Bug#990743: unblock: ncbi-entrez-direct/14.6.20210224+dfsg-4
Package: release.debian.org
Severity: normal
User: release.debian.org@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 <ucko@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 = ();
{
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