From d4e9e58f17973595ecc98eeb1846254b4ead1968 Mon Sep 17 00:00:00 2001
From: George Katsikas <giorgakis.katsikas@gmail.com>
Date: Fri, 14 Feb 2025 17:21:41 +0100
Subject: [PATCH] =?UTF-8?q?refactor(metadata):=20=E2=99=BB=EF=B8=8F=20simp?=
=?UTF-8?q?lify=20and=20beautify=20specifying=20author=20affiliations?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
More reliable method of extracting affiliations. Improve table presentation. Sticky form submit buttons. Use clientside validation for the form. Allow non-numerical identifiers for affiliations.
---
scipost_django/journals/models/publication.py | 40 ++----
.../journals/author_affiliations.html | 115 +++++++++++-------
.../journals/author_affiliations_orgcell.html | 34 ++++--
scipost_django/journals/views.py | 64 ++++------
4 files changed, 136 insertions(+), 117 deletions(-)
diff --git a/scipost_django/journals/models/publication.py b/scipost_django/journals/models/publication.py
index 5016779bb..d355dc29a 100644
--- a/scipost_django/journals/models/publication.py
+++ b/scipost_django/journals/models/publication.py
@@ -590,32 +590,18 @@ class Publication(models.Model):
| models.Q(doi_label__startswith=f"{doi_anchor}-")
).order_by("doi_label")
- @staticmethod
- def extract_affiliations_from_tex(tex_contents: str) -> list[str]:
- """
- Extracts the affiliations from the TeX contents, constructing a list with each affiliation as a string.
- This list is used to render the affiliation list in the add_author view.
- """
- affiliation_field = re.findall("%%%%%%%%%% TODO: AFFILIATIONS(.*?)%%%%%%%%%% END TODO: AFFILIATIONS", tex_contents, re.DOTALL)[0]
- affiliation_texts = affiliation_field.strip().split("\n\\\\")
-
- affiliation_list = []
- for affiliation_text in affiliation_texts:
- affiliation = re.findall("{\\\\bf\s*\d+} (.*)", affiliation_text, re.DOTALL) or [affiliation_text]
- affiliation = affiliation[0].strip()
- affiliation_list.append(affiliation)
-
- return affiliation_list
-
- def construct_affiliation_list(self) -> list[str]:
+ @cached_property
+ def tex_affiliations(self) -> list[tuple[str, str]]:
"""
- Constructs a list of affiliations from the TeX file of the publication.
- This list is used to render the affiliation list in the add_author view.
+ Extracts the affiliations from the TeX contents, constructing a list
+ with each affiliation as an (identifier, text) pair
+ Matches the pattern: `{\\bf #} Affiliation Text ...\\\\`
+ Returns a list of tuples with the affiliation identifier (number) and the affiliation text.
"""
- if self.tex_contents:
- return Publication.extract_affiliations_from_tex(self.tex_contents)
- return []
+ return re.findall(
+ r"{\\bf (.+?)\}\s?(.+?)(?:\\\\\n|%{5,})", self.tex_contents, re.DOTALL
+ )
@cached_property
def tex_contents(self) -> str | None:
@@ -624,7 +610,7 @@ class Publication(models.Model):
return self.proofs_repository.fetch_tex()
- def construct_tex_author_info(self) -> tuple[list[str], list[list[int]]]:
+ def construct_tex_author_info(self) -> tuple[list[str], list[list[str]]]:
"""Puts together information for each author from the TeX file of the publication."""
