Athemis/doi2dataset
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fix: Update AbstractProcessor to accept optional console parameter

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This commit is contained in:
Alexander Minges 2025-07-10 11:18:00 +02:00
parent 2f7400e6c0
commit 4fdf50673d
Signed by: Athemis
SSH key fingerprint: SHA256:TUXshgulbwL+FRYvBNo54pCsI0auROsSEgSvueKbkZ4
1 changed files with 20 additions and 11 deletions
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31
doi2dataset.py
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@ -489,7 +489,7 @@ class Config:
if not config_path.exists(): if not config_path.exists():
raise FileNotFoundError(f"Config file not found: {config_path}") 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) config_data = yaml.safe_load(f)
# Validate PI email addresses # Validate PI email addresses
@ -769,14 +769,16 @@ class AbstractProcessor:
""" """
Retrieves and processes abstracts from CrossRef and OpenAlex. 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. Initialize with an APIClient instance.
Args: Args:
api_client (APIClient): The API client to use for requests. api_client (APIClient): The API client to use for requests.
console (Console | None): Rich console instance for output.
""" """
self.api_client = api_client self.api_client = api_client
self.console = console or Console()
def get_abstract(self, doi: str, data: dict[str, Any], license: License) -> Abstract: 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"} license_ok = {"cc-by", "cc-by-sa", "cc-by-nc", "cc-by-nc-sa", "cc0", "pd"}
if license.short in license_ok: 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) crossref_abstract = self._get_crossref_abstract(doi)
if crossref_abstract: if crossref_abstract:
return Abstract(text=crossref_abstract, source="crossref") return Abstract(text=crossref_abstract, source="crossref")
else: 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: else:
if license.name: 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: 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) openalex_abstract = self._get_openalex_abstract(data)
if openalex_abstract: if openalex_abstract:
return Abstract(text=openalex_abstract, source="openalex") return Abstract(text=openalex_abstract, source="openalex")
else: 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") return Abstract(text="", source="none")
def _get_crossref_abstract(self, doi: str) -> str | None: def _get_crossref_abstract(self, doi: str) -> str | None:
@ -1332,7 +1334,7 @@ class MetadataProcessor:
dict[str, Any]: The complete metadata dictionary. dict[str, Any]: The complete metadata dictionary.
""" """
license_info = LicenseProcessor.process_license(data) 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) abstract = abstract_processor.get_abstract(self.doi, data, license_info)
citation_builder = CitationBuilder(data, self.doi, self.pi_finder, self.ror) 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", default_subject: str = "Medicine, Health and Life Sciences",
contact_mail: str | None = None, contact_mail: str | None = None,
upload: bool = False, upload: bool = False,
ror: bool = False ror: bool = False,
console: Console | None = None
) -> dict[str, list[Any]]: ) -> dict[str, list[Any]]:
""" """
Process a batch of DOIs and return a summary of results. 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. contact_mail (str | None): Contact email address.
upload (bool): Flag indicating whether to upload metadata to Dataverse. upload (bool): Flag indicating whether to upload metadata to Dataverse.
ror (bool): Flag indication whether to use ROR id for affiliation. ror (bool): Flag indication whether to use ROR id for affiliation.
console (Console | None): Rich console instance for output.
Returns: Returns:
dict[str, list[Any]]: Dictionary with keys 'success' and 'failed'. dict[str, list[Any]]: Dictionary with keys 'success' and 'failed'.
""" """
results: dict[str, list[Any]] = {"success": [], "failed": []} results: dict[str, list[Any]] = {"success": [], "failed": []}
# Use provided console or create a new one
if console is None:
console = Console()
progress_columns = [ progress_columns = [
SpinnerColumn(), SpinnerColumn(),
TextColumn("[bold blue]{task.description:<50}"), TextColumn("[bold blue]{task.description:<50}"),
@ -1791,7 +1799,8 @@ def main():
default_subject=args.subject, default_subject=args.subject,
contact_mail=args.contact_mail, contact_mail=args.contact_mail,
upload=args.upload, upload=args.upload,
ror=args.use_ror ror=args.use_ror,
console=console
) )