diff --git a/scipost_django/journals/models/publication.py b/scipost_django/journals/models/publication.py
index d0013b94c96e3491c811f60720daa0192ca18e73..07f48f3b7fa1392b9412f5319c828200a107b188 100644
--- a/scipost_django/journals/models/publication.py
+++ b/scipost_django/journals/models/publication.py
@@ -473,6 +473,11 @@ class Publication(models.Model):
def pubfracs_sum_to_1(self):
"""Checks that the support fractions sum up to one."""
return self.pubfracs.aggregate(Sum("fraction"))["fraction__sum"] == 1
+
+ @property
+ def proofs_repository(self):
+ """Return the proofs repository for the publication."""
+ return self.accepted_submission.production_stream.proofs_repository
@property
def compensated_expenditures(self):
diff --git a/scipost_django/journals/views.py b/scipost_django/journals/views.py
index b6f90a157eea878421c69d68889da245b9eacb45..14eac8adfdb810b9b2b728ed44c26444ff936694 100644
--- a/scipost_django/journals/views.py
+++ b/scipost_django/journals/views.py
@@ -7,6 +7,8 @@ import hashlib
import json
import os
import re
+
+import gitlab
from profiles.models import Profile
import random
import string
@@ -923,11 +925,16 @@ def reset_author_associations(publication_object: Publication) -> None:
"""Deletes all PublicationAuthorsTable entries for the given publication_object and repopulates it based on the author_list."""
PublicationAuthorsTable.objects.filter(publication=publication_object).delete()
- author_query_list = search_for_authors(publication_object)
- author_dict_list = build_author_dict_list(publication_object, author_query_list)
+ author_string_list, author_affiliation_ids = fetch_tex_author_info(
+ publication_object
+ )
+ author_query_list = search_for_authors(publication_object, author_string_list)
+ author_render_list = build_author_render_list(
+ author_string_list, author_query_list, author_affiliation_ids
+ )
- # We add the succesful authors from the author_dict_list to the PublicationAuthorsTable.
- for author_dict in author_dict_list:
+ # We add the succesful authors from the author_render_list to the PublicationAuthorsTable.
+ for author_dict in author_render_list:
PublicationAuthorsTable.objects.create(
publication=publication_object, profile=author_dict["profile"]
)
@@ -977,40 +984,51 @@ def add_author(request, doi_label: str) -> HttpResponse:
),
)
- author_query_list = search_for_authors(publication)
- author_dict_list = build_author_dict_list(publication, author_query_list)
+ author_string_list, author_affiliation_ids = fetch_tex_author_info(publication)
+ author_query_list = search_for_authors(publication, author_string_list)
+ author_render_list = build_author_render_list(
+ author_string_list, author_query_list, author_affiliation_ids
+ )
return render(
request,
"journals/add_author_list.html",
{
- "author_list": author_dict_list,
+ "author_list": author_render_list,
"selected_author_id": int(request.POST["selected_author_id"]),
},
)
- author_query_list = search_for_authors(publication)
- author_dict_list = build_author_dict_list(publication, author_query_list)
+ # Fetch authors and affiliations as they appear in the TeX file.
+ author_string_list, author_affiliation_ids = fetch_tex_author_info(publication)
+ author_query_list = search_for_authors(publication, author_string_list)
+ author_render_list = build_author_render_list(
+ author_string_list, author_query_list, author_affiliation_ids
+ )
+
+ # Update and save the author_list in the publication object.
+ publication.author_list = ", ".join(author_string_list)
+ publication.save()
context = {
"publication": publication,
"form": form,
- "author_list": author_dict_list,
+ "author_list": author_render_list,
}
return render(request, "journals/add_author.html", context)
-def search_for_authors(publication_object: Publication) -> list:
- """Creates a list of (Profile) queryset objects based on the publication_object's.author_list [string]."""
+def search_for_authors(
+ publication_object: Publication, author_string_list: list[str]
+) -> list:
+ """Creates a list of (Profile) queryset objects based on the strings in author_string_list."""
author_profile_query_list = []
authors_metadata_table = PublicationAuthorsTable.objects.filter(
publication=publication_object
)
- for i, tex_author in enumerate(
- publication_object.author_list.split(", ")
- ): # Author1, Author2, ...
