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Develop into Master #683

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Sep 30, 2024
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8d5cd01
Update rspec-rails to version 6.1.4
depfu[bot] Aug 16, 2024
b60338a
Merge pull request #665 from sanger/depfu/update/rspec-rails-6.1.4
SHIV5T3R Aug 21, 2024
4de4f31
Update rexml to version 3.3.6
depfu[bot] Aug 22, 2024
14b090d
Merge pull request #666 from sanger/depfu/update/rexml-3.3.6
SHIV5T3R Aug 23, 2024
4b7158e
Update rspec-rails to version 6.1.5
depfu[bot] Sep 3, 2024
2890646
Update Ruby to version 3.3.5
depfu[bot] Sep 5, 2024
54840c1
Merge pull request #669 from sanger/depfu/update/rspec-rails-6.1.5
stevieing Sep 13, 2024
2f5cbfe
Update rspec-rails to version 7.0.1
depfu[bot] Sep 13, 2024
31c1e3e
Merge pull request #670 from sanger/depfu/update/rspec-rails-7.0.1
stevieing Sep 13, 2024
6637afc
Update rubocop to version 1.66.1
depfu[bot] Sep 13, 2024
6fc0364
Update rubocop-rails to version 2.26.1
depfu[bot] Sep 13, 2024
2263a34
Update rubocop-rspec to version 3.0.5
depfu[bot] Sep 13, 2024
022c3cf
Merge pull request #672 from sanger/depfu/update/rubocop-1.66.1
dasunpubudumal Sep 18, 2024
7acfe6a
Increase size of id_sample_lims column in sample table
stevieing Sep 19, 2024
f3374a4
Reverted views schema
stevieing Sep 20, 2024
48c7b68
Merge pull request #678 from sanger/675-y24-316-as-developers-we-want…
stevieing Sep 20, 2024
b2101a8
Merge pull request #671 from sanger/depfu/engine/ruby-3.3.5
stevieing Sep 20, 2024
5dddd19
Update ffi gem version to 1.17.0
stevieing Sep 20, 2024
662b025
Merge pull request #679 from sanger/update-ffi-to-fix-errors
stevieing Sep 20, 2024
6fa7b15
Update spec_helper.rb to use Rails.root.glob for requiring support files
stevieing Sep 20, 2024
7babd64
Merge pull request #673 from sanger/depfu/update/rubocop-rails-2.26.1
stevieing Sep 20, 2024
0ea609e
Merge pull request #674 from sanger/depfu/update/rubocop-rspec-3.0.5
stevieing Sep 20, 2024
f2f9540
Update .release-version
stevieing Sep 30, 2024
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2 changes: 1 addition & 1 deletion .release-version
Original file line number Diff line number Diff line change
@@ -1 +1 @@
1.20.0
1.21.0
2 changes: 1 addition & 1 deletion .ruby-version
Original file line number Diff line number Diff line change
@@ -1 +1 @@
3.3.4
3.3.5
2 changes: 1 addition & 1 deletion Dockerfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM ruby:3.3.4
FROM ruby:3.3.5

