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ORM update and extension #244

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merged 2 commits into from
Oct 14, 2024
Merged

ORM update and extension #244

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13c8082
Added new delegated methods, sample_uuid and sample_lims
mgcam Oct 9, 2024
9b03c7d
Updated ORM classes
mgcam Oct 9, 2024
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4 changes: 4 additions & 0 deletions Changes
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
LIST OF CHANGES
---------------

- Added new delegated methods to WTSI::DNAP::Warehouse::Schema::Result::IseqFlowcell,
sample_uuid and sample_lims.
- Updated ORM classes by ingesting changes from the prod database,

release 6.33.1 (2024-10-04)
- Added .github/dependabot.yml file to auto-update GitHub actions
- GitHub CI - updated deprecated v2 runner action to v3
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2 changes: 2 additions & 0 deletions lib/WTSI/DNAP/Warehouse/Schema/Result/IseqFlowcell.pm
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Expand Up @@ -601,7 +601,9 @@ Readonly my @USER_ROLES => qw/manager follower owner/;

Readonly my %DELEGATION_TO_SAMPLE => {
'sample_id' => 'id_sample_lims',
'sample_uuid' => 'uuid_sample_lims',
'sample_name' => 'name',
'sample_lims' => 'id_lims',
'sample_reference_genome' => 'reference_genome',
'organism' => 'organism',
'sample_accession_number' => 'accession_number',
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8 changes: 4 additions & 4 deletions lib/WTSI/DNAP/Warehouse/Schema/Result/Sample.pm
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Expand Up @@ -67,7 +67,7 @@ LIMS-specific sample uuid

data_type: 'varchar'
is_nullable: 0
size: 20
size: 255

LIMS-specific sample identifier

Expand Down Expand Up @@ -459,7 +459,7 @@ __PACKAGE__->add_columns(
'uuid_sample_lims',
{ data_type => 'varchar', is_nullable => 1, size => 36 },
'id_sample_lims',
{ data_type => 'varchar', is_nullable => 0, size => 20 },
{ data_type => 'varchar', is_nullable => 0, size => 255 },
'last_updated',
{
data_type => 'datetime',
Expand Down Expand Up @@ -798,8 +798,8 @@ __PACKAGE__->has_many(
);


# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:SBUvcjIuSMo1rqiCwp0AEA
# Created by DBIx::Class::Schema::Loader v0.07052 @ 2024-10-09 15:42:26
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:S5eGEf8q9fTn5qKSp/Et/g

our $VERSION = '0';

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12 changes: 10 additions & 2 deletions lib/WTSI/DNAP/Warehouse/Schema/Result/Study.pm
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Expand Up @@ -306,6 +306,12 @@ The data destination type(s) for the study. It could be 'standard', '14mg' or 'g
is_nullable: 1
size: 255

=head2 programme

data_type: 'varchar'
is_nullable: 1
size: 255

=cut

__PACKAGE__->add_columns(
Expand Down Expand Up @@ -412,6 +418,8 @@ __PACKAGE__->add_columns(
{ data_type => 'varchar', is_nullable => 1, size => 255 },
'contaminated_human_data_access_group',
{ data_type => 'varchar', is_nullable => 1, size => 255 },
'programme',
{ data_type => 'varchar', is_nullable => 1, size => 255 },
);

=head1 PRIMARY KEY
Expand Down Expand Up @@ -580,8 +588,8 @@ __PACKAGE__->has_many(
);


# Created by DBIx::Class::Schema::Loader v0.07052 @ 2024-08-08 13:33:16
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:cSZp6NXki9BI3+HAAlBY9w
# Created by DBIx::Class::Schema::Loader v0.07052 @ 2024-10-09 15:42:26
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:5p/5azacjlWMHTtTSrJtew

with 'WTSI::DNAP::Warehouse::Schema::Query::LimsFlags';

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7 changes: 4 additions & 3 deletions lib/WTSI/DNAP/Warehouse/Schema/Result/TolSampleBioproject.pm
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Expand Up @@ -61,7 +61,7 @@ __PACKAGE__->table('tol_sample_bioproject');
=head2 library_type

data_type: 'enum'
extra: {list => ['Chromium genome','Haplotagging','Hi-C','Hi-C - Arima v1','Hi-C - Arima v2','Hi-C - Dovetail','Hi-C - Omni-C','Hi-C - Qiagen','PacBio - CLR','PacBio - HiFi','ONT','RNA PolyA','RNA-seq dUTP eukaryotic','Standard','unknown','HiSeqX PCR free','PacBio - HiFi (ULI)','PacBio - IsoSeq']}
extra: {list => ['Chromium genome','Haplotagging','Hi-C','Hi-C - Arima v1','Hi-C - Arima v2','Hi-C - Dovetail','Hi-C - Omni-C','Hi-C - Qiagen','PacBio - CLR','PacBio - HiFi','ONT','RNA PolyA','RNA-seq dUTP eukaryotic','Standard','unknown','HiSeqX PCR free','PacBio - HiFi (ULI)','PacBio - IsoSeq','ATAC-seq']}
is_nullable: 1

=head2 tolid
Expand Down Expand Up @@ -144,6 +144,7 @@ __PACKAGE__->add_columns(
'HiSeqX PCR free',
'PacBio - HiFi (ULI)',
'PacBio - IsoSeq',
'ATAC-seq',
],
},
is_nullable => 1,
Expand Down Expand Up @@ -221,8 +222,8 @@ __PACKAGE__->belongs_to(
);


# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-04-21 14:32:17
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:+03wqzLzH0LFAZwFGbEKOA
# Created by DBIx::Class::Schema::Loader v0.07052 @ 2024-10-09 15:42:26
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:P7s1muBNrElt8Hd3xqTL3w

our $VERSION = '0';

Expand Down