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Merge branch 'merge_25.0_into_25.1_oct' into merge_25.1_into_dev_oct
2 parents f23a469 + 14b118a commit 92d9f03

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‎.github/release-drafter.yml‎

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# Release Drafter Configuration for Galaxy
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# Implements YY.N.P versioning scheme using existing Galaxy labels
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#
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# IMPORTANT: Galaxy's versioning scheme is YY.N.P where:
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# - YY = Two-digit year (25 for 2025)
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# - N = Feature release number (0, 1, 2... - typically 2-3 per year)
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# - P = Patch/point release number (0, 1, 2, 3...)
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#
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# Year transitions (24→25) must be handled manually when creating releases.
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name-template: 'Galaxy $RESOLVED_VERSION'
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tag-template: 'v$RESOLVED_VERSION'
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# Categories for organizing release notes using existing Galaxy labels
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categories:
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- title: '🎉 Major Changes'
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labels:
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- 'major'
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- 'highlight'
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- title: '🚀 New Features'
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labels:
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- 'kind/feature'
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- title: '🔧 Enhancements'
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labels:
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- 'kind/enhancement'
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- title: '🐛 Bug Fixes'
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labels:
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- 'kind/bug'
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- title: '🔒 Security Updates'
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labels:
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- 'area/security'
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- title: '⚡ Performance'
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labels:
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- 'area/performance'
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- title: '🧰 Refactoring'
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labels:
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- 'kind/refactoring'
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- title: '📚 Documentation'
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labels:
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- 'area/documentation'
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- title: '🔧 Admin & Configuration'
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labels:
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- 'area/admin'
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- 'area/configuration'
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- title: '🛠️ API Changes'
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labels:
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- 'area/API'
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- title: '🧪 Testing'
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labels:
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- 'area/testing'
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- 'area/testing/api'
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- 'area/testing/integration'
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- 'area/testing/selenium'
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- title: '🏗️ Infrastructure & Dependencies'
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labels:
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- 'area/dependencies'
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- 'area/client-build'
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# Exclude certain labels from release notes
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exclude-labels:
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- 'triage'
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- 'procedures'
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- 'planning'
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- 'merge'
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- 'status/needs feedback'
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- 'status/planning'
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# Template for each change line
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change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
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# Characters to escape in titles
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change-title-escapes: '\<*_&'
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# Version is read from lib/galaxy/version.py by the workflow
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# No version-resolver needed since Galaxy manages versions manually
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# Template for the release body
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template: |
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## Changes in $RESOLVED_VERSION
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$CHANGES
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**Full Changelog**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION

‎.github/workflows/build_container_image.yaml‎

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id: buildargs
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run: |
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echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT
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echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
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echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3

‎.github/workflows/release-drafter.yml‎

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name: Release Drafter
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on:
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push:
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branches:
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- dev
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- master
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- 'release_*'
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pull_request_target:
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types: [opened, reopened, synchronize]
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permissions:
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contents: read
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jobs:
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update_release_draft:
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permissions:
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contents: write
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pull-requests: write
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if: github.repository == 'galaxyproject/galaxy'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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ref: dev
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sparse-checkout: |
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lib/galaxy/version.py
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- name: Read Galaxy version
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id: galaxy-version
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run: |
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# Extract VERSION_MAJOR from version.py (e.g., "25.1")
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VERSION_MAJOR=$(grep '^VERSION_MAJOR' lib/galaxy/version.py | cut -d'"' -f2)
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RELEASE_VERSION="${VERSION_MAJOR}.0"
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echo "version=${RELEASE_VERSION}" >> $GITHUB_OUTPUT
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echo "Galaxy release version: ${RELEASE_VERSION}"
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- uses: release-drafter/release-drafter@v6
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with:
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config-name: release-drafter.yml
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version: ${{ steps.galaxy-version.outputs.version }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.k8s_ci.Dockerfile‎

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locales \
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vim-tiny \
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nano-tiny \
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netcat-openbsd \
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curl \
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procps \
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less \
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bzip2 \
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tini \
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nodejs \
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wget \
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&& update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 0 \
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&& update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 0 \
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&& echo "set nocompatible\nset backspace=indent,eol,start" >> /usr/share/vim/vimrc.tiny \

