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galaxy package¶
Galaxy root package – this is a namespace package.
Subpackages¶
- galaxy.actions package
- galaxy.app_unittest_utils package
- Submodules
- galaxy.app_unittest_utils.galaxy_mock module
buildMockEnviron()
MockApp
MockApp.config
MockApp.amqp_type
MockApp.job_search
MockApp.toolbox
MockApp.tool_cache
MockApp.install_model
MockApp.watchers
MockApp.dataset_collection_manager
MockApp.hda_manager
MockApp.workflow_manager
MockApp.history_manager
MockApp.job_metrics
MockApp.stop
MockApp.is_webapp
MockApp.__init__()
MockApp.wait_for_toolbox_reload()
MockApp.reindex_tool_search()
MockLock
MockAppConfig
MockWebapp
MockTrans
MockVisualizationsRegistry
MockDir
MockTemplateHelpers
- galaxy.app_unittest_utils.tools_support module
- galaxy.auth package
- galaxy.authnz package
IdentityProvider
- Submodules
- galaxy.authnz.custos_authnz module
- galaxy.authnz.managers module
AuthnzManager
AuthnzManager.__init__()
AuthnzManager.get_allowed_idps()
AuthnzManager.can_user_assume_authn()
AuthnzManager.try_get_authz_config()
AuthnzManager.refresh_expiring_oidc_tokens_for_provider()
AuthnzManager.refresh_expiring_oidc_tokens()
AuthnzManager.authenticate()
AuthnzManager.callback()
AuthnzManager.create_user()
AuthnzManager.logout()
AuthnzManager.disconnect()
AuthnzManager.get_cloud_access_credentials()
AuthnzManager.get_cloud_access_credentials_in_file()
- galaxy.authnz.psa_authnz module
PSAAuthnz
Strategy
Strategy.__init__()
Strategy.get_setting()
Strategy.session_get()
Strategy.session_set()
Strategy.session_pop()
Strategy.request_data()
Strategy.request_host()
Strategy.build_absolute_uri()
Strategy.redirect()
Strategy.html()
Strategy.render_html()
Strategy.start()
Strategy.complete()
Strategy.continue_pipeline()
Storage
on_the_fly_config()
contains_required_data()
verify()
allowed_to_disconnect()
disconnect()
- galaxy.celery package
- galaxy.config package
LOGGING_CONFIG_DEFAULT
DEPENDENT_CONFIG_DEFAULTS
configure_logging()
find_root()
expand_pretty_datetime_format()
BaseAppConfiguration
BaseAppConfiguration.renamed_options
BaseAppConfiguration.deprecated_dirs
BaseAppConfiguration.paths_to_check_against_root
BaseAppConfiguration.add_sample_file_to_defaults
BaseAppConfiguration.listify_options
BaseAppConfiguration.object_store_store_by
BaseAppConfiguration.__init__()
BaseAppConfiguration.is_set()
BaseAppConfiguration.resolve_path()
CommonConfigurationMixin
GalaxyAppConfiguration
GalaxyAppConfiguration.renamed_options
GalaxyAppConfiguration.deprecated_options
GalaxyAppConfiguration.default_config_file_name
GalaxyAppConfiguration.deprecated_dirs
GalaxyAppConfiguration.paths_to_check_against_root
GalaxyAppConfiguration.add_sample_file_to_defaults
GalaxyAppConfiguration.listify_options
GalaxyAppConfiguration.database_connection
GalaxyAppConfiguration.tool_path
GalaxyAppConfiguration.tool_data_path
GalaxyAppConfiguration.new_file_path
GalaxyAppConfiguration.drmaa_external_runjob_script
GalaxyAppConfiguration.track_jobs_in_database
GalaxyAppConfiguration.monitor_thread_join_timeout
GalaxyAppConfiguration.manage_dependency_relationships
GalaxyAppConfiguration.enable_tool_shed_check
GalaxyAppConfiguration.builds_file_path
GalaxyAppConfiguration.len_file_path
GalaxyAppConfiguration.integrated_tool_panel_config
GalaxyAppConfiguration.toolbox_filter_base_modules
GalaxyAppConfiguration.tool_filters
GalaxyAppConfiguration.tool_label_filters
GalaxyAppConfiguration.tool_section_filters
GalaxyAppConfiguration.user_tool_filters
GalaxyAppConfiguration.user_tool_section_filters
GalaxyAppConfiguration.user_tool_label_filters
GalaxyAppConfiguration.password_expiration_period
GalaxyAppConfiguration.shed_tool_data_path
GalaxyAppConfiguration.hours_between_check
GalaxyAppConfiguration.galaxy_data_manager_data_path
GalaxyAppConfiguration.use_remote_user
GalaxyAppConfiguration.preserve_python_environment
GalaxyAppConfiguration.email_from
GalaxyAppConfiguration.workflow_resource_params_mapper
GalaxyAppConfiguration.sanitize_allowlist_file
GalaxyAppConfiguration.allowed_origin_hostnames
GalaxyAppConfiguration.trust_jupyter_notebook_conversion
GalaxyAppConfiguration.user_library_import_symlink_allowlist
GalaxyAppConfiguration.user_library_import_dir_auto_creation
GalaxyAppConfiguration.container_resolvers_config_file
GalaxyAppConfiguration.tool_dependency_dir
GalaxyAppConfiguration.involucro_path
GalaxyAppConfiguration.mulled_channels
GalaxyAppConfiguration.nginx_upload_store
GalaxyAppConfiguration.tus_upload_store
GalaxyAppConfiguration.pretty_datetime_format
GalaxyAppConfiguration.visualization_plugins_directory
GalaxyAppConfiguration.galaxy_infrastructure_url
GalaxyAppConfiguration.themes
GalaxyAppConfiguration.themes_by_host
GalaxyAppConfiguration.__init__()
GalaxyAppConfiguration.config_value_for_host()
GalaxyAppConfiguration.reload_sanitize_allowlist()
GalaxyAppConfiguration.ensure_tempdir()
GalaxyAppConfiguration.check()
GalaxyAppConfiguration.is_fetch_with_celery_enabled()
Configuration
reload_config_options()
get_database_engine_options()
- Submodules
- galaxy.config.config_manage module
- galaxy.config.schema module
- galaxy.config.script module
- galaxy.datatypes package
- Subpackages
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.converters.bed_to_gff_converter module
- galaxy.datatypes.converters.bgzip module
- galaxy.datatypes.converters.cram_to_bam module
- galaxy.datatypes.converters.fasta_to_len module
- galaxy.datatypes.converters.fasta_to_tabular_converter module
- galaxy.datatypes.converters.fastq_to_fqtoc module
- galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
- galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
- galaxy.datatypes.converters.gff_to_bed_converter module
- galaxy.datatypes.converters.gff_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_bed_converter module
- galaxy.datatypes.converters.interval_to_bedstrict_converter module
- galaxy.datatypes.converters.interval_to_fli module
- galaxy.datatypes.converters.interval_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_tabix_converter module
- galaxy.datatypes.converters.lped_to_fped_converter module
- galaxy.datatypes.converters.lped_to_pbed_converter module
- galaxy.datatypes.converters.maf_to_fasta_converter module
- galaxy.datatypes.converters.maf_to_interval_converter module
- galaxy.datatypes.converters.parquet_to_csv_converter module
- galaxy.datatypes.converters.pbed_ldreduced_converter module
- galaxy.datatypes.converters.pbed_to_lped_converter module
- galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
- galaxy.datatypes.converters.pileup_to_interval_index_converter module
- galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module
- galaxy.datatypes.converters.tabular_csv module
- galaxy.datatypes.converters.tabular_to_dbnsfp module
- galaxy.datatypes.converters.vcf_to_interval_index_converter module
- galaxy.datatypes.converters.vcf_to_vcf_bgzip module
- galaxy.datatypes.converters.wiggle_to_simple_converter module
- galaxy.datatypes.dataproviders package
- Submodules
- galaxy.datatypes.dataproviders.base module
- galaxy.datatypes.dataproviders.chunk module
- galaxy.datatypes.dataproviders.column module
- galaxy.datatypes.dataproviders.dataset module
- galaxy.datatypes.dataproviders.decorators module
- galaxy.datatypes.dataproviders.exceptions module
- galaxy.datatypes.dataproviders.external module
- galaxy.datatypes.dataproviders.hierarchy module
- galaxy.datatypes.dataproviders.line module
- galaxy.datatypes.display_applications package
- galaxy.datatypes.util package
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.annotation module
- galaxy.datatypes.anvio module
- galaxy.datatypes.assembly module
- galaxy.datatypes.binary module
Binary
Ab1
Idat
Cel
MashSketch
CompressedArchive
Meryldb
Visium
Bref3
DynamicCompressedArchive
GzDynamicCompressedArchive
Bz2DynamicCompressedArchive
CompressedZipArchive
GenericAsn1Binary
BamNative
BamNative.edam_format
BamNative.edam_data
BamNative.file_ext
BamNative.sort_flag
BamNative.set_meta()
BamNative.merge()
BamNative.init_meta()
BamNative.sniff()
BamNative.is_bam()
BamNative.set_peek()
BamNative.display_peek()
BamNative.to_archive()
BamNative.groom_dataset_content()
BamNative.get_chunk()
BamNative.display_data()
BamNative.validate()
BamNative.metadata_spec
Bam
Bam.edam_format
Bam.edam_data
Bam.file_ext
Bam.track_type
Bam.data_sources
Bam.get_index_flag()
Bam.dataset_content_needs_grooming()
Bam.set_meta()
Bam.sniff()
Bam.line_dataprovider()
Bam.regex_line_dataprovider()
Bam.column_dataprovider()
Bam.dict_dataprovider()
Bam.header_dataprovider()
Bam.id_seq_qual_dataprovider()
Bam.genomic_region_dataprovider()
Bam.genomic_region_dict_dataprovider()
Bam.samtools_dataprovider()
Bam.dataproviders
Bam.metadata_spec
ProBam
BamInputSorted
BamQuerynameSorted
CRAM
BaseBcf
Bcf
BcfUncompressed
H5
Loom
Anndata
Grib
GmxBinary
Trr
Cpt
Xtc
Edr
Biom2
Cool
MCool
H5MLM
H5MLM.file_ext
H5MLM.TARGET_URL
