Clinical-Genomics / cg

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• master
• 2396-update-latest-archivedf-lowcell
• 2792-new-seq-models
• 2871-calculate-reads-for-negative-controls
• 2871-revert-changes
• 2871-store-fastq-hk-negative-controls
• 2871-test-calculate-reads-for-negative-controls
• 29-balsamic-configurator
• 29-balsamic-link-files
• 2906-add-capture-kit-filter
• 30-balsamic-submit-command
• 3025-remove-flow-cell-sample
• 3064-fix-loging-for-service
• 3092-allow-tomte-order
• 31-balsamic-dev-commands
• 3179-remove-remnant-sars-cov-2
• 3182-add-retrieve-commands
• 3184-replace-parameter-yes-with-skip_confirmation
• 32-balsamic-class-factory
• 3245-add-relationships-seq
• 3254-empty-folder-creation-when-cloning-cg-repo
• 3307-not-exiting-multi-case-upload-process-when-one-gens-upload-fails
• 35-balsamic-tracker
• 3642-add-case-validation
• 3679-update-sample-reads
• 3714-validating-sample-sex-in-add-relationship
• 3722-Add-Volume-Validation
• 3765-pass-case-prio-to-scout-load-config
• 3767-allow-micro-seq-only-excel
• 3804-high-prio-decompress
• 3831-microsalt-sequencing-qc-logic
• 3843-same-file-archived
• 3843-same-file-archived-to-pdc-the-same-day
• 39-address-balsamic-issues
• 3997-add-balsamic-order-validation-rule
• 3998-exact-matches-for-links-in-sample-and-case-tables
• 4000-hide-apptag-version-from-delivery-report
• 4044-fix-rna-upload
• 4047-fix-nfanalysis-configs
• 4153-sla-for-order-tickets
• 4173-validate-container-name
• 4222-change-delivery-message-for-taxprofiler
• 4232-skip-rna-omics-files
• 4251-add-limit-option
• 4275-upload-files-to-scout
• 4307-fix-seq-cleaning-logic
• 4313-batchwise-pacbio-post-processing
• 4421-move-cases-to-analyse
• 4423-fix-nallo-cleaning
• 4465-add-apptag-archived-filter
• 4468-add-filter-application_version
• 4480-remove-case-arg
• 4527-fix-microsalt-SLURM-tracking
• 4541-show-run-name-and-plate
• 4588-pass-head-job-partition-to-balsamic18
• 4589-remove-flow-cell-ref
• 575-add-get-related-dna-cases-from-rna-case
• 575-add-mip-rna-messages
• Add-CaseSample-RNAFusion
• Add-RNAFusion-CaseSample
• Refactor-ensure-valid-config
• Remove-deprecated-flags
• Vince-janv-patch-1
• Vince-janv-patch-test-1
• Vince-janv-patch-test-2
• Vince-janv-patch-test-3
• Vince-janv-patch-test-4
• Vince-janv-patch-test-5
• adapt-cli-get-illumina
• adapt-cli-set-illumina
• add-RNA-metrics-to-report
• add-admin-view-illumina-fc
• add-admin-view-sample-metrics
• add-affected-rule
• add-analysis-delivery-message
• add-application-archived-validation
• add-application-version-filter
• add-application-workflow-compatibility
• add-archive-to-cust-view
• add-aud-claim
• add-balsamic
• add-balsamic-rules
• add-balsamic-sample-errors
• add-balsamic-umi
• add-balsamic-validation-rules
• add-bam-delivery-message
• add-barcode-metrics-dto
• add-barcoded-fixtures
• add-buffer-required-rule
• add-cascading
• add-case-check-to-orderform-parser
• add-case-names-to-delivery-messages
• add-case-sample-cascading
• add-chanjo2-api
• add-cli-delete-fc
• add-cli-post-processing
• add-config-case-dev-command
• add-control-samples-check-case
• add-dad-validation
• add-default-command
• add-default-value-is-cancelled
• add-delivery-service-factory
• add-dev-cli-commands
• add-dev-endpoints
• add-dry-run-store
• add-dto-validation
• add-error-handling-rn
• add-error-log
• add-existing-case-collaboration-rule
• add-existing-sample-check
• add-existing-sample-model
• add-extension-ensure-method
