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[automated] Merge Develop into Master #2049

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merged 42 commits into from
Nov 12, 2024
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f472079
feat(rnaf): adds rna ffpe pipeline, robot steps and purposes
BenTopping Oct 17, 2024
3a9deb7
feat(rnaf): removes lrnaf cherrypick in favour of using lbr cherrypick
BenTopping Oct 18, 2024
de60306
Refactor pipeline configuration for Hi-C in bespoke PCR
dasunpubudumal Oct 23, 2024
5cfa76a
Refactor pipeline configuration for Hi-C in bespoke PCR
dasunpubudumal Oct 23, 2024
b1ce713
Refactor active_pipelines_for method in PipelineList
dasunpubudumal Oct 23, 2024
c6d8ff4
Update vite to version 5.4.10
depfu[bot] Oct 24, 2024
85c7d58
Refactor pipeline configuration to include Hi-C in bespoke PCR
dasunpubudumal Oct 24, 2024
458297c
Refactor pipeline configuration to include Hi-C in bespoke PCR
dasunpubudumal Oct 24, 2024
e675ff3
Refactor active_pipelines_for method in PipelineList
dasunpubudumal Oct 24, 2024
28ce2af
Refactor pipeline configuration to include Haplotagging in bespoke PCR
dasunpubudumal Oct 24, 2024
fe551b2
misc: wip rnaf pipeline
BenTopping Oct 28, 2024
26834c7
Update rexml to version 3.3.9
depfu[bot] Oct 28, 2024
4f9550f
Update eslint-plugin-vue to version 9.30.0
depfu[bot] Oct 29, 2024
adebf9a
Customer-requested bed number change
KatyTaylor Oct 30, 2024
8fa9c1d
Update oj to version 3.16.7
depfu[bot] Nov 2, 2024
498b2fb
Revert "Revert "Y24-022 UI Submit Pool XP tube to traction""
seenanair Nov 5, 2024
d3948a3
Merge pull request #2048 from sanger/revert-2046-revert-2008-y24-022-…
seenanair Nov 5, 2024
5938412
Merge pull request #2037 from sanger/scrna-core-bed-verification-chan…
KatyTaylor Nov 5, 2024
e2bf5b3
Merge pull request #2031 from sanger/depfu/update/rexml-3.3.9
StephenHulme Nov 5, 2024
7db5324
Merge pull request #2045 from sanger/depfu/update/oj-3.16.7
StephenHulme Nov 5, 2024
5af4eb7
Update rails to version 7.1.5
depfu[bot] Nov 5, 2024
ae416aa
Add bespoke Hi-C configuration to pipeline and remove redundant entri…
dasunpubudumal Nov 6, 2024
9a56469
WIP flagging new pipeline config
dasunpubudumal Nov 6, 2024
a6bc921
WIP flagging hic norm plate purpose
dasunpubudumal Nov 6, 2024
d3da88f
Merge pull request #2041 from sanger/depfu/update/group/rails-7.1.5
StephenHulme Nov 6, 2024
6145703
Merge pull request #2020 from sanger/depfu/update/yarn/vite-5.4.10
StephenHulme Nov 6, 2024
a0ea116
Merge pull request #2035 from sanger/depfu/update/yarn/eslint-plugin-…
StephenHulme Nov 6, 2024
2c1f96d
Update Node.js to version 22.11.0
depfu[bot] Nov 6, 2024
2223eb7
Merge pull request #2004 from sanger/y24-265-rna-ffpe
BenTopping Nov 6, 2024
c01e8ce
Merge pull request #2038 from sanger/depfu/engine/yarn/nodejs-22.11.0