H5MLM.max_peek_size
H5MLM.max_preview_size
H5MLM.CONFIG
H5MLM.HTTP_REPR
H5MLM.HYPERPARAMETER
H5MLM.REPR
H5MLM.URL
H5MLM.set_meta()
H5MLM.sniff()
H5MLM.get_attribute()
H5MLM.get_repr()
H5MLM.get_html_repr()
H5MLM.get_config_string()
H5MLM.set_peek()
H5MLM.display_peek()
H5MLM.display_data()
H5MLM.metadata_spec
LudwigModel
HexrdMaterials
Scf
Sff
BigWig
BigBed
TwoBit
SQlite
GeminiSQLite
ChiraSQLite
CuffDiffSQlite
MzSQlite
PQP
OSW
SQmass
BlibSQlite
DlibSQlite
ElibSQlite
IdpDB
GAFASQLite
NcbiTaxonomySQlite
Xlsx
ExcelXls
Sra
RData
RDS
OxliBinary
OxliCountGraph
OxliNodeGraph
OxliTagSet
OxliStopTags
OxliSubset
OxliGraphLabels
PostgresqlArchive
MongoDBArchive
GeneNoteBook
Fast5Archive
Fast5ArchiveGz
Fast5ArchiveBz2
SearchGuiArchive
NetCDF
Dcd
Vel
DAA
RMA6
DMND
ICM
Parquet
BafTar
YepTar
TdfTar
MassHunterTar
MassLynxTar
WiffTar
Wiff2Tar
Pretext
JP2
Npz
HexrdImagesNpz
HexrdEtaOmeNpz
FITS
- galaxy.datatypes.blast module
- galaxy.datatypes.checkers module
- galaxy.datatypes.chrominfo module
- galaxy.datatypes.constructive_solid_geometry module
- galaxy.datatypes.coverage module
- galaxy.datatypes.data module
DatatypeConverterNotFoundException
DatatypeValidation
validate()
get_params_and_input_name()
DataMeta
Data
Data.edam_data
Data.edam_format
Data.file_ext
Data.CHUNKABLE
Data.metadata_spec
Data.is_binary
Data.composite_type
Data.primary_file_name
Data.allow_datatype_change
Data.track_type
Data.data_sources
Data.dataproviders
Data.__init__()
Data.supported_display_apps
Data.composite_files
Data.is_datatype_change_allowed()
Data.dataset_content_needs_grooming()
Data.groom_dataset_content()
Data.init_meta()
Data.set_meta()
Data.missing_meta()
Data.set_max_optional_metadata_filesize()
Data.get_max_optional_metadata_filesize()
Data.max_optional_metadata_filesize
Data.set_peek()
Data.display_peek()
Data.to_archive()
Data.display_data()
Data.display_as_markdown()
Data.display_name()
Data.display_info()
Data.get_mime()
Data.add_display_app()
Data.remove_display_app()
Data.clear_display_apps()
Data.add_display_application()
Data.get_display_application()
Data.get_display_applications_by_dataset()
Data.get_display_types()
Data.get_display_label()
Data.as_display_type()
Data.get_display_links()
Data.get_converter_types()
Data.find_conversion_destination()
Data.convert_dataset()
Data.after_setting_metadata()
Data.before_setting_metadata()
Data.add_composite_file()
Data.writable_files
Data.get_writable_files_for_dataset()
Data.get_composite_files()
Data.generate_primary_file()
Data.has_resolution
Data.matches_any()
Data.merge()
Data.has_dataprovider()
Data.dataprovider()
Data.validate()
Data.base_dataprovider()
Data.chunk_dataprovider()
Data.chunk64_dataprovider()
Data.handle_dataset_as_image()
Text
Directory
GenericAsn1
LineCount
Newick
Nexus
get_test_fname()
get_file_peek()
- galaxy.datatypes.flow module
- galaxy.datatypes.genetics module
GenomeGraphs
rgTabList
rgSampleList
rgFeatureList
Rgenetics
SNPMatrix
Lped
Pphe
Fphe
Phe
Fped
Pbed
ldIndep
Eigenstratgeno
Eigenstratpca
Snptest
IdeasPre
Pheno
RexpBase
RexpBase.file_ext
RexpBase.html_table
RexpBase.composite_type
RexpBase.__init__()
RexpBase.generate_primary_file()
RexpBase.get_mime()
RexpBase.get_phecols()
RexpBase.get_pheno()
RexpBase.set_peek()
RexpBase.get_peek()
RexpBase.get_file_peek()
RexpBase.regenerate_primary_file()
RexpBase.init_meta()
RexpBase.set_meta()
RexpBase.make_html_table()
RexpBase.display_peek()
RexpBase.metadata_spec
Affybatch
Eset
MAlist
LinkageStudies
GenotypeMatrix
MarkerMap
DataIn
AllegroLOD
- galaxy.datatypes.gis module
- galaxy.datatypes.goldenpath module
- galaxy.datatypes.graph module
- galaxy.datatypes.hdf5 module
HDF5SummarizedExperiment
HDF5SummarizedExperiment.file_ext
HDF5SummarizedExperiment.composite_type
HDF5SummarizedExperiment.allow_datatype_change
HDF5SummarizedExperiment.__init__()
HDF5SummarizedExperiment.init_meta()
HDF5SummarizedExperiment.generate_primary_file()
HDF5SummarizedExperiment.sniff()
HDF5SummarizedExperiment.get_mime()
HDF5SummarizedExperiment.metadata_spec
- galaxy.datatypes.images module
- galaxy.datatypes.interval module
Interval
Interval.edam_data
Interval.edam_format
Interval.file_ext
Interval.line_class
Interval.track_type
Interval.data_sources
Interval.__init__()
Interval.init_meta()
Interval.set_meta()
Interval.displayable()
Interval.get_estimated_display_viewport()
Interval.as_ucsc_display_file()
Interval.display_peek()
Interval.ucsc_links()
Interval.validate()
Interval.sniff_prefix()
Interval.genomic_region_dataprovider()
Interval.genomic_region_dict_dataprovider()
Interval.interval_dataprovider()
Interval.interval_dict_dataprovider()
Interval.dataproviders
Interval.metadata_spec
Interval.sniff()
BedGraph
Bed
ProBed
BedStrict
Bed6
Bed12
Gff
Gff.edam_data
Gff.edam_format
Gff.file_ext
Gff.valid_gff_frame
Gff.column_names
Gff.data_sources
Gff.track_type
Gff.__init__()
Gff.set_attribute_metadata()
Gff.set_meta()
Gff.display_peek()
Gff.get_estimated_display_viewport()
Gff.ucsc_links()
Gff.gbrowse_links()
Gff.sniff_prefix()
Gff.genomic_region_dataprovider()
Gff.genomic_region_dict_dataprovider()
Gff.interval_dataprovider()
Gff.interval_dict_dataprovider()
Gff.dataproviders
Gff.metadata_spec
Gff.sniff()
Gff3
Gtf
Wiggle
Wiggle.edam_format
Wiggle.file_ext
Wiggle.track_type
Wiggle.data_sources
Wiggle.__init__()
Wiggle.get_estimated_display_viewport()
Wiggle.gbrowse_links()
Wiggle.ucsc_links()
Wiggle.display_peek()
Wiggle.set_meta()
Wiggle.sniff_prefix()
Wiggle.wiggle_dataprovider()
Wiggle.wiggle_dict_dataprovider()
Wiggle.dataproviders
Wiggle.metadata_spec
Wiggle.sniff()
CustomTrack
ENCODEPeak
ChromatinInteractions
ScIdx
IntervalTabix
JuicerMediumTabix
BedTabix
GffTabix
- galaxy.datatypes.isa module
- galaxy.datatypes.media module
- galaxy.datatypes.metacyto module
- galaxy.datatypes.metadata module
Statement
MetadataCollection
MetadataCollection.__init__()
MetadataCollection.get_parent()
MetadataCollection.set_parent()
MetadataCollection.parent
MetadataCollection.spec
MetadataCollection.remove_key()
MetadataCollection.element_is_set()
MetadataCollection.get_metadata_parameter()
MetadataCollection.make_dict_copy()
MetadataCollection.requires_dataset_id
MetadataCollection.from_JSON_dict()
MetadataCollection.to_JSON_dict()
MetadataSpecCollection
MetadataParameter
MetadataParameter.__init__()
MetadataParameter.get_field()
MetadataParameter.to_string()
MetadataParameter.to_safe_string()
MetadataParameter.make_copy()
MetadataParameter.marshal()
MetadataParameter.validate()
MetadataParameter.unwrap()
MetadataParameter.wrap()
MetadataParameter.from_external_value()
MetadataParameter.to_external_value()
MetadataElementSpec
SelectParameter
DBKeyParameter
RangeParameter
ColumnParameter
ColumnTypesParameter
ListParameter
DictParameter
PythonObjectParameter
FileParameter
MetadataTempFile
- galaxy.datatypes.microarrays module
- galaxy.datatypes.molecules module
- galaxy.datatypes.mothur module
- galaxy.datatypes.msa module
- galaxy.datatypes.neo4j module
- galaxy.datatypes.ngsindex module
- galaxy.datatypes.phylip module
- galaxy.datatypes.plant_tribes module
- galaxy.datatypes.proteomics module
Wiff
Wiff2
MzTab
MzTab2
Kroenik
PepList
PSMS
PEFF
PepXmlReport
ProtXmlReport
Dta
Dta2d
Edta
ProteomicsXml
ParamXml
PepXml
MascotXML
MzML
NmrML
ProtXML
MzXML
MzData
MzIdentML
TraML
TrafoXML
MzQuantML
ConsensusXML
FeatureXML
IdXML
TandemXML
UniProtXML
XquestXML
XquestSpecXML
QCML
Mgf
MascotDat
ThermoRAW
Msp
SPLibNoIndex
SPLib
Ms2
XHunterAslFormat
Sf3
ImzML
- galaxy.datatypes.qiime2 module
- galaxy.datatypes.qualityscore module
- galaxy.datatypes.registry module
ConfigurationError
Registry
Registry.__init__()
Registry.load_datatypes()
Registry.get_legacy_sites_by_build()
Registry.get_display_sites()
Registry.load_datatype_sniffers()
Registry.get_datatype_from_filename()
Registry.is_extension_unsniffable_binary()
Registry.get_datatype_class_by_name()
Registry.get_available_tracks()
Registry.get_mimetype_by_extension()
Registry.get_datatype_by_extension()
Registry.change_datatype()
Registry.load_datatype_converters()
Registry.load_display_applications()
Registry.reload_display_applications()
Registry.load_external_metadata_tool()
Registry.set_default_values()
Registry.get_converters_by_datatype()
Registry.get_converter_by_target_type()
Registry.find_conversion_destination_for_dataset_by_extensions()
Registry.get_composite_extensions()
Registry.get_upload_metadata_params()
Registry.edam_formats
Registry.edam_data
Registry.to_xml_file()
Registry.get_extension()
example_datatype_registry_for_sample()
- galaxy.datatypes.sequence module
SequenceSplitLocations
Sequence
Alignment
Fasta
csFasta
Fastg
BaseFastq
BaseFastq.edam_format
BaseFastq.file_ext
BaseFastq.bases_regexp
BaseFastq.set_meta()
BaseFastq.sniff_prefix()
BaseFastq.display_data()
BaseFastq.split()
BaseFastq.process_split_file()
BaseFastq.quality_check()
BaseFastq.check_first_block()
BaseFastq.check_block()
BaseFastq.validate()
BaseFastq.metadata_spec
