Update affiliation.py

jdhapi/utils/affiliation.py

@@ -3,10 +3,25 @@
 import pycountry
 from jdhseo.utils import get_affiliation
 from jdhapi.models import Author
+
 logger = logging.getLogger(__name__)
 
 
 def get_authors(article_authors, affiliations):
+    """
+    Extracts and returns a list of authors with their respective affiliations.
+
+    Args:
+        article_authors (list): A list of author objects, where each object contains
+                                attributes like 'firstname', 'lastname', and 'orcid'.
+        affiliations (list): A list of affiliation dictionaries, where each dictionary
+                             contains 'aff_id', 'aff_pub_id', and 'authors_link' which
+                             is a list of author last names linked to the affiliation.
+
+    Returns:
+        list: A list of dictionaries, where each dictionary represents an author with
+              their 'given_names', 'surname', 'orcid', 'aff_id', and 'aff_pub_id'.
+    """
     authors = []
     for author in article_authors:
         for affiliation in affiliations:
@@ -18,20 +33,36 @@ def get_authors(article_authors, affiliations):
                         "surname": author.lastname,
                         "orcid": author.orcid,
                         "aff_id": affiliation["aff_id"],
-                        "aff_pub_id": affiliation["aff_pub_id"]
+                        "aff_pub_id": affiliation["aff_pub_id"],
                     }
         authors.append(contrib)
         # logger.debug(f'authors {authors}')
     return authors
 
 
+# ici qu'il faut chnger
 def get_affiliation_json_one(author_id, orcid_url, affiliation):
-    logger.debug('START get_affiliation_json_one')
+    """
+    Retrieve the affiliation details for an author based on ORCID URL or database information.
+
+    Args:
+        author_id (int): The ID of the author in the database.
+        orcid_url (str): The ORCID URL of the author.
+        affiliation (str): The institution affiliation of the author.
+
+    Returns:
+        dict: A dictionary containing the affiliation details with keys:
+            - "institution" (str): The institution affiliation.
+            - "city" (str): The city of the institution.
+            - "country" (str): The country code of the institution.
+            - "country_name" (str): The full country name of the institution.
+    """
+    logger.debug("START get_affiliation_json_one")
     default_affiliation = {
         "institution": affiliation,
         "city": "NOT FOUND",
         "country": "NOT FOUND",
-        "country_name": "NOT FOUND"
+        "country_name": "NOT FOUND",
     }
     if orcid_url:
         # contact_orcid
@@ -40,69 +71,107 @@ def get_affiliation_json_one(author_id, orcid_url, affiliation):
         city_country = get_affiliation(orcid)
         if city_country:
             # if city_country.find('-') != -1:
-            city = city_country.partition('-')[0].strip()
-            country = city_country.partition('-')[2].strip()
+            city = city_country.partition("-")[0].strip()
+            country = city_country.partition("-")[2].strip()
             country_name = pycountry.countries.get(alpha_2=country).name
             affiliation = {
                 "institution": affiliation,
                 "city": city,
                 "country": country,
-                "country_name": country_name
+                "country_name": country_name,
             }
         else:
             # go to retrieve from the author
-            author = Author.objects.get(
-                id=author_id)
+            author = Author.objects.get(id=author_id)
             if author.city and author.country:
-                logger.debug(f'ORCID but no city and country found - find in DB {author.lastname}')
+                logger.debug(
+                    f"ORCID but no city and country found - find in DB {author.lastname}"
+                )
                 affiliation = {
-                "institution": affiliation,
-                "city": author.city,
-                "country": author.country,
-                "country_name": author.country.name
-            }
+                    "institution": affiliation,
+                    "city": author.city,
+                    "country": author.country,
+                    "country_name": author.country.name,
+                }
             else:
-                logger.debug(f'ORCID but no city and country found - NOT found in DB - default_affiliation {author.lastname}')
-                affiliation= default_affiliation
+                logger.debug(
+                    f"ORCID but no city and country found - NOT found in DB - default_affiliation {author.lastname}"
+                )
+                affiliation = default_affiliation
     else:
         # go to retrieve from the author
-        author = Author.objects.get(
-                id=author_id)
+        author = Author.objects.get(id=author_id)
         if author.city and author.country:
-            logger.debug(f'NO ORCID but no city and country found - find in DB {author.lastname}')
+            logger.debug(
+                f"NO ORCID but no city and country found - find in DB {author.lastname}"
+            )
             affiliation = {
                 "institution": affiliation,
                 "city": author.city,
                 "country": author.country,
-                "country_name": author.country.name
+                "country_name": author.country.name,
             }
         else:
-            logger.debug(f'NO ORCID but no city and country found - NOT found in DB - default_affiliation {author.lastname}')
+            logger.debug(
+                f"NO ORCID but no city and country found - NOT found in DB - default_affiliation {author.lastname}"
+            )
             return default_affiliation
-    logger.debug('END get_affiliation_json_one')
+    logger.debug("END get_affiliation_json_one")
     return affiliation
 
