Add support for ROR institution identifiers in affiliations
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1 changed files with 112 additions and 20 deletions
120
doi2dataset.py
120
doi2dataset.py
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@ -158,6 +158,7 @@ class BaseMetadataField[T]:
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multiple: bool
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value: T
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type: FieldType = field(init=False)
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expanded_value: dict[str, str] | None = field(default=None)
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def __post_init__(self) -> None:
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"""
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@ -196,13 +197,23 @@ class PrimitiveMetadataField(BaseMetadataField[str]):
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def _set_type(self) -> None:
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self.type = FieldType.PRIMITIVE
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def to_dict(self) -> dict[str, str | bool]:
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def to_dict(self) -> dict[str, str | bool | dict[str, str]]:
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"""
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Convert the primitive metadata field to a dictionary representation.
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Returns:
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dict[str, str | bool]: Dictionary with field properties.
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"""
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if self.expanded_value:
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return {
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"typeName": self.name,
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"typeClass": self.type.value,
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"multiple": self.multiple,
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"value": self.value,
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"expandedValue": self.expanded_value
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}
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else:
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return {
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"typeName": self.name,
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"typeClass": self.type.value,
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@ -264,6 +275,22 @@ class CompoundMetadataField(
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"value": value_list
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}
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@dataclass
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class Institution:
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display_name: str
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ror: str = ""
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def affiliation_field(self) -> PrimitiveMetadataField:
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if self.ror:
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expanded_value = {
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"scheme": "http://www.grid.ac/ontology/",
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"termName": self.display_name,
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"@type": "https://schema.org/Organization"
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}
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return PrimitiveMetadataField("authorAffiliation", False, self.ror, expanded_value)
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else:
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return PrimitiveMetadataField("authorAffiliation", False, self.display_name)
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@dataclass
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class Person:
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"""
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@ -274,16 +301,36 @@ class Person:
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given_name (str): Given name of the person.
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orcid (str): ORCID identifier (optional).
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email (str): Email address (optional).
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affiliation (str): Affiliation of the person (optional).
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affiliation (Institution): Affiliation of the person (optional).
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project (list[str]): List of associated projects.
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"""
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family_name: str
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given_name: str
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orcid: str = ""
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email: str = ""
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affiliation: str = ""
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affiliation: Institution | str = ""
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project: list[str] = field(default_factory=list)
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def to_dict(self) -> dict[str, str | list[str]]:
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"""Convert Person to a dictionary for JSON serialization."""
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return_dict = {
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"family_name": self.family_name,
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"given_name": self.given_name,
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"orcid": self.orcid,
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"email": self.email,
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"project": self.project
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}
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if self.affiliation.ror:
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return_dict["affiliation"] = self.affiliation.ror
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elif self.affiliation.display_name:
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return_dict["affiliation"] = self.affiliation.display_name
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else:
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return_dict["affiliation"] = ""
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return return_dict
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def format_name(self) -> str:
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"""
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Format the name in 'Family, Given' order.
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@ -300,17 +347,23 @@ class Person:
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Returns:
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list: List of metadata fields representing the author.
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"""
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affiliation_field = None
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if isinstance(self.affiliation, Institution):
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affiliation_field = self.affiliation.affiliation_field()
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else:
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affiliation_field = PrimitiveMetadataField("authorAffiliation", False, self.affiliation)
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if self.orcid:
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return [
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PrimitiveMetadataField("authorName", False, self.format_name()),
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PrimitiveMetadataField("authorAffiliation", False, self.affiliation),
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affiliation_field,
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ControlledVocabularyMetadataField("authorIdentifierScheme", False, "ORCID"),
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PrimitiveMetadataField("authorIdentifier", False, self.orcid)
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]
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else:
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return [
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PrimitiveMetadataField("authorName", False, self.format_name()),
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PrimitiveMetadataField("authorAffiliation", False, self.affiliation)
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affiliation_field
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]
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def dataset_contact_fields(self) -> list[PrimitiveMetadataField]:
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@ -320,12 +373,20 @@ class Person:
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Returns:
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list: List of metadata fields for the dataset contact.
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"""
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affiliation_field = None
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if isinstance(self.affiliation, Institution):
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affiliation_field = self.affiliation.affiliation_field()
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else:
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affiliation_field = PrimitiveMetadataField("authorAffiliation", False, self.affiliation)
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return [
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PrimitiveMetadataField("datasetContactName", False, self.format_name()),
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PrimitiveMetadataField("datasetContactAffiliation", False, self.affiliation),
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affiliation_field,
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PrimitiveMetadataField("datasetContactEmail", False, self.email)
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]
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@dataclass
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class License:
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"""
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@ -898,7 +959,7 @@ class CitationBuilder:
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"""
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Builds various citation-related metadata fields.
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"""
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def __init__(self, data: dict[str, Any], doi: str, pi_finder: PIFinder) -> None:
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def __init__(self, data: dict[str, Any], doi: str, pi_finder: PIFinder, ror: bool = False) -> None:
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"""
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Initialize the CitationBuilder with data, DOI, and a PIFinder.