• add-extraction-method-enum
• add-family-graph-rules
• add-fastq-rules
• add-fields
• add-file-fetcher
• add-file-mover
• add-file-reformatters
• add-file-tests
• add-force-storage-comment
• add-freshdesk-client
• add-gene-panel-validation
• add-gunicorn-config
• add-head-partition
• add-hifi-yield
• add-illumina-flow-cell-model
• add-illumina-metrics-filter
• add-illumina-run-model
• add-illumina-seq-metrics
• add-illumna-sample-run
• add-input-fetcher
• add-integration-test
• add-internal-id-exists-validation
• add-limit-to-mip-balsamic
• add-logging-to-cli
• add-macros-to-report
• add-maf-order
• add-manifest-to-nf-workflows
• add-metagenome-classes
• add-metagenome-rules
• add-metrics-dto
• add-microbial-fastq-orderin
• add-microbial-fastq-validation
• add-microbial-order
• add-microbial-submitter
• add-microsalt-analysis-starter-to-factory
• add-microsalt-assembly-to-delivery
• add-microsalt-configurator
• add-microsalt-order-validation
• add-microsalt-validate-application-not-archived
• add-mip-dna-case-config
• add-mip-dna-dev-cli
• add-mip-dna-gene-panel
• add-mip-dna-rules
• add-mip-dna-skeleton
• add-mip-dna-to-starter-factory
• add-mip-dna-tracker
• add-missing-test
• add-multiple-smrt-cell-support
• add-multiqc-report-to-mip-dna-delivery
• add-mut-rules
• add-mutant-fields
• add-mutant-qc
• add-mutant-upload
• add-mutant-upload-api
• add-mutant-validation-models
• add-nallo-config-case
• add-nallo-delivery-report
• add-nallo-gene-panel
• add-nallo-loqusdb-cust
• add-nallo-loqusdb-upload
• add-nallo-metrics-deliver
• add-nallo-ordertype
• add-nallo-run
• add-nallo-start-available
• add-nallo-statusdb-limitations
• add-nallo-store-available
• add-nallo-storing
• add-nallo-to-analysis-options
• add-nallo-to-cg-workflow
• add-nallo-workflow-start
• add-nanpore-run-device
• add-new-cli
• add-new-tech
• add-nf-stub-run
• add-ngsbits-sex-check-raredisease
• add-no-repeated-panels-validation
• add-order-name-length-restriction
• add-order-validation-response-test
• add-ordertype-application-table
• add-ordertype-endpoint
• add-other-alias
• add-pacbio-admin-views
• add-pacbio-data-transfer-service
• add-pacbio-dto
• add-pacbio-endpoints
• add-pacbio-file-manager
• add-pacbio-hk-service
• add-pacbio-order-sample
• add-pacbio-order-submitter
• add-pacbio-orderin
• add-pacbio-ordertype
• add-pacbio-run-data-generator
• add-pacbio-run-name-to-db
• add-pacbio-run-validator
• add-pacbio-sample-metrics
• add-pacbio-sequencing-run
• add-pacbio-sequencing-run-endpoint
• add-pacbio-smrt-cell-model
• add-pacbio-store-service
• add-pacbio-val-rules
• add-pacbio-validation-service
• add-pagination-cases-samples-pools
• add-panel-to-master-list
• add-panels-to-raredisease-params-file
• add-params-file-taxprofiler
• add-pon-to-dr
• add-pool-rules
• add-pp-complete
• add-pytest-to-replicate-issue
• add-questions-to-template
• add-rank-model-to-scout-rd
• add-rarediseas-orderform
• add-raredisease-clinical-delivery
• add-raredisease-delivery-report
• add-raredisease-gens-upload
• add-raredisease-metrics-deliver
• add-raredisease-ordertype
• add-raredisease-panel-to-start
• add-raredisease-pedigree-check
• add-raredisease-scout-upload
• add-raredisease-sex-relatedness-check
• add-raredisease-upload
• add-rd-genotype-upload-no-tests
• add-report-rd
• add-retry-strategies-freshdesk
• add-rich-click
• add-rna-sample-subject-id-validation
• add-rnafusion-analysisstarter
• add-rnafusion-dev-commands