 
 def get_aff_pub_id(publisher_id, aff_id):
+    """
+    Generate a formatted affiliation publisher ID.
+
+    Args:
+        publisher_id (str): The ID of the publisher.
+        aff_id (int): The affiliation ID.
+
+    Returns:
+        str: A string in the format "j_<publisher_id>_aff_00<aff_id>".
+    """
     return "j_" + publisher_id.lower() + "_aff_00" + str(aff_id)
 
 
 def get_affiliation_json(authors, publisher_id):
+    """
+    Generate a list of affiliation JSON objects for a given list of authors and a publisher ID.
+
+    Args:
+        authors (list): A list of author objects. Each author object should have the attributes 'id', 'orcid', 'affiliation', and 'lastname'.
+        publisher_id (str): The ID of the publisher.
+
+    Returns:
+        list: A list of dictionaries, each representing an affiliation. Each dictionary contains the following keys:
+            - aff_id (int): The affiliation ID.
+            - authors_link (list): A list of author last names associated with the affiliation.
+            - aff_pub_id (str): The formatted affiliation publisher ID.
+            - institution (str): The institution name (from the author's affiliation).
+    """
     affiliations = []
     i = 1
     for author in authors:
-        affiliation_one = get_affiliation_json_one(author.id, author.orcid, author.affiliation)
+        affiliation_one = get_affiliation_json_one(
+            author.id, author.orcid, author.affiliation
+        )
         if len(affiliations) == 0:
             affiliation_one["aff_id"] = i
             affiliation_one["authors_link"] = [author.lastname]
             # format j_publisherId_aff_00sup Ex: j_jdh-2021-1006_aff_001
-            affiliation_one["aff_pub_id"] = get_aff_pub_id(publisher_id, affiliation_one["aff_id"])
+            affiliation_one["aff_pub_id"] = get_aff_pub_id(
+                publisher_id, affiliation_one["aff_id"]
+            )
             affiliations.append(affiliation_one)
         else:
             # need to check if already exist
             result = next(
-                (item for item in affiliations if item['institution'] == affiliation_one['institution']),
-                {}
+                (
+                    item
+                    for item in affiliations
+                    if item["institution"] == affiliation_one["institution"]
+                ),
+                {},
             )
             if result:
                 # need to add author
@@ -111,16 +180,38 @@ def get_affiliation_json(authors, publisher_id):
                 i += 1
                 affiliation_one["aff_id"] = i
                 affiliation_one["authors_link"] = [author.lastname]
-                affiliation_one["aff_pub_id"] = get_aff_pub_id(publisher_id, affiliation_one["aff_id"])
+                affiliation_one["aff_pub_id"] = get_aff_pub_id(
+                    publisher_id, affiliation_one["aff_id"]
+                )
                 affiliations.append(affiliation_one)
     # logger.info(f'affiliations: {affiliations}')
     return affiliations
 
 
-# method to check if affiliation is default_affiliation or not
 def is_default_affiliation(affiliations):
+    """
+    Checks if any affiliation in the list has default values.
+
+    This function iterates through a list of affiliations and checks if any
+    affiliation has "NOT FOUND" as the value for the keys "city", "country",
+    or "country_name". If any of these keys have the value "NOT FOUND", the
+    function returns True, indicating that the affiliation has default values.
+
+    Args:
+        affiliations (list of dict): A list of affiliation dictionaries, where
+                                     each dictionary contains keys "city",
+                                     "country", and "country_name".
+
+    Returns:
+        bool: True if any affiliation has "NOT FOUND" as the value for "city",
+              "country", or "country_name". False otherwise.
+    """
     for affiliation in affiliations:
         # if in the affiliation the city is NOT FOUND  or country is NOT FOUND or country_name is NOT FOUND return True
-        if affiliation["city"] == "NOT FOUND" or affiliation["country"] == "NOT FOUND" or affiliation["country_name"] == "NOT FOUND":
+        if (
+            affiliation["city"] == "NOT FOUND"
+            or affiliation["country"] == "NOT FOUND"
+            or affiliation["country_name"] == "NOT FOUND"
+        ):
             return True
     return False