+ for i, tex_author in enumerate(author_string_list): # Author1, Author2, ...
# If an author is already on the index of authors_metadata_table, do not search.
if (
not authors_metadata_table.exists()
@@ -1028,14 +1046,16 @@ def search_for_authors(publication_object: Publication) -> list:
return author_profile_query_list
-def build_author_dict_list(
- publication_object: Publication, author_profile_query_list: list
+def build_author_render_list(
+ author_string_list: list[str],
+ author_profile_query_list: list,
+ author_affiliation_ids: list[list[int]],
) -> list:
- """Creates a list of dictionaries for each author in the publication_object's.author_list [string]. This list is used to render the author list in the add_author view."""
+ """Creates a list of dictionaries for each author. This list is used to render the author list in the add_author view."""
author_dict_lsit = []
- for author_profile_query, tex_author in zip(
- author_profile_query_list, publication_object.author_list.split(", ")
+ for author_profile_query, tex_author, their_affiliations in zip(
+ author_profile_query_list, author_string_list, author_affiliation_ids
): # Author1, Author2, ...
author_profile = (
author_profile_query.first() if len(author_profile_query) < 2 else None
@@ -1055,7 +1075,7 @@ def build_author_dict_list(
{
"tex_name": tex_author,
"profile": author_profile,
- "affiliations": [1, 2],
+ "affiliations": their_affiliations,
"first_name_guess": first_name_guess,
"last_name_guess": last_name_guess,
"has_name_warning": has_name_warning,
@@ -1066,6 +1086,83 @@ def build_author_dict_list(
return author_dict_lsit
+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 fetch_affiliation_list(publication: Publication) -> list[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.
+ """
+
+ tex_contents = publication.proofs_repository.fetch_publication_tex()
+ return extract_affiliations_from_tex(tex_contents)
+
+
+def fetch_tex_author_info(
+ publication: Publication,
+) -> tuple[list[str], list[list[int]]]:
+ """Fetches information for each author from the TeX file of the publication."""
+
+ tex_contents = publication.proofs_repository.fetch_publication_tex()
+ author_field = re.findall(
+ "%%%%%%%%%% TODO: AUTHORS(.*?)%%%%%%%%%% END TODO: AUTHORS",
+ tex_contents,
+ re.DOTALL,
+ )[0]
+ author_texts = author_field.strip().split("\n")
+
+ if len(author_texts) > 1 and " and" in author_texts[-2]:
+ author_texts[-2] = author_texts[-2].replace(" and", ",").replace("\nand ", "\n")
+
+ author_list = []
+ affiliation_list = []
+ for author_text in author_texts:
+ has_supperscript = re.search("textsuperscript", author_text) is not None
+ has_affiliation = re.search("\d", author_text) is not None
+
+ delimiter: str = r"\\textsuperscript" if has_supperscript else ","
+
+ author = re.findall(rf"(.*?){delimiter}", author_text)[0]
+ author_list.append(author)
+
+ # If no affiliation is present, we add them all.
