Upstream MEtadata GAthered with YAml (UMEGAYA)
Introduction
This is an effort to collect meta-information about upstream in a file called debian/upstream in the source packages maintained in a publicly accessible version control system (VCS), currently Subversion or Git. Since this information is directly accessed from the VCS, it can be updated without uploading the source packages to the Debian archive.
Umegaya is also the name of a draft collector system that is implemented on upstream-metadata.debian.net. Its source is available on git.debian.org. It is used in to feed the data in the UltimateDebianDatabase.
Proof of principle (in progress)
To make the DebianMed web sentinels use the UDD, fed from the debian/upstream via upstream-metadata.debian.net, to display bibliographic information about which academic article to cite when using our packages. This is currently done by collecting the information in the central file used to create the med-* metapackages.
The Umegaya instance running at http://upstream-metadata.debian.net is collecting and organising debian/upstream and debian/copyright files as pools. Currently they are pushed daily in the QA team's Subversion repository's directory packages-metadata. An UDD importer is in development.
Syntax
The debian/upstream file is in YAML format. In its simplest form, it looks much like the paragraph format used in Debian control files. Nevertheless, there may be some times unexpected behaviours, for instance field contents that have a colon inside have to be quoted in some cases. In doubt, there are validaters available, like this Online YAML Parser. With the libyaml-libyaml-perl package installed, the following command can also validate YAML files:
perl -MYAML::XS -e '$/=""; Load(<STDIN>)' < upstream
Be careful not to use the plain Perl YAML module as it accepts files with invalid syntax (661700).
Fields
In alphabetic order. Let's try to use the same vocabulary as in DOAP as much as possible. Fields that are the same as in DOAP are followed by an asterisk.
- Archive
- When the upstream work is part of a large archive, like CPAN.
- Bug-Database
- A URL to the list of known bugs for the project.
- Bug-Submit
- A URL that is the place where new bug reports should be sent.
- Cite-As
The way the authors want their software be cited in publications. The value is a string which might contain a link in valid HTML syntax. (see discussion on Debian Science list)
- Contact
- Which person, mailing list, forum,… to send messages in the first place.
- Donation
- An URL to a donation form (or instructions).
- FAQ
- An URL to the online FAQ.
- Gallery
- An URL to a gallery of pictures made with the program (not screenshots).
- Name *
- Upstream name of the packaged work.
- Homepage *
- The packaged work's homepage.
- Other-References
- An URL to a upstream page containing more references.
- Reference
- One or more bibliographic references, represented as a mapping or sequence of mappings containing the one or more of the following keys. The values for the keys are always scalars, and the keys that correspond to standard BibTeX entries must provide the same content.
- Author
Author list in BibTeX friendly syntax (separating multiple authors by the keyword "and" and using as few as possible abbreviations in the names, as proposed in http://nwalsh.com/tex/texhelp/bibtx-23.html).
- DOI
- This is the digital object identifier of the academic publication describing the packaged work.
- Eprint
- Hyperlink to the PDF file of the article.
- Journal
- Abbreviated journal name [To be discussed: which standard to recommend ?].
- Number
- Issue number.
- Pages
- Article page number(s). [To be discussed] Page number separator must be a single ASCII hyphen. What do we do with condensed notations like 401-10 ?
- PMID
ID number in the PubMed database.
- Title
- Article title.
- Type
A BibTeX entry type indicating what is cited. Typical values are article, book, or inproceedings. [To be discussed]. In case this field is not present, article is assumed.
- URL
- Hyperlink to the abstract of the article. This should not point to the full version because this is specified by Eprint. Please also do not drop links to pubmed here because this would be redundant to PMID.
- Volume
- Journal volume.
- Year
- Year of publication
- Debian-package
- Optional: citation information can be restricted to some specific binary package of a multi-binary package if the reference is only concerning this package; Note: This is just a proposal and might change in the future
- Registration
- An URL to a registration form (or instructions).
- Repository
- URL to a repository containing the upstream sources.
- Repository-Browse
- An URL to browse the repository containing the upstream sources.
- Screenshots
One or more URLs to upstream pages containing screenshots (not screenshots.debian.net), repesented by a scalar or a sequence of scalars.
- Watch
Currently it contains the main line of debian/watch. It is therefore assumed to be in format version 3. For surveying multiple locations, it could contain a YAML sequence.
- Webservice
- URL to an web page where the packaged program can also be used.
Reserved fields
The following fields are used internally and must not be present in debian/upstream.
- YAML-ALL
- Used to dump the loaded record.
- YAML-URL
- Used to override the repository's URL provided by debcheckout.
- YAML-REFRESH-DATE
Used to deduce how long umegaya will ignore calls to refresh (to avoid hammering Alioth).
TODO: ignore them safely.
Discussion
Let's discuss here, on a mailing list (debian-med or debian-qa), or a discussion page, if available.
The data is not really Debian-specific, lets put it outside Debian and use the ?PackageMap to map between Debian package names and the data:
http://lists.debian.org/debian-mentors/2009/11/msg00450.html
To do: formalise the above using ?http://search.cpan.org/~ddumont/Config-Model/lib/Config/Model/Backend/Yaml.pm, and generate docs as explained in http://ddumont.wordpress.com/2011/04/08/configuration-doc-generation-with-configmodel/ .
* In addition to ?DOAP, other Semantic Web ontologies/namespaces/schemas should be reused in order to not reinvent the wheel, and enable such metadata to participate to the ?Semantic Web (see also Open Linked Data matters). As such, SPDX would be an interesting standard to link to, as well as ADMS.F/OSS, for packages description, IMHO. Syntactically, any form of RDF would be interesting to explicitely convey the prefixes in the field names... and I'm not sure it can be done in ?YAML -- OlivierBerger
Template
Here is a template for a debian/upstream file which can be used to specify citations:
Reference: Author: <please use full names and separate multiple author by the keyword "and"> Title: Journal: Year: Volume: Number: Pages: DOI: PMID: URL: eprint:
Deprecated features
Hyphen shortcut for mappings
Only a subset of YAML is used: sequences are only expected to contain scalars and mappings are only expected to contain a scalar or a mapping, but with only one level of imbrication.
In addition, two conventions that are not part of the YAML format are used:
- Field names are case-insensitive.
- Nested mappings are shortcuts for longer field names composed of both mapping field names separated by a dash. The following two examples are equivalent:
Foo: Bar: baz
Foo-Bar: baz
UDD loading through a YAML intermediate
The bibliographic data was refreshed daily at http://upstream-metadata.debian.net/for_UDD/biblio.yaml via a local cron job. As specified in config-org.yaml, it was retreived by the script fetch_bibref.sh and loaded in the UDD as triples (package, key, value) with the bibref_gatherer.
Notes
debian/upstream-metadata.yaml was formerly used instead of debian/upstream. See http://lists.debian.org/debian-devel/2012/01/msg00426.html.