BaseFastq.sniff()
Fastq
FastqSanger
FastqSolexa
FastqIllumina
FastqCSSanger
Maf
MafCustomTrack
Axt
Lav
RNADotPlotMatrix
DotBracket
Genbank
MemePsp
- galaxy.datatypes.sniff module
get_test_fname()
sniff_with_cls()
handle_composite_file()
ConvertResult
ConvertFunction
convert_newlines()
convert_sep2tabs()
convert_newlines_sep2tabs()
iter_headers()
validate_tabular()
get_headers()
is_column_based()
guess_ext()
guess_ext_from_file_name()
FilePrefix
run_sniffers_raw()
zip_single_fileobj()
build_sniff_from_prefix()
disable_parent_class_sniffing()
HandleCompressedFileResponse
handle_compressed_file()
handle_uploaded_dataset_file()
HandleUploadedDatasetFileInternalResponse
convert_function()
handle_uploaded_dataset_file_internal()
InappropriateDatasetContentError
- galaxy.datatypes.spaln module
- galaxy.datatypes.speech module
- galaxy.datatypes.tabular module
TabularData
TabularData.edam_format
TabularData.CHUNKABLE
TabularData.data_line_offset
TabularData.max_peek_columns
TabularData.set_meta()
TabularData.set_peek()
TabularData.displayable()
TabularData.get_chunk()
TabularData.display_data()
TabularData.display_as_markdown()
TabularData.make_html_table()
TabularData.make_html_peek_header()
TabularData.make_html_peek_rows()
TabularData.display_peek()
TabularData.is_int()
TabularData.is_float()
TabularData.guess_type()
TabularData.column_dataprovider()
TabularData.dataset_column_dataprovider()
TabularData.dict_dataprovider()
TabularData.dataset_dict_dataprovider()
TabularData.dataproviders
TabularData.metadata_spec
Tabular
SraManifest
Taxonomy
Sam
Sam.edam_format
Sam.edam_data
Sam.file_ext
Sam.track_type
Sam.data_sources
Sam.__init__()
Sam.display_peek()
Sam.sniff_prefix()
Sam.set_meta()
Sam.merge()
Sam.line_dataprovider()
Sam.regex_line_dataprovider()
Sam.column_dataprovider()
Sam.dataset_column_dataprovider()
Sam.dict_dataprovider()
Sam.dataset_dict_dataprovider()
Sam.header_dataprovider()
Sam.id_seq_qual_dataprovider()
Sam.genomic_region_dataprovider()
Sam.genomic_region_dict_dataprovider()
Sam.dataproviders
Sam.metadata_spec
Sam.sniff()
Pileup
BaseVcf
Vcf
VcfGz
Eland
ElandMulti
FeatureLocationIndex
BaseCSV
CSV
TSV
ConnectivityTable
ConnectivityTable.edam_format
ConnectivityTable.file_ext
ConnectivityTable.header_regexp
ConnectivityTable.structure_regexp
ConnectivityTable.__init__()
ConnectivityTable.set_meta()
ConnectivityTable.sniff_prefix()
ConnectivityTable.get_chunk()
ConnectivityTable.metadata_spec
ConnectivityTable.sniff()
MatrixMarket
CMAP
Psl
- galaxy.datatypes.text module
- galaxy.datatypes.tracks module
- galaxy.datatypes.triples module
- galaxy.datatypes.upload_util module
- galaxy.datatypes.xml module
- Subpackages
- galaxy.dependencies package
ConditionalDependencies
ConditionalDependencies.__init__()
ConditionalDependencies.parse_configs()
ConditionalDependencies.get_conditional_requirements()
ConditionalDependencies.check()
ConditionalDependencies.check_psycopg2_binary()
ConditionalDependencies.check_mysqlclient()
ConditionalDependencies.check_drmaa()
ConditionalDependencies.check_galaxycloudrunner()
ConditionalDependencies.check_total_perspective_vortex()
ConditionalDependencies.check_pbs_python()
ConditionalDependencies.check_pykube()
ConditionalDependencies.check_chronos_python()
ConditionalDependencies.check_boto3_python()
ConditionalDependencies.check_fluent_logger()
ConditionalDependencies.check_sentry_sdk()
ConditionalDependencies.check_statsd()
ConditionalDependencies.check_python_ldap()
ConditionalDependencies.check_ldap3()
ConditionalDependencies.check_python_pam()
ConditionalDependencies.check_azure_storage()
ConditionalDependencies.check_kamaki()
ConditionalDependencies.check_python_irodsclient()
ConditionalDependencies.check_fs_dropboxfs()
ConditionalDependencies.check_fs_webdavfs()
ConditionalDependencies.check_fs_anvilfs()
ConditionalDependencies.check_fs_sshfs()
ConditionalDependencies.check_fs_googledrivefs()
ConditionalDependencies.check_fs_gcsfs()
ConditionalDependencies.check_google_cloud_storage()
ConditionalDependencies.check_fs_onedatafs()
ConditionalDependencies.check_fs_basespace()
ConditionalDependencies.check_watchdog()
ConditionalDependencies.check_python_gitlab()
ConditionalDependencies.check_pygithub()
ConditionalDependencies.check_influxdb()
ConditionalDependencies.check_tensorflow()
ConditionalDependencies.check_weasyprint()
ConditionalDependencies.check_custos_sdk()
ConditionalDependencies.check_hvac()
ConditionalDependencies.check_pkce()
optional()
- galaxy.exceptions package
MessageException
ItemDeletionException
ObjectInvalid
AcceptedRetryLater
NoContentException
ActionInputError
DuplicatedSlugException
DuplicatedIdentifierException
ObjectAttributeInvalidException
ObjectAttributeMissingException
MalformedId
UserInvalidRunAsException
MalformedContents
UnknownContentsType
RequestParameterMissingException
ToolMetaParameterException
ToolMissingException
RequestParameterInvalidException
ToolInputsNotReadyException
ToolInputsNotOKException
RealUserRequiredException
AuthenticationFailed
AuthenticationRequired
ItemAccessibilityException
ItemOwnershipException
ItemImmutableException
ConfigDoesNotAllowException
InsufficientPermissionsException
UserCannotRunAsException
AdminRequiredException
UserActivationRequiredException
ObjectNotFound
Conflict
DeprecatedMethod
ConfigurationError
InconsistentDatabase
InternalServerError
ToolExecutionError
NotImplemented
InvalidFileFormatError
ReferenceDataError
ServerNotConfiguredForRequest
HandlerAssignmentError
- Submodules
- galaxy.exceptions.error_codes module
- galaxy.files package
FileSourcePath
FileSourceScore
NoMatchingFileSource
ConfiguredFileSources
ConfiguredFileSources.__init__()
ConfiguredFileSources.find_best_match()
ConfiguredFileSources.get_file_source_path()
ConfiguredFileSources.validate_uri_root()
ConfiguredFileSources.looks_like_uri()
ConfiguredFileSources.plugins_to_dict()
ConfiguredFileSources.to_dict()
ConfiguredFileSources.from_app_config()
ConfiguredFileSources.from_dict()
NullConfiguredFileSources
ConfiguredFileSourcesConfig
FileSourceDictifiable
ProvidesUserFileSourcesUserContext
ProvidesUserFileSourcesUserContext.__init__()
ProvidesUserFileSourcesUserContext.email
ProvidesUserFileSourcesUserContext.username
ProvidesUserFileSourcesUserContext.ftp_dir
ProvidesUserFileSourcesUserContext.preferences
ProvidesUserFileSourcesUserContext.role_names
ProvidesUserFileSourcesUserContext.group_names
ProvidesUserFileSourcesUserContext.is_admin
ProvidesUserFileSourcesUserContext.user_vault
ProvidesUserFileSourcesUserContext.app_vault
ProvidesUserFileSourcesUserContext.file_sources
DictFileSourcesUserContext
DictFileSourcesUserContext.__init__()
DictFileSourcesUserContext.email
DictFileSourcesUserContext.username
DictFileSourcesUserContext.ftp_dir
DictFileSourcesUserContext.preferences
DictFileSourcesUserContext.role_names
DictFileSourcesUserContext.group_names
DictFileSourcesUserContext.is_admin
DictFileSourcesUserContext.user_vault
DictFileSourcesUserContext.app_vault
DictFileSourcesUserContext.file_sources
- Subpackages
- galaxy.files.sources package
FilesSourceProperties
FilesSourceOptions
SingleFileSource
SupportsBrowsing
FilesSource
BaseFilesSource
uri_join()
slash_join()
- Submodules
- galaxy.files.sources.anvil module
- galaxy.files.sources.basespace module
- galaxy.files.sources.dropbox module
- galaxy.files.sources.ftp module
- galaxy.files.sources.galaxy module
- galaxy.files.sources.googlecloudstorage module
- galaxy.files.sources.googledrive module
- galaxy.files.sources.onedata module
- galaxy.files.sources.posix module
- galaxy.files.sources.s3 module
- galaxy.files.sources.s3fs module
- galaxy.files.sources.ssh module
- galaxy.files.sources.webdav module
- galaxy.files.unittest_utils package
- galaxy.files.sources package
- Submodules
- galaxy.files.uris module
- galaxy.forms package
- Submodules
- galaxy.forms.forms module
- galaxy.job_execution package
- Subpackages
- Submodules
- galaxy.job_execution.compute_environment module
dataset_path_to_extra_path()
ComputeEnvironment
ComputeEnvironment.output_names()
ComputeEnvironment.input_path_rewrite()
ComputeEnvironment.output_path_rewrite()
ComputeEnvironment.input_extra_files_rewrite()
ComputeEnvironment.output_extra_files_rewrite()
ComputeEnvironment.input_metadata_rewrite()
ComputeEnvironment.unstructured_path_rewrite()
ComputeEnvironment.working_directory()
ComputeEnvironment.config_directory()
ComputeEnvironment.env_config_directory()
ComputeEnvironment.sep()
ComputeEnvironment.new_file_path()
ComputeEnvironment.tool_directory()
ComputeEnvironment.version_path()
ComputeEnvironment.home_directory()
ComputeEnvironment.tmp_directory()
ComputeEnvironment.galaxy_url()
ComputeEnvironment.get_file_sources_dict()
SimpleComputeEnvironment
SharedComputeEnvironment
SharedComputeEnvironment.job_id
SharedComputeEnvironment.__init__()
SharedComputeEnvironment.job
SharedComputeEnvironment.get_file_sources_dict()