StephenHulme Nov 6, 2024
a09fcce
Update selenium-webdriver to version 4.26.0
depfu[bot] Nov 6, 2024
0ef9d9b
Merge pull request #2053 from sanger/depfu/update/selenium-webdriver-…
StephenHulme Nov 6, 2024
30d6457
build: remove rspec-rails version lock and update
StephenHulme Nov 6, 2024
4a05005
Merge pull request #2054 from sanger/sh51/remove-rspec-rails-version-…
StephenHulme Nov 6, 2024
64ef6ba
Update @vitest/coverage-v8 to version 2.1.4
StephenHulme Nov 7, 2024
b36de72
build: update vitest to compatible version
StephenHulme Nov 7, 2024
caadb9e
build: regenerate lockfile
StephenHulme Nov 7, 2024
779563f
Merge pull request #2023 from sanger/y24-335-barcode-for-norm-plate-t…
dasunpubudumal Nov 7, 2024
0402678
Merge pull request #2036 from sanger/depfu/update/yarn/@vitest/covera…
StephenHulme Nov 8, 2024
38c1eb9
misc: unwip rnaf pipeline
BenTopping Nov 12, 2024
7737ff3
Merge pull request #2066 from sanger/unwip-rna-ffpe
BenTopping Nov 12, 2024
6f3529a
misc: bumps release version
BenTopping Nov 12, 2024
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2 changes: 1 addition & 1 deletion .nvmrc
Original file line number Diff line number Diff line change
@@ -1 +1 @@
v20.16.0
v22.11.0
2 changes: 1 addition & 1 deletion .release-version
Original file line number Diff line number Diff line change
@@ -1 +1 @@
3.63.0
3.64.0
2 changes: 1 addition & 1 deletion Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ group :test do
gem 'launchy' # Used by capybara for eg. save_and_open_screenshot
gem 'rails-controller-testing'
gem 'rspec-json_expectations'
gem 'rspec-rails', '6.1.3'
gem 'rspec-rails'
gem 'selenium-webdriver', '~> 4.1', require: false
gem 'simplecov', require: false
gem 'simplecov-lcov', require: false
Expand Down
139 changes: 70 additions & 69 deletions Gemfile.lock
Original file line number Diff line number Diff line change
Expand Up @@ -28,84 +28,88 @@ GIT
GEM
remote: https://rubygems.org/
specs:
actioncable (7.1.4)
actionpack (= 7.1.4)
activesupport (= 7.1.4)
actioncable (7.1.5)
actionpack (= 7.1.5)
activesupport (= 7.1.5)
nio4r (~> 2.0)
websocket-driver (>= 0.6.1)
zeitwerk (~> 2.6)
actionmailbox (7.1.4)
actionpack (= 7.1.4)
activejob (= 7.1.4)
activerecord (= 7.1.4)
activestorage (= 7.1.4)
activesupport (= 7.1.4)
actionmailbox (7.1.5)
actionpack (= 7.1.5)
activejob (= 7.1.5)
activerecord (= 7.1.5)
activestorage (= 7.1.5)
activesupport (= 7.1.5)
mail (>= 2.7.1)
net-imap
net-pop
net-smtp
actionmailer (7.1.4)
actionpack (= 7.1.4)
actionview (= 7.1.4)
activejob (= 7.1.4)
activesupport (= 7.1.4)
actionmailer (7.1.5)
actionpack (= 7.1.5)
actionview (= 7.1.5)
activejob (= 7.1.5)
activesupport (= 7.1.5)
mail (~> 2.5, >= 2.5.4)
net-imap
net-pop
net-smtp
rails-dom-testing (~> 2.2)
actionpack (7.1.4)
actionview (= 7.1.4)
activesupport (= 7.1.4)
