diff --git a/doi2dataset.py b/doi2dataset.py index 9cbd676..683f4dc 100755 --- a/doi2dataset.py +++ b/doi2dataset.py @@ -158,7 +158,6 @@ class BaseMetadataField[T]: multiple: bool value: T type: FieldType = field(init=False) - expanded_value: dict[str, str] | None = field(default=None) def __post_init__(self) -> None: """ @@ -197,29 +196,19 @@ class PrimitiveMetadataField(BaseMetadataField[str]): def _set_type(self) -> None: self.type = FieldType.PRIMITIVE - def to_dict(self) -> dict[str, str | bool | dict[str, str]]: + def to_dict(self) -> dict[str, str | bool]: """ Convert the primitive metadata field to a dictionary representation. Returns: dict[str, str | bool]: Dictionary with field properties. """ - - if self.expanded_value: - return { - "typeName": self.name, - "typeClass": self.type.value, - "multiple": self.multiple, - "value": self.value, - "expandedValue": self.expanded_value - } - else: - return { - "typeName": self.name, - "typeClass": self.type.value, - "multiple": self.multiple, - "value": self.value, - } + return { + "typeName": self.name, + "typeClass": self.type.value, + "multiple": self.multiple, + "value": self.value, + } @dataclass class ControlledVocabularyMetadataField(BaseMetadataField[str | list[str]]): @@ -275,36 +264,6 @@ class CompoundMetadataField( "value": value_list } -@dataclass -class Institution: - """ - Represents an institution or organization. - - Attributes: - display_name (str): The name of the institution. - ror (str): Research Organization Registry identifier (optional). - """ - display_name: str - ror: str = "" - - def affiliation_field(self) -> PrimitiveMetadataField: - """ - Create a metadata field for the affiliation. - - Returns: - PrimitiveMetadataField: A metadata field representing the institution, - using ROR ID when available. - """ - if self.ror: - expanded_value = { - "scheme": "http://www.grid.ac/ontology/", - "termName": self.display_name, - "@type": "https://schema.org/Organization" - } - return PrimitiveMetadataField("authorAffiliation", False, self.ror, expanded_value) - else: - return PrimitiveMetadataField("authorAffiliation", False, self.display_name) - @dataclass class Person: """ @@ -315,47 +274,16 @@ class Person: given_name (str): Given name of the person. orcid (str): ORCID identifier (optional). email (str): Email address (optional). - affiliation (Institution): Affiliation of the person (optional). + affiliation (str): Affiliation of the person (optional). project (list[str]): List of associated projects. """ family_name: str given_name: str orcid: str = "" email: str = "" - affiliation: Institution | str = "" + affiliation: str = "" project: list[str] = field(default_factory=list) - def to_dict(self) -> dict[str, str | list[str] | dict[str, str]]: - """ - Convert Person to a dictionary for JSON serialization. - - Handles affiliations properly by checking if the affiliation - is an Institution object or a string. - - Returns: - dict: A dictionary containing the person's information including - name, contact details, and affiliation. - """ - return_dict: dict[str, str | list[str] | dict[str, str]] = { - "family_name": self.family_name, - "given_name": self.given_name, - "orcid": self.orcid, - "email": self.email, - "project": self.project - } - - if isinstance(self.affiliation, Institution): - if self.affiliation.ror: - return_dict["affiliation"] = self.affiliation.ror - elif self.affiliation.display_name: - return_dict["affiliation"] = self.affiliation.display_name - else: - return_dict["affiliation"] = "" - else: - return_dict["affiliation"] = "" - - return return_dict - def format_name(self) -> str: """ Format the name in 'Family, Given' order. @@ -367,59 +295,37 @@ class Person: def author_fields(self) -> list[PrimitiveMetadataField | ControlledVocabularyMetadataField]: """ - Build metadata fields for the author. - - The method handles both Institution objects and string values for affiliations. - Different fields are generated depending on whether ORCID is available. + Build metadata fields for an author. Returns: - list: List of metadata fields representing the author, including name, - affiliation, and optionally ORCID identifier information. + list: List of metadata fields representing the author. """ - affiliation_field = None - if isinstance(self.affiliation, Institution): - affiliation_field = self.affiliation.affiliation_field() - else: - affiliation_field = PrimitiveMetadataField("authorAffiliation", False, self.affiliation) - if self.orcid: return [ PrimitiveMetadataField("authorName", False, self.format_name()), - affiliation_field, + PrimitiveMetadataField("authorAffiliation", False, self.affiliation), ControlledVocabularyMetadataField("authorIdentifierScheme", False, "ORCID"), PrimitiveMetadataField("authorIdentifier", False, self.orcid) ] else: return [ PrimitiveMetadataField("authorName", False, self.format_name()), - affiliation_field + PrimitiveMetadataField("authorAffiliation", False, self.affiliation) ] def dataset_contact_fields(self) -> list[PrimitiveMetadataField]: """ - Generate metadata fields for dataset contact. - - The method handles both Institution objects and string values for affiliations. - Creates fields for the contact name, affiliation, and email address. + Build metadata fields for dataset contact information. Returns: - list: List of metadata fields for the dataset contact including name, - affiliation, and email address. + list: List of metadata fields for the dataset contact. """ - - affiliation_field = None - if isinstance(self.affiliation, Institution): - affiliation_field = self.affiliation.affiliation_field() - else: - affiliation_field = PrimitiveMetadataField("datasetContactAffiliation", False, self.affiliation) - return [ PrimitiveMetadataField("datasetContactName", False, self.format_name()), - affiliation_field, + PrimitiveMetadataField("datasetContactAffiliation", False, self.affiliation), PrimitiveMetadataField("datasetContactEmail", False, self.email) ] - @dataclass class License: """ @@ -447,12 +353,6 @@ class Abstract: source: str def __post_init__(self): - """ - Validate that the abstract source is one of the allowed values. - - Raises: - ValueError: If source is not one of the allowed values. - """ allowed_sources = ["crossref", "openalex", "none"] if self.source not in allowed_sources: raise ValueError(f"{self.source} is not valid! Needs to be one of {str(allowed_sources)}.") @@ -998,7 +898,7 @@ class CitationBuilder: """ Builds various citation-related metadata fields. """ - def __init__(self, data: dict[str, Any], doi: str, pi_finder: PIFinder, ror: bool = False) -> None: + def __init__(self, data: dict[str, Any], doi: str, pi_finder: PIFinder) -> None: """ Initialize the CitationBuilder with data, DOI, and a PIFinder. @@ -1009,7 +909,6 @@ class CitationBuilder: """ self.data = data self.doi = doi - self.ror = ror self.pi_finder = pi_finder def build_other_ids(self) -> list[list[PrimitiveMetadataField]]: @@ -1096,7 +995,7 @@ class CitationBuilder: authorship (dict[str, Any]): Authorship metadata. Returns: - Person: Processed author + Person: Processed author. """ display_name = author.get("display_name", "") given_name, family_name = NameProcessor.split_name(display_name) @@ -1104,19 +1003,9 @@ class CitationBuilder: person = Person(family_name, given_name) if affiliations := authorship.get("affiliations"): - affiliation = Institution(affiliations[0].get("raw_affiliation_string", "").strip()) - + affiliation = affiliations[0].get("raw_affiliation_string", "").strip() person.affiliation = affiliation - if self.ror: - if institutions := authorship.get("institutions"): - institution = institutions[0] - if institution.get("ror"): - affiliation = Institution(institution.get("display_name"), institution.get("ror")) - - person.affiliation = affiliation - - if orcid := author.get("orcid"): person.orcid = normalize_orcid(orcid) @@ -1213,7 +1102,6 @@ class MetadataProcessor: default_subject: str = "Other", contact_mail: str | None = None, upload: bool = False, - ror: bool= False, console: Console | None = None, progress: Progress | None = None, task_id: TaskID | None = None @@ -1227,7 +1115,6 @@ class MetadataProcessor: output_path (Path | None): Path where metadata will be saved. default_subject (str): Default subject. contact_mail (str | None): Contact email address. - ror (bool): Whether to use ROR id for affiliation upload (bool): Whether to upload metadata. console (Console | None): Rich console instance. progress (Progress | None): Progress bar instance. @@ -1247,7 +1134,6 @@ class MetadataProcessor: pi_objects = [Person(**pi) for pi in config.PIS] self.pi_finder = PIFinder(pi_objects) self.upload = upload - self.ror = ror self.progress = progress self.task_id = task_id @@ -1364,10 +1250,9 @@ class MetadataProcessor: license_info = LicenseProcessor.process_license(data) abstract_processor = AbstractProcessor(self.api_client) 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) authors, corresponding_authors = citation_builder.build_authors() - author_fields: list[list[PrimitiveMetadataField | ControlledVocabularyMetadataField]] = [] corresponding_author_fields: list[list[PrimitiveMetadataField]] = [] for author in authors: @@ -1566,28 +1451,8 @@ class MetadataProcessor: """ if self.output_path: try: - # Custom JSON encoder to handle custom objects - class CustomEncoder(json.JSONEncoder): - """ - Custom JSON encoder that handles objects with to_dict method. - - This allows for proper serialization of custom classes like - Institution and Person by calling their to_dict method when - available. - - Args: - o: The object to serialize. - - Returns: - A JSON-serializable representation of the object. - """ - def default(self, o: Any) -> Any: - if hasattr(o, 'to_dict'): - return o.to_dict() - return super().default(o) - with open(self.output_path, "w", encoding="utf-8") as f: - json.dump(metadata, f, indent=4, ensure_ascii=False, cls=CustomEncoder) + json.dump(metadata, f, indent=4, ensure_ascii=False) self.console.print(f"{ICONS['save']} Metadata saved in: {self.output_path}", style="info") except Exception as e: self.console.print(f"{ICONS['error']} Error saving metadata: {str(e)}\n", style="error") @@ -1672,8 +1537,7 @@ def process_doi_batch( depositor: str | None = None, default_subject: str = "Medicine, Health and Life Sciences", contact_mail: str | None = None, - upload: bool = False, - ror: bool = False + upload: bool = False ) -> dict[str, list[Any]]: """ Process a batch of DOIs and return a summary of results. @@ -1685,7 +1549,6 @@ def process_doi_batch( default_subject (str): Default subject for metadata. 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. Returns: dict[str, list[Any]]: Dictionary with keys 'success' and 'failed'. @@ -1754,7 +1617,6 @@ def process_doi_batch( default_subject=default_subject, contact_mail=contact_mail, upload=upload, - ror=ror, console=console, progress=progress, task_id=status_task @@ -1826,12 +1688,7 @@ if __name__ == "__main__": parser.add_argument( "-u", "--upload", help="Upload to Dataverse", - action="store_true" - ) - parser.add_argument( - "-r", "--use-ror", - help="Use ROR ID if available", - action="store_true" + action='store_true' ) args = parser.parse_args() @@ -1870,8 +1727,7 @@ if __name__ == "__main__": depositor=args.depositor, default_subject=args.subject, contact_mail=args.contact_mail, - upload=args.upload, - ror=args.use_ror + upload=args.upload )