SharedComputeEnvironment.output_names()
SharedComputeEnvironment.output_paths()
SharedComputeEnvironment.input_path_rewrite()
SharedComputeEnvironment.output_path_rewrite()
SharedComputeEnvironment.input_extra_files_rewrite()
SharedComputeEnvironment.output_extra_files_rewrite()
SharedComputeEnvironment.input_metadata_rewrite()
SharedComputeEnvironment.unstructured_path_rewrite()
SharedComputeEnvironment.working_directory()
SharedComputeEnvironment.env_config_directory()
SharedComputeEnvironment.new_file_path()
SharedComputeEnvironment.version_path()
SharedComputeEnvironment.tool_directory()
SharedComputeEnvironment.home_directory()
SharedComputeEnvironment.tmp_directory()
SharedComputeEnvironment.galaxy_url()
- galaxy.job_execution.datasets module
- galaxy.job_execution.output_collect module
PermissionProvider
MetadataSourceProvider
collect_dynamic_outputs()
BaseJobContext
JobContext
JobContext.__init__()
JobContext.job_working_directory
JobContext.tool_provided_metadata
JobContext.discovered_file_count
JobContext.tag_handler
JobContext.work_context
JobContext.sa_session
JobContext.permission_provider
JobContext.metadata_source_provider
JobContext.job
JobContext.flush_per_n_datasets
JobContext.input_dbkey
JobContext.object_store
JobContext.user
JobContext.persist_object()
JobContext.flush()
JobContext.get_library_folder()
JobContext.get_hdca()
JobContext.create_library_folder()
JobContext.create_hdca()
JobContext.add_output_dataset_association()
JobContext.add_library_dataset_to_folder()
JobContext.add_datasets_to_history()
JobContext.output_collection_def()
JobContext.output_def()
JobContext.job_id()
JobContext.get_job_id()
JobContext.get_implicit_collection_jobs_association_id()
SessionlessJobContext
SessionlessJobContext.__init__()
SessionlessJobContext.tool_provided_metadata
SessionlessJobContext.discovered_file_count
SessionlessJobContext.output_collection_def()
SessionlessJobContext.output_def()
SessionlessJobContext.job_id()
SessionlessJobContext.get_hdca()
SessionlessJobContext.add_dataset_collection()
SessionlessJobContext.add_output_dataset_association()
SessionlessJobContext.get_job_id()
SessionlessJobContext.get_implicit_collection_jobs_association_id()
SessionlessJobContext.job_working_directory
collect_primary_datasets()
discover_files()
walk_over_file_collectors()
walk_over_extra_files()
dataset_collector()
ToolMetadataDatasetCollector
DatasetCollector
read_exit_code_from()
default_exit_code_file()
collect_extra_files()
collect_shrinked_content_from_path()
- galaxy.job_execution.setup module
JobOutput
JobOutputs
JobIO
JobIO.dict_collection_visible_keys
JobIO.__init__()
JobIO.job
JobIO.from_json()
JobIO.from_dict()
JobIO.to_dict()
JobIO.to_json()
JobIO.file_sources
JobIO.dataset_path_rewriter
JobIO.output_paths
JobIO.output_hdas_and_paths
JobIO.get_input_dataset_fnames()
JobIO.get_input_fnames()
JobIO.get_input_paths()
JobIO.get_input_path()
JobIO.get_output_basenames()
JobIO.get_output_fnames()
JobIO.get_output_path()
JobIO.get_mutable_output_fnames()
JobIO.get_output_hdas_and_fnames()
JobIO.compute_outputs()
JobIO.get_output_file_id()
ensure_configs_directory()
create_working_directory_for_job()
- galaxy.job_metrics package
JobInstrumenter
Safety
- Subpackages
- galaxy.job_metrics.instrumenters package
InstrumentPlugin
- Submodules
- galaxy.job_metrics.instrumenters.cgroup module
- galaxy.job_metrics.instrumenters.core module
- galaxy.job_metrics.instrumenters.cpuinfo module
- galaxy.job_metrics.instrumenters.env module
- galaxy.job_metrics.instrumenters.hostname module
- galaxy.job_metrics.instrumenters.meminfo module
- galaxy.job_metrics.instrumenters.uname module
- galaxy.job_metrics.instrumenters package
- Submodules
- galaxy.job_metrics.formatting module
- galaxy.job_metrics.safety module
- galaxy.jobs package
JobDestination
NoopQueue
JobToolConfiguration
JobConfiguration
JobConfiguration.DEFAULT_BASE_HANDLER_POOLS
JobConfiguration.DEFAULT_NWORKERS
JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE
JobConfiguration.JOB_RESOURCE_CONDITIONAL_XML
JobConfiguration.__init__()
JobConfiguration.runner_plugins
JobConfiguration.handlers
JobConfiguration.handler_runner_plugins
JobConfiguration.destinations
JobConfiguration.tools
JobConfiguration.tool_classes
JobConfiguration.resource_groups
JobConfiguration.resource_parameters
JobConfiguration.get_tool_resource_xml()
JobConfiguration.get_params()
JobConfiguration.get_envs()
JobConfiguration.get_resubmits()
JobConfiguration.default_job_tool_configuration
JobConfiguration.get_job_tool_configurations()
JobConfiguration.get_destination()
JobConfiguration.get_destinations()
JobConfiguration.get_job_runner_plugins()
JobConfiguration.is_id()
JobConfiguration.is_tag()
JobConfiguration.convert_legacy_destinations()
JobWrapper
TaskWrapper
TaskWrapper.is_task
TaskWrapper.__init__()
TaskWrapper.can_split()
TaskWrapper.get_job()
TaskWrapper.get_task()
TaskWrapper.get_id_tag()
TaskWrapper.prepare()
TaskWrapper.fail()
TaskWrapper.change_state()
TaskWrapper.get_state()
TaskWrapper.get_exit_code()
TaskWrapper.set_runner()
TaskWrapper.finish()
TaskWrapper.cleanup()
TaskWrapper.get_command_line()
TaskWrapper.get_session_id()
TaskWrapper.get_output_file_id()
TaskWrapper.get_tool_provided_job_metadata()
TaskWrapper.get_dataset_finish_context()
TaskWrapper.setup_external_metadata()
TaskWrapper.get_output_destination()
- Subpackages
- galaxy.jobs.rules package
- galaxy.jobs.runners package
RunnerParams
BaseJobRunner
JobState
AsynchronousJobState
AsynchronousJobRunner
- Subpackages
- Submodules
- galaxy.jobs.runners.chronos module
- galaxy.jobs.runners.cli module
- galaxy.jobs.runners.condor module
- galaxy.jobs.runners.drmaa module
- galaxy.jobs.runners.godocker module
- galaxy.jobs.runners.kubernetes module
- galaxy.jobs.runners.local module
- galaxy.jobs.runners.pbs module
- galaxy.jobs.runners.pulsar module
- galaxy.jobs.runners.slurm module
- galaxy.jobs.runners.state_handler_factory module
- galaxy.jobs.runners.tasks module
- galaxy.jobs.runners.univa module
- galaxy.jobs.splitters package
- Submodules
- galaxy.jobs.command_factory module
- galaxy.jobs.dynamic_tool_destination module
priority_list
destination_list
max_edit_dist
MalformedYMLException
ScannerError
get_keys_from_dict()
RuleValidator
parse_yaml()
validate_destination()
validate_config()
bytes_to_str()
str_to_bytes()
importer()
map_tool_to_destination()
get_destination_list_from_job_config()
get_edit_distance()
get_typo_correction()
verbose
- galaxy.jobs.handler module
JobHandlerI
JobHandler
ItemGrabber
StopSignalException
BaseJobHandlerQueue
JobHandlerQueue
JobHandlerQueue.__init__()
JobHandlerQueue.start()
JobHandlerQueue.job_wrapper()
JobHandlerQueue.job_pair_for_id()
JobHandlerQueue.get_user_job_count()
JobHandlerQueue.get_user_job_count_per_destination()
JobHandlerQueue.increase_running_job_count()
JobHandlerQueue.get_total_job_count_per_destination()
JobHandlerQueue.put()
JobHandlerQueue.shutdown()
JobHandlerQueue.queue
JobHandlerStopQueue
DefaultJobDispatcher
- galaxy.jobs.manager module
- galaxy.jobs.mapper module
- galaxy.jobs.rule_helper module
- galaxy.jobs.stock_rules module
- galaxy.managers package
- Submodules
- galaxy.managers.annotatable module
- galaxy.managers.api_keys module
- galaxy.managers.base module
ParsedFilter
parsed_filter
security_check()
get_class()
decode_id()
decode_with_security()
encode_with_security()
get_object()
munge_lists()
ModelManager
ModelManager.model_class
ModelManager.foreign_key_name
ModelManager.__init__()
ModelManager.app
ModelManager.session()
ModelManager.query()
ModelManager.one()
ModelManager.by_id()
ModelManager.list()
ModelManager.count()
ModelManager.by_ids()
ModelManager.create()
ModelManager.copy()
ModelManager.update()
ModelManager.associate()
ModelManager.query_associated()
HasAModelManager
ModelSerializingError
ModelDeserializingError
SkipAttribute
Serializer
ModelSerializer
ModelSerializer.__init__()
ModelSerializer.views
ModelSerializer.default_view
ModelSerializer.url_for()
ModelSerializer.add_serializers()
ModelSerializer.add_view()
ModelSerializer.serialize()
ModelSerializer.skip()
ModelSerializer.default_serializer()
ModelSerializer.serialize_date()
ModelSerializer.serialize_id()
ModelSerializer.serialize_type_id()
ModelSerializer.serialize_to_view()
ModelValidator
Deserializer
ModelDeserializer
ModelDeserializer.validate
ModelDeserializer.app
ModelDeserializer.__init__()
ModelDeserializer.add_deserializers()
ModelDeserializer.deserialize()
ModelDeserializer.default_deserializer()
ModelDeserializer.deserialize_basestring()
ModelDeserializer.deserialize_bool()
ModelDeserializer.deserialize_int()
ModelDeserializer.deserialize_genome_build()
ModelFilterParser
ModelFilterParser.model_class
ModelFilterParser.parsed_filter
ModelFilterParser.__init__()
ModelFilterParser.date_string_re
ModelFilterParser.orm_filter_parsers
ModelFilterParser.fn_filter_parsers
ModelFilterParser.build_filter_params()
