[Debian-med-packaging] Bug#990741: ncbi-entrez-direct: efetch and einfo wrappers warn about some supported options

[Aaron M. Ucko]

Package: ncbi-entrez-direct
Version: 14.6.20210224+dfsg-3+b2
Severity: serious
Justification: maintainer prerogative

In the course of checking whether
https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/1934402
affects ncbi-blast+ in testing and unstable, I observed -- *only* -- a
different issue: the efetch wrapper Debian deploys to avoid needing a
formal conflict with acedb-other doesn't account for NCBI efetch's
undocumented -docsum shorthand, which get_species_taxids uses.  The
wrapper's heuristics conclude that the NCBI implementation is probably
in order, but it's a close call, and somewhat noisy:

  $ get_species_taxids -n 'Homo sapiens'
  Launching NCBI efetch rather than AceDB efetch despite misgivings,
  due to more severe misgivings about AceDB syntax compatibility.  If you
  meant to run AceDB efetch, please explicitly run it via efetch.acedb.
  AceDB misgivings (1 major, 2 minor):
    -mode (major)
    -db (minor)
    taxonomy json (minor)
  NCBI misgivings (1 major, 0 minor):
    -docsum (major)
  WARNING: Redundant -db 'taxonomy' argument
   
  Taxid : 9606 
   rank : species 
   division : primates 
   scientific name : Homo sapiens 
   common name : human 
  
  1 matche(s) found.

I could certainly patch get_species_taxids, but would prefer to adjust
ncbi-entrez-direct's efetch wrapper, since -docsum is legitimate, just
undocumented.  A full sweep revealed some other gaps in both this
wrapper and the analogous einfo wrapper, mostly around other
undocumented options.  AFAICT, these arguments are all at *best*
unlikely for these commands' homonyms; for instance, -docsum could
only correspond to

       -d <dbfile> Specify database file (avoid this)

with an inline value "ocsum"(!)

-- System Information:
Debian Release: 11.0
  APT prefers testing-security
  APT policy: (500, 'testing-security'), (500, 'testing-debug'), (500, 'testing'), (500, 'stable'), (300, 'unstable-debug'), (300, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386, x32

Kernel: Linux 5.10.0-7-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ncbi-entrez-direct depends on:
ii  curl                7.74.0-1.3
ii  libc6               2.31-12
ii  libwww-perl         6.52-1
ii  libxml-simple-perl  2.25-1
ii  perl                5.32.1-4
ii  wget                1.21-1+b1

ncbi-entrez-direct recommends no packages.

Versions of packages ncbi-entrez-direct suggests:
ii  curl           7.74.0-1.3
ii  libxml2-utils  2.9.10+dfsg-6.7
ii  python3        3.9.2-3

-- no debconf information