by Django 4.2.10 on 2024-08-05 13:50
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+ dependencies = [
+ ("journals", "0134_journal_alternative_journals"),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name="publicationresource",
+ name="_type",
+ field=models.CharField(
+ choices=[
+ ("source_repo", "Publication source files repository"),
+ ("release_repo", "Codebase release version (archive) repository"),
+ ("live_repo", "Live (external) repository"),
+ ("supplemental_info", "Supplemental information"),
+ ],
+ max_length=32,
+ ),
+ ),
+ ]
diff --git a/scipost_django/journals/models/resource.py b/scipost_django/journals/models/resource.py
index 30580074d..ecc10045e 100644
--- a/scipost_django/journals/models/resource.py
+++ b/scipost_django/journals/models/resource.py
@@ -11,10 +11,12 @@ class PublicationResource(models.Model):
TYPE_SOURCE_REPO = "source_repo"
TYPE_RELEASE_ARCHIVE_REPO = "release_repo"
TYPE_LIVE_REPO = "live_repo"
+ TYPE_SUP_INFO = "supplemental_info"
TYPE_CHOICES = (
(TYPE_SOURCE_REPO, "Publication source files repository"),
(TYPE_RELEASE_ARCHIVE_REPO, "Codebase release version (archive) repository"),
(TYPE_LIVE_REPO, "Live (external) repository"),
+ (TYPE_SUP_INFO, "Supplemental information"),
)
_type = models.CharField(max_length=32, choices=TYPE_CHOICES)
publication = models.ForeignKey(
diff --git a/scipost_django/journals/templates/journals/manage_publication_resources.html b/scipost_django/journals/templates/journals/manage_publication_resources.html
index 5a400bcda..e3045e99e 100644
--- a/scipost_django/journals/templates/journals/manage_publication_resources.html
+++ b/scipost_django/journals/templates/journals/manage_publication_resources.html
@@ -26,6 +26,10 @@
<div hx-get="{% url "journals:_hx_publication_resource_list" doi_label=publication.doi_label %}"
hx-trigger="load once"></div>
- <a class="btn btn-sm btn-primary"
- href="{{ publication.get_absolute_url }}">Back to Publication</a>
+ <div class="d-flex flex-row">
+ <a class="btn btn-sm btn-secondary"
+ href="{{ publication.get_absolute_url }}">Back to Publication</a>
+ <a class="btn btn-sm btn-primary ms-auto"
+ href="{% url "journals:fetch_publication_resources" publication.doi_label %}">Fetch from preprint server</a>
+ </div>
{% endblock content %}
diff --git a/scipost_django/journals/templates/journals/publication_detail.html b/scipost_django/journals/templates/journals/publication_detail.html
index bcd95c126..9c8e1c6fd 100644
--- a/scipost_django/journals/templates/journals/publication_detail.html
+++ b/scipost_django/journals/templates/journals/publication_detail.html
@@ -85,38 +85,56 @@
{% endif %}
<hr class="mt-5 mb-4"/>
- {% if publication.topics.all or perms.scipost.can_manage_ontology %}
- <h3 class="mt-2">Ontology / Topics</h3>
- See full <a href="{% url 'ontology:ontology' %}">Ontology</a> or <a href="{% url 'ontology:topics' %}">Topics</a> database.
- <br>
- <br>
-
- <div>
- {% for topic in publication.topics.all %}
- <span class="label label-secondary"><a href="{% url 'ontology:topic_details' slug=topic.slug %}">{{ topic }}</a>{% if perms.scipost.can_manage_ontology %} <a href="{% url 'journals:publication_remove_topic' doi_label=publication.doi_label slug=topic.slug %}"><span class="text-danger">{% include 'bi/x-circle-fill.html' %}</span></a>{% endif %}</span>
- {% empty %}
- <div>No Topic has yet been associated to this Publication</div>
- {% endfor %}
- </div>
+ <div class="row">
+ <div class="col">
+ {% if publication.topics.all or perms.scipost.can_manage_ontology %}
+ <h3 class="mt-2">Ontology / Topics</h3>
+ See full <a href="{% url 'ontology:ontology' %}">Ontology</a> or <a href="{% url 'ontology:topics' %}">Topics</a> database.