ModelFilterParser.parse_query_filters()
ModelFilterParser.parse_filters()
ModelFilterParser.parse_filter()
ModelFilterParser.UNDERSCORED_OPS
ModelFilterParser.string_standard_ops()
ModelFilterParser.parse_id_list()
ModelFilterParser.parse_int_list()
ModelFilterParser.parse_date()
ModelFilterParser.contains_non_orm_filter()
parse_bool()
raise_filter_err()
is_valid_slug()
SortableManager
StorageCleanerManager
- galaxy.managers.citations module
- galaxy.managers.cloud module
- galaxy.managers.cloudauthzs module
- galaxy.managers.collections module
DatasetCollectionManager
DatasetCollectionManager.ELEMENTS_UNINITIALIZED
DatasetCollectionManager.__init__()
DatasetCollectionManager.precreate_dataset_collection_instance()
DatasetCollectionManager.precreate_dataset_collection()
DatasetCollectionManager.create()
DatasetCollectionManager.create_dataset_collection()
DatasetCollectionManager.get_converters_for_collection()
DatasetCollectionManager.collection_builder_for()
DatasetCollectionManager.delete()
DatasetCollectionManager.update()
DatasetCollectionManager.copy()
DatasetCollectionManager.history_dataset_collections()
DatasetCollectionManager.match_collections()
DatasetCollectionManager.get_dataset_collection_instance()
DatasetCollectionManager.get_dataset_collection()
DatasetCollectionManager.apply_rules()
DatasetCollectionManager.get_collection_contents()
DatasetCollectionManager.write_dataset_collection()
- galaxy.managers.collections_util module
- galaxy.managers.configuration module
- galaxy.managers.context module
ProvidesAppContext
ProvidesUserContext
ProvidesUserContext.galaxy_session
ProvidesUserContext.tag_handler
ProvidesUserContext.async_request_user
ProvidesUserContext.user
ProvidesUserContext.user_vault
ProvidesUserContext.get_user()
ProvidesUserContext.anonymous
ProvidesUserContext.get_current_user_roles()
ProvidesUserContext.user_is_admin
ProvidesUserContext.user_is_bootstrap_admin
ProvidesUserContext.user_can_do_run_as
ProvidesUserContext.user_is_active
ProvidesUserContext.check_user_activation()
ProvidesUserContext.user_ftp_dir
ProvidesHistoryContext
- galaxy.managers.datasets module
DatasetManager
DatasetManager.model_class
DatasetManager.foreign_key_name
DatasetManager.app
DatasetManager.__init__()
DatasetManager.create()
DatasetManager.copy()
DatasetManager.purge()
DatasetManager.purge_datasets()
DatasetManager.error_unless_dataset_purge_allowed()
DatasetManager.is_accessible()
DatasetManager.has_access_permission()
DatasetManager.compute_hash()
DatasetRBACPermissions
DatasetSerializer
DatasetSerializer.model_manager_class
DatasetSerializer.__init__()
DatasetSerializer.default_view
DatasetSerializer.add_serializers()
DatasetSerializer.serialize_file_name()
DatasetSerializer.serialize_extra_files_path()
DatasetSerializer.serialize_permissions()
DatasetSerializer.views
DatasetSerializer.serializable_keyset
DatasetSerializer.serializers
DatasetSerializer.app
DatasetAssociationManager
DatasetAssociationManager.app
DatasetAssociationManager.__init__()
DatasetAssociationManager.is_accessible()
DatasetAssociationManager.delete()
DatasetAssociationManager.purge()
DatasetAssociationManager.by_user()
DatasetAssociationManager.creating_job()
DatasetAssociationManager.stop_creating_job()
DatasetAssociationManager.is_composite()
DatasetAssociationManager.extra_files()
DatasetAssociationManager.serialize_dataset_association_roles()
DatasetAssociationManager.ensure_can_change_datatype()
DatasetAssociationManager.ensure_can_set_metadata()
DatasetAssociationManager.detect_datatype()
DatasetAssociationManager.set_metadata()
DatasetAssociationManager.overwrite_metadata()
DatasetAssociationManager.update_permissions()
DatasetAssociationSerializer
DatasetAssociationSerializer.add_serializers()
DatasetAssociationSerializer.serialize()
DatasetAssociationSerializer.default_view
DatasetAssociationSerializer.views
DatasetAssociationSerializer.serializable_keyset
DatasetAssociationSerializer.serializers
DatasetAssociationSerializer.model_manager_class
DatasetAssociationSerializer.app
DatasetAssociationDeserializer
DatasetAssociationDeserializer.add_deserializers()
DatasetAssociationDeserializer.deserialize_metadata()
DatasetAssociationDeserializer.deserialize_metadatum()
DatasetAssociationDeserializer.deserialize_datatype()
DatasetAssociationDeserializer.app
DatasetAssociationDeserializer.deserializable_keyset
DatasetAssociationDeserializer.model_manager_class
DatasetAssociationFilterParser
DatasetAssociationFilterParser.eq_datatype()
DatasetAssociationFilterParser.isinstance_datatype()
DatasetAssociationFilterParser.model_class
DatasetAssociationFilterParser.orm_filter_parsers
DatasetAssociationFilterParser.fn_filter_parsers
DatasetAssociationFilterParser.model_manager_class
DatasetAssociationFilterParser.app
- galaxy.managers.datatypes module
- galaxy.managers.deletable module
- galaxy.managers.display_applications module
- galaxy.managers.executables module
- galaxy.managers.folders module
SecurityParams
FolderManager
FolderManager.get()
FolderManager.secure()
FolderManager.check_modifyable()
FolderManager.check_manageable()
FolderManager.check_accessible()
FolderManager.get_folder_dict()
FolderManager.create()
FolderManager.update()
FolderManager.delete()
FolderManager.get_current_roles()
FolderManager.can_add_item()
FolderManager.cut_the_prefix()
FolderManager.decode_folder_id()
FolderManager.cut_and_decode()
FolderManager.get_contents()
FolderManager.build_folder_path()
- galaxy.managers.genomes module
- galaxy.managers.group_roles module
- galaxy.managers.group_users module
- galaxy.managers.groups module
- galaxy.managers.hdas module
HistoryDatasetAssociationNoHistoryException
HDAManager
HDAManager.model_class
HDAManager.foreign_key_name
HDAManager.tag_assoc
HDAManager.annotation_assoc
HDAManager.app
HDAManager.__init__()
HDAManager.get_owned_ids()
HDAManager.is_accessible()
HDAManager.is_owner()
HDAManager.create()
HDAManager.materialize()
HDAManager.copy()
HDAManager.copy_ldda()
HDAManager.purge()
HDAManager.error_if_uploading()
HDAManager.has_been_resubmitted()
HDAManager.data_conversion_status()
HDAManager.text_data()
HDAManager.annotation()
HDAStorageCleanerManager
HDASerializer
HDASerializer.model_manager_class
HDASerializer.app
HDASerializer.__init__()
HDASerializer.serialize_copied_from_ldda_id()
HDASerializer.add_serializers()
HDASerializer.serialize()
HDASerializer.serialize_display_apps()
HDASerializer.serialize_old_display_applications()
HDASerializer.serialize_urls()
HDADeserializer
HDAFilterParser
- galaxy.managers.hdcas module
stream_dataset_collection()
write_dataset_collection()
set_collection_attributes()
HDCAManager
DCESerializer
DCSerializer
DCASerializer
HDCASerializer
HDCASerializer.__init__()
HDCASerializer.default_view
HDCASerializer.add_serializers()
HDCASerializer.generate_contents_url()
HDCASerializer.serialize_job_state_summary()
HDCASerializer.serialize_elements_datatypes()
HDCASerializer.app
HDCASerializer.views
HDCASerializer.serializable_keyset
HDCASerializer.serializers
HDCASerializer.model_manager_class
- galaxy.managers.histories module
HistoryManager
HistoryManager.model_class
HistoryManager.foreign_key_name
HistoryManager.user_share_model
HistoryManager.tag_assoc
HistoryManager.annotation_assoc
HistoryManager.rating_assoc
HistoryManager.__init__()
HistoryManager.copy()
HistoryManager.by_user()
HistoryManager.is_owner()
HistoryManager.most_recent()
HistoryManager.purge()
HistoryManager.get_current()
HistoryManager.set_current()
HistoryManager.set_current_by_id()
HistoryManager.parse_order_by()
HistoryManager.non_ready_jobs()
HistoryManager.queue_history_import()
HistoryManager.legacy_serve_ready_history_export()
HistoryManager.get_ready_history_export_file_path()
HistoryManager.queue_history_export()
HistoryManager.get_sharing_extra_information()
HistoryManager.is_history_shared_with()
HistoryManager.make_members_public()
HistoryManager.archive_history()
HistoryManager.restore_archived_history()
HistoryManager.get_active_count()
HistoryStorageCleanerManager
HistoryStorageCleanerManager.__init__()
HistoryStorageCleanerManager.sort_map
HistoryStorageCleanerManager.get_discarded_summary()
HistoryStorageCleanerManager.get_discarded()
HistoryStorageCleanerManager.get_archived_summary()
HistoryStorageCleanerManager.get_archived()
HistoryStorageCleanerManager.cleanup_items()
HistoryExportManager
HistoryExportManager.export_object_type
HistoryExportManager.__init__()
HistoryExportManager.get_task_exports()
HistoryExportManager.get_task_export_by_id()
HistoryExportManager.create_export_association()
HistoryExportManager.get_record_metadata()
HistoryExportManager.get_exports()
HistoryExportManager.serialize()
HistoryExportManager.get_ready_jeha()
HistorySerializer
HistorySerializer.model_manager_class
HistorySerializer.SINGLE_CHAR_ABBR
HistorySerializer.__init__()
HistorySerializer.add_serializers()
HistorySerializer.serialize_state_ids()
HistorySerializer.serialize_state_counts()
