Ensembl / ensembl-datacheck

96%

master: 99%

LAST BUILD ON BRANCH feature/pipeline_emails

branch: feature/pipeline_emails

CHANGE BRANCH

x

Reset

• feature/pipeline_emails
• bugfix/travis_skip_tests
• master
• feature/more_testing_of_tests
• new_test/RegulatoryFeatureIsActive
• new_test/SampleRegulatoryFeatureExists
• feature/hook_update_index
• new_test/ExperimentHasFeatureSet
• feature/improve_test_coverage
• feature/new_datachecks
• feature/better_diag_message
• feature/collection_db_test
• feature/advisory_dc
• bugfix/skipping_in_collections
• new_test/SegmentationFileHasBigBed
• new_test/AltAllele
• new_test/ExonRank
• new_test/feature_position
• new_test/exon_strand_order
• fix_travis_slack_credentials
• new_test/exonsBoundaries
• feature/gene_datachecks
• bugfix/test_databases
• bugfix/test_dbs_and_obsolete_files
• release/96
• merge/release/96
• feature/pipeline_script
• feature/extend_gene_stats
• feature/datacheck_groups
• feature/schema_datachecks
• feature/analysis_and_attribs
• feature/amonida/dc
• feature/multidb
• feature/assembly_metakeys
• feature/more_meta_checks
• feature/old_dba
• feature/xref_datachecks
• feature/funcgen_datachecks
• feature/config_file
• feature/compare_variation
• feature/compara_datachecks
• feature/desc_group_tidy
• feature/filter_behaviour
• feature/statistics
• bugfix/controlledtables
• feature/misc_tweaks
• feature/update_test
• release/97
• bug_fix/sundry_minor_fixes
• new_datacheck/db_species_name
• bugfix/missing_library
• release/98
• bugfix/email_reports
• bugfix/remove_stable_id_check
• feature/update_datachecks
• Compare_previous_version_go
• evidence_free_go
• predicted_xrefs
• unreviewed_xrefs
• xref_prefixes
• compare_previous_version_synonyms
• xref_html
• duplicate_xref
• gene_stable_id_display_xref
• stable_id_display_xref
• shared_display_xref
• transcript_display_xref_suffix
• xref_desc_special_char
• uniprotkb_diplayxref_ids
• compare_previous_version_projected_synonym
• compara_projected_gene_name
• Simple_features_analysis_type
• merge_release_98
• update_test_db
• release/99
• transcript_same_name
• transcript_same_name_99
• fix_release_99
• merge_release_99
• feature/repo_release_versions
• bug_fix/embedded_dc_output
• EmailNotify
• readme-dependencies
• fix_index
• dnadb_creation
• merge_release_99_master
• mem_update
• copyright-2020
• release/100
• bugfix/misc
• feature/update_cpanfile
• Adaptive_memory_ENSPROD-4787
• attrib_value_update
• fix_synteny_sanity
• bugfix/ancestral_sequences_species_set
• fix_view_problem
• sundry_fixes
• funcgen_updates
• datacheck_fixes
• merge_release_100
• biomart_dc
• ENSPROD-4980
• feature/updated_datachecks
• compara_datachecks
• datacheck_for_description_newline
• feature/pipeline_fixes
• update_tests_101
• release/101
• biomart_dc_fix
• bugfix/schema_patch_sort
• datachecks_for_Xref
• healthchecks_to_datachecks
• bugfix/shared_species
• revert-193-assembly_longer
• bugfix/catch_errors
• bugfix/assorted_fixes
• bugfix/variation
• bugfix/mt_chr_updates
• bugfix/end_timestamp
• tmp
• xref_prefix_fix
• revert-229-xref_prefix_fix
• bug_fix/skip_data_files
• bugfix/fk_multi_db
• hotfixes/viruses-division
• hotfix/gene-servionned-viruses
• feature/force_multi
• feature/versioned_genes
• email_notify
• bugfix/motif_feature_file
• bugfix/variation_datachecks
• bugfix/old_ontology_compara
• bugfix/go_xrefs
• bugfix/xref_fixes
• feature/ancestral_group
• compara/cafe_dc
• TapToJson
• xref_prefix_update
• feature/ncbi_gene_name
• feature/ancestral_sequences_name
• feature/dupe_xref_advisory
• release/102
• bugfix/remove_skeletons
• bugfix/seqlevel_toplevel
• feature/assembly_geneset_change
• bugfix/species_id
• feature/pipeline_xref_datacheck
• bugfix/db_name_format
• bugfix/gene_biotype_of
• bugfix/undef_adaptor_test
• convert_tap_json
• tap_to_json_bug
• bugfix/variation_fk
• feature/update_group_script
• feature/update_group
• bugfix/display_xref_exists
• bugfix/optimise_query
• feature/fix_conflicts
• feature/merge_102_to_master
• feature/update_test_db
• feature/exon_rank_sequential
• release/103
• feature/remove_stable_id
• feature/add_core_sync_group
• bugfix/exon_bounds
• non_core_dc_pipeline
• feature/non_core_dc_pipeline
• hotfix/MetaKeyFormat
• bugfix/sundry_fixes
• bugfix/nonprinting_chars
• bugfix/seqregion_synonyms
• bugfix/homology_mlss
• bugfix/cmp_end
• bugfix/core_stats_limit
• feature/check_unique_keys
• bugfix/blank_sets
• feature/sample_text_placeholder
• feature/fk_prod_db
• feature/test_update
• bugfix/plastid_annotation
• bugfix/config_flock
• feature/compara_schema
• hotfix/repeatmodeler_meta_key
