Merge pull request #480 from afuetterer/yaml

chore: convert json files to yaml

fuji_server/config/server.ini

@@ -9,9 +9,10 @@ debug_mode = true
 data_files_limit = 5
 log_config = config/logging.ini
 logdir = logs
+verify_pids = false
 # the URI which triggers the remote logging all other F-UJI server requests are ignored
-remote_log_host = fuji.localhost
-remote_log_path = /loghandler/index.php
+remote_log_host =
+remote_log_path =
 rate_limit = 100 per minute
 # limits the maximum size of content (metadata) which can be downloaded
 max_content_size = 5000000

fuji_server/controllers/fair_check.py

@@ -71,7 +71,7 @@ class FAIRCheck:
     LONG_TERM_FILE_FORMATS = None
     OPEN_FILE_FORMATS = None
     DEFAULT_NAMESPACES = None
-    VOCAB_NAMESPACES = None
+    # VOCAB_NAMESPACES = None
     ARCHIVE_MIMETYPES = Mapper.ARCHIVE_COMPRESS_MIMETYPES.value
     STANDARD_PROTOCOLS = None
     SCHEMA_ORG_CONTEXT = []
@@ -242,8 +242,8 @@ def load_predata(cls):
             cls.OPEN_FILE_FORMATS = Preprocessor.get_open_file_formats()
         if not cls.DEFAULT_NAMESPACES:
             cls.DEFAULT_NAMESPACES = Preprocessor.getDefaultNamespaces()
-        if not cls.VOCAB_NAMESPACES:
-            cls.VOCAB_NAMESPACES = Preprocessor.getLinkedVocabs()
+        # if not cls.VOCAB_NAMESPACES:
+        #    cls.VOCAB_NAMESPACES = Preprocessor.getLinkedVocabs()
         if not cls.STANDARD_PROTOCOLS:
             cls.STANDARD_PROTOCOLS = Preprocessor.get_standard_protocols()
         if not cls.SCHEMA_ORG_CONTEXT:

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.)