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@ -909,6 +970,7 @@ class CitationBuilder:
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"""
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self.data = data
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self.doi = doi
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self.ror = ror
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self.pi_finder = pi_finder
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def build_other_ids(self) -> list[list[PrimitiveMetadataField]]:
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@ -995,7 +1057,7 @@ class CitationBuilder:
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authorship (dict[str, Any]): Authorship metadata.
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Returns:
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Person: Processed author.
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Person: Processed author
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"""
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display_name = author.get("display_name", "")
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given_name, family_name = NameProcessor.split_name(display_name)
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@ -1003,9 +1065,19 @@ class CitationBuilder:
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person = Person(family_name, given_name)
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if affiliations := authorship.get("affiliations"):
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affiliation = affiliations[0].get("raw_affiliation_string", "").strip()
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affiliation = Institution(affiliations[0].get("raw_affiliation_string", "").strip())
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person.affiliation = affiliation
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if self.ror:
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if institutions := authorship.get("institutions"):
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institution = institutions[0]
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if institution.get("ror"):
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affiliation = Institution(institution.get("display_name"), institution.get("ror"))
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person.affiliation = affiliation
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if orcid := author.get("orcid"):
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person.orcid = normalize_orcid(orcid)
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@ -1102,6 +1174,7 @@ class MetadataProcessor:
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default_subject: str = "Other",
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contact_mail: str | None = None,
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upload: bool = False,
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ror: bool= False,
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console: Console | None = None,
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progress: Progress | None = None,
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task_id: TaskID | None = None
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@ -1115,6 +1188,7 @@ class MetadataProcessor:
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output_path (Path | None): Path where metadata will be saved.
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default_subject (str): Default subject.
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contact_mail (str | None): Contact email address.
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ror (bool): Whether to use ROR id for affiliation
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upload (bool): Whether to upload metadata.
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console (Console | None): Rich console instance.
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progress (Progress | None): Progress bar instance.
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@ -1134,6 +1208,7 @@ class MetadataProcessor:
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pi_objects = [Person(**pi) for pi in config.PIS]
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self.pi_finder = PIFinder(pi_objects)
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self.upload = upload
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self.ror = ror
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self.progress = progress
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self.task_id = task_id
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@ -1250,9 +1325,10 @@ class MetadataProcessor:
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license_info = LicenseProcessor.process_license(data)
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abstract_processor = AbstractProcessor(self.api_client)
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abstract = abstract_processor.get_abstract(self.doi, data, license_info)
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citation_builder = CitationBuilder(data, self.doi, self.pi_finder)
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citation_builder = CitationBuilder(data, self.doi, self.pi_finder, self.ror)
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authors, corresponding_authors = citation_builder.build_authors()
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author_fields: list[list[PrimitiveMetadataField | ControlledVocabularyMetadataField]] = []
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corresponding_author_fields: list[list[PrimitiveMetadataField]] = []
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for author in authors:
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@ -1451,8 +1527,15 @@ class MetadataProcessor:
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"""
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if self.output_path:
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try:
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# Custom JSON encoder to handle custom objects
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class CustomEncoder(json.JSONEncoder):
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def default(self, obj):
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if hasattr(obj, 'to_dict'):
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return obj.to_dict()
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return super().default(obj)
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with open(self.output_path, "w", encoding="utf-8") as f:
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json.dump(metadata, f, indent=4, ensure_ascii=False)
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json.dump(metadata, f, indent=4, ensure_ascii=False, cls=CustomEncoder)
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self.console.print(f"{ICONS['save']} Metadata saved in: {self.output_path}", style="info")
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except Exception as e:
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self.console.print(f"{ICONS['error']} Error saving metadata: {str(e)}\n", style="error")
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@ -1537,7 +1620,8 @@ def process_doi_batch(
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depositor: str | None = None,
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default_subject: str = "Medicine, Health and Life Sciences",
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contact_mail: str | None = None,
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upload: bool = False
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upload: bool = False,
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ror: bool = False
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) -> dict[str, list[Any]]:
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"""
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Process a batch of DOIs and return a summary of results.
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@ -1549,6 +1633,7 @@ def process_doi_batch(
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default_subject (str): Default subject for metadata.
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contact_mail (str | None): Contact email address.
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upload (bool): Flag indicating whether to upload metadata to Dataverse.
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ror (bool): Flag indication whether to use ROR id for affiliation.
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Returns:
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dict[str, list[Any]]: Dictionary with keys 'success' and 'failed'.
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@ -1617,6 +1702,7 @@ def process_doi_batch(
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default_subject=default_subject,
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contact_mail=contact_mail,
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upload=upload,
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ror=ror,
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console=console,
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progress=progress,
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task_id=status_task
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@ -1688,7 +1774,12 @@ if __name__ == "__main__":
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parser.add_argument(
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"-u", "--upload",
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help="Upload to Dataverse",
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action='store_true'
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action="store_true"
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)
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parser.add_argument(
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"-r", "--use-ror",
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help="Use ROR ID if available",
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action="store_true"
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)
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args = parser.parse_args()
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@ -1727,7 +1818,8 @@ if __name__ == "__main__":
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depositor=args.depositor,
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default_subject=args.subject,
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contact_mail=args.contact_mail,
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upload=args.upload
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upload=args.upload,
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ror=args.use_ror
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)
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