[med-svn] [Git][med-team/bioperl-run][master] 4 commits: Disable tests for RemoteBlast
Pranav Ballaney
gitlab at salsa.debian.org
Sun Apr 5 17:28:51 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / bioperl-run
Commits:
e7338903 by Pranav Ballaney at 2020-04-05T18:27:46+05:30
Disable tests for RemoteBlast
- - - - -
6935cf3b by Pranav Ballaney at 2020-04-05T21:51:06+05:30
Disable tests for RemoteBlast_rpsblast
- - - - -
a2bab072 by Pranav Ballaney at 2020-04-05T21:51:49+05:30
Extract BEDTools version properly
- - - - -
ff4658f3 by Pranav Ballaney at 2020-04-05T21:58:15+05:30
Update changelog
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/Extract_version_from_BEDTools_properly.patch
- debian/patches/series
- + debian/patches/skip_tests_for_RemoteBlast.patch
- + debian/patches/skip_tests_for_RemoteBlast_rpsblast.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,16 @@
bioperl-run (1.7.3-5) UNRELEASED; urgency=medium
+ [ Michael R. Crusoe ]
* Team upload.
* Add build-dep on libfile-sort-perl as that has arrived in Debian
* debian/upstream/metadata: Add Repository & Repository-Browse
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 04 Apr 2020 11:57:03 +0200
+ [ Pranav Ballaney ]
+ * Disable tests for RemoteBlast
+ * Disable tests for RemoteBlast_rpsblast
+ * Extract BEDTools version properly
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Sun, 05 Apr 2020 21:55:41 +0530
bioperl-run (1.7.3-4) unstable; urgency=medium
=====================================
debian/patches/Extract_version_from_BEDTools_properly.patch
=====================================
@@ -0,0 +1,20 @@
+Description: Tests 8 and 26 in BEDTools.t failed because BEDTools.pm couldn't
+ extract versions of tools properly. This patch fixes it. Related test 44 still fails
+ due to an unknown error.
+Author: Pranav Ballaney <ballaneypranav at gmail.com>
+Last-Update: 2020-04-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/lib/Bio/Tools/Run/BEDTools.pm
++++ b/lib/Bio/Tools/Run/BEDTools.pm
+@@ -895,8 +895,8 @@ sub version{
+ # We don't bother trying to catch this: version is returned as an illegal file seek
+
+ my @details = split("\n",$self->stderr);
+- (my $version) = grep /^Program: .*$/, @details;
+- $version =~ s/^Program: //;
++ (my $version) = grep /^Version: .*$/, @details;
++ $version =~ s/^Version: //;
+
+ return $version;
+ }
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,6 @@
+Extract_version_from_BEDTools_properly.patch
+skip_tests_for_RemoteBlast_rpsblast.patch
+skip_tests_for_RemoteBlast.patch
kalign-input-via-piping.patch
kalign-version-regex.patch
skip_tests_for_wise.patch
=====================================
debian/patches/skip_tests_for_RemoteBlast.patch
=====================================
@@ -0,0 +1,150 @@
+Description: RemoteBlast.t needs internet access for some tests - disabled.