‎client/src/components/Collections/ListWizard.vue‎

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import type { WhichListBuilder } from "./ListWizard/types";
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import { useAutoPairing } from "./usePairing";
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import LoadingSpan from "../LoadingSpan.vue";
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import ListCollectionCreator from "./ListCollectionCreator.vue";
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import WhichBuilder from "./ListWizard/WhichBuilder.vue";
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import PairedOrUnpairedListCollectionCreator from "./PairedOrUnpairedListCollectionCreator.vue";
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<template>
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<div v-if="currentHistoryId">
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<div v-if="creationError">
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<BAlert variant="danger">
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<BAlert variant="danger" show>
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{{ creationError }}
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</BAlert>
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</div>
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<div v-if="collectionCreated">
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<BAlert variant="success" show> Collection created and it has been added to your history. </BAlert>
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</div>
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<div v-else-if="!selectedItems">Loading...</div>
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<div v-else-if="!selectedItems">
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<BAlert variant="info" show>
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<LoadingSpan />
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</BAlert>
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</div>
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<div v-else-if="selectedItems.length == 0">
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<p>Select datasets from history panel to use the Galaxy list building wizard.</p>
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<BAlert variant="info" show>
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Select datasets from the history panel to use the Galaxy list building wizard.
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</BAlert>
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</div>
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<GenericWizard v-else :use="wizard" :is-busy="isBusy" :submit-button-label="buildButtonLabel" @submit="submit">
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<div v-if="wizard.isCurrent('which-builder')">

‎client/src/components/Collections/ListWizard/WhichBuilder.vue‎

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<b>Flat List</b>
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</BCardTitle>
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<div>
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This options creates a simple flat list of files. If your data isn't nested and does not contained
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This option creates a simple flat list of files. If your data isn't nested and does not contained
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paired datasets, this is the the option to choose.
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</div>
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</BCard>
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<b>List of Paired Datasets</b>
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</BCardTitle>
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<div>
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This options creates a uniform list of paired datasets, use this option if all of your data should
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be paired off.
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This option creates a uniform list of paired datasets, use this option if all of your data should be
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paired off.
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</div>
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</BCard>
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<BCard

‎client/src/components/Collections/wizard/WhichWorkbookCollectionType.vue‎

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<b>Flat List</b>
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</BCardTitle>
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<div>
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This options creates a simple flat list of files. If your data isn't nested and does not contained
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paired datasets, this is the the option to choose.
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This option creates a simple flat list of files. If your data isn't nested and does not contained
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paired datasets, this is the option to choose.
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</div>
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</BCard>
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<BCard
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<b>List of Paired Datasets</b>
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</BCardTitle>
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<div>
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This options creates a uniform list of paired datasets, use this option if all of your data should
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be paired off.
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This option creates a uniform list of paired datasets, use this option if all of your data should be
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paired off.
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</div>
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</BCard>
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</BCardGroup>

‎client/src/components/Common/Wizard/GenericWizard.vue‎

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.card-header {
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border-radius: 0;
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}
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&:hover {
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border-color: lighten($brand-primary, 20%);
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cursor: pointer;
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}
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}
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}
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</style>

‎client/src/components/History/CurrentCollection/CollectionOperations.vue‎

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);
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const disableDownload = props.dsc.populated_state !== "ok";
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const hasSampleSheet = computed(() => {
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return props.dsc.collection_type && props.dsc.collection_type.startsWith("sample_sheet");
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});
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const sheetUrl = computed(() => {
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return `${getAppRoot()}collection/${props.dsc.id}/sheet`;
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});
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<span>Run Job Again</span>
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</b-button>
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<b-button
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v-if="sheetUrl"
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v-if="hasSampleSheet && sheetUrl"
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class="rounded-0 text-decoration-none"
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size="sm"
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variant="link"

‎client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue‎

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const { setSelectedItems } = useCollectionBuilderItemSelection();
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const selection = Array.from(this.contentSelection.values());
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setSelectedItems(selection);
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this.$router.push({ path: `/collection/new_list?advanced=${advanced}` });
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if (this.$route.path === "/collection/new_list") {
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// vue-router 4 supports a native force push with clean URLs, but we're using a __vkey__
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// bit as a workaround to allow the builder to be invoked consecutively
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this.$router.push({ path: `/collection/new_list?advanced=${advanced}` }, { force: true });
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} else {
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this.$router.push(`/collection/new_list?advanced=${advanced}`);
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}
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},
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// Selected content manipulation, hide/show/delete/purge
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hideSelected() {

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