diff --git a/MANIFEST b/MANIFEST index 80a8f6b77..f95cf38e9 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1057,14 +1057,6 @@ t/data/qc/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa t/data/qc/references/PhiX/default/all/fasta/PhiX.fasta t/data/qc/samplesheet_14043.csv t/data/qc/samplesheet_14353.csv -t/data/qc_outcomes/fixtures/000-mqc_library_outcome_dict.yml -t/data/qc_outcomes/fixtures/000-mqc_outcome_dict.yml -t/data/qc_outcomes/fixtures/000-uqc_outcome_dict.yml -t/data/qc_outcomes/fixtures/200-seq_component.yml -t/data/qc_outcomes/fixtures/300-seq_component_composition.yml -t/data/qc_outcomes/fixtures/300-seq_composition.yml -t/data/qc_outcomes/fixtures/400-mqc_library_outcome_ent.yml -t/data/qc_outcomes/fixtures/README t/data/release/config/archive_off/product_release.yml t/data/release/config/archive_on/product_release.yml t/data/release/config/bqsr_off/product_release.yml diff --git a/lib/npg_pipeline/base.pm b/lib/npg_pipeline/base.pm index 0fe98efbf..c1490e269 100644 --- a/lib/npg_pipeline/base.pm +++ b/lib/npg_pipeline/base.pm @@ -60,22 +60,6 @@ within npg_pipeline package =head2 npg_tracking_schema -=head2 qc_schema - -An attribute caching a connection to a QC database. -The attribute is allowed to be undefined and is implicitly undefined -since no default or build method is provided. This is done in order -to prevent the automatic connection to a database in child classes. - -=cut - -has 'qc_schema' => ( - metaclass => 'NoGetopt', - isa => 'Maybe[npg_qc::Schema]', - is => 'ro', - required => 0, -); - =head2 flowcell_id =head2 tracking_run diff --git a/lib/npg_pipeline/product.pm b/lib/npg_pipeline/product.pm index 91663f9c1..06cab424e 100644 --- a/lib/npg_pipeline/product.pm +++ b/lib/npg_pipeline/product.pm @@ -598,116 +598,6 @@ sub chunk_as_product { return __PACKAGE__->new($ref); } - -=head2 final_seqqc_objs - - Returns a list of DBIx row objects representing a sequencing QC outcomes - for component lanes of this product. If not all lanes have a final outcome, - an empty list is returned. - - npg_qc::Schema object argument is required. - - use List::MoreUtils qw/all any/; - my @seq_qc_objs = $p->final_seqqc_objs($schema); - my $passed = @seq_qc_objs && (all { $_->is_accepted } @seq_qc_objs); - my $failed = !@seq_qc_objs || (any { $_->is_rejected } @seq_qc_objs); -=cut - -sub final_seqqc_objs { - my ($self, $schema) = @_; - - $schema or croak 'qc schema argument is required'; - - my @lp = $self->lanes_as_products; - my @seqqc = grep { $_->has_final_outcome } - $schema->resultset('MqcOutcomeEnt') - ->search_via_composition([map{$_->composition}@lp])->all; - if (@lp != @seqqc) { - return; - } - - return @seqqc; -} - -=head2 seqqc_objs - - Returns a list of DBIx row objects representing a sequencing QC outcomes - for component lanes of this product, even if not all outcomes are final. - - npg_qc::Schema object argument is required. - - use List::MoreUtils qw/all any/; - my @seq_qc_objs = $p->seqqc_objs($schema); - #these may or may not be final outcomes - my $passed = @seq_qc_objs && (all { $_->is_accepted } @seq_qc_objs); - my $failed = !