+ <br>
+ <br>
- {% if perms.scipost.can_manage_ontology %}
-
- <br>
- <ul class="list-inline">
- <li class="list-inline-item">
- <form class="form-inline" action="{% url 'journals:publication_add_topic' doi_label=publication.doi_label %}" method="post">
- <ul class="list-inline">
- <li class="list-inline-item">Add an existing Topic:</li>
- <li class="list-inline-item">{% csrf_token %}{{ select_topic_form }}</li>
- <li class="list-inline-item"><input class="btn btn-outline-secondary" type="submit" value="Link"></li>
- </ul>
- </form>
- </li>
- <li class="list-inline-item p-2">Can't find the Topic you need? <a href="{% url 'ontology:topic_create' %}" target="_blank">Create it</a> (opens in new window)</li>
- </ul>
- {% endif %}
+ <div>
+ {% for topic in publication.topics.all %}
+ <span class="label label-secondary"><a href="{% url 'ontology:topic_details' slug=topic.slug %}">{{ topic }}</a>{% if perms.scipost.can_manage_ontology %} <a href="{% url 'journals:publication_remove_topic' doi_label=publication.doi_label slug=topic.slug %}"><span class="text-danger">{% include 'bi/x-circle-fill.html' %}</span></a>{% endif %}</span>
+ {% empty %}
+ <div>No Topic has yet been associated to this Publication</div>
+ {% endfor %}
+ </div>
- {% endif %}
+ {% if perms.scipost.can_manage_ontology %}
+
+ <br>
+ <ul class="list-inline">
+ <li class="list-inline-item">
+ <form class="form-inline" action="{% url 'journals:publication_add_topic' doi_label=publication.doi_label %}" method="post">
+ <ul class="list-inline">
+ <li class="list-inline-item">Add an existing Topic:</li>
+ <li class="list-inline-item">{% csrf_token %}{{ select_topic_form }}</li>
+ <li class="list-inline-item"><input class="btn btn-outline-secondary" type="submit" value="Link"></li>
+ </ul>
+ </form>
+ </li>
+ <li class="list-inline-item p-2">Can't find the Topic you need? <a href="{% url 'ontology:topic_create' %}" target="_blank">Create it</a> (opens in new window)</li>
+ </ul>
+ {% endif %}
+
+ {% endif %}
+ </div>
+ {% if publication.resources.sup_info %}
+ <div class="col-12 col-md col-xl-4">
+ <details {% if publication.resources.sup_info|length < 4 %}open{% endif %}
+ class="hcard hcard-secondary bg-opacity-25">
+ <summary class="list-triangle"><h3>Supplemental Information</h3></summary>
+ <p class="text-muted">External links to supplemental resources; opens in a new tab.</p>
+ <ul class="list-unstyled">
+ {% for sup_info in publication.resources.sup_info.all %}
+ <li><a class="fs-6" href="{{ sup_info.url }}" target="_blank">{{ sup_info.comments }}</a></li>
+ {% endfor %}
+ </ul>
+ </details>
+ </div>
+ {% endif %}
+ </div>
<h3 class="mt-4">
Author{{ publication.authors.all|length|pluralize }} / Affiliation{{ affiliations_list|length|pluralize }}: mappings to Contributors and Organizations
diff --git a/scipost_django/journals/urls/general.py b/scipost_django/journals/urls/general.py
index d258dd286..93f940bec 100644
--- a/scipost_django/journals/urls/general.py
+++ b/scipost_django/journals/urls/general.py
@@ -218,6 +218,11 @@ urlpatterns = [
journals_views.HTMXInlinePublicationResourceListView.as_view(),
name="_hx_publication_resource_list",
),
+ path(
+ "admin/<publication_doi_label:doi_label>/fetch_publication_resources",
+ journals_views.fetch_publication_resources,
+ name="fetch_publication_resources",
+ ),
# Admin: Volumes and Issues
path(
"admin/volumes/",
diff --git a/scipost_django/journals/views.py b/scipost_django/journals/views.py
index d6f18a81d..36ddd23f6 100644
--- a/scipost_django/journals/views.py
+++ b/scipost_django/journals/views.py
@@ -735,14 +735,62 @@ def draft_accompanying_publication(request, doi_label):
@permission_required("scipost.can_draft_publication", raise_exception=True)
def manage_publication_resources(request, doi_label):
publication = get_object_or_404(Publication, doi_label=doi_label)
+
+ # Determine whether to display button with automatic creation of resource
+ # Currently, only possible for ChemaRxiv submissions
+ can_fetch_resources = (
+ "chemrxiv"
+ in publication.accepted_submission.preprint.identifier_w_vn_nr.lower()
+ )
+
context = {
"publication": publication,
+ "can_fetch_resources": can_fetch_resources,
}
return TemplateResponse(
request, "journals/manage_publication_resources.html", context
)
+def fetch_publication_resources(request, doi_label):
+ publication = get_object_or_404(Publication, doi_label=doi_label)
+ if (
+ "chemrxiv"
+ not in publication.accepted_submission.preprint.identifier_w_vn_nr.lower()
+ ):
+ messages.error(
+ request, "Resource fetching is only available for ChemRxiv submissions"
+ )
+ return redirect(
+ reverse("journals:manage_publication_resources", args=(doi_label,))
+ )
+
+ # Fetch resources from ChemRxiv
+ response = requests.get(
+ f"https://chemrxiv.org/engage/chemrxiv/public-api/v1/items/doi/"
+ + publication.accepted_submission.preprint.identifier_w_vn_nr
+ )
+
+ if response.status_code != 200:
+ messages.error(request, "Resource fetching failed.")
+ return redirect(
+ reverse("journals:manage_publication_resources", args=(doi_label,))
+ )
+
+ if resources := response.json().get("suppItems", []):
+ resources = sorted(resources, key=lambda x: x.get("id"))
+
+ for resource in resources:
+ PublicationResource.objects.get_or_create(
+ publication=publication,
+ comments=resource.get("title"),
+ url=resource.get("asset", {}).get("original", {}).get("url", ""),
+ _type=PublicationResource.TYPE_SUP_INFO,
+ )
+
+ return redirect(reverse("journals:manage_publication_resources", args=(doi_label,)))
+
+
@method_decorator(login_required, name="dispatch")
@method_decorator(
permission_required("scipost.can_draft_publication", raise_exception=True),
--
GitLab