tex_contents = self.tex_contents or ""
@@ -661,8 +647,8 @@ class Publication(models.Model):
# If no affiliation is present, we add them all.
if not has_affiliation:
- total_affiliations = len(Publication.extract_affiliations_from_tex(tex_contents))
- default_affiliations = list(range(1, total_affiliations +1))
+ total_affiliations = len(self.tex_affiliations)
+ default_affiliations = list(range(1, total_affiliations + 1))
affiliation_list.append(default_affiliations)
continue
@@ -670,7 +656,7 @@ class Publication(models.Model):
# We remove anything following the first "$" character which separates affiliations from emails.
affiliations = superscript.split("$")[0].strip().split(",")
- affiliations = [int(aff.strip()) for aff in affiliations]
+ affiliations = [aff.strip() for aff in affiliations]
affiliation_list.append(affiliations)
return author_list, affiliation_list
diff --git a/scipost_django/journals/templates/journals/author_affiliations.html b/scipost_django/journals/templates/journals/author_affiliations.html
index f277f632a..a752216b9 100644
--- a/scipost_django/journals/templates/journals/author_affiliations.html
+++ b/scipost_django/journals/templates/journals/author_affiliations.html
@@ -1,6 +1,8 @@
{% extends 'scipost/base.html' %}
-{% block pagetitle %}: Author Affiliations{% endblock pagetitle %}
+{% block pagetitle %}
+ : Author Affiliations
+{% endblock pagetitle %}
{% load bootstrap %}
{% load common_extras %}
@@ -19,51 +21,76 @@
{% block content %}
- <div class="row">
- <div class="col-12">
- <h1 class="highlight">Author affiliations for <a href="{{ publication.get_absolute_url }}">{{ publication.doi_label }}</a></h1>
- <br>
- <div>
- <p>Can't find it in the selector? <a href="{% url 'organizations:organization_create' %}" target="_blank">Add a new organization to our database</a> (opens in new window)</p>
- </div>
-
- <div class="d-flex flex-row gap-2">
- <form hx-post="{% url 'journals:author_affiliations' doi_label=publication.doi_label%}" id="add_affiliation_form" hx-swap="outerHTML">
- {% csrf_token %}
- {{ form|bootstrap_inline }}
- <input name="add" class="btn btn-primary" type="submit" value="Add Organization" form="add_affiliation_form"/>
- </form>
- <form action="{% url 'journals:author_affiliations' doi_label=publication.doi_label%}" id="submit_affiliation_form" method="POST">
- {% csrf_token %}
- <input name="submit" class="btn btn-secondary" type="submit" value="Submit" form="submit_affiliation_form"/>
- <input type="hidden" name="total_affiliations" value="{{ affiliation_texts|length }}"/>
- </form>
- </div>
-
- <br>
- <h3>List of affiliations:</h3>
- <table class = "ms-4" id="author_affiliations_list">
+ <h1 class="highlight">
+ Author affiliations for <a href="{{ publication.get_absolute_url }}">{{ publication.doi_label }}</a>
+ </h1>
+ <br />
+ <div>
+ <p>
+ Can't find it in the selector? <a href="{% url 'organizations:organization_create' %}" target="_blank">Add a new organization to our database</a> (opens in new window)
+ </p>
+ </div>
+
+ <div class="position-relative">
+
+ <form class="d-flex flex-row gap-2 p-2 position-sticky top-0 bg-white"
+ hx-post="{% url 'journals:author_affiliations' doi_label=publication.doi_label %}"
+ id="add_affiliation_form"
+ hx-swap="outerHTML">
+ <input name="add"
+ class="btn btn-primary"
+ type="submit"
+ value="Add Organization"
+ form="add_affiliation_form" />
+ {{ form|bootstrap_inline }}
+ </form>
+
+ <h3>List of affiliations:</h3>
+ <form action="{% url 'journals:author_affiliations' doi_label=publication.doi_label %}"
+ id="submit_affiliation_form"
+ method="POST">
+ {% csrf_token %}
+ <table class="table mb-4" id="author_affiliations_list">
<tr>
- <th> </th>
- <th class="ps-3"> # </th>
- <th class="ps-2"> Affiliation Text </th>
- <th class="ps-4"> Organization </th>
+ <th></th>
+ <th>#</th>
+ <th>Affiliation Text</th>
+ <th>Organization</th>
</tr>