@seq_qc_objs || (any { $_->is_rejected } @seq_qc_objs); - -=cut - -sub seqqc_objs { - my ($self, $schema) = @_; - - $schema or croak 'qc schema argument is required'; - - my @lp = $self->lanes_as_products; - my @seqqc = $schema->resultset('MqcOutcomeEnt') - ->search_via_composition([map{$_->composition}@lp])->all; - if (@lp != @seqqc) { - return; - } - return @seqqc; -} - -=head2 final_libqc_obj - - Returns a DBIx row object representing a final library QC outcome. - Returns an undefined value if the final library QC outcome is - not available for this product. - - npg_qc::Schema object argument is required. - - my $lib_qc_obj = $p->final_libqc_obj($schema); - print $lib_qc_obj->is_accepted; - -=cut - -sub final_libqc_obj { - my ($self, $schema) = @_; - - $schema or croak 'qc schema argument is required'; - - my $libqc = $schema->resultset('MqcLibraryOutcomeEnt') - ->search_via_composition([$self->composition])->next; - if ($libqc && $libqc->has_final_outcome) { - return $libqc; - } - - return; -} - -=head2 libqc_obj - - Returns a DBIx row object representing the library QC outcome. - Returns an undefined value if the library QC outcome is - not available for this product. - - npg_qc::Schema object argument is required. - - my $lib_qc_obj = $p->libqc_obj($schema); - -=cut - -sub libqc_obj { - my ($self, $schema) = @_; - - $schema or croak 'qc schema argument is required'; - - return $schema->resultset('MqcLibraryOutcomeEnt') - ->search_via_composition([$self->composition])->next; -} - - - __PACKAGE__->meta->make_immutable; 1; diff --git a/lib/npg_pipeline/validation.pm b/lib/npg_pipeline/validation.pm index 3296d9f8e..1e106ac27 100644 --- a/lib/npg_pipeline/validation.pm +++ b/lib/npg_pipeline/validation.pm @@ -403,9 +403,11 @@ a database connection. =cut -has '+qc_schema' => ( - lazy => 1, - builder => '_build_qc_schema', +has 'qc_schema' => ( + isa => 'npg_qc::Schema', + is => 'ro', + required => 0, + lazy_build => 1, ); sub _build_qc_schema { return npg_qc::Schema->connect(); diff --git a/t/15-product-release.t b/t/15-product-release.t index cf3901e11..08db9308b 100644 --- a/t/15-product-release.t +++ b/t/15-product-release.t @@ -24,11 +24,6 @@ Log::Log4perl->easy_init({level => $INFO, with 'npg_testing::db'; } -# See README in fixtures for a description of the test data. -my $qc = TestDB->new ( - sqlite_utf8_enabled => 1, - verbose => 0)->create_test_db('npg_qc::Schema'); - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/novaseq/180709_A00538_0010_BH3FCMDRXX/' . 'Data/Intensities/BAM_basecalls_20180805-013153/' . @@ -49,8 +44,7 @@ subtest 'expected_files' => sub { (conf_path => "t/data/release/config/archive_on", runfolder_path => $runfolder_path, id_run => 26291, - timestamp => $timestamp, - qc_schema => $qc); + timestamp => $timestamp); my $product = shift @{$archiver->products->{data_products}}; @@ -85,8 +79,7 @@ subtest 'expected_unaligned_files' => sub { (conf_path => "t/data/release/config/archive_on", runfolder_path => $runfolder_path, id_run => 26291, - timestamp => $timestamp, - qc_schema => $qc); + timestamp => $timestamp); my $product = shift @{$archiver->products->{data_products}}; diff --git a/t/data/qc_outcomes/fixtures/000-mqc_library_outcome_dict.yml b/t/data/qc_outcomes/fixtures/000-mqc_library_outcome_dict.yml deleted file mode 100644 index de310d9fb..000000000 --- a/t/data/qc_outcomes/fixtures/000-mqc_library_outcome_dict.yml +++ /dev/null @@ -1,32 +0,0 @@ ---- -- id_mqc_library_outcome : 1 - short_desc : 'Accepted preliminary' - long_desc : 'Library is preliminary accepted.' - iscurrent : 1 - isvisible : 1 -- id_mqc_library_outcome : 2 - short_desc : 'Rejected preliminary' - long_desc : 'Library is preliminary rejected.' - iscurrent : 1 - isvisible : 1 -- id_mqc_library_outcome : 3 - short_desc : 'Accepted final' - long_desc : 'Library has been accepted