[adamjohnwright]

Replaces #85, with its review's findings fixed.

Spec 001, T023.

• The species: -s now takes a list of species ids, each written to its own file (one id still works). The Jenkinsfile passes the 15 species of release 98's published biopax.zip, read from those files' own xml:base. Whether to add Mycobacterium tuberculosis, which has events of its own but has never been published, is Should the release's BioPAX files include Mycobacterium tuberculosis? #84. If yes, it is one more id in the Jenkinsfile.
• The Jenkinsfile: the stray quote that ended its docker run line, which would have stopped the shell, is gone. The jar is the image's entry point, and -o ./output lands in the mounted folder.
• The release's check is the DownloadDirectory step's grep (release-download-directory's Jenkinsfile): every .owl in biopax.zip must hold xml:base="http://www.reactome.org/biopax/{release}. CI's fixture job now runs the same check. It passes for the fixture's release (98) and fails for another (97).
• Run as written, as far as this host allows:
  • an image built from this branch;
  • the command's own shape (--network=host, the mount, -o ./output, -s with the two species the fixture graph holds) against the private fixture graph;
  • then the Jenkinsfile's zip -r, and the release's check on the unzipped files: two files, both with the release's base.
    The release server's own run is the release's, and its timing is T024.
• Checked: the fixture's output is unchanged with -s 48887,170928. A bad species id exits 1. 93 tests pass, and actionlint is clean.
• From T023: the release's 15 species, the Jenkinsfile's command, the xml:base check #85's review:
  • Empty species: a species named with -s that has no events now ends the run with exit 1. The release's check counts files, so it wouldn't notice one missing. Shown with a species added to the private fixture graph for the run and removed after.
  • CI: the fixture job's second run uses the list form, and its byte comparison holds it to the one-by-one run.
  • Credentials: the Jenkinsfile's credentials reach the shell as $user/$pass instead of being filled in by Groovy.
  • Noted, not changed: the release's own pattern has no / after the release number, so release 9 would match 98's files. The list of 15 is kept in step by hand.

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