• add-rnafusion-rules
• add-run-params-hk
• add-sample-application-exists-validation
• add-sample-cancel-filter
• add-sample-id-delivery-error-message
• add-sample-metrics-dto
• add-sample-sequencing-dto
• add-sample-sheet-taxprofiler
• add-scout-delivery-tomte
• add-sentieon-balsamic-cli
• add-sentieon-to-config
• add-seqera-dtos
• add-seqera-platform-client
• add-sequencing-qc-cli
• add-sex-delivery-report
• add-sex-validation
• add-skip-rc-buffer-validation
• add-standalone-capture-kit-validation
• add-start-available
• add-starter-factory
• add-status-required-if-new-sample-validation
• add-store-service
• add-string-length-constraint
• add-structure
• add-subject-id-case-name-validation
• add-subject-id-validation
• add-subprocess-submitter
• add-taxprofiler-configurator
• add-taxprofiler-report
• add-taxprofiler-rules-models
• add-taxprofiler-sample-sheet
• add-taxprofiler-submitter
• add-taxprofiler-support
• add-taxprofiler-to-starter-factory
• add-test-structure
• add-time-stamps-to-flow-cell
• add-to-factories
• add-tomte-delivery-report-to-scout
• add-tomte-report
• add-tomte-validation-rules
• add-tomte-validation-service
• add-tower-config
• add-tumour-to-mip-rna
• add-typing-for-slurm_qos
• add-und-reads-new-flow
• add-validation-case-name-sample-name-different
• add-validation-container
• add-validation-flow-structure
• add-validation-mip-all-samples-unknown
• add-validation-rule
• add-verification-aud
• add-version-id-column-to-analysis
• add-version-id-to-analysis
• add-well-validation
• add-wgs-loqusdb-flag
• add-workflow-id-to-analysis
• add-yield
• add/CHILDHYPOTONIA-to-clinical-master-list
• add/bwa-mem-to-fluffy-command
• add/report-email-to-upload
• add_apply_balsamic_exome_tag
• add_artefact_loqusdb_argument
• add_d4_rd
• add_d4file_to_scout
• add_genotype_upload_to_rd
• add_internal_id_device
• add_nallo_store_command
• add_nallo_upload
• add_path_target_bed
• add_peddy_nallo_filepaths
• add_peddy_to_nallo_scout
• add_raredisease_start
• add_resources_nallo
• add_scout_for_tomte
• add_somatic_normal_sv_artefacts
• add_tomte_scout_upload_to_dna_case
• add_validation_tube_names
• add_validation_tube_names_case
• add_well_position_validation
• add_well_position_validation_case
• adjust-col-type
• allow-all-order-types-json-orders
• allow-mip-rna-json
• allow-tomte-orders
• allow-unknown-sex
• always-force-reupload
• app-compatibility
• balsamic-18-loqusdb-uploads
• balsamic_v16
• balsamic_v18_changes
• bug-fix-nallo-delivery-report-correct-scout
• bug-fix-raredisease-delivery-tags
• bug-fix-raredisease-qc-duplication
• bump-archive-rate
• centralise-app-config
• change-endpoint-limitations
• change-order-type-application-enum
• change-path-ownership
• change-return-type
• change-taxprofiler-sequencing-qc
• changes_for_balsamic_submit
• choose-correct-scout-instance
• clarify-downsample-help
• clean-case-dirs
• clean-dead-code
• clean-pacbio-fixtures
• clean-up-validation-rules
• clean_past_run_dirs
• cli-search
• collect-seq-times
• concatenate-w-pseudo-workflow
• config-separate-services
• configurator-factory
• containerize-cg
• convert-empty-strings-to-none
• correct-analysis-api
• correct-type
• count-cases-in-topup
• create-maf-case
• create-validation-sample
• create_cust_acc_csv
• debug-log-selected-cases
• decompose-sample-file-formatter
• decompression-service
• delete-unused-crud-functions
• deliver-order
• deliver-sample-file
• deliver_params_file_tomte