as a final decision.' - iscurrent : 1 - isvisible : 1 -- id_mqc_library_outcome : 4 - short_desc : 'Rejected final' - long_desc : 'Library has been rejected as a final decision.' - iscurrent : 1 - isvisible : 1 -- id_mqc_library_outcome : 5 - short_desc : 'Undecided' - long_desc : 'Library has no current outcome.' - iscurrent : 1 - isvisible : 1 -- id_mqc_library_outcome : 6 - short_desc : 'Undecided final' - long_desc : 'Library has no outcome as final decision.' - iscurrent : 1 - isvisible : 1 - diff --git a/t/data/qc_outcomes/fixtures/000-mqc_outcome_dict.yml b/t/data/qc_outcomes/fixtures/000-mqc_outcome_dict.yml deleted file mode 100644 index 654811236..000000000 --- a/t/data/qc_outcomes/fixtures/000-mqc_outcome_dict.yml +++ /dev/null @@ -1,27 +0,0 @@ ---- -- id_mqc_outcome : 1 - short_desc : 'Accepted preliminary' - long_desc : 'Lane is preliminary accepted.' - iscurrent : 1 - isvisible : 1 -- id_mqc_outcome : 2 - short_desc : 'Rejected preliminary' - long_desc : 'Lane is preliminary rejected.' - iscurrent : 1 - isvisible : 1 -- id_mqc_outcome : 3 - short_desc : 'Accepted final' - long_desc : 'Lane has been accepted as a final decision.' - iscurrent : 1 - isvisible : 1 -- id_mqc_outcome : 4 - short_desc : 'Rejected final' - long_desc : 'Lane has been rejected as a final decision.' - iscurrent : 1 - isvisible : 1 -- id_mqc_outcome : 5 - short_desc : 'Undecided' - long_desc : 'Lane has no current outcome.' - iscurrent : 1 - isvisible : 1 - diff --git a/t/data/qc_outcomes/fixtures/000-uqc_outcome_dict.yml b/t/data/qc_outcomes/fixtures/000-uqc_outcome_dict.yml deleted file mode 100755 index 320ec47e4..000000000 --- a/t/data/qc_outcomes/fixtures/000-uqc_outcome_dict.yml +++ /dev/null @@ -1,16 +0,0 @@ ---- -- id_uqc_outcome : 1 - short_desc : 'Accepted' - long_desc : 'End user would like to utilise the product' - iscurrent : 1 - isvisible : 1 -- id_uqc_outcome : 2 - short_desc : 'Rejected' - long_desc : 'End user will not utilise the product' - iscurrent : 1 - isvisible : 1 -- id_uqc_outcome : 3 - short_desc : 'Undecided' - long_desc : 'No decision, follow mqc outcome when determining utility' - iscurrent : 1 - isvisible : 1 \ No newline at end of file diff --git a/t/data/qc_outcomes/fixtures/200-seq_component.yml b/t/data/qc_outcomes/fixtures/200-seq_component.yml deleted file mode 100644 index f73ea5149..000000000 --- a/t/data/qc_outcomes/fixtures/200-seq_component.yml +++ /dev/null @@ -1,158 +0,0 @@ ---- -- digest: 64013f487492f493d06c360266c75179fca9e5e3bd9cdf4715656c05e484d04a - id_run: 26291 - id_seq_component: 1 - position: 1 - subset: ~ - tag_index: 10 -- digest: 1575e3fa8cfc5b0684045f1b2a132076e9ac088f630c90790fbe36f7e0589d00 - id_run: 26291 - id_seq_component: 2 - position: 2 - subset: ~ - tag_index: 10 -- digest: f1c6a2b1a081645eceec70070e0900ed11e4ef7527cdbe5311738629d759e97b - id_run: 26291 - id_seq_component: 3 - position: 1 - subset: ~ - tag_index: 4 -- digest: 247284cbb9248db81a44b4ea1dba9e6abff3137f99c2f4a138555b120f5eaf8c - id_run: 26291 - id_seq_component: 4 - position: 2 - subset: ~ - tag_index: 4 -- digest: cdf72931d7b0ccce78922cec587b0bfa1c6ba0bad8c7ecb217d48af7c0e08a19 - id_run: 26291 - id_seq_component: 5 - position: 1 - subset: ~ - tag_index: 7 -- digest: ac2b116498fe0f7085a75f6f2f4bdb8e5ffadf7068d724fb08771cd6302b24e3 - id_run: 26291 - id_seq_component: 6 - position: 2 - subset: ~ - tag_index: 7 -- digest: a8ee737489b8ae763c3e53056ca2638da44859177584ba2ba7abf73168c55f5e - id_run: 26291 - id_seq_component: 