actionpack (7.1.5)
actionview (= 7.1.5)
activesupport (= 7.1.5)
nokogiri (>= 1.8.5)
racc
rack (>= 2.2.4)
rack-session (>= 1.0.1)
rack-test (>= 0.6.3)
rails-dom-testing (~> 2.2)
rails-html-sanitizer (~> 1.6)
actiontext (7.1.4)
actionpack (= 7.1.4)
activerecord (= 7.1.4)
activestorage (= 7.1.4)
activesupport (= 7.1.4)
actiontext (7.1.5)
actionpack (= 7.1.5)
activerecord (= 7.1.5)
activestorage (= 7.1.5)
activesupport (= 7.1.5)
globalid (>= 0.6.0)
nokogiri (>= 1.8.5)
actionview (7.1.4)
activesupport (= 7.1.4)
actionview (7.1.5)
activesupport (= 7.1.5)
builder (~> 3.1)
erubi (~> 1.11)
rails-dom-testing (~> 2.2)
rails-html-sanitizer (~> 1.6)
activejob (7.1.4)
activesupport (= 7.1.4)
activejob (7.1.5)
activesupport (= 7.1.5)
globalid (>= 0.3.6)
activemodel (7.1.4)
activesupport (= 7.1.4)
activerecord (7.1.4)
activemodel (= 7.1.4)
activesupport (= 7.1.4)
activemodel (7.1.5)
activesupport (= 7.1.5)
activerecord (7.1.5)
activemodel (= 7.1.5)
activesupport (= 7.1.5)
timeout (>= 0.4.0)
activestorage (7.1.4)
actionpack (= 7.1.4)
activejob (= 7.1.4)
activerecord (= 7.1.4)
activesupport (= 7.1.4)
activestorage (7.1.5)
actionpack (= 7.1.5)
activejob (= 7.1.5)
activerecord (= 7.1.5)
activesupport (= 7.1.5)
marcel (~> 1.0)
activesupport (7.1.4)
activesupport (7.1.5)
base64
benchmark (>= 0.3)
bigdecimal
concurrent-ruby (~> 1.0, >= 1.0.2)
connection_pool (>= 2.2.5)
drb
i18n (>= 1.6, < 2)
logger (>= 1.4.2)
minitest (>= 5.1)
mutex_m
securerandom (>= 0.3)
tzinfo (~> 2.0)
addressable (2.8.7)
public_suffix (>= 2.0.2, < 7.0)
ast (2.4.2)
base64 (0.2.0)
benchmark (0.3.0)
bigdecimal (3.1.8)
bindex (0.8.1)
bootsnap (1.18.4)
Expand All @@ -132,7 +136,7 @@ GEM
bigdecimal
rexml
crass (1.0.6)
date (3.3.4)
date (3.4.0)
diff-lcs (1.5.1)
docile (1.4.0)
drb (2.2.1)
Expand Down Expand Up @@ -206,8 +210,8 @@ GEM
listen (3.9.0)
rb-fsevent (~> 0.10, >= 0.10.3)
rb-inotify (~> 0.9, >= 0.9.10)
logger (1.6.0)
loofah (2.22.0)
logger (1.6.1)
loofah (2.23.1)
crass (~> 1.0.2)
nokogiri (>= 1.12.0)
lumberjack (1.2.10)
Expand All @@ -227,7 +231,7 @@ GEM
multipart-post (2.4.0)
mutex_m (0.2.0)
nenv (0.3.0)
net-imap (0.4.14)
net-imap (0.5.0)
date
net-protocol
net-pop (0.1.2)
Expand All @@ -236,14 +240,14 @@ GEM
timeout
net-smtp (0.5.0)
net-protocol
nio4r (2.7.3)
nio4r (2.7.4)
nokogiri (1.16.7)
mini_portile2 (~> 2.8.2)
racc (~> 1.4)
notiffany (0.1.3)
nenv (~> 0.1)
shellany (~> 0.0)
oj (3.16.5)
oj (3.16.7)
bigdecimal (>= 3.0)
ostruct (>= 0.2)
ostruct (0.6.0)
Expand Down Expand Up @@ -273,23 +277,22 @@ GEM
rack (>= 3.0.0)
rack-test (2.1.0)
rack (>= 1.3)
rackup (2.1.0)
rackup (2.2.0)
rack (>= 3)
webrick (~> 1.8)
rails (7.1.4)
actioncable (= 7.1.4)
actionmailbox (= 7.1.4)
actionmailer (= 7.1.4)
actionpack (= 7.1.4)
actiontext (= 7.1.4)
actionview (= 7.1.4)
activejob (= 7.1.4)
activemodel (= 7.1.4)
activerecord (= 7.1.4)
