Package: release.debian.org Severity: normal User: release.debian....@packages.debian.org Usertags: unblock
[ Introduction / Reason ] I would like to issue a new ncbi-entrez-direct upload (patch attached) adjusting two wrapper scripts to account fully for their wrappees' repertoire of options, or at minimum acknowledging that NCBI's efetch accepts -docsum as shorthand for -format docsum for the sake of ncbi-blast+'s get_species_taxids script. (https://bugs.debian.org/990741 has more details.) [ Impact ] Without this patch, on systems with ncbi-entrez-direct and acedb-other both installed, some legitimate usage of efetch intended to pick up NCBI's version will yield warnings; likewise for einfo with epub-utils installed alongside ncbi-entrez-direct. (In some corner cases, these wrapper scripts might even wind up running the wrong efetch or einfo, though they should at least warn about doing so.) [ Tests ] #990741 has an example of the current misbehavior; with this patch in place, the only diagnostics should be the single WARNING: line from NCBI's efetch itself, which is entirely safe to disregard. [ Risks ] AFAICT, this patch should not affect any command lines intended for acedb-other's efetch or epub-utils's einfo, but if you want to be extra cautious, I can limit it to adding -docsum for efetch for now. [ Checklist ] [x] all changes are documented in the d/changelog [x] I reviewed all changes and I approve them [x] attach debdiff against the package in testing [ Other info ] I am holding off on uploading anything pending feedback on whether to go forward with the full patch or a scaled-down version that only adds an acknowledgment of the -docsum shorthand. Thanks! unblock ncbi-entrez-direct/14.6.20210224+dfsg-4
diff --git a/debian/changelog b/debian/changelog index f8b2667..5bb4c46 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,12 @@ +ncbi-entrez-direct (14.6.20210224+dfsg-4) UNRELEASED; urgency=medium + + * debian/{efetch,einfo}: Refresh %ncbi_supported, taking care to include + undocumented options. (In particular, ncbi-blast+'s + get_species_taxids uses efetch's undocumented -docsum shorthand.) + (Closes: #990741.) + + -- Aaron M. Ucko <u...@debian.org> Mon, 05 Jul 2021 22:12:10 -0400 + ncbi-entrez-direct (14.6.20210224+dfsg-3) unstable; urgency=medium * debian/man/eblast.1: Extend deprecation notice to eblast. diff --git a/debian/efetch b/debian/efetch index 603bdaa..79a2726 100755 --- a/debian/efetch +++ b/debian/efetch @@ -28,6 +28,7 @@ my %ncbi_supported = ( 'id' => 's', 'input' => 's', 'format' => 's', + 'docsum' => undef, 'style' => 's', 'mode' => 's', 'seq_start' => 'i', @@ -38,10 +39,14 @@ my %ncbi_supported = ( 'complexity' => 'i', 'chr_start' => 'i', 'chr_stop' => 'i', + 'showgi' => undef, 'extend' => 'i', 'extrafeat' => 'i', + 'showgaps' => undef, + 'show-gaps' => undef, 'start' => 'i', 'stop' => 'i', + 'api_key' => 's', 'raw' => undef, 'json' => undef, 'nogi' => undef, @@ -49,14 +54,26 @@ my %ncbi_supported = ( 'tool' => 's', 'pipe' => undef, 'help' => undef, + 'example' => undef, + 'examples' => undef, + 'error' => undef, + 'errors' => undef, 'silent' => undef, 'verbose' => undef, 'debug' => undef, + 'oldmode' => undef, + 'newmode' => undef, 'log' => undef, + 'compact' => undef, 'http' => 's', 'https' => 's', 'alias' => 's', - 'base' => 's'); + 'base' => 's', + 'web' => 's', + 'step' => 'i', + 'label' => 's', + 'timer' => undef, + 'version' => undef); my %ncbi_abbrev = (); { diff --git a/debian/einfo b/debian/einfo index 570c088..a4d202a 100755 --- a/debian/einfo +++ b/debian/einfo @@ -26,19 +26,36 @@ my $epub_keys = 't'; my %ncbi_supported = ( 'db' => 's', 'dbs' => undef, + 'field' => undef, 'fields' => undef, + 'link' => undef, 'links' => undef, + 'test' => undef, + 'tests' => undef, + 'api_key' => undef, 'email' => 's', 'tool' => 's', + 'repeat' => undef, + 'repeats' => undef, + 'error' => undef, + 'errors' => undef, 'help' => undef, 'silent' => undef, 'verbose' => undef, 'debug' => undef, + 'oldmode' => undef, + 'newmode' => undef, 'log' => undef, + 'compact' => undef, 'http' => 's', 'https' => 's', 'alias' => 's', - 'base' => 's'); + 'base' => 's', + 'web' => 's', + 'step' => 'i', + 'label' => 's', + 'timer' => undef, + 'version' => undef); my %ncbi_abbrev = (); {