+Author: Pranav Ballaney <ballaneypranav at gmail.com>
+Last-Update: 2020-04-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/t/Tools/Run/RemoteBlast.t
++++ b/t/Tools/Run/RemoteBlast.t
+@@ -7,7 +7,7 @@ BEGIN {
+ use lib '.';
+ use Bio::Root::Test;
+
+- test_begin(-tests => 21,
++ test_begin(-tests => 15,
+ -requires_modules => [qw(IO::String
+ LWP
+ LWP::UserAgent)],
+@@ -67,36 +67,36 @@ SKIP: {
+ }
+ }
+
+- if ($rc) {
+- ok(1,'retrieve_blast succeeded');
+- $remote_blast->remove_rid($rids[0]);
+- my $count = 0;
+- isa_ok($rc, 'Bio::SearchIO');
+- while (my $result = $rc->next_result) {
+- while ( my $hit = $result->next_hit ) {
+- $count++;
+- next unless ( $v > 0);
+- print "sbjct name is ", $hit->name, "\n";
+- while ( my $hsp = $hit->next_hsp ) {
+- print "score is ", $hsp->bits, "\n";
+- }
+- }
+- }
+- is($count, 3, 'HSPs returned');
+- }
+- elsif ($attempt > $max_attempts) {
+- # have a test fail here (there should not be repeated failed attempts to
+- # get reports)
+- ok(0,'Exceeded maximum attempts on server to retrieve report');
+- diag("Timeout, did not return report after ".($attempt - 1)." attempts");
+- skip('Remote server timeout problems', 2);
+- }
+- else {
+- # have a test fail here (whatever is returned should be eval as true and
+- # be a SearchIO)
+- ok(0,"Other problem on remote server, no report returned: $rc");
+- skip('Possible remote server problems', 2);
+- }
++ # if ($rc) {
++ # ok(1,'retrieve_blast succeeded');
++ # $remote_blast->remove_rid($rids[0]);
++ # my $count = 0;
++ # isa_ok($rc, 'Bio::SearchIO');
++ # while (my $result = $rc->next_result) {
++ # while ( my $hit = $result->next_hit ) {
++ # $count++;
++ # next unless ( $v > 0);
++ # print "sbjct name is ", $hit->name, "\n";
++ # while ( my $hsp = $hit->next_hsp ) {
++ # print "score is ", $hsp->bits, "\n";
++ # }
++ # }
++ # }
++ # is($count, 3, 'HSPs returned');
++ # }
++ # elsif ($attempt > $max_attempts) {
++ # # have a test fail here (there should not be repeated failed attempts to
++ # # get reports)
++ # ok(0,'Exceeded maximum attempts on server to retrieve report');
++ # diag("Timeout, did not return report after ".($attempt - 1)." attempts");
++ # skip('Remote server timeout problems', 2);
++ # }
++ # else {
++ # # have a test fail here (whatever is returned should be eval as true and
++ # # be a SearchIO)
++ # ok(0,"Other problem on remote server, no report returned: $rc");
++ # skip('Possible remote server problems', 2);
++ # }
+ }
+
+ SKIP: {
+@@ -146,36 +146,36 @@ SKIP: {
+ }
+ }
+
+- if ($rc) {
+- ok(1,'retrieve_blast succeeded');
+- $remote_blast->remove_rid($rids[0]);
+- my $count = 0;
+- isa_ok($rc, 'Bio::SearchIO');
+- while (my $result = $rc->next_result) {
+- while ( my $hit = $result->next_hit ) {
+- $count++;
+- next unless ( $v > 0);
+- print "sbjct name is ", $hit->name, "\n";
+- while ( my $hsp = $hit->next_hsp ) {
+- print "score is ", $hsp->bits, "\n";
+- }
+- }
+- }
+- is($count, 3, 'HSPs returned');
+- }
+- elsif ($attempt > $max_attempts) {
+- # have a test fail here (there should not be repeated failed attempts to
+- # get reports)
+- ok(0,'Exceeded maximum attempts on server to retrieve report');
+- diag("Timeout, did not return report after ".($attempt - 1)." attempts");
+- skip('Remote server timeout problems', 2);
+- }
+- else {
+- # have a test fail here (whatever is returned should be eval as true and
+- # be a SearchIO)
+- ok(0,"Other problem on remote server, no report returned: $rc");
+- skip('Possible remote server problems', 2);
+- }
++ # if ($rc) {
++ # ok(1,'retrieve_blast succeeded');
++ # $remote_blast->remove_rid($rids[0]);
++ # my $count = 0;
++ # isa_ok($rc, 'Bio::SearchIO');
++ # while (my $result = $rc->next_result) {
++ # while ( my $hit = $result->next_hit ) {
++ # $count++;
