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merge devel to master, preparation for release 62.6 #396

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merged 52 commits into from
Dec 13, 2016
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01301a0
consistent branch in Travis CI builds
mgcam Sep 20, 2016
ae75f6d
fix for dbix schema loader
mgcam Nov 22, 2016
af68338
translation from a database composition representation to the npg_tra…
mgcam Nov 22, 2016
6689246
comments rearranged
mgcam Nov 22, 2016
7d31cb2
collection search reimplemented - was implemented wrongly for composi…
mgcam Nov 22, 2016
855e060
add result role to SamtoolsStats DBIx object
mgcam Nov 23, 2016
c247331
typos fixed; tests for db-based results
mgcam Nov 23, 2016
ca13c3b
Force comparison as numbers so 0 and 0.00 are considered equal
mgcam Nov 24, 2016
6f0f097
Merge pull request #376 from mgcam/test_fix
jmtcsngr Nov 24, 2016
6618a1f
back to mysql 5.7.13
jmtcsngr Nov 17, 2016
c8576de
no templates rna_seqc results - we should not try rendering
mgcam Nov 18, 2016
e764ce6
fix release number
mgcam Nov 21, 2016
a7ebec0
Force comparison as numbers so 0 and 0.00 are considered equal
mgcam Nov 24, 2016
f447b5a
update Changes
jmtcsngr Nov 24, 2016
74741fd
fix conflict in Changes
jmtcsngr Nov 24, 2016
6350b64
Merge pull request #377 from jmtcsngr/mysql_5_7_13
mgcam Nov 24, 2016
a78f8a7
drop node 0.12 & add perl 5.22-shrplib in travis
jmtcsngr Nov 24, 2016
7db4d1b
fixing tests after move to perl 22
jmtcsngr Nov 24, 2016
7535710
merged in wtsi/devel and resolved changes
mgcam Nov 24, 2016
4ce62bd
beter version
mgcam Nov 24, 2016
129c9e6
better change description
mgcam Nov 24, 2016
7bfd192
treat the perl-dnap-utilities package in line with other dependencies
mgcam Nov 24, 2016
9af1b7a
switch some for Undecided manual qc outcome
jmtcsngr Nov 24, 2016
b0911fc
Merge pull request #378 from jmtcsngr/perl_22
mgcam Nov 24, 2016
44a6901
move variable definition closer to where it is used
mgcam Nov 28, 2016
6e006b4
Merge pull request #359 from mgcam/follow_branch
jmtcsngr Nov 28, 2016
45596a3
reduce uncertainty in ranking close results for teh old contamination…
mgcam Nov 28, 2016
ae94c0f
Merge pull request #379 from mgcam/better_contam_comparison
jmtcsngr Nov 29, 2016
6ec01ca
typo fixed
mgcam Nov 29, 2016
b0bf5ea
merged in wtsi/devel and resolved conflict
mgcam Nov 29, 2016
1975777
call_gtck_composite_rpt.pl: supply rpt list to genotype check
dozy Nov 30, 2016
9e95d77
Merge pull request #381 from dozy/rpt_list_for_gtck
jenniferliddle Nov 30, 2016
1677846
fix SeqQC db query for composition-based tables
mgcam Dec 1, 2016
b859c56
do not force numeric comparison on a potentially string argument
mgcam Dec 2, 2016
ad06aab
PBP, BuiltinFunctions::ProhibitUselessTopic - Useless use of $_
mgcam Dec 2, 2016
08acc26
proper NULL expression in YAML to avoid warnings when loading the dat…
mgcam Dec 2, 2016
8639b21
Changes update
mgcam Dec 2, 2016
ff25d8f
Merge pull request #384 from mgcam/perl5.22_fixes
dkj Dec 2, 2016
45ccb37
PDL return values fix
mgcam Dec 2, 2016
6038b1e
be very specific when dropping tag_index parameter from a query
mgcam Dec 5, 2016
572c3d0
Merge remote-tracking branch 'wtsi/devel' into rpt4composition
mgcam Dec 5, 2016
d37bdce
Use disposable-irods in Travis build; use perl-irods-wrap
Dec 5, 2016
5ca50f4
Fix for rare out of order mpileup failures in genotype qc
ces Dec 5, 2016
385fefa
Merge pull request #389 from ces/genosort
dozy Dec 5, 2016
edb7620
Merge pull request #388 from iainrb/irods_travis_and_interface_2
Dec 5, 2016
54ec786
Merge pull request #385 from mgcam/pdl_return_values_fix
dkj Dec 5, 2016
5af8343
Added -u to require initialised variables.
kjsanger Dec 6, 2016
c45aa35
Merge pull request #390 from keithj/initialise-variables
Dec 7, 2016
5944151
Merge commit 'refs/pull/375/head' of https://github.com/wtsi-npg/npg_…
dkj Dec 7, 2016
f0ca881
Merge branch 'devel' of https://github.com/wtsi-npg/npg_qc into devel
dkj Dec 8, 2016
3df99b2
Made building the iRODS handle of npg_qc::autoqc::checks::genotype
kjsanger Dec 12, 2016
3614434
Merge pull request #395 from keithj/lazy-irods
dozy Dec 12, 2016
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4 changes: 2 additions & 2 deletions npg_qc_viewer/t/40-controller-QcOutcomes.t
Original file line number Diff line number Diff line change
@@ -216,15 +216,15 @@ subtest 'data validation for update requests' => sub {
like ($response->content, qr/rpt string should not contain \';\'/,
'multi-component compositions are not allowed');

$data->{'lib'} = {'1:2' => {'mqc_outcome' => 'some'}, '1:4' => {'mqc_outcome' => ''}};
$data->{'lib'} = {'1:2' => {'mqc_outcome' => 'Undecided'}, '1:4' => {'mqc_outcome' => ''}};
$request = _new_post_request();
$request->content(encode_json($data));
$response = request($request);
is($response->code, $error_code, "error code is $error_code");
like ($response->content, qr/Outcome description is missing for 1:4/,
'outcome description should be present');

$data->{'lib'} = {'1:2' => {'mqc_outcome' => 'some'}, '1:4' => {'qc_outcome' => ''}};
$data->{'lib'} = {'1:2' => {'mqc_outcome' => 'Undecided'}, '1:4' => {'qc_outcome' => ''}};
$request = _new_post_request();
$request->content(encode_json($data));
$response = request($request);