- {% for affiliation_tex, default_affiliation in affiliation_texts|zip_dj:default_affiliations %}
- <tr>
- <td> <input type="radio" name="checked_row_id" value="{{ forloop.counter }}" form = "add_affiliation_form" id="{{ forloop.counter }}" {% if forloop.counter == checked_row_id %}checked{% endif %}> </td>
- <td class="ps-3"><label for="{{ forloop.counter }}">{{ forloop.counter }}.</label></td>
- <td class="ps-2"><label for="{{ forloop.counter }}">{{affiliation_tex}}</label></td>
- {% include "journals/author_affiliations_orgcell.html" with checked_row_id=forloop.counter organization=default_affiliation %}
- </tr>
- {% endfor %}
- </table>
+
+ {% for identifier, text, organization in affiliations %}
+ <tr class="align-middle">
+ <td>
+ <input class="me-2" type="radio" name="checked_row_id" value="{{ identifier }}" form = "add_affiliation_form" id="{{ identifier }}"
+ {% if identifier == checked_row_id %}checked{% endif %}
+ />
+ </td>
+ <td>
+ <label for="{{ identifier }}">{{ identifier }}.</label>
+ </td>
+ <td>
+ <label class="w-100" for="{{ identifier }}">{{ text }}</label>
+ </td>
+ {% include "journals/author_affiliations_orgcell.html" with checked_row_id=identifier organization=organization %}
+ </tr>
+ {% endfor %}
+
+
+ </table>
+ <input name="submit"
+ class="btn btn-primary"
+ type="submit"
+ value="Submit"
+ form="submit_affiliation_form" />
+ </form>
+
</div>
- </div>
-{% endblock %}
+ {% endblock %}
+
+
-{% block footer_script %}
- {{ block.super }}
- {{ form.media }}
-{% endblock footer_script %}
+ {% block footer_script %}
+ {{ block.super }}
+ {{ form.media }}
+ {% endblock footer_script %}
diff --git a/scipost_django/journals/templates/journals/author_affiliations_orgcell.html b/scipost_django/journals/templates/journals/author_affiliations_orgcell.html
index f6752ba99..235b2b35f 100644
--- a/scipost_django/journals/templates/journals/author_affiliations_orgcell.html
+++ b/scipost_django/journals/templates/journals/author_affiliations_orgcell.html
@@ -1,9 +1,25 @@
-<td class="ps-4" id="organization_column_{{checked_row_id}}">
- <input type="hidden" value="{{organization.id}}" form="submit_affiliation_form" name="affiliation_id_{{checked_row_id}}">
- {% if organization is not None %}
- <img src="{{ organization.country.flag }}" style="width:15px;" alt="{{ organization.country }} flag" title="{{organization.get_country_display}}" data-bs-toggle="tooltip"/>
- <a href="{{ organization.get_absolute_url }}">{{ organization.name }} </a>
- {% else %}
- -- No affiliation --
- {% endif %}
-</td>
\ No newline at end of file
+<td id="organization_column_{{ checked_row_id }}">
+
+ {% if organization is not None %}
+ <input type="hidden"
+ value="{{ organization.id }}"
+ form="submit_affiliation_form"
+ name="affiliation_id_{{ checked_row_id }}"
+ required />
+ <img src="{{ organization.country.flag }}"
+ style="width:15px"
+ alt="{{ organization.country }} flag"
+ title="{{ organization.get_country_display }}"
+ data-bs-toggle="tooltip" />
+ <a href="{{ organization.get_absolute_url }}">{{ organization.name }}</a>
+ {% else %}
+ <div class="text-nowrap">
+ <input type="text"
+ form="submit_affiliation_form"
+ name="affiliation_id_{{ checked_row_id }}"
+ placeholder="-- No affiliation --"
+ required />
+ </div>
+ {% endif %}
+
+</td>
diff --git a/scipost_django/journals/views.py b/scipost_django/journals/views.py
index 013267520..79cfd1bf7 100644
--- a/scipost_django/journals/views.py
+++ b/scipost_django/journals/views.py
@@ -1043,28 +1043,32 @@ def build_author_render_list(
@permission_required("scipost.can_draft_publication", return_403=True)
@transaction.atomic
def author_affiliations(request, doi_label: str) -> HttpResponse:
- def _affiliations_from_post(request: HttpRequest) -> list[Organization | None]:
- """Iterate over the POST request keys 'affiliation_id_k' to build a list of affiliation Organization objects."""