HistorySerializer.serialize_history_state()
HistorySerializer.serialize_contents()
HistorySerializer.serialize_contents_states()
HistorySerializer.serialize_contents_active()
HistoryDeserializer
HistoryFilters
- galaxy.managers.history_contents module
HistoryContentsManager
HistoryContentsManager.root_container_class
HistoryContentsManager.contained_class
HistoryContentsManager.contained_class_manager_class
HistoryContentsManager.contained_class_type_name
HistoryContentsManager.subcontainer_class
HistoryContentsManager.subcontainer_class_manager_class
HistoryContentsManager.subcontainer_class_type_name
HistoryContentsManager.common_columns
HistoryContentsManager.default_order_by
HistoryContentsManager.__init__()
HistoryContentsManager.contained()
HistoryContentsManager.subcontainers()
HistoryContentsManager.contents()
HistoryContentsManager.contents_count()
HistoryContentsManager.contents_query()
HistoryContentsManager.parse_order_by()
HistoryContentsManager.state_counts()
HistoryContentsManager.active_counts()
HistoryContentsManager.map_datasets()
HistoryContentsManager.passes_filters()
HistoryContentsSerializer
HistoryContentsSerializer.model_manager_class
HistoryContentsSerializer.__init__()
HistoryContentsSerializer.default_view
HistoryContentsSerializer.add_serializers()
HistoryContentsSerializer.serialize_id_or_skip()
HistoryContentsSerializer.views
HistoryContentsSerializer.serializable_keyset
HistoryContentsSerializer.serializers
HistoryContentsSerializer.app
HistoryContentsFilters
HistoryContentsFilters.model_class
HistoryContentsFilters.parse_query_filters_with_relations()
HistoryContentsFilters.get_query_filters_with_relations()
HistoryContentsFilters.decode_type_id()
HistoryContentsFilters.parse_type_id_list()
HistoryContentsFilters.orm_filter_parsers
HistoryContentsFilters.fn_filter_parsers
HistoryContentsFilters.model_manager_class
HistoryContentsFilters.app
- galaxy.managers.interactivetool module
InteractiveToolSqlite
InteractiveToolManager
InteractiveToolManager.__init__()
InteractiveToolManager.create_entry_points()
InteractiveToolManager.configure_entry_point()
InteractiveToolManager.configure_entry_points()
InteractiveToolManager.save_entry_point()
InteractiveToolManager.create_interactivetool()
InteractiveToolManager.get_nonterminal_for_user_by_trans()
InteractiveToolManager.can_access_job()
InteractiveToolManager.can_access_entry_point()
InteractiveToolManager.can_access_entry_points()
InteractiveToolManager.stop()
InteractiveToolManager.remove_entry_points()
InteractiveToolManager.remove_entry_point()
InteractiveToolManager.target_if_active()
InteractiveToolManager.get_entry_point_subdomain()
InteractiveToolManager.get_entry_point_path()
InteractiveToolManager.access_entry_point_target()
- galaxy.managers.jobs module
- galaxy.managers.lddas module
- galaxy.managers.libraries module
LibraryManager
LibraryManager.get()
LibraryManager.create()
LibraryManager.update()
LibraryManager.delete()
LibraryManager.list()
LibraryManager.secure()
LibraryManager.check_accessible()
LibraryManager.get_library_dict()
LibraryManager.get_current_roles()
LibraryManager.get_access_roles()
LibraryManager.get_modify_roles()
LibraryManager.get_manage_roles()
LibraryManager.get_add_roles()
LibraryManager.make_public()
LibraryManager.is_public()
get_containing_library_from_library_dataset()
- galaxy.managers.library_datasets module
LibraryDatasetsManager
LibraryDatasetsManager.model_class
LibraryDatasetsManager.__init__()
LibraryDatasetsManager.app
LibraryDatasetsManager.get()
LibraryDatasetsManager.update()
LibraryDatasetsManager.secure()
LibraryDatasetsManager.check_accessible()
LibraryDatasetsManager.check_modifiable()
LibraryDatasetsManager.serialize()
LibraryDatasetsManager.foreign_key_name
- galaxy.managers.licenses module
LicenseMetadataModel
LicenseMetadataModel.licenseId
LicenseMetadataModel.name
LicenseMetadataModel.reference
LicenseMetadataModel.referenceNumber
LicenseMetadataModel.isDeprecatedLicenseId
LicenseMetadataModel.isOsiApproved
LicenseMetadataModel.seeAlso
LicenseMetadataModel.detailsUrl
LicenseMetadataModel.recommended
LicenseMetadataModel.url
LicenseMetadataModel.spdxUrl
LicensesManager
- galaxy.managers.markdown_parse module
- galaxy.managers.markdown_util module
- galaxy.managers.metrics module
- galaxy.managers.model_stores module
ModelStoreUserContext
ModelStoreManager
ModelStoreManager.__init__()
ModelStoreManager.setup_history_export_job()
ModelStoreManager.prepare_history_download()
ModelStoreManager.prepare_history_content_download()
ModelStoreManager.prepare_invocation_download()
ModelStoreManager.write_invocation_to()
ModelStoreManager.write_history_content_to()
ModelStoreManager.write_history_to()
ModelStoreManager.set_history_export_request_metadata()
ModelStoreManager.set_history_export_result_metadata()
ModelStoreManager.import_model_store()
create_objects_from_store()
- galaxy.managers.pages module
PageManager
PageManager.model_class
PageManager.foreign_key_name
PageManager.user_share_model
PageManager.tag_assoc
PageManager.annotation_assoc
PageManager.rating_assoc
PageManager.__init__()
PageManager.index_query()
PageManager.create_page()
PageManager.save_new_revision()
PageManager.rewrite_content_for_import()
PageManager.rewrite_content_for_export()
PageSerializer
PageDeserializer
PageContentProcessor
PageContentProcessor.bare_ampersand
PageContentProcessor.elements_no_end_tag
PageContentProcessor.__init__()
PageContentProcessor.reset()
PageContentProcessor.feed()
PageContentProcessor.handle_starttag()
PageContentProcessor.handle_endtag()
PageContentProcessor.handle_charref()
PageContentProcessor.handle_entityref()
PageContentProcessor.handle_data()
PageContentProcessor.handle_comment()
PageContentProcessor.handle_decl()
PageContentProcessor.handle_pi()
PageContentProcessor.output()
get_page_identifiers()
placeholderRenderForEdit()
placeholderRenderForSave()
- galaxy.managers.quotas module
QuotaManager
QuotaManager.__init__()
QuotaManager.sa_session
QuotaManager.quota_agent
QuotaManager.create_quota()
QuotaManager.rename_quota()
QuotaManager.manage_users_and_groups_for_quota()
QuotaManager.edit_quota()
QuotaManager.set_quota_default()
QuotaManager.unset_quota_default()
QuotaManager.delete_quota()
QuotaManager.undelete_quota()
QuotaManager.purge_quota()
QuotaManager.get_quota()
- galaxy.managers.ratable module
- galaxy.managers.rbac_secured module
- galaxy.managers.remote_files module
- galaxy.managers.roles module
- galaxy.managers.secured module
AccessibleManagerMixin
OwnableManagerMixin
OwnableManagerMixin.model_class
OwnableManagerMixin.by_id()
OwnableManagerMixin.is_owner()
OwnableManagerMixin.get_owned()
OwnableManagerMixin.error_unless_owner()
OwnableManagerMixin.list_owned()
OwnableManagerMixin.filter_owned()
OwnableManagerMixin.get_mutable()
OwnableManagerMixin.error_unless_mutable()
- galaxy.managers.session module
- galaxy.managers.sharable module
SharableModelDeserializer
SharableModelDeserializer.__init__()
SharableModelDeserializer.add_deserializers()
SharableModelDeserializer.deserialize_published()
SharableModelDeserializer.deserialize_importable()
SharableModelDeserializer.deserialize_users_shared_with()
SharableModelDeserializer.app
SharableModelDeserializer.deserializers
SharableModelDeserializer.deserializable_keyset
SharableModelDeserializer.model_manager_class
SharableModelFilters
SharableModelManager
SharableModelManager.user_share_model
SharableModelManager.SINGLE_CHAR_ABBR
SharableModelManager.__init__()
SharableModelManager.by_user()
SharableModelManager.is_owner()
SharableModelManager.is_accessible()
SharableModelManager.make_importable()
SharableModelManager.make_non_importable()
SharableModelManager.publish()
SharableModelManager.unpublish()
SharableModelManager.list_published()
SharableModelManager.get_share_assocs()
SharableModelManager.share_with()
SharableModelManager.unshare_with()
SharableModelManager.list_shared_with()
SharableModelManager.get_sharing_extra_information()
SharableModelManager.make_members_public()
SharableModelManager.update_current_sharing_with_users()
SharableModelManager.set_slug()
SharableModelManager.is_valid_slug()
SharableModelManager.get_unique_slug()
SharableModelManager.create_unique_slug()
SharableModelSerializer
SharableModelSerializer.SINGLE_CHAR_ABBR
SharableModelSerializer.__init__()
SharableModelSerializer.add_serializers()
SharableModelSerializer.serialize_email_hash()
SharableModelSerializer.serialize_title()
SharableModelSerializer.serialize_username()
SharableModelSerializer.serialize_username_and_slug()
SharableModelSerializer.serialize_users_shared_with()
SharingOptions
ShareWithExtra
SlugBuilder
- galaxy.managers.taggable module
- galaxy.managers.tags module
- galaxy.managers.tool_data module
- galaxy.managers.tools module
DynamicToolManager
DynamicToolManager.model_class
DynamicToolManager.get_tool_by_uuid()
DynamicToolManager.get_tool_by_tool_id()