activestorage (= 7.1.4)
activesupport (= 7.1.4)
rails (7.1.5)
actioncable (= 7.1.5)
actionmailbox (= 7.1.5)
actionmailer (= 7.1.5)
actionpack (= 7.1.5)
actiontext (= 7.1.5)
actionview (= 7.1.5)
activejob (= 7.1.5)
activemodel (= 7.1.5)
activerecord (= 7.1.5)
activestorage (= 7.1.5)
activesupport (= 7.1.5)
bundler (>= 1.15.0)
railties (= 7.1.4)
railties (= 7.1.5)
rails-controller-testing (1.0.5)
actionpack (>= 5.0.1.rc1)
actionview (>= 5.0.1.rc1)
Expand All @@ -301,9 +304,9 @@ GEM
rails-html-sanitizer (1.6.0)
loofah (~> 2.21)
nokogiri (~> 1.14)
railties (7.1.4)
actionpack (= 7.1.4)
activesupport (= 7.1.4)
railties (7.1.5)
actionpack (= 7.1.5)
activesupport (= 7.1.5)
irb
rackup (>= 1.0.0)
rake (>= 12.2)
Expand All @@ -321,8 +324,7 @@ GEM
regexp_parser (2.9.2)
reline (0.5.10)
io-console (~> 0.5)
rexml (3.3.6)
strscan
rexml (3.3.9)
rspec (3.13.0)
rspec-core (~> 3.13.0)
rspec-expectations (~> 3.13.0)
Expand All @@ -336,7 +338,7 @@ GEM
rspec-mocks (3.13.1)
diff-lcs (>= 1.2.0, < 2.0)
rspec-support (~> 3.13.0)
rspec-rails (6.1.3)
rspec-rails (6.1.4)
actionpack (>= 6.1)
activesupport (>= 6.1)
railties (>= 6.1)
Expand Down Expand Up @@ -370,7 +372,8 @@ GEM
ruby-units (4.0.3)
ruby2_keywords (0.0.5)
rubyzip (2.3.2)
selenium-webdriver (4.23.0)
securerandom (0.3.1)
selenium-webdriver (4.26.0)
base64 (~> 0.2)
logger (~> 1.4)
rexml (~> 3.2, >= 3.2.5)
Expand All @@ -392,7 +395,6 @@ GEM
sprint_client (0.1.0)
state_machines (0.6.0)
stringio (3.1.1)
strscan (3.1.0)
syntax_tree (6.2.0)
prettier_print (>= 1.2.0)
syntax_tree-haml (4.0.3)
Expand Down Expand Up @@ -427,15 +429,14 @@ GEM
addressable (>= 2.8.0)
crack (>= 0.3.2)
hashdiff (>= 0.4.0, < 2.0.0)
webrick (1.8.2)
websocket (1.2.11)
websocket-driver (0.7.6)
websocket-extensions (>= 0.1.0)
websocket-extensions (0.1.5)
xpath (3.2.0)
nokogiri (~> 1.8)
yard (0.9.36)
zeitwerk (2.6.18)
zeitwerk (2.7.1)

PLATFORMS
ruby
Expand All @@ -461,7 +462,7 @@ DEPENDENCIES
rails-controller-testing
rake
rspec-json_expectations
rspec-rails (= 6.1.3)
rspec-rails
rubocop
rubocop-performance
rubocop-rails
Expand Down
1 change: 1 addition & 0 deletions app/frontend/entrypoints/application.js
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ import '@/javascript/multi-stamp/index.js'
import '@/javascript/qc-information/index.js'
import '@/javascript/tubes-to-rack/index.js'
import '@/javascript/validate-paired-tubes/index.js'
import '@/javascript/pool-xp-tube-panel/index.js'

// Load simple javascript files
import '@/javascript/plain-javascript/page-reloader.js'
Expand Down
19 changes: 19 additions & 0 deletions app/frontend/javascript/icons/ErrorIcon.vue
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
<template>
<svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 -960 960 960" width="24" :fill="color" :stroke="color">
<path