• delivery-type-support
• deparameterize-test_cli_mip_dna
• depr-os-ticket
• dev-commands-raredisease
• dev-freshdesk
• dev-new-delivery-service
• dev-new-start-balsamic
• dev-new-start-taxprofiler
• dev-pacbio-flow
• dev-raredisease-tags
• dev-start-mip-dna
• dev-start-pipelines
• dev-to-dev-balsamic-loqusdb
• dev-update-pacbio-models
• develop-illumina-devices
• develop-new-devices
• different-external-apis
• disallow-reusing-sample-names
• do-not-parse-index-sequence
• downgrade-wtforms
• draft-post-process-all
• drop-workflow
• eliottBo-patch-1
• enable_tga_matched_normal_soft_filter
• enhance-tests
• ensure-fields-optional
• ensure-valid-config-MIP-DNA
• error-handling-crud-seq-run
• existing-data-tag
• existing-sample-collaboration-rule
• export-skip-reception-control
• extract-analysis-endpoints
• extract-application-endpoints
• extract-case-endpoints
• extract-flowcell-endpoints
• extract-order-endpoints
• extract-pool-endpoints
• extract-sample-endpoints
• extract-user-ep
• feat-add-pacbio-dates-db
• feat-add-to-hk-new-models
• feat-keycloak
• feat-modernize-config
• feat-pacbio-post-processing
• feat-parse-smrtlnk
• feat-post-process-all
• feat-rm-osticket
• feat-run-name-service
• feat-zip-reports-pacbio
• feat/add-freshdesk-properties
• feat/connect-order-to-ticket
• feat/rm-OsTicket
• feature-request-downsample
• fetche_tissue_type_from_original_sample
• fill-illumina-sequencing-run
• filter-orders-by-delivered
• filter-rna-related-samples
• finish-integration-tests
• fix-add-pk-device-tables
• fix-alembic-script-names
• fix-all-fastq-cli
• fix-all-fc-on-disk
• fix-annotation-warinings
• fix-annoying-hk-warning
• fix-auto-fastq-upload
• fix-balsamic-fetch
• fix-bug
• fix-bug-report-template
• fix-bump-bump2version-version
• fix-caesar-rsync-permissions
• fix-case-file-storing
• fix-case-sample-view
• fix-certifi-vuln
• fix-clean-fastq
• fix-cli-store-name
• fix-clinical-delivery
• fix-col-type
• fix-comments-vj
• fix-concat-bug
• fix-conflicts-pacbio
• fix-contributing-doc-fmt
• fix-dataset-metrics
• fix-ddn-retrievals
• fix-delivery-cli
• fix-delivery-error-handling
• fix-delivery-files-empty
• fix-delivery-types
• fix-dockerfile-poetry2
• fix-downsample
• fix-dragen-cpu-allocation
• fix-dragen-cpu-and-exclusiveness
• fix-dragen-demux-slurm
• fix-duplicated-summaries
• fix-encrypt-sbatch
• fix-endpoint-sample-metrics
• fix-enum-serialisation
• fix-excel-fixtures
• fix-fastq-cleaning
• fix-fastq-delivery
• fix-fastq-delivery-message
• fix-flag-handling
• fix-flow-cell-mode-parsing
• fix-flow-cell-paths
• fix-fluffly-samplesheet
• fix-fohm-upload
• fix-gene-panel-tests
• fix-index-sequence-mismatch
• fix-indices
• fix-internal_id
• fix-invoicing-errors
• fix-last-excluded-test
• fix-maf-orders
• fix-merge-conflict-dev-start-pipelines
• fix-microbial-fastq-internal-id
• fix-microbial-sample-sheet
• fix-microsalt-delivery-message
• fix-microsalt-old-attributes
• fix-microsalt-single-sample-tracking
• fix-mip-data-type
• fix-mutant-qc-constant-typo
• fix-new-db-models
• fix-nf-config-models
• fix-nf-tests
• fix-no-delivery-parse
• fix-no-sample-post
• fix-order-view
• fix-pacbio-db-columns
• fix-pacbio-metrics-as-properties
• fix-patch-IDT10-indices
• fix-pedigree-validation
• fix-percent-q30
• fix-poetry-publish-timout
• fix-post-processing
• fix-post-processing-error
• fix-pre-commit
• fix-premature-processing
• fix-primary-keys-autoincrement
• fix-priority-order
• fix-pydantic-field