++ # next unless ( $v > 0);
++ # print "sbjct name is ", $hit->name, "\n";
++ # while ( my $hsp = $hit->next_hsp ) {
++ # print "score is ", $hsp->bits, "\n";
++ # }
++ # }
++ # }
++ # is($count, 3, 'HSPs returned');
++ # }
++ # elsif ($attempt > $max_attempts) {
++ # # have a test fail here (there should not be repeated failed attempts to
++ # # get reports)
++ # ok(0,'Exceeded maximum attempts on server to retrieve report');
++ # diag("Timeout, did not return report after ".($attempt - 1)." attempts");
++ # skip('Remote server timeout problems', 2);
++ # }
++ # else {
++ # # have a test fail here (whatever is returned should be eval as true and
++ # # be a SearchIO)
++ # ok(0,"Other problem on remote server, no report returned: $rc");
++ # skip('Possible remote server problems', 2);
++ # }
+ }
+
+ SKIP: {
=====================================
debian/patches/skip_tests_for_RemoteBlast_rpsblast.patch
=====================================
@@ -0,0 +1,78 @@
+--- a/t/Tools/Run/RemoteBlast_rpsblast.t
++++ b/t/Tools/Run/RemoteBlast_rpsblast.t
+@@ -14,7 +14,7 @@ BEGIN {
+ use lib '.';
+ use Bio::Root::Test;
+
+- test_begin(-tests => 7,
++ test_begin(-tests => 4,
+ -requires_modules => [qw(IO::String
+ LWP
+ LWP::UserAgent)],
+@@ -71,36 +71,36 @@ SKIP: {
+ }
+ $remote_rpsblast->remove_rid($rids[0]);
+
+- if ($rc) {
+- ok(1,'retrieve_blast succeeded');
+- $remote_rpsblast->remove_rid($rids[0]);
+- my $count = 0;
+- isa_ok($rc, 'Bio::SearchIO');
+- while (my $result = $rc->next_result) {
+- while ( my $hit = $result->next_hit ) {
+- $count++;
+- next unless ( $v > 0);
+- print "sbjct name is ", $hit->name, "\n";
+- while ( my $hsp = $hit->next_hsp ) {
+- print "score is ", $hsp->bits, "\n";
+- }
+- }
+- }
+- cmp_ok($count, '>=', 45, 'HSPs returned');
+- }
+- elsif ($attempt > 10) {
+- # have a test fail here (there should not be repeated failed attempts to
+- # get reports)
+- ok(0,'Exceeded maximum attempts on server to retrieve report');
+- diag("Timeout, did not return report after ".($attempt - 1)." attempts");
+- skip('Remote server timeout problems', 2);
+- }
+- else {
+- # have a test fail here (whatever is returned should be eval as true and
+- # be a SearchIO)
+- ok(0,"Other problem on remote server, no report returned: $rc");
+- skip('Possible remote server problems', 2);
+- }
++ # if ($rc) {
++ # ok(1,'retrieve_blast succeeded');
++ # $remote_rpsblast->remove_rid($rids[0]);
++ # my $count = 0;
++ # isa_ok($rc, 'Bio::SearchIO');
++ # while (my $result = $rc->next_result) {
++ # while ( my $hit = $result->next_hit ) {
++ # $count++;
++ # next unless ( $v > 0);
++ # print "sbjct name is ", $hit->name, "\n";
++ # while ( my $hsp = $hit->next_hsp ) {
++ # print "score is ", $hsp->bits, "\n";
++ # }
++ # }
++ # }
++ # cmp_ok($count, '>=', 45, 'HSPs returned');
++ # }
++ # elsif ($attempt > 10) {
++ # # have a test fail here (there should not be repeated failed attempts to
++ # # get reports)
++ # ok(0,'Exceeded maximum attempts on server to retrieve report');
++ # diag("Timeout, did not return report after ".($attempt - 1)." attempts");
++ # skip('Remote server timeout problems', 2);
++ # }
++ # else {
++ # # have a test fail here (whatever is returned should be eval as true and
++ # # be a SearchIO)
++ # ok(0,"Other problem on remote server, no report returned: $rc");
++ # skip('Possible remote server problems', 2);
++ # }
+ }
+
+ # To be a good citizen, we should restore the default NCBI service
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/53b73472efe072ef8f377c21a9ece535a14b0c1b...ff4658f3507a773ad485cd01f72bc09a531a6b4a
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/53b73472efe072ef8f377c21a9ece535a14b0c1b...ff4658f3507a773ad485cd01f72bc09a531a6b4a
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