• bugfix/genebuild_version_integer
• bugfix/biomart_branch
• feature/merge_103
• bugfix/xref_prefixes_group
• update_db_spec
• release/104
• bugfix/xref_types_critical
• bugfix/metakey_url_format
• refseq_peptide_prefix_rw
• bugfix/empty_output
• copyright-2021
• feature/analysis_db_version
• bugfixes/fix-query-check-previous-db
• bugfixes/344-on-release-103
• bugfixes/344-on-release-104
• bugfix/old_db_variation
• hotfix/repeatdetector_metakey
• features/long-running-dc-group
• bugfix/synonym_names
• bugfix/old_assembly_chr
• feature/split_appris_tsl
• feature/ccds_xref
• hotfix/repeatmasking_metakeys
• hotfix/division_specific_repeatmasking
• feature/sample_group
• bugfix/core_db_type
• merge/release_104
• feature/server_uri
• feature/test_db_update
• feature/codon_migration
• features/codo-updates
• hotfix/repeatfeature
• bugfix/species_common_name
• release/105
• bugfix/server_uri_exceptions
• hotfix/repeat_nonvert
• bugfix/advisory_common_name
• bugfix/karyotype_chr_name
• bugfix/ont_advisory
• feature/ena_format_gff3
• one_karyotype_rank_dc
• feature/website_packed_status
• bugfix/genebuild_start_date
• feature/gene_biotype_timeout
• bugfix/mt_location
• bugfix/insdc_rapid
• fix/metadata-default-main
• main
• release/106
• bugfix/compara_div_conditional
• feature/collective_advisory_dc_report
• features/ep-7119
• archive/master
• bugfix/multi_coredb_selection
• luca-drf-display-name-format-regex
• features/ep-7140
• bugfix/rename_dc_module
• bau/copyright-2022
• bugfix/display_name_extra_character
• bugfix/release-105-build-clone
• DisplayName-with-commas-fix
• DisplayName-with-commas-fix-release/105
• DisplayNameFormat_update_main
• DisplayNameFormat_update_105
• DisplayNameFormat_update_107
• DisplayNameFormat_update_106
• release/107
• feature/test_db_patch_107
• bugfix/compara-species-url
• bugfix/transcript-support-operator
• bugfix/transcript-support-operator-106
• feature/ENSPROD-7673_division_name_include_in_report
• bugfix/method_new_genebuild_metakeys
• bugfix/method_new_genebuild_metakeys1
• bugfix/typo-adivisory-report
• alphafold_datacheck
• fix/fan_funnel_dc
• bugfix/rr_display_name_format
• feature/ENSPROD_7736_disallow_species_strain_group
• feature/ENSPROD_7736_disallow_species_strain_group_106
• features/allow-subspecies-for-plants
• bugfix/genebuild_stable_id_prefix
• feature/raise_fail_status
• features/perl-5.26
• strain_type_dc
• bug/param_in_analysis
• feature/test_db_patch_108
• release/108
• fix/genebuild_anno_metakey
• fix/genebuild_anno_metakey1
• fix/genebuild_anno_metakey2
• merge-conflicts-108-106
• feature/dc_results_to_es
• features/ENSPROD-7978
• feature/dependency_module_es
• bugfix/data-file-division-path
• bug/fix_old_db_uri
• feature/test_db_patch_109
• update/skip_human_repeats
• skip_human_polymorphic_pseudogenes
• update/gene_biotypes_fix
• canonical_transcript_fix_projection
• release/109
• feature/testcase_old_uri_array
• valid_display_name_fix
• vsitnik-patch-allowed_dispnames_107
• vsitnik-display_name_pat_108
• vsitnik-patch-allowed_disp_name_pat_109
• update/check_annotation_source
• hotfix/check_mt_karyotype
• feature/xref_gene_symbol_transformer
• feature/test_db_patch_110
• bau/copyright-2023
• vsitnik-fix-mt-only-chr
• release/110
• vsitnik-patch-1_prokka
• update/gene_symbols_dc
• feature/dc_sequence_checksum
• bugfix/release-109-conflicts
• bugfix/merge-109
• feature/CompareSpeciesAlias
• features/alphafold-logicname
• 110
• merge-release-110
• features/es-no-port
• feature/test_db_patch_111
• bugfix/checksums_cds
• bugfix/lrgsequence-checksum
• feature/cactus_meta_consistency
• bugfix/elastic
• release/111
• feature/test_db_patch_112
• feature/biomart_species_metazoa
• features/slurm_112
• patch-1
• feature/mvp_110
• bau/copyright-2024
• bugfix/test-update-plants
• feature/mvp-rebase-main
• jalvarez/support_gcf
• jalvarez/mupport_gcf_main
• update/allow_blanks_core_meta
• feature/mvp
• feature/canonical_member_core
• funcgen-dc-cleanup
• mbarba/brc_seqregions
• feature/ncrna_canonic_member_core

Build # 275

Build Type

Pull #63

travis-ci

Committed by web-flow

Commit Message

Restructure pipeline to have a module that deals with datacheck submissions. This allows the pipeline to be used with an eternal beekeeper, isolating submissions from each other. Submission metadata is stored in a table in the hive, for easier lookup. The default is now to receive a single summary email per submission.

Pull Request Pull Request #63: Restructure datacheck pipeline

Run Details

4 of 4 new or added lines in 1 file covered. (100.0%)

1588 of 1646 relevant lines covered (96.48%)

18.15 hits per line