RUN gem install bundler

Expand Down
46 changes: 21 additions & 25 deletions Gemfile.lock
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ GEM
amq-protocol (~> 2.3, >= 2.3.1)
sorted_set (~> 1, >= 1.0.2)
coderay (1.1.3)
concurrent-ruby (1.3.3)
concurrent-ruby (1.3.4)
connection_pool (2.2.5)
crass (1.0.6)
diff-lcs (1.5.1)
Expand All @@ -50,7 +50,7 @@ GEM
factory_bot_rails (6.4.3)
factory_bot (~> 6.4)
railties (>= 5.0.0)
ffi (1.15.5)
ffi (1.17.0)
formatador (1.1.0)
guard (2.18.1)
formatador (>= 0.2.4)
Expand Down Expand Up @@ -84,19 +84,19 @@ GEM
lumberjack (1.2.9)
method_source (1.1.0)
mini_portile2 (2.8.7)
minitest (5.24.1)
minitest (5.25.1)
msgpack (1.7.2)
multi_json (1.15.0)
mysql2 (0.5.6)
nenv (0.3.0)
nokogiri (1.16.6)
nokogiri (1.16.7)
mini_portile2 (~> 2.8.2)
racc (~> 1.4)
notiffany (0.1.3)
nenv (~> 0.1)
shellany (~> 0.0)
parallel (1.25.1)
parser (3.3.4.0)
parallel (1.26.3)
parser (3.3.5.0)
ast (~> 2.4.1)
racc
pry (0.14.2)
Expand Down Expand Up @@ -127,51 +127,48 @@ GEM
ffi (~> 1.0)
rbtree (0.4.6)
regexp_parser (2.9.2)
rexml (3.3.4)
strscan
rspec (3.13.0)
rspec-core (~> 3.13.0)
rspec-expectations (~> 3.13.0)
rspec-mocks (~> 3.13.0)
rspec-core (3.13.0)
rspec-core (3.13.1)
rspec-support (~> 3.13.0)
rspec-expectations (3.13.1)
rspec-expectations (3.13.3)
diff-lcs (>= 1.2.0, < 2.0)
rspec-support (~> 3.13.0)
rspec-mocks (3.13.1)
diff-lcs (>= 1.2.0, < 2.0)
rspec-support (~> 3.13.0)
rspec-rails (6.1.3)
actionpack (>= 6.1)
activesupport (>= 6.1)
railties (>= 6.1)
rspec-rails (7.0.1)
actionpack (>= 7.0)
activesupport (>= 7.0)
railties (>= 7.0)
rspec-core (~> 3.13)
rspec-expectations (~> 3.13)
rspec-mocks (~> 3.13)
rspec-support (~> 3.13)
rspec-support (3.13.1)
rubocop (1.65.1)
rubocop (1.66.1)
json (~> 2.3)
language_server-protocol (>= 3.17.0)
parallel (~> 1.10)
parser (>= 3.3.0.2)
rainbow (>= 2.2.2, < 4.0)
regexp_parser (>= 2.4, < 3.0)
rexml (>= 3.2.5, < 4.0)
rubocop-ast (>= 1.31.1, < 2.0)
rubocop-ast (>= 1.32.2, < 2.0)
ruby-progressbar (~> 1.7)
unicode-display_width (>= 2.4.0, < 3.0)
rubocop-ast (1.32.0)
rubocop-ast (1.32.3)
parser (>= 3.3.1.0)
rubocop-performance (1.21.1)
rubocop (>= 1.48.1, < 2.0)
rubocop-ast (>= 1.31.1, < 2.0)
rubocop-rails (2.25.1)
rubocop-rails (2.26.1)
activesupport (>= 4.2.0)
rack (>= 1.1)
rubocop (>= 1.33.0, < 2.0)
rubocop (>= 1.52.0, < 2.0)
rubocop-ast (>= 1.31.1, < 2.0)
rubocop-rspec (3.0.4)
rubocop-rspec (3.0.5)
rubocop (~> 1.61)
ruby-progressbar (1.13.0)
sanger_warren (0.4.1)
Expand All @@ -190,12 +187,11 @@ GEM
sorted_set (1.0.3)
rbtree
set (~> 1.0)
strscan (3.1.0)
thor (1.3.1)
thor (1.3.2)
tzinfo (2.0.6)
concurrent-ruby (~> 1.0)
unicode-display_width (2.5.0)
zeitwerk (2.6.16)
unicode-display_width (2.6.0)
zeitwerk (2.6.18)

PLATFORMS
ruby
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
class IncreaseSizeOfIdSampleLimsColumnInSample < ActiveRecord::Migration[7.0]
def up
change_column :sample, :id_sample_lims, :string, limit: 255
end

def down
change_column :sample, :id_sample_lims, :string, limit: 20
end
end
6 changes: 3 additions & 3 deletions db/schema.rb
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
#
# It's strongly recommended that you check this file into your version control system.

ActiveRecord::Schema[7.0].define(version: 2024_08_14_125331) do
ActiveRecord::Schema[7.0].define(version: 2024_09_19_134424) do
create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
t.string "aliquot_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
Expand Down Expand Up @@ -305,7 +305,7 @@
create_table "sample", primary_key: "id_sample_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
t.string "id_lims", limit: 10, null: false, comment: "LIM system identifier, e.g. CLARITY-GCLP, SEQSCAPE"
t.string "uuid_sample_lims", limit: 36, comment: "LIMS-specific sample uuid"
t.string "id_sample_lims", limit: 20, null: false, comment: "LIMS-specific sample identifier"
t.string "id_sample_lims", null: false, comment: "LIMS-specific sample identifier"
t.datetime "last_updated", precision: nil, null: false, comment: "Timestamp of last update"
t.datetime "recorded_at", precision: nil, null: false, comment: "Timestamp of warehouse update"
t.datetime "deleted_at", precision: nil, comment: "Timestamp of sample deletion"
Expand Down Expand Up @@ -463,7 +463,7 @@
t.string "programme"
t.index ["accession_number"], name: "study_accession_number_index"
t.index ["id_lims", "id_study_lims"], name: "study_id_lims_id_study_lims_index", unique: true
t.index ["id_study_lims"], name: "index_study_on_id_study_lims", unique: false
t.index ["id_study_lims"], name: "index_study_on_id_study_lims"
t.index ["name"], name: "study_name_index"
t.index ["uuid_study_lims"], name: "study_uuid_study_lims_index", unique: true
end
Expand Down
2 changes: 1 addition & 1 deletion db/views_schema.rb
Original file line number Diff line number Diff line change
Expand Up @@ -29,4 +29,4 @@
'lh_biosero_cp_error_recovered_destination_plate_completed','lh_biosero_cp_error_recovered_destination_plate_partial_completed'
)
SQL
)
)
2 changes: 1 addition & 1 deletion spec/models/sample_spec.rb
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@

let(:json) do
{
'id' => 1,
'id' => '1' * 255.to_i,
'name' => 'name',
'reference_genome' => 'reference genome',
'organism' => 'organism',
Expand Down
2 changes: 1 addition & 1 deletion spec/spec_helper.rb
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

# Requires supporting ruby files with custom matchers and macros, etc,
# in spec/support/ and its subdirectories.
Dir[Rails.root.join('spec/support/**/*.rb')].each { |f| require f }
Rails.root.glob('spec/support/**/*.rb').each { |f| require f }

RSpec.configure do |config|
config.use_transactional_fixtures = true
Expand Down
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