[med-svn] [Git][med-team/kaptive][master] kaptive 0.7.3-3: Further extend crash recognition (#986592).

[Aaron M. Ucko]

Aaron M. Ucko pushed to branch master at Debian Med / kaptive


Commits:
61bc03e0 by Aaron M. Ucko at 2021-04-16T17:35:21-04:00
kaptive 0.7.3-3: Further extend crash recognition (#986592).

d/p/extend_bad_versions: Account for crashes with error output too.
If a relevant tblastn version failed with error text starting with
"terminate called ", prepend the usual "tblastn crashed!" message.

Team upload, urgency high.

- - - - -


2 changed files:

- debian/changelog
- debian/patches/extend_bad_versions


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+kaptive (0.7.3-3) unstable; urgency=high
+
+  * Team upload.
+  * d/p/extend_bad_versions: Account for crashes with error output too.
+    If a relevant tblastn version failed with error text starting with
+    "terminate called ", prepend the usual "tblastn crashed!" message.
+    (Closes: #986592.)
+
+ -- Aaron M. Ucko <ucko at debian.org>  Fri, 16 Apr 2021 17:33:52 -0400
+
 kaptive (0.7.3-2) unstable; urgency=high
 
   * Team upload.


=====================================
debian/patches/extend_bad_versions
=====================================
@@ -8,12 +8,37 @@
  from collections import OrderedDict
  from Bio import SeqIO
  
-@@ -912,7 +913,7 @@ def get_blast_hits(database, query, thre
+@@ -904,22 +905,27 @@ def get_blast_hits(database, query, thre
+     out, err = process.communicate()
+     out = convert_bytes_to_str(out)
+     err = convert_bytes_to_str(err)
+-    if err:
+-        quit_with_error(command[0] + ' encountered an error:\n' + err)
+-    if process.returncode != 0:
++    if err or process.returncode != 0:
+         msg = command[0] + ' crashed!\n'
+ 
          # A known crash can occur with tblastn and recent versions of BLAST+ when multiple threads
          # are used. Check for this case and display an informative error message if so.
          version = get_blast_version(command[0])
 -        bad_version = (version == '2.4.0') or (version == '2.5.0') or (version == '2.6.0')
+-        if threads > 1 and bad_version:
 +        bad_version = re.match(r'2\.(?:[4-9]|1[01])\.\d+$', version)
-         if threads > 1 and bad_version:
++        if threads > 1 and bad_version \
++           and (not err or err.startswith("terminate called ")):
              msg += '\nYou are using BLAST+ v' + version + ' which may crash when running with '
              msg += 'multiple threads.\n\n'
+             msg += 'To avoid this issue, try one of the following:\n'
+             msg += '  1) Use an unaffected version of BLAST+ (v2.3.0 or earlier should work)\n'
+             msg += '  2) Run Kaptive with "--threads 1" (will probably be slower)\n'
+-        quit_with_error(msg)
++            if err:
++                msg += "\nRaw error:\n" + err
++            quit_with_error(msg)
++        elif err:
++            quit_with_error(command[0] + ' encountered an error:\n' + err)
++        else:
++            quit_with_error(msg)
+ 
+     if genes:
+         blast_hits = [GeneBlastHit(line) for line in line_iterator(out)]



View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/commit/61bc03e075a93af23653f5d3aabec210444f91a7

-- 
View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/commit/61bc03e075a93af23653f5d3aabec210444f91a7
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