From 4fdf50673d4c87d20d1cf1c7ccd6eff92aaf2c86 Mon Sep 17 00:00:00 2001
From: Alexander Minges <alexander.minges@uni-due.de>
Date: Thu, 10 Jul 2025 11:18:00 +0200
Subject: [PATCH] fix: Update AbstractProcessor to accept optional console
 parameter

---
 doi2dataset.py | 31 ++++++++++++++++++++-----------
 1 file changed, 20 insertions(+), 11 deletions(-)

diff --git a/doi2dataset.py b/doi2dataset.py
index 2aac6e5..936b571 100755
--- a/doi2dataset.py
+++ b/doi2dataset.py
@@ -489,7 +489,7 @@ class Config:
         if not config_path.exists():
             raise FileNotFoundError(f"Config file not found: {config_path}")
 
-        with open(config_path, 'r', encoding='utf-8') as f:
+        with open(config_path, encoding='utf-8') as f:
             config_data = yaml.safe_load(f)
 
         # Validate PI email addresses
@@ -769,14 +769,16 @@ class AbstractProcessor:
     """
     Retrieves and processes abstracts from CrossRef and OpenAlex.
     """
-    def __init__(self, api_client: APIClient):
+    def __init__(self, api_client: APIClient, console: Console | None = None):
         """
         Initialize with an APIClient instance.
 
         Args:
             api_client (APIClient): The API client to use for requests.
+            console (Console | None): Rich console instance for output.
         """
         self.api_client = api_client
+        self.console = console or Console()
 
     def get_abstract(self, doi: str, data: dict[str, Any], license: License) -> Abstract:
         """
@@ -793,26 +795,26 @@ class AbstractProcessor:
         license_ok = {"cc-by", "cc-by-sa", "cc-by-nc", "cc-by-nc-sa", "cc0", "pd"}
 
         if license.short in license_ok:
-            console.print(f"\n{ICONS['info']} License {license.name} allows derivative works. Pulling abstract from CrossRef.", style="info")
+            self.console.print(f"\n{ICONS['info']} License {license.name} allows derivative works. Pulling abstract from CrossRef.", style="info")
             crossref_abstract = self._get_crossref_abstract(doi)
             if crossref_abstract:
                 return Abstract(text=crossref_abstract, source="crossref")
             else:
-                console.print(f"\n{ICONS['warning']} No abstract found in CrossRef!", style="warning")
+                self.console.print(f"\n{ICONS['warning']} No abstract found in CrossRef!", style="warning")
         else:
             if license.name:
-                console.print(f"\n{ICONS['info']} License {license.name} does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
+                self.console.print(f"\n{ICONS['info']} License {license.name} does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
             else:
-                console.print(f"\n{ICONS['info']} Custom license does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
+                self.console.print(f"\n{ICONS['info']} Custom license does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
 
 
         openalex_abstract = self._get_openalex_abstract(data)
         if openalex_abstract:
             return Abstract(text=openalex_abstract, source="openalex")
         else:
-            console.print(f"\n{ICONS['warning']} No abstract found in OpenAlex!", style="warning")
+            self.console.print(f"\n{ICONS['warning']} No abstract found in OpenAlex!", style="warning")
 
-        console.print(f"\n{ICONS['warning']} No abstract found in either CrossRef nor OpenAlex!", style="warning")
+        self.console.print(f"\n{ICONS['warning']} No abstract found in either CrossRef nor OpenAlex!", style="warning")
         return Abstract(text="", source="none")
 
     def _get_crossref_abstract(self, doi: str) -> str | None:
@@ -1332,7 +1334,7 @@ class MetadataProcessor:
             dict[str, Any]: The complete metadata dictionary.
         """
         license_info = LicenseProcessor.process_license(data)
-        abstract_processor = AbstractProcessor(self.api_client)
+        abstract_processor = AbstractProcessor(self.api_client, self.console)
         abstract = abstract_processor.get_abstract(self.doi, data, license_info)
         citation_builder = CitationBuilder(data, self.doi, self.pi_finder, self.ror)
 
@@ -1593,7 +1595,8 @@ def process_doi_batch(
     default_subject: str = "Medicine, Health and Life Sciences",
     contact_mail: str | None = None,
     upload: bool = False,
-    ror: bool = False
+    ror: bool = False,
+    console: Console | None = None
 ) -> dict[str, list[Any]]:
     """
     Process a batch of DOIs and return a summary of results.
@@ -1606,12 +1609,17 @@ def process_doi_batch(
         contact_mail (str | None): Contact email address.
         upload (bool): Flag indicating whether to upload metadata to Dataverse.
         ror (bool): Flag indication whether to use ROR id for affiliation.
+        console (Console | None): Rich console instance for output.
 
     Returns:
         dict[str, list[Any]]: Dictionary with keys 'success' and 'failed'.
     """
     results: dict[str, list[Any]] = {"success": [], "failed": []}
 
+    # Use provided console or create a new one
+    if console is None:
+        console = Console()
+
     progress_columns = [
         SpinnerColumn(),
         TextColumn("[bold blue]{task.description:<50}"),
@@ -1791,7 +1799,8 @@ def main():
             default_subject=args.subject,
             contact_mail=args.contact_mail,
             upload=args.upload,
-            ror=args.use_ror
+            ror=args.use_ror,
+            console=console
         )