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Clean mapper class
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@genie9
genie9 committed Apr 5, 2022
1 parent 00c2618 commit 05ab87c
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Showing 2 changed files with 16 additions and 124 deletions.
1 change: 0 additions & 1 deletion metadata_backend/helpers/metax_api_handler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,6 @@ async def update_dataset_with_doi_info(self, doi_info: Dict, _metax_ids: List) -
mapped_metax_data = mapper.map_metadata()
bulk_data.append({"identifier": id["metaxIdentifier"], "research_dataset": mapped_metax_data})

# for id in metax_ids:
async with ClientSession() as sess:
resp = await sess.patch(
f"{self.metax_url}{self.rest_route}",
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139 changes: 16 additions & 123 deletions metadata_backend/helpers/metax_mapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,104 +15,6 @@ class MetaDataMapper:
https://raw.githubusercontent.com/CSCfi/metax-api/master/src/metax_api/api/rest/v2/schemas/att_dataset_schema.json
"""

{
"Person": {
"properties": {
"@type": {"type": "string", "enum": ["Person"]},
"identifier": {
"description": "An unambiguous reference to the resource within a given context.",
"type": "string",
"format": "uri",
"example": ["http://orcid.org/0000-0002-1825-0097"],
},
"name": {
"title": "Name",
"description": (
"This property contains a name of the agent. This property can be repeated for different "
"versions of the name (e.g. the name in different languages)"
),
"type": "string",
},
"member_of": {
"description": (
"Indicates that a person is a member of the Organization with no indication of the "
"nature of that membership or the role played."
),
"type": "object",
"$ref": "#/definitions/Organization",
},
"contributor_type": {
"description": "Contributor type of the Agent. Reference data from DataCite.",
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/Concept"},
},
},
"required": ["@type", "name", "member_of"],
},
}
{
"Organization": {
"description": "An organization.",
"type": "object",
"properties": {
"@type": {"type": "string", "enum": ["Organization"]},
"identifier": {
"type": "string",
"format": "uri",
"example": ["http://orcid.org/0000-0002-1825-0097"],
},
"name": {
"type": "object",
"$ref": "#/definitions/langString",
},
"contributor_type": {
"@id": "http://uri.suomi.fi/datamodel/ns/mrd#contributorType",
"description": (
"Contributor type of the Organization. Based on the subset of the DataCite reference data."
),
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/Concept"},
},
},
"required": ["@type"],
}
}
{
"Concept": {
"description": "An idea or notion; a unit of thought.",
"type": "object",
"properties": {
"identifier": {
"description": "This is the IRI identifier for the concept",
"type": "string",
"format": "uri",
},
"pref_label": {
"description": (
"The preferred lexical label for a resource, in a given language. A resource has no more than "
"one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel "
"without language tag. The range of skos:prefLabel is the class of RDF plain literals. "
"skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."
),
"type": "object",
"$ref": "#/definitions/langString",
},
"definition": {
"description": "A statement or formal explanation of the meaning of a concept.",
"type": "object",
"$ref": "#/definitions/langString",
},
"in_scheme": {
"description": (
"Relates a resource (for example a concept) to a concept scheme in which it is included."
),
"type": "string", # "uri": "http://uri.suomi.fi/codelist/fairdata/identifier_type/code/doi",
"format": "uri",
},
"required": ["identifier"],
},
}
}
{
"ResearchDataset": {
# DOI
Expand Down Expand Up @@ -183,16 +85,16 @@ class MetaDataMapper:
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/ResearchAgent"},
},
# TODO: need more info
# the only field with FUNDER, study
# TODO: will be implemented later
# describes study from same folder/submission for mapped datasets
"is_output_of": {
"title": "Producer project",
"description": "A project that has caused the dataset to be created",
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/Project"},
},
# contributor - Rights Holder
# can this be also organisation?
# TODO: This can be an organisation at some point
"rights_holder": {
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/ResearchAgent"},
Expand All @@ -204,7 +106,7 @@ class MetaDataMapper:
"items": {"type": "object", "$ref": "#/definitions/Concept"},
},
# language
# cannot be mapped to Metax unless we take Lexvo schema in to use
# TODO: cannot be mapped as is to Metax unless we take Lexvo schema in to use
"language": {
"type": "array",
"items": {
Expand All @@ -230,7 +132,7 @@ class MetaDataMapper:
},
},
},
# geoLocations
# geoLocations, MUST be WGS84 coordinates, https://epsg.io/4326
"spatial": {
"geographic_name": {
"description": (
Expand Down Expand Up @@ -260,7 +162,8 @@ class MetaDataMapper:
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/PeriodOfTime"},
},
# dataset from same folder/submission ?
# TODO: will be implemented later
# dataset from same folder/submission
"relation": {
"type": "array",
"items": {
Expand Down Expand Up @@ -303,17 +206,17 @@ class MetaDataMapper:
},
},
},
# subject Yrjö Leino
# TODO: will be implemented later
"field_of_science": {
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/Concept"},
},
# TODO: Needs clarification
# TODO: Need clarification on necessarity of this field
"remote_resources": {
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/WebResource"},
},
# restricted - ask Metax team for a link to REMS
# restricted
"access_rights": {
"type": "object",
"$ref": "#/definitions/RightsStatement",
Expand All @@ -323,8 +226,7 @@ class MetaDataMapper:
"type": "array",
"items": {"type": "object", "$ref": "#/definitions/ResearchAgent"},
},
# sizes field need either some indication on incomming type of data or MUST be in bytes
# Though now dates schema is array so maybe data type is better solution for multiple object inputs
# TODO: will be implemented later
"total_remote_resources_byte_size": {
"type": "integer",
},
Expand Down Expand Up @@ -399,12 +301,7 @@ def _map_creators(self, creators: List) -> None:
def _map_contributors(self, contributors: List) -> None:
"""Map contributors.
contributors (other then Rights Holder, Data Curator, Distributor)
-> contributor
contributors Rights Holder -> rights_holder
contributors Data Curator -> curator
:param submitter_data: Contributors data from
:param contributors: Contributors data from
"""
LOG.info("Mapping contributors")
LOG.debug(contributors)
Expand Down Expand Up @@ -449,11 +346,7 @@ def _map_contributors(self, contributors: List) -> None:
def _map_dates(self, dates: List) -> None:
"""Map dates.
dates Updated -> modified
dates Issued -> issued
dates Collected -> temporal
:param submitter_data: Dates data from datacite
:param dates: Dates data from datacite
"""
LOG.info("Mapping dates")
LOG.debug(dates)
Expand Down Expand Up @@ -495,9 +388,9 @@ def _map_spatial(self, locations: List) -> None:
If geoLocationPoint or geoLocationBox is comming with location data
lat lon coordinates will be mapped to wkt geometric presentation.
Inputs should be in degrees as geographic coordinate system (GCS) is used here.
Inputs MUST be WGS84 degrees coordinates as geographic coordinate system (GCS) is used here.
:param location: GeoLocations data from datacite
:param locations: GeoLocations data from datacite
"""
LOG.info("Mapping locations")
LOG.debug(locations)
Expand Down Expand Up @@ -528,7 +421,7 @@ def _map_spatial(self, locations: List) -> None:
def _map_other_identifier(self, identifiers: List) -> None:
"""Map alternateIdentifiers.
:param location: Alternate identifiers data from datacite
:param identifiers: Alternate identifiers data from datacite
"""
LOG.info("Mapping alternate identifiers")
LOG.debug(identifiers)
Expand Down

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