- total_affiliations_from_tex = int(request.POST.get("total_affiliations"))
-
- affiliations = []
- for i in range(total_affiliations_from_tex):
- affiliation_id = request.POST.get(f"affiliation_id_{i +1}")
- affiliation_id = int(affiliation_id) if affiliation_id else None
- affiliation = Organization.objects.filter(pk=affiliation_id).first()
- affiliations.append(affiliation)
-
- return affiliations
-
- # -------------
publication = get_object_or_404(Publication, doi_label=doi_label)
if not publication.is_draft and not request.user.has_perm(
"can_publish_accepted_submission"
):
- raise Http404("You do not have permission to edit this non-draft Publication")
+ raise PermissionDenied(
+ "You do not have permission to edit this non-draft Publication"
+ )
form = AuthorsTableOrganizationSelectForm(request.POST or None)
+ organizations = {
+ identifier: Organization.objects.filter(pk=value).first()
+ if request.POST and (value := request.POST.get(f"affiliation_id_{identifier}"))
+ else None
+ for identifier, _ in publication.tex_affiliations
+ }
+ affiliations = [
+ (i, t, o)
+ for (i, t), o in zip(publication.tex_affiliations, organizations.values())
+ ]
+ context = {
+ "publication": publication,
+ "form": form,
+ "affiliations": affiliations,
+ }
+
if request.POST:
if not request.POST.get("submit"):
context = {
@@ -1084,11 +1088,13 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
return response
else:
# First we need to check if all of the affiliations exist.
- affiliations = _affiliations_from_post(request)
- total_affiliations_from_tex = int(request.POST.get("total_affiliations"))
+ total_affiliations_from_tex = len(
+ list(filter(lambda x: x.startswith("affiliation_id_"), request.POST))
+ )
total_non_empty_affiliations = len(
- list(filter(lambda x: x is not None, affiliations))
+ list(filter(lambda x: x is not None, organizations.values()))
)
+ print(total_affiliations_from_tex, total_non_empty_affiliations)
if total_non_empty_affiliations != total_affiliations_from_tex:
messages.warning(
@@ -1097,24 +1103,15 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
% publication.doi_label,
)
- tex_affiliations = publication.construct_affiliation_list()
- context = {
- "publication": publication,
- "form": form,
- "affiliation_texts": tex_affiliations,
- "default_affiliations": affiliations, # To reconstruct the form.
- }
return render(request, "journals/author_affiliations.html", context)
else:
authors = PublicationAuthorsTable.objects.filter(
publication=publication
)
- authors_list, affiliations_of_authors = (
- publication.construct_tex_author_info()
- )
- for author, their_affiliations in zip(authors, affiliations_of_authors):
+ _, author_aff_ids = publication.construct_tex_author_info()
+ for author, aff_ids in zip(authors, author_aff_ids):
author.affiliations.set(
- [affiliations[index - 1] for index in their_affiliations]
+ [organizations.get(i) for i in aff_ids] or None
)
publication.cf_author_affiliation_indices_list = []
@@ -1122,13 +1119,6 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
return publication_detail(request, doi_label)
- tex_affiliations = publication.construct_affiliation_list()
- context = {
- "publication": publication,
- "form": form,
- "affiliation_texts": tex_affiliations,
- "default_affiliations": [None] * len(tex_affiliations),
- }
return render(request, "journals/author_affiliations.html", context)
--
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