DynamicToolManager.get_tool_by_id()
DynamicToolManager.create_tool()
DynamicToolManager.list_tools()
DynamicToolManager.deactivate()
DynamicToolManager.foreign_key_name
DynamicToolManager.app
ToolFilterMixin
- galaxy.managers.users module
UserManager
UserManager.foreign_key_name
UserManager.__init__()
UserManager.model_class
UserManager.register()
UserManager.create()
UserManager.delete()
UserManager.undelete()
UserManager.purge()
UserManager.by_id()
UserManager.by_email()
UserManager.by_api_key()
UserManager.check_bootstrap_admin_api_key()
UserManager.is_admin()
UserManager.admins()
UserManager.error_unless_admin()
UserManager.is_anonymous()
UserManager.error_if_anonymous()
UserManager.get_user_by_identity()
UserManager.current_user()
UserManager.user_can_do_run_as()
UserManager.preferences()
UserManager.private_role()
UserManager.sharing_roles()
UserManager.default_permissions()
UserManager.quota()
UserManager.quota_bytes()
UserManager.tags_used()
UserManager.change_password()
UserManager.send_activation_email()
UserManager.send_reset_email()
UserManager.get_reset_token()
UserManager.send_subscription_email()
UserManager.activate()
UserManager.app
UserSerializer
UserSerializer.model_manager_class
UserSerializer.__init__()
UserSerializer.default_view
UserSerializer.add_serializers()
UserSerializer.serialize_disk_usage()
UserSerializer.serialize_disk_usage_for()
UserSerializer.views
UserSerializer.serializable_keyset
UserSerializer.serializers
UserSerializer.app
UserDeserializer
CurrentUserSerializer
AdminUserFilterParser
- galaxy.managers.visualizations module
VisualizationManager
VisualizationSerializer
VisualizationSerializer.model_manager_class
VisualizationSerializer.SINGLE_CHAR_ABBR
VisualizationSerializer.__init__()
VisualizationSerializer.default_view
VisualizationSerializer.add_serializers()
VisualizationSerializer.views
VisualizationSerializer.serializable_keyset
VisualizationSerializer.serializers
VisualizationSerializer.app
VisualizationDeserializer
- galaxy.managers.workflows module
WorkflowsManager
WorkflowsManager.model_class
WorkflowsManager.foreign_key_name
WorkflowsManager.user_share_model
WorkflowsManager.__init__()
WorkflowsManager.app
WorkflowsManager.index_query()
WorkflowsManager.get_stored_workflow()
WorkflowsManager.get_stored_accessible_workflow()
WorkflowsManager.attach_stored_workflow()
WorkflowsManager.get_owned_workflow()
WorkflowsManager.check_security()
WorkflowsManager.get_invocation()
WorkflowsManager.get_invocation_report()
WorkflowsManager.cancel_invocation()
WorkflowsManager.get_invocation_step()
WorkflowsManager.update_invocation_step()
WorkflowsManager.build_invocations_query()
WorkflowsManager.annotation_assoc
WorkflowsManager.rating_assoc
CreatedWorkflow
WorkflowSerializer
WorkflowContentsManager
WorkflowContentsManager.__init__()
WorkflowContentsManager.ensure_raw_description()
WorkflowContentsManager.read_workflow_from_path()
WorkflowContentsManager.normalize_workflow_format()
WorkflowContentsManager.build_workflow_from_raw_description()
WorkflowContentsManager.update_workflow_from_raw_description()
WorkflowContentsManager.workflow_to_dict()
WorkflowContentsManager.store_workflow_artifacts()
WorkflowContentsManager.store_workflow_to_path()
WorkflowContentsManager.get_step_map_over()
WorkflowContentsManager.do_refactor()
WorkflowContentsManager.refactor()
WorkflowContentsManager.get_all_tools()
RefactorRequest
RefactorResponse
WorkflowStateResolutionOptions
WorkflowUpdateOptions
WorkflowCreateOptions
WorkflowCreateOptions.import_tools
WorkflowCreateOptions.publish
WorkflowCreateOptions.importable
WorkflowCreateOptions.install_repository_dependencies
WorkflowCreateOptions.install_resolver_dependencies
WorkflowCreateOptions.install_tool_dependencies
WorkflowCreateOptions.new_tool_panel_section_label
WorkflowCreateOptions.tool_panel_section_id
WorkflowCreateOptions.tool_panel_section_mapping
WorkflowCreateOptions.shed_tool_conf
WorkflowCreateOptions.archive_source
WorkflowCreateOptions.trs_tool_id
WorkflowCreateOptions.trs_version_id
WorkflowCreateOptions.trs_server
WorkflowCreateOptions.trs_url
WorkflowCreateOptions.is_importable
WorkflowCreateOptions.install_options
MissingToolsException
RawWorkflowDescription
Format2ConverterGalaxyInterface
- galaxy.metadata package
get_metadata_compute_strategy()
MetadataCollectionStrategy
PortableDirectoryMetadataGenerator
PortableDirectoryMetadataGenerator.portable
PortableDirectoryMetadataGenerator.write_object_store_conf
PortableDirectoryMetadataGenerator.__init__()
PortableDirectoryMetadataGenerator.setup_external_metadata()
PortableDirectoryMetadataGenerator.load_metadata()
PortableDirectoryMetadataGenerator.external_metadata_set_successfully()
ExtendedDirectoryMetadataGenerator
- Submodules
- galaxy.metadata.set_metadata module
- galaxy.model package
now()
get_uuid()
Base
RepresentById
NoConverterException
ConverterDependencyException
set_datatypes_registry()
HasTags
SerializeFilesHandler
SerializationOptions
Serializable
HasName
UsesCreateAndUpdateTime
WorkerProcess
cached_id()
JobLike
calculate_user_disk_usage_statements()
UserQuotaBasicUsage
UserQuotaUsage
User
User.use_pbkdf2
User.bootstrap_admin_user
User.id
User.create_time
User.update_time
User.last_password_change
User.form_values_id
User.preferred_object_store_id
User.disk_usage
User.activation_token
User.addresses
User.cloudauthz
User.custos_auth
User.default_permissions
User.groups
User.histories
User.active_histories
User.galaxy_sessions
User.quotas
User.quota_source_usages
User.social_auth
User.stored_workflow_menu_entries
User.values
User.api_keys
User.data_manager_histories
User.roles
User.stored_workflows
User.all_notifications
User.non_private_roles
User.preferences
User.dict_collection_visible_keys
User.dict_element_visible_keys
User.__init__()
User.email
User.password
User.external
User.deleted
User.purged
User.active
User.username
User.extra_preferences
User.set_password_cleartext()
User.set_random_password()
User.check_password()
User.system_user_pwent()
User.all_roles()
User.all_roles_exploiting_cache()
User.get_disk_usage()
User.set_disk_usage()
User.total_disk_usage
User.adjust_total_disk_usage()
User.get_oidc_tokens()
User.nice_total_disk_usage
User.calculate_disk_usage_default_source()
User.calculate_and_set_disk_usage()
User.user_template_environment()
User.expand_user_properties()
User.is_active()
User.is_authenticated()
User.attempt_create_private_role()
User.dictify_usage()
User.dictify_usage_for()
User.quota_source_usage_for()
User.current_galaxy_session
User.table
PasswordResetToken
DynamicTool
DynamicTool.id
DynamicTool.create_time
DynamicTool.update_time
DynamicTool.tool_id
DynamicTool.tool_version
DynamicTool.tool_format
DynamicTool.tool_path
DynamicTool.tool_directory
DynamicTool.value
DynamicTool.dict_collection_visible_keys
DynamicTool.dict_element_visible_keys
DynamicTool.__init__()
DynamicTool.active
DynamicTool.hidden
DynamicTool.uuid
DynamicTool.table
BaseJobMetric
JobMetricText
JobMetricNumeric
TaskMetricText
TaskMetricNumeric
IoDicts
Job
Job.id
Job.create_time
Job.update_time
Job.history_id
Job.library_folder_id
Job.tool_id
Job.tool_version
Job.galaxy_version
Job.dynamic_tool_id
Job.info
Job.copied_from_job_id
Job.command_line
Job.job_messages
Job.param_filename
Job.runner_name
Job.job_stdout
Job.job_stderr
Job.tool_stdout
Job.tool_stderr
Job.exit_code
Job.traceback
Job.session_id
Job.user_id
Job.job_runner_name
Job.job_runner_external_id
Job.destination_id
Job.destination_params
Job.object_store_id
Job.params
Job.handler
Job.preferred_object_store_id
Job.object_store_id_overrides
Job.user
Job.galaxy_session
Job.history
Job.library_folder
Job.parameters
Job.input_datasets
Job.input_dataset_collections
Job.input_dataset_collection_elements
Job.output_dataset_collection_instances
Job.output_dataset_collections
Job.post_job_actions
Job.input_library_datasets
Job.output_library_datasets
Job.external_output_metadata
Job.tasks
Job.output_datasets
Job.state_history
Job.text_metrics
Job.numeric_metrics
Job.interactivetool_entry_points
Job.implicit_collection_jobs_association
Job.container
Job.data_manager_association
Job.history_dataset_collection_associations
Job.workflow_invocation_step
Job.any_output_dataset_collection_instances_deleted
Job.any_output_dataset_deleted
Job.dict_collection_visible_keys
Job.dict_element_visible_keys
Job.states
Job.terminal_states
Job.non_ready_states
Job.__init__()
Job.dependencies
Job.state
Job.imported
Job.running
Job.finished
Job.io_dicts()
Job.get_external_output_metadata()
Job.get_session_id()
Job.get_user_id()
Job.get_tool_id()
Job.get_tool_version()
Job.get_command_line()
Job.get_dependencies()
Job.get_param_filename()
Job.get_parameters()
Job.get_copied_from_job_id()
Job.get_input_datasets()
Job.get_output_datasets()
Job.get_input_library_datasets()
Job.get_output_library_datasets()
Job.get_state()
Job.get_info()
Job.get_job_runner_name()