• fix-raredisease-delivery-report-percentage
• fix-raredisease-sample-pairs-list
• fix-rd-fixtures
• fix-rd-tags
• fix-redirect
• fix-remaining-tests
• fix-remove-rsync-permission-flag
• fix-revision
• fix-rna-messages
• fix-rna-upload-with-dna-case
• fix-rna-uploads
• fix-rnafusion-config
• fix-rsync-bug
• fix-sample-archiving
• fix-sample-error
• fix-sample-fk
• fix-sample-response
• fix-sample-sheet-validation
• fix-sample-status
• fix-scout-no-drop
• fix-scout38-url
• fix-search-illumina-run
• fix-serialization
• fix-set-case
• fix-single-sample-microsalt-start
• fix-start-microsalt
• fix-started-at-balsamic
• fix-store-handlers
• fix-store-validation
• fix-tags-hk
• fix-tests-iof
• fix-tests-orders-api
• fix-ticket-clashes
• fix-tomte-del
• fix-tomte-delivery-messages
• fix-tomte-uploads
• fix-type-hinting
• fix-typo
• fix-validation-integration-tests
• fix-view-links
• fix-volume-rule
• fix-workflow-models
• fix/add-only-files-with-reads
• fix/issue-3555
• fix/issue-3555-incorrect-error-handled
• fix_dry_run_conflict
• fix_germlinecaller
• fix_nallo_filepaths
• fix_raredisease_custom_images
• fix_rd_filepaths
• fix_snv_vcf
• fohm-gsaid-in-upload
• fohm-upload-file-fetcher
• folder-cleanup
• force-storage-incomplete-cases
• force-storage-prevent-upload
• frame-out-ticketing-system
• freshdesk-connection
• generate-mutant-fields
• gens_for_tga
• handle-all-orders-delivered
• handle-completed-delivered
• handle-unassigned-reads
• hide-cancelled-samples-from-customers
• hide-development-analyses
• implement-convert-errors
• implement-seqera-submitter
• improve-dr-tests
• improve-order-flow
• improve-order-flow-fluffy
• improve-order-flow-main
• improve-order-flow-mip-rna
• improve-order-flow-storing-main
• improve-order-view
• improve-ticketing-log
• include-delivered-in-order-response
• include-hidden-analysis-trailblazer
• increase_click_character
• init-freshdesk-client
• init-tickethandler-freshdesk
• integrate-microsalt
• integrate-raredisease-command
• integration_test
• internal_control_get_higher_prio
• issue-3712
• jasen-add-config-case
• jasen-add-to-analysis-options
• lessen-archiving-limit
• licensing
• limit-mip-balsamic-starts
• lims-sample-model
• link_trailblazer_and_cg_analyses
• log-number-of-cases-to-start
• lower-archive-rate
• make-fetching-sample-specific
• make-nallo-orderable
• make-panels-optional
• make-raredisease-orderable
• make-source-optionable
• make-ticket-number-private
• make_migration_idempotent
• managed_variants_in_params
• map-errors
• map-sample-errors
• merge-prepare-fastq-api
• microbial-fastq-order-classes
• microbial-fastq-rules
• minimal-implementation
• mip-check-pass
• mip-dna-submitter
• mirosalt-version-storage
• model-validate-tests
• move-balsamic-rules
• move-case-limit
• move-delivery-factory
• move-general-rules
• move-order-api
• move-stuff
• move-validation-service
• multiqc_patch
• mutant
• mutant-file-formatter
• nallo-add-loqusdb-to-cg-upload
• nallo-delivery-message
• nallo-delivery-types-report
• nallo-form-and-bump-pacbio
• nallo-qc-peddy-parent-somalier-sex
• nallo-qcmetrics-production
• nallo-remove-assembly-scout-upload
• nallo-resume-new-revision
• nallo-upload-bug
• netxflow-config-file
• new-analysis-table-flow
• new-micro-seq-of
• new-rml-form
• new-rule-sample-case-name
• nipt-qc-service
• no-content-instead-of-error
• no-gens-for-hg38
• non-nullable-att-pacbio
• old-model-cleaning
• one-case-per-sample-fastq