+ if not has_affiliation:
+ total_affiliations = len(extract_affiliations_from_tex(tex_contents))
+ default_affiliations = list(range(1, total_affiliations + 1))
+ affiliation_list.append(default_affiliations)
+ continue
+
+ superscript = re.findall("textsuperscript\{(.*?)\}", author_text)[0]
+
+ # 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]
+ affiliation_list.append(affiliations)
+
+ return author_list, affiliation_list
+
+
@permission_required("scipost.can_draft_publication", return_403=True)
@transaction.atomic
def author_affiliations(request, doi_label: str) -> HttpResponse:
@@ -1123,7 +1220,7 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
% publication.doi_label,
)
- tex_affiliations = get_affiliations()
+ tex_affiliations = fetch_affiliation_list(publication)
context = {
"publication": publication,
"form": form,
@@ -1135,15 +1232,10 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
authors = PublicationAuthorsTable.objects.filter(
publication=publication
)
- affiliations_for_author = [
- [1, 2],
- [1],
- [2],
- [1, 2],
- [1, 2],
- [1],
- ] # TODO: TEX DATA
- for author, their_affiliations in zip(authors, affiliations_for_author):
+ authors_list, affiliations_of_authors = fetch_tex_author_info(
+ publication
+ )
+ for author, their_affiliations in zip(authors, affiliations_of_authors):
author.affiliations.set(
[affiliations[index - 1] for index in their_affiliations]
)
@@ -1153,7 +1245,7 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
return publication_detail(request, doi_label)
- tex_affiliations = get_affiliations()
+ tex_affiliations = fetch_affiliation_list(publication)
context = {
"publication": publication,
"form": form,
@@ -1163,41 +1255,6 @@ def author_affiliations(request, doi_label: str) -> HttpResponse:
return render(request, "journals/author_affiliations.html", context)
-def get_affiliations() -> dict:
- # First we find the section where the affiliations exist. --TODO: Enable below for git integration.
- # section = re.findall('TODO: AFFILIATIONS\n(.*?)\n%%%%%%%%%% END', paper, re.DOTALL)[0] + "%" # We add a % to the end to make sure the regex works.
- section = (
- r"""{\bf 1} Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
-\\
-{\bf 2} California Institute of Technology, Pasadena, California 91125, USA"""
- + "%"
- )
- affids = re.findall(
- r"\{\\bf (\d+)\}", section
- ) # We look for affiliations based on the {\bf k} format.
- if affids:
- affids = [int(i) for i in affids] # We count the number of affiliations.
-
- if affids != list(range(1, len(affids) + 1)):
- raise ValueError(
- "Affiliation numbers not in correct order! Check the TeX file. Are they all present?"
- )
-
- affiliations = [] # We create a list of affiliations.
- for k in affids: # Extract the affiliation text for each affiliation id.
- aff = re.findall(rf"bf {k}}} (.*?)({{|\%)", section, re.DOTALL)[0][0]
- aff = (
- aff.replace("\\", " ").replace(" ", " ").strip()
- ) # Remove leading and trailing whitespaces.
-
- affiliations.append(aff)
- return affiliations
- else:
- # There is only one affiliation OR something went wrong. We return all as is.
- # We remove the % at the end (which was put for the other case to work).
- return [section[:-1]]
-
-
@permission_required("scipost.can_draft_publication", return_403=True)
def update_references(request, doi_label):
"""
diff --git a/scipost_django/production/models.py b/scipost_django/production/models.py
index b21bee18a61819bf19ae30a284c7764eea070b05..48ce75866e657de11c0e8a4a04c16677ec0b6f32 100644
--- a/scipost_django/production/models.py
+++ b/scipost_django/production/models.py
@@ -15,6 +15,7 @@ from django.dispatch import receiver
from django.db.models import Value
from django.db.models.functions import Concat
from django.conf import settings
+import gitlab
from guardian.shortcuts import assign_perm, remove_perm
@@ -47,6 +48,7 @@ from scipost.storage import SecureFileStorage
if TYPE_CHECKING:
from submissions.models import Submission
+ from journals.models import Publication
class ProductionUser(models.Model):
@@ -534,6 +536,20 @@ class ProofsRepository(models.Model):
return paths
+ def fetch_publication_tex(self) -> str:
+ """ Fetches the TeX file of the publication. """
+ gl = gitlab.Gitlab("https://" + settings.GITLAB_URL, private_token = settings.GITLAB_KEY)
+ gl.auth()
+
+ project = gl.projects.get(self.git_path)
+ publication: "Publication" = self.stream.submission.publications.first()
+
+ main_file_path = publication.doi_label.replace(".", "_") +".tex"
+ publication_file = project.files.get(file_path = main_file_path, ref = "main")
+ tex_contents = publication_file.decode().decode("utf-8")
+
+ return tex_contents
+
def __str__(self) -> str:
return f"Proofs repo for {self.stream}"