Job.get_job_runner_external_id()
Job.get_post_job_actions()
Job.get_imported()
Job.get_handler()
Job.get_params()
Job.get_user()
Job.get_tasks()
Job.get_id_tag()
Job.set_session_id()
Job.set_user_id()
Job.set_tool_id()
Job.get_user_email()
Job.set_tool_version()
Job.set_command_line()
Job.set_dependencies()
Job.set_param_filename()
Job.set_parameters()
Job.set_copied_from_job_id()
Job.set_input_datasets()
Job.set_output_datasets()
Job.set_input_library_datasets()
Job.set_output_library_datasets()
Job.set_info()
Job.set_runner_name()
Job.get_job()
Job.set_runner_external_id()
Job.set_post_job_actions()
Job.set_imported()
Job.set_handler()
Job.set_params()
Job.add_parameter()
Job.add_input_dataset()
Job.add_output_dataset()
Job.add_input_dataset_collection()
Job.add_input_dataset_collection_element()
Job.add_output_dataset_collection()
Job.add_implicit_output_dataset_collection()
Job.add_input_library_dataset()
Job.add_output_library_dataset()
Job.add_post_job_action()
Job.all_entry_points_configured
Job.set_state()
Job.get_param_values()
Job.raw_param_dict()
Job.check_if_output_datasets_deleted()
Job.mark_stopped()
Job.mark_deleted()
Job.mark_failed()
Job.resume()
Job.requires_shareable_storage()
Job.to_dict()
Job.update_hdca_update_time_for_job()
Job.set_final_state()
Job.get_destination_configuration()
Job.command_version
Job.update_output_states()
Job.remappable()
Job.hide_outputs()
Job.table
Task
Task.id
Task.create_time
Task.execution_time
Task.update_time
Task.command_line
Task.param_filename
Task.runner_name
Task.job_stdout
Task.job_stderr
Task.tool_stdout
Task.tool_stderr
Task.exit_code
Task.job_messages
Task.info
Task.traceback
Task.job_id
Task.task_runner_name
Task.task_runner_external_id
Task.text_metrics
Task.numeric_metrics
Task.states
Task.__init__()
Task.state
Task.working_directory
Task.job
Task.prepare_input_files_cmd
Task.get_param_values()
Task.get_id_tag()
Task.get_command_line()
Task.get_parameters()
Task.get_state()
Task.get_info()
Task.get_working_directory()
Task.get_task_runner_name()
Task.get_task_runner_external_id()
Task.get_job()
Task.get_prepare_input_files_cmd()
Task.get_external_output_metadata()
Task.get_job_runner_name()
Task.get_job_runner_external_id()
Task.get_session_id()
Task.set_id()
Task.set_command_line()
Task.set_parameters()
Task.set_state()
Task.set_info()
Task.set_working_directory()
Task.set_task_runner_name()
Task.set_job_runner_external_id()
Task.set_task_runner_external_id()
Task.set_job()
Task.set_prepare_input_files_cmd()
Task.table
JobParameter
JobToInputDatasetAssociation
JobToInputDatasetAssociation.id
JobToInputDatasetAssociation.job_id
JobToInputDatasetAssociation.dataset_id
JobToInputDatasetAssociation.job
JobToInputDatasetAssociation.__init__()
JobToInputDatasetAssociation.name
JobToInputDatasetAssociation.dataset
JobToInputDatasetAssociation.dataset_version
JobToInputDatasetAssociation.table
JobToOutputDatasetAssociation
JobToOutputDatasetAssociation.id
JobToOutputDatasetAssociation.job_id
JobToOutputDatasetAssociation.dataset_id
JobToOutputDatasetAssociation.job
JobToOutputDatasetAssociation.__init__()
JobToOutputDatasetAssociation.name
JobToOutputDatasetAssociation.dataset
JobToOutputDatasetAssociation.item
JobToOutputDatasetAssociation.table
JobToInputDatasetCollectionAssociation
JobToInputDatasetCollectionAssociation.id
JobToInputDatasetCollectionAssociation.job_id
JobToInputDatasetCollectionAssociation.dataset_collection_id
JobToInputDatasetCollectionAssociation.job
JobToInputDatasetCollectionAssociation.__init__()
JobToInputDatasetCollectionAssociation.name
JobToInputDatasetCollectionAssociation.dataset_collection
JobToInputDatasetCollectionAssociation.table
JobToInputDatasetCollectionElementAssociation
JobToInputDatasetCollectionElementAssociation.id
JobToInputDatasetCollectionElementAssociation.job_id
JobToInputDatasetCollectionElementAssociation.dataset_collection_element_id
JobToInputDatasetCollectionElementAssociation.job
JobToInputDatasetCollectionElementAssociation.__init__()
JobToInputDatasetCollectionElementAssociation.name
JobToInputDatasetCollectionElementAssociation.dataset_collection_element
JobToInputDatasetCollectionElementAssociation.table
JobToOutputDatasetCollectionAssociation
JobToOutputDatasetCollectionAssociation.id
JobToOutputDatasetCollectionAssociation.job_id
JobToOutputDatasetCollectionAssociation.dataset_collection_id
JobToOutputDatasetCollectionAssociation.job
JobToOutputDatasetCollectionAssociation.__init__()
JobToOutputDatasetCollectionAssociation.name
JobToOutputDatasetCollectionAssociation.dataset_collection_instance
JobToOutputDatasetCollectionAssociation.item
JobToOutputDatasetCollectionAssociation.table
JobToImplicitOutputDatasetCollectionAssociation
JobToImplicitOutputDatasetCollectionAssociation.id
JobToImplicitOutputDatasetCollectionAssociation.job_id
JobToImplicitOutputDatasetCollectionAssociation.dataset_collection_id
JobToImplicitOutputDatasetCollectionAssociation.job
JobToImplicitOutputDatasetCollectionAssociation.__init__()
JobToImplicitOutputDatasetCollectionAssociation.name
JobToImplicitOutputDatasetCollectionAssociation.dataset_collection
JobToImplicitOutputDatasetCollectionAssociation.table
JobToInputLibraryDatasetAssociation
JobToInputLibraryDatasetAssociation.id
JobToInputLibraryDatasetAssociation.job_id
JobToInputLibraryDatasetAssociation.ldda_id
JobToInputLibraryDatasetAssociation.job
JobToInputLibraryDatasetAssociation.__init__()
JobToInputLibraryDatasetAssociation.name
JobToInputLibraryDatasetAssociation.dataset
JobToInputLibraryDatasetAssociation.table
JobToOutputLibraryDatasetAssociation
JobToOutputLibraryDatasetAssociation.id
JobToOutputLibraryDatasetAssociation.job_id
JobToOutputLibraryDatasetAssociation.ldda_id
JobToOutputLibraryDatasetAssociation.job
JobToOutputLibraryDatasetAssociation.__init__()
JobToOutputLibraryDatasetAssociation.name
JobToOutputLibraryDatasetAssociation.dataset
JobToOutputLibraryDatasetAssociation.table
JobStateHistory
ImplicitlyCreatedDatasetCollectionInput
ImplicitlyCreatedDatasetCollectionInput.id
ImplicitlyCreatedDatasetCollectionInput.dataset_collection_id
ImplicitlyCreatedDatasetCollectionInput.input_dataset_collection_id
ImplicitlyCreatedDatasetCollectionInput.__init__()
ImplicitlyCreatedDatasetCollectionInput.name
ImplicitlyCreatedDatasetCollectionInput.input_dataset_collection
ImplicitlyCreatedDatasetCollectionInput.table
ImplicitCollectionJobs
ImplicitCollectionJobsJobAssociation
ImplicitCollectionJobsJobAssociation.id
ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id
ImplicitCollectionJobsJobAssociation.job_id
ImplicitCollectionJobsJobAssociation.order_index
ImplicitCollectionJobsJobAssociation.implicit_collection_jobs
ImplicitCollectionJobsJobAssociation.job
ImplicitCollectionJobsJobAssociation.__init__()
ImplicitCollectionJobsJobAssociation.table
PostJobAction
PostJobActionAssociation
JobExternalOutputMetadata
JobExternalOutputMetadata.id
JobExternalOutputMetadata.job_id
JobExternalOutputMetadata.history_dataset_association_id
JobExternalOutputMetadata.library_dataset_dataset_association_id
JobExternalOutputMetadata.is_valid
JobExternalOutputMetadata.filename_in
JobExternalOutputMetadata.filename_out
JobExternalOutputMetadata.filename_results_code
JobExternalOutputMetadata.filename_kwds
JobExternalOutputMetadata.filename_override_metadata
JobExternalOutputMetadata.job_runner_external_pid
JobExternalOutputMetadata.__init__()
JobExternalOutputMetadata.job
JobExternalOutputMetadata.history_dataset_association
JobExternalOutputMetadata.library_dataset_dataset_association
JobExternalOutputMetadata.dataset
JobExternalOutputMetadata.table
FakeDatasetAssociation
JobExportHistoryArchive
JobExportHistoryArchive.id
JobExportHistoryArchive.job_id
JobExportHistoryArchive.history_id
JobExportHistoryArchive.dataset_id
JobExportHistoryArchive.history_attrs_filename
JobExportHistoryArchive.job
JobExportHistoryArchive.dataset
JobExportHistoryArchive.history
JobExportHistoryArchive.ATTRS_FILENAME_HISTORY
JobExportHistoryArchive.__init__()
JobExportHistoryArchive.compressed
JobExportHistoryArchive.fda
JobExportHistoryArchive.temp_directory
JobExportHistoryArchive.up_to_date
JobExportHistoryArchive.ready
JobExportHistoryArchive.preparing
JobExportHistoryArchive.export_name
JobExportHistoryArchive.create_for_history()
JobExportHistoryArchive.to_dict()
JobExportHistoryArchive.table
JobImportHistoryArchive
StoreExportAssociation
JobContainerAssociation
JobContainerAssociation.id
JobContainerAssociation.job_id
JobContainerAssociation.container_type
JobContainerAssociation.container_name
JobContainerAssociation.created_time
JobContainerAssociation.modified_time
JobContainerAssociation.job
JobContainerAssociation.__init__()
JobContainerAssociation.container_info
JobContainerAssociation.table
InteractiveToolEntryPoint
InteractiveToolEntryPoint.id
InteractiveToolEntryPoint.job_id
InteractiveToolEntryPoint.name
InteractiveToolEntryPoint.tool_port
InