chore: convert json files in data directory to yaml

fuji_server/data/README.md

@@ -1,21 +1,18 @@
 # Data files
 
-
-- [`linked_vocabs/*_ontologies.json`](./linked_vocabs)
-- [`access_rights.json`](./access_rights.json): Lists COAR, EPRINTS, EU, OPENAIRE access rights. Used for evaluation of the data access level, FsF-A1-01M, which looks for metadata item `access_level`.
+- [`linked_vocabs/*_ontologies.yaml`](./linked_vocabs)
+- [`access_rights.yaml`](./access_rights.yaml): Lists COAR, EPRINTS, EU, OPENAIRE access rights. Used for evaluation of the data access level, FsF-A1-01M, which looks for metadata item `access_level`.
 - [`bioschemastypes.txt`](./bioschemastypes.txt)
 - [`creativeworktypes.txt`](./creativeworktypes.txt)
 - [`default_namespaces.txt`](./default_namespaces.txt): Excluded during evaluation of the semantic vocabulary, FsF-I2-01M.
-- [`file_formats.json`](./file_formats.json): Dictionary of scientific file formats. Used in evaluation of R1.3-02D to check the file format of the data.
+- [`file_formats.yaml`](./file_formats.yaml): Dictionary of scientific file formats. Used in evaluation of R1.3-02D to check the file format of the data.
 - [`google_cache.db`](./google_cache.db): Used for evaluating FsF-F4-01M (searchability in major catalogues like DataCite registry, Google Dataset, Mendeley, ...). Google Data search is queried for a PID in column `google_links`. It's a dataset with metadata about datasets that have a DOI or persistent identifier from `identifer.org`.
-- [`identifiers_org_resolver_data.json`](./identifiers_org_resolver_data.json): Used in [`IdentifierHelper`](fuji_server/helper/identifier_helper.py).
-- [`jsonldcontext.json`](./jsonldcontext.json)
-- [`licenses.json`](./licenses.json): Used to populate `Preprocessor.license_names`, a list of SPDX licences. Used in evaluation of licenses, FsF-R1.1-01M.
-- [`linked_vocab.json`](./linked_vocab.json)
-- [`longterm_formats.json`](./longterm_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json).
-- [`metadata_standards_uris.json`](./metadata_standards_uris.json)
-- [`metadata_standards.json`](./metadata_standards.json): Used in evaluation of community metadata, FsF-R1.3-01M.
-- [`open_formats.json`](./open_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json).
+- [`identifiers_org_resolver_data.yaml`](./identifiers_org_resolver_data.yaml): Used in [`IdentifierHelper`](fuji_server/helper/identifier_helper.py).
+- [`jsonldcontext.yaml`](./jsonldcontext.yaml)
+- [`licenses.yaml`](./licenses.yaml): Used to populate `Preprocessor.license_names`, a list of SPDX licences. Used in evaluation of licenses, FsF-R1.1-01M.
+- [`linked_vocab.yaml`](./linked_vocab.yaml)
+- [`metadata_standards_uris.yaml`](./metadata_standards_uris.yaml)
+- [`metadata_standards.yaml`](./metadata_standards.yaml): Used in evaluation of community metadata, FsF-R1.3-01M.
 - [`repodois.yaml`](./repodois.yaml): DOIs from re3data (Datacite).
 - [`ResourceTypes.txt`](./ResourceTypes.txt)
-- [`standard_uri_protocols.json`](./standard_uri_protocols.json): Used for evaluating access through standardised protocols (FsF-A1-03D). Mapping of acronym to long name (e.g. FTP, SFTP, HTTP etc.)
+- [`standard_uri_protocols.yaml`](./standard_uri_protocols.yaml): Used for evaluating access through standardised protocols (FsF-A1-03D). Mapping of acronym to long name (e.g. FTP, SFTP, HTTP etc.)

fuji_server/data/access_rights.yaml

@@ -0,0 +1,121 @@
+COAR_access_right:
+  id: COAR_access_rights
+  identifier:
+    type: namespace
+    value: https://vocabularies.coar-repositories.org/access_rights
+  label: COAR access rights
+  members:
+  - access_condition: embargoed
+    id: c_f1cf
+    label: embargoed access
+    source: coar-repositories.org
+    uri: http://purl.org/coar/access_right/c_f1cf
+  - access_condition: metadataonly
+    id: c_14cb
+    label: metadata only access
+    source: coar-repositories.org
+    uri: http://purl.org/coar/access_right/c_14cb
+  - access_condition: restricted
+    id: c_16ec
+    label: restricted access
+    source: coar-repositories.org
+    uri: http://purl.org/coar/access_right/c_16ec
+  - access_condition: public
+    id: c_abf2
+    label: open access
+    source: coar-repositories.org
+    uri: http://purl.org/coar/access_right/c_abf2
+  source: coar-repositories.org
+EPRINTS_access_rights:
+  id: EPRINTS_access_rights
+  identifier:
+    type: namespace
+    value: http://purl.org/eprint/accessRights/
+  label: ePrints access rights vocabulary
+  members:
+  - access_condition: public
+    id: OpenAccess
+    label: Open Access
+    source: ukoln.ac.uk
+    uri: http://purl.org/eprint/accessRights/OpenAccess
+  - access_condition: restricted
+    id: RestrictedAccess
+    label: Restricted Access
+    source: ukoln.ac.uk
+    uri: http://purl.org/eprint/accessRights/RestrictedAccess
+  - access_condition: closed
+    id: ClosedAccess
+    label: Closed Access
+    source: ukoln.ac.uk
+    uri: http://purl.org/eprint/accessRights/ClosedAccess
+  source: ukoln.ac.uk
+EU_access_rights:
+  id: EU_access_rights
+  identifier:
+    type: namespace
+    value: http://publications.europa.eu/resource/authority/access-right/
+  label: EU publications office access-right authority table
+  members:
+  - access_condition: restricted
+    id: NON_PUBLIC
+    label: non-public
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
+  - access_condition: embargoed
+    id: OP_DATPRO
+    label: Provisional data
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/OP_DATPRO
+  - access_condition: public
+    id: PUBLIC
+    label: public
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/PUBLIC
+  - access_condition: restricted
+    id: RESTRICTED
+    label: restricted
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/RESTRICTED
+  - access_condition: restricted
+    id: SENSITIVE
+    label: sensitive
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/SENSITIVE
+  - access_condition: restricted
+    id: CONFIDENTIAL
+    label: confidential
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/CONFIDENTIAL
+  - access_condition: public
+    id: NORMAL
+    label: normal
+    source: publications.europa.eu
+    uri: http://publications.europa.eu/resource/authority/access-right/NORMAL
+  source: publications.europa.eu
+OPENAIRE_access_rights:
+  id: OPENAIRE_access_rights
+  identifier:
+    value: info:eu-repo/semantics/
+  label: OpenAire access rights list
+  members:
+  - access_condition: closed
+    id: closedAccess
+    label: closed Access
+    source: openaire.eu
+    uri: info:eu-repo/semantics/closedAccess
+  - access_condition: embargoed
+    id: embargoedAccess
+    label: embargoed Access
+    source: openaire.eu
+    uri: info:eu-repo/semantics/embargoedAccess
+  - access_condition: restricted
+    id: restrictedAccess
+    label: restricted Access
+    source: openaire.eu
+    uri: info:eu-repo/semantics/restrictedAccess
+  - access_condition: public
+    id: openAccess
+    label: open Access
+    source: openaire.eu
+    uri: info:eu-repo/semantics/openAccess
+  source: openaire.eu