• one-case-per-sample-metagenome
• one-sample-per-case-rule
• only-bclconvert-in-validation
• open-pending-ticket
• open-status-for-only-existing-samples-ticket
• order-flow-RML-model
• order-flow-fastq
• order-in-db-ui
• order-message-filter-delivered
• order-validation-for-bait-sets
• orderform-validation-error
• ordertype-application-creation
• override-microbial-dump
• pacbio-alembic-script
• pacbio-control-metrics
• pacbio-loading-metrics
• pacbio-metric-parsing
• pacbio-models
• pacbio-raw-data-metrics
• param-test-as-dict
• parametrise-param-file-tests
• parametrise-with-dict
• params-file
• parse-barcodes-report
• parse-failed-reads-pacbio
• parse-into-sequencing-run
• parse-new-ccs-report
• parse-pacbio-of
• patch-analysis-storing
• patch-application-filter
• patch-balsamic
• patch-balsamic-orders-filter
• patch-balsamic-uploads
• patch-capture-kit
• patch-case-sample-cascading
• patch-case-sample-validation
• patch-control-parsing
• patch-delivered-filter
• patch-discriminator
• patch-elution-buffer-parsing
• patch-error-sample-rule
• patch-existing-parents
• patch-existing-sample
• patch-existing-samples-reference
• patch-file-filter
• patch-fluffy-samplesheet
• patch-get-sequencing-run
• patch-imports
• patch-latest-analysed
• patch-microbial-fastq-models
• patch-microsalt-clean
• patch-microsalt-version-fetching
• patch-mip-scout-upload
• patch-mutant-validation
• patch-nextflow-store-cli
• patch-nextflow-store-cli2
• patch-nip-uploads
• patch-order-case-linking
• patch-order-message
• patch-order-table
• patch-order-view
• patch-ordered-date
• patch-orders-pagination
• patch-organism-parsing
• patch-override-cycles
• patch-pacbio-order-in
• patch-pagination
• patch-pedigree-validation
• patch-pydantic-error-mappings
• patch-raredisease-wes-uploads
• patch-recent-migration
• patch-reference-genome
• patch-repeated-case-names-rule
• patch-repeated-case-sample-name-rule
• patch-response-type
• patch-sample-properties
• patch-samples-in-collaboration-endpoint
• patch-scout-upload
• patch-skip-reception-control
• patch-string-lengths
• patch-subprocess-check
• patch-subprocess-check-false
• patch-ticket-id
• patch-tissue-block-enum
• patch-tomte-rule-placement
• patch-tube-well-positions
• patch-typing
• patch-user-rule
• patch-users-endpoint
• patch-validate-fathers-are-male
• patch-validate-unique-sample-names
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Build # 18002484328

Build Type

push

github

Committed by web-flow

Commit Message

Block retrieval of SPRING files if any file is still archiving (#4616)(patch)

## Description
The retrieval of SPRING files behaves unexpectedly when their archiving takes too long. Specifically, when retrieving files from a sample that is currently being archived, it results in unexpected behaviour, as documented in https://github.com/Clinical-Genomics/bug-reports/issues/42. For this reason, this PR implements a check that stops a retrieval process of a sample if any of its files are currently being archived, raising a `SampleFilesCurrentlyArchivingError`.

### Added

- Support for checking if any of a sample's files is being archived, and raise an error if that is the case.
- Test for this new functionality

### Changed

- Modified existing tests to account for new functionality

### Fixed

- Removed unused fixtures

Run Details

7 of 10 new or added lines in 2 files covered. (70.0%)

27610 of 32092 relevant lines covered (86.03%)

0.86 hits per line