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Bug#990743: marked as done (unblock: ncbi-entrez-direct/14.6.20210224+dfsg-4)

Your message dated Sun, 11 Jul 2021 22:27:11 +0200
with message-id <6b1cac41-41ca-3b9f-5efe-b2bd8f2c8be3@debian.org>
and subject line Re: Bug#990743: unblock: ncbi-entrez-direct/14.6.20210224+dfsg-4
has caused the Debian Bug report #990743,
regarding unblock: ncbi-entrez-direct/14.6.20210224+dfsg-4
to be marked as done.

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-- 
990743: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=990743
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
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 = ();
 {

--- End Message ---
--- Begin Message --- 
Hi,

On 08-07-2021 23:43, Aaron M. Ucko wrote:
> Uploaded.  Thanks again!

Unblocked

Paul

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