d="M480-280q17 0 28.5-11.5T520-320q0-17-11.5-28.5T480-360q-17 0-28.5 11.5T440-320q0 17 11.5 28.5T480-280Zm-40-160h80v-240h-80v240Zm40 360q-83 0-156-31.5T197-197q-54-54-85.5-127T80-480q0-83 31.5-156T197-763q54-54 127-85.5T480-880q83 0 156 31.5T763-763q54 54 85.5 127T880-480q0 83-31.5 156T763-197q-54 54-127 85.5T480-80Zm0-80q134 0 227-93t93-227q0-134-93-227t-227-93q-134 0-227 93t-93 227q0 134 93 227t227 93Zm0-320Z"
/>
</svg>
</template>

<script>
export default {
name: 'ErrorIcon',
props: {
color: {
type: String,
default: 'currentColor',
},
},
}
</script>
19 changes: 19 additions & 0 deletions app/frontend/javascript/icons/ReadyIcon.vue
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
<template>
<svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 -960 960 960" width="24" :fill="color" :stroke="color">
<path
d="M480-360q50 0 85-35t35-85q0-50-35-85t-85-35q-50 0-85 35t-35 85q0 50 35 85t85 35Zm0 280q-83 0-156-31.5T197-197q-54-54-85.5-127T80-480q0-83 31.5-156T197-763q54-54 127-85.5T480-880q83 0 156 31.5T763-763q54 54 85.5 127T880-480q0 83-31.5 156T763-197q-54 54-127 85.5T480-80Zm0-80q134 0 227-93t93-227q0-134-93-227t-227-93q-134 0-227 93t-93 227q0 134 93 227t227 93Zm0-320Z"
/>
</svg>
</template>

<script>
export default {
name: 'ReadyIcon',
props: {
color: {
type: String,
default: 'currentColor',
},
},
}
</script>
19 changes: 19 additions & 0 deletions app/frontend/javascript/icons/SuccessIcon.vue
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
<template>
<svg xmlns="http://www.w3.org/2000/svg" height="24" viewBox="0 -960 960 960" width="24" :fill="color" :stroke="color">
<path
d="m424-296 282-282-56-56-226 226-114-114-56 56 170 170Zm56 216q-83 0-156-31.5T197-197q-54-54-85.5-127T80-480q0-83 31.5-156T197-763q54-54 127-85.5T480-880q83 0 156 31.5T763-763q54 54 85.5 127T880-480q0 83-31.5 156T763-197q-54 54-127 85.5T480-80Zm0-80q134 0 227-93t93-227q0-134-93-227t-227-93q-134 0-227 93t-93 227q0 134 93 227t227 93Zm0-320Z"
/>
</svg>
</template>

<script>
export default {
name: 'SuccessIcon',
props: {
color: {
type: String,
default: 'currentColor',
},
},
}
</script>
19 changes: 19 additions & 0 deletions app/frontend/javascript/icons/TubeIcon.vue
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
<template>
<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#5f6368">
<path
d="M480-80q-83 0-141.5-58.5T280-280v-360q-33 0-56.5-23.5T200-720v-80q0-33 23.5-56.5T280-880h400q33 0 56.5 23.5T760-800v80q0 33-23.5 56.5T680-640v360q0 83-58.5 141.5T480-80ZM280-720h400v-80H280v80Zm200 560q50 0 85-35t35-85H480v-80h120v-80H480v-80h120v-120H360v360q0 50 35 85t85 35ZM280-720v-80 80Z"
/>
</svg>
</template>

<script>
export default {
name: 'ErrorIcon',
props: {
color: {
type: String,
default: 'currentColor',
},
},
}
</script>
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