0.7.0

Release notes for pymetadata 0.7.0

Security

• Locations of COMBINE archive entries are validated: absolute locations and locations pointing outside of the archive, e.g., ../model.xml, are rejected, so a manifest cannot write or delete files outside of the archive directory (#95).
• The attributes of the manifest.xml are escaped, locations with &, " or < produced an unreadable manifest (#95).
• ChEBI ids and InChIKeys are validated before they are used in request urls and cache file names; cache file names are derived with pymetadata.cache.cache_file and stay inside the cache directory (#95).
• Omex.from_url only accepts http and https urls, downloads with retries and a timeout, streams the archive to disk and removes the download afterwards (#95).

Fixes

• COMBINE archives (#95):
  • Omex.entries_by_format matches the names of EntryFormat, e.g., csv or SBML_L3V2.
  • Locations are normalized once when an entry is created; adding model.xml twice replaces the entry and get_path("model.xml") works.
  • Omex.add_entry no longer modifies the entry passed by the caller.
  • The temporary directory of an archive is removed by the new Omex.close, by the context manager, or at the latest when the archive is garbage collected.
  • Omex.to_omex writes atomically, a failing write does not destroy an existing archive.
  • Omex.guess_format does not depend on the encoding of .xml files and handles .XML.
• Annotations (#95): terms of namespaces embedded in the LUI without their prefix (chebi/33699, go/0005829), DOIs and other compact ids containing /, lowercase percent encoding in urn:miriam resources, upper case url schemes, query strings, fragments and trailing slashes in urls, registry patterns without anchors, RDFAnnotation.validate for resources which cannot be parsed, and the mapping of legacy collections (obo.go, biomodels.sbo).
• Web services (#95): OLSQuery(cache=False) disabled the cache again; ChEBI and UniChem wrote the cache with cache=False; a corrupt cache file is treated as a cache miss; unknown ChEBI ids return {}; failed ontology downloads raise and downloads are written atomically.
• Archives written by Omex.to_omex and downloaded ontologies get regular file permissions instead of owner-only ones.
• Canonical FMA IRIs for the OLS metadata resolution (#90).

Changes

• Invalid archive locations raise a pydantic.ValidationError, Omex.from_omex raises a ValueError for a zip archive without manifest.xml.
• Namespace.resources of the registry is a list[Resource], dictionaries are still converted.
• urllib3 is a declared dependency.

Performance

• Reading and writing archives no longer copies every file twice.
• The registry compiles the patterns once and determines the dataclass fields once.

Your pymetadata team