7 - position: 1 - subset: ~ - tag_index: 8 -- digest: b4178cdaf8d6f7d5c1c1179a524e1489ca89a45eea7aad99c96e9706a5fc8ec8 - id_run: 26291 - id_seq_component: 8 - position: 2 - subset: ~ - tag_index: 8 -- digest: c957145416114cd41df343db734e2de29921fb6aac1c4494ac8ab738d69a714a - id_run: 26291 - id_seq_component: 9 - position: 1 - subset: ~ - tag_index: 1 -- digest: 78d0a76c780c449ac12645d642e7f98888a895f400f4a879fe7f28455d6a602e - id_run: 26291 - id_seq_component: 10 - position: 2 - subset: ~ - tag_index: 1 -- digest: 5b6320cc7f823853bb4e4373bd99156957e0162fd56c594160678237f148b08e - id_run: 26291 - id_seq_component: 11 - position: 1 - subset: ~ - tag_index: 9 -- digest: 4b9361de5a2e4f739a3a5f29c5c85a6d1765ba92f6516c36997a2f385e1cc4d8 - id_run: 26291 - id_seq_component: 12 - position: 2 - subset: ~ - tag_index: 9 -- digest: 8dd53961be4c48398a33239805839bbcfef01198f46d5f1d847c52da2483f852 - id_run: 26291 - id_seq_component: 13 - position: 1 - subset: ~ - tag_index: 12 -- digest: 9099df4b8546270b01d1fe62288bd142ac7f0121995fcd84a13700ad29735496 - id_run: 26291 - id_seq_component: 14 - position: 2 - subset: ~ - tag_index: 12 -- digest: 2172da71cf35ae59316f93b1f8e45b28e7f2f1a53c641d956ba8be5611623ea5 - id_run: 26291 - id_seq_component: 15 - position: 1 - subset: ~ - tag_index: 11 -- digest: bf51062197cb45b27beaa5901d2c2f7ab5ecf9370e1955873c4a4f07bcef1dc9 - id_run: 26291 - id_seq_component: 16 - position: 2 - subset: ~ - tag_index: 11 -- digest: a142d0df20a8362a241e571ed480b741a192a5f70108ee3af41cf1d701365b06 - id_run: 26291 - id_seq_component: 17 - position: 1 - subset: ~ - tag_index: 6 -- digest: f05db0e533f9072826078aa3ee34e60c7638a77c58135427a7cf54ec8d8fdaeb - id_run: 26291 - id_seq_component: 18 - position: 2 - subset: ~ - tag_index: 6 -- digest: b62e703d047c360a5830bd46d7f48439efb25e6852302fd21d56778c26a35b76 - id_run: 26291 - id_seq_component: 19 - position: 1 - subset: ~ - tag_index: 2 -- digest: 4e18a830a0756c837343aae86871259481523173486c6e94a5cf0f0ac3b16561 - id_run: 26291 - id_seq_component: 20 - position: 2 - subset: ~ - tag_index: 2 -- digest: ad5ec898f6e5407f5a80ec68c0967acf20a5e4809d21cd29b5b2d39c0f731534 - id_run: 26291 - id_seq_component: 21 - position: 1 - subset: ~ - tag_index: 5 -- digest: 7458fe6b0b88f8fefd75f21862bed23e7b342caf2d51a726a324a228613c677f - id_run: 26291 - id_seq_component: 22 - position: 2 - subset: ~ - tag_index: 5 -- digest: f4013ca42106e02a488361206d845005a21c0917d7b7dbcb6a878f7322194c2a - id_run: 26291 - id_seq_component: 23 - position: 1 - subset: ~ - tag_index: 3 -- digest: 28f8a790af34647bc75d61b07e2506b84612dfd58ada09da2edc5bb6eead8873 - id_run: 26291 - id_seq_component: 24 - position: 2 - subset: ~ - tag_index: 3 -- digest: cd87cabb80ce5105c7924a3bc56a383afb7b72afda6b5867856373403b0913a2 - id_run: 26291 - id_seq_component: 25 - position: 1 - subset: ~ - tag_index: ~ -- digest: 98af9d7a81091699a06cfd97624f0049c87fca8229c8133fda245caeff0a194c - id_run: 26291 - id_seq_component: 26 - position: 2 - subset: ~ - tag_index: ~ - diff --git a/t/data/qc_outcomes/fixtures/300-seq_component_composition.yml b/t/data/qc_outcomes/fixtures/300-seq_component_composition.yml deleted file mode 100644 index bb1a90041..000000000 --- a/t/data/qc_outcomes/fixtures/300-seq_component_composition.yml +++ /dev/null @@ -1,106 +0,0 @@ ---- -- id_seq_comcom: 1 - id_seq_component: 1 - id_seq_composition: 1 - size: 2 -- id_seq_comcom: 2 - id_seq_component: 2 - id_seq_composition: 1 - size: 2 -- id_seq_comcom: 3 - id_seq_component: 3 - id_seq_composition: 2 - size: 2 -- id_seq_comcom: 4 - id_seq_component: 4 - id_seq_composition: 2 - size: 2 -- id_seq_comcom: 5 - id_seq_component: 5 - id_seq_composition: 3 - size: 2 -- id_seq_comcom: 6 - id_seq_component: 6 - id_seq_composition: 3 - size: 2 -- id_seq_comcom: 7 - id_seq_component: 7 - id_seq_composition: 4 - size: 2 -- id_seq_comcom: 8 - id_seq_component: 8 - id_seq_composition: 4 - size: 2 -- id_seq_comcom: 9 - id_seq_component: 9 - id_seq_composition: 5 - size: 2 -- id_seq_comcom: 10 - id_seq_component: 10 - id_seq_composition: 5 - size: 2 -- id_seq_comcom: 11 - id_seq_component: 11 - id_seq_composition: 6 - size: 2 -- id_seq_comcom: 12 - id_seq_component: 12 - id_seq_composition: 6 - size: 2 -- id_seq_comcom: 13 - id_seq_component: 13 - id_seq_composition: 7 - size: 2 -- id_seq_comcom: 14 - id_seq_component: 14 - id_seq_composition: 7 - size: 2 -- id_seq_comcom: 15 - id_seq_component: 15 - id_seq_composition: 8 - size: 2 -- id_seq_comcom: 16 - id_seq_component: 16 - id_seq_composition: 8 - size: 2 -- id_seq_comcom: 17 - id_seq_component: 17 - id_seq_composition: 9 - size: 2 -- id_seq_comcom: 18 - id_seq_component: 18 - id_seq_composition: 9 - size: 2 -- id_seq_comcom: 19 - id_seq_component: 19 - id_seq_composition: 10 - size: 2 -- id_seq_comcom: 20 - id_seq_component: 20 - id_seq_composition: 10 - size: 2 -- id_seq_comcom: 21 - id_seq_component: 21 - id_seq_composition: 11 - size: 2 -- id_seq_comcom: 22 - id_seq_component: 22 - id_seq_composition: 11 - size: 2 -- id_seq_comcom: 23 - id_seq_component: 23 - id_seq_composition: 12 - size: 2 -- id_seq_comcom: 24 - id_seq_component: 24 - id_seq_composition: 12 - size: 2 -- id_seq_comcom: 25 - id_seq_component: 25 - id_seq_composition: 13 - size: 1 -- id_seq_comcom: 26 - id_seq_component: 26 - id_seq_composition: 14 - size: 1 - diff --git a/t/data/qc_outcomes/fixtures/300-seq_composition.yml b/t/data/qc_outcomes/fixtures/300-seq_composition.yml deleted file mode 100644 index 81d1f1839..000000000 --- a/t/data/qc_outcomes/fixtures/300-seq_composition.yml +++ /dev/null @@ -1,44 +0,0 @@ ---- -- digest: d00e47ab46e2b4e5cbf1d7d67a5a0f4f3f5ca6c14c8c9994fa7b1cb5b83505c2 - id_seq_composition: 1 - size: 2 -- digest: 40ec8ffb930b2e661e5a496a263dcf09bb096cd85508f9bac1f5e32298bb3381 - id_seq_composition: 2 - size: 2 -- digest: 477c2257c18c6895320f532f347b51133e4126dded129c070488988ca65fa4ea - id_seq_composition: 3 - size: 2 -- digest: af6877094c0031f61ba6847a5d3f14d891c00a40ca660cb95571d4e2df102cca - id_seq_composition: 4 - size: 2 -- digest: b65be328691835deeff44c4025fadecd9af6512c10044754dd2161d8a7c85000 - id_seq_composition: 5 - size: 2 -- digest: b5a2c4b928e74dedf08adb31b558849ab927bb4ad60636554414d4bcc2d924ea - id_seq_composition: 6 - size: 2 -- digest: 333ecb63f21d80de0c2affc0458e168f79f77ee9cf26771b655e17220e46cc50 - id_seq_composition: 7 - size: 2 -- digest: 446d78a664d9939cd3e603a133e43f22b99b3b35e2ec893c5f9b6e0d1c00a1a7 - id_seq_composition: 8 - size: 2 -- digest: 654571abbf002fe3db014b1886bc676d54325816c3464e855ed3fe234e4ab15c - id_seq_composition: 9 - size: 2 -- digest: e7acb7b9924267e06abcaf2f0ceb76e9c9e0692908d04d4edfac4a8dc35843c0 - id_seq_composition: 10 - size: 2 -- digest: a3649dc48ec3511ad99817086e84ceb05df5d5749c45e597517c2b3e3cebd0e8 - id_seq_composition: 11 - size: 2 -- digest: 05858d03dadcd624f4c33c8766828f89fd44a3cc67582aa68a8dc257e95bd519 - id_seq_composition: 12 - size: 2 -- digest: ec20309571a4ee83d19cbec42a4837e33a3361881d781acce2bc9b88d3a4b763 - id_seq_composition: 13 - size: 1 -- digest: f14be2eeb5fd199883138473f915cdf9bd2b66bda5592e122a4b4b9e5e3110ad - id_seq_composition: 14 - size: 1 - diff --git a/t/data/qc_outcomes/fixtures/400-mqc_library_outcome_ent.yml b/t/data/qc_outcomes/fixtures/400-mqc_library_outcome_ent.yml deleted file mode 100644 index a1651e898..000000000 --- a/t/data/qc_outcomes/fixtures/400-mqc_library_outcome_ent.yml +++ /dev/null @@ -1,121 +0,0 @@ ---- -- id_mqc_library_outcome_ent: 1 - id_mqc_outcome: 4 - id_run: ~ - id_seq_composition: 1 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 2 - id_mqc_outcome: 4 - id_run: ~ - id_seq_composition: 2 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 3 - id_mqc_outcome: 1 - id_run: ~ - id_seq_composition: 3 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 4 - id_mqc_outcome: 2 - id_run: ~ - id_seq_composition: 4 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 5 - id_mqc_outcome: 1 - id_run: ~ - id_seq_composition: 5 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 6 - id_mqc_outcome: 3 - id_run: ~ - id_seq_composition: 6 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 7 - id_mqc_outcome: 6 - id_run: ~ - id_seq_composition: 7 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 8 - id_mqc_outcome: 5 - id_run: ~ - id_seq_composition: 8 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 9 - id_mqc_outcome: 6 - id_run: ~ - id_seq_composition: 9 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 10 - id_mqc_outcome: 2 - id_run: ~ - id_seq_composition: 10 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 11 - id_mqc_outcome: 5 - id_run: ~ - id_seq_composition: 11 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 -- id_mqc_library_outcome_ent: 12 - id_mqc_outcome: 3 - id_run: ~ - id_seq_composition: 12 - last_modified: 2018-08-14 12:06:28 - modified_by: 'user' - position: ~ - reported: ~ - tag_index: ~ - username: u1 diff --git a/t/data/qc_outcomes/fixtures/400-mqc_outcome_ent.yml b/t/data/qc_outcomes/fixtures/400-mqc_outcome_ent.yml deleted file mode 100644 index c4588de0e..000000000 --- a/t/data/qc_outcomes/fixtures/400-mqc_outcome_ent.yml +++ /dev/null @@ -1,20 +0,0 @@ ---- -- id_mqc_outcome: 3 - id_mqc_outcome_ent: 1 - id_run: 26291 - id_seq_composition: 13 - last_modified: 2019-03-18 15:54:32 - modified_by: ~ - position: 1 - reported: ~ - username: ~ -- id_mqc_outcome: 3 - id_mqc_outcome_ent: 2 - id_run: 26291 - id_seq_composition: 14 - last_modified: 2019-03-18 15:54:32 - modified_by: ~ - position: 2 - reported: ~ - username: ~ - diff --git a/t/data/qc_outcomes/fixtures/README b/t/data/qc_outcomes/fixtures/README deleted file mode 100644 index 3f8af79b0..000000000 --- a/t/data/qc_outcomes/fixtures/README +++ /dev/null @@ -1,18 +0,0 @@ -Run 26291 has the following library manual QC results: - -# 26291:1:1;26291:2:1 => 1 # 1: Accepted preliminary -# 26291:1:2;26291:2:2 => 2 # 2: Rejected preliminary -# 26291:1:3;26291:2:3 => 3 # 3: Accepted final -# 26291:1:4;26291:2:4 => 4 # 4: Rejected final -# 26291:1:5;26291:2:5 => 5 # 5: Undecided -# 26291:1:6;26291:2:6 => 6 # 6: Undecided final -# 26291:1:7;26291:2:7 => 1 -# 26291:1:8;26291:2:8 => 2 -# 26291:1:9;26291:2:9 => 3 # 3: Accepted final -# 26291:1:10;26291:2:10 => 4 # 4: Rejected final -# 26291:1:11;26291:2:11 => 5 -# 26291:1:12;26291:2:12 => 6 - -These results are used to test that pipeline jobs take the -correct action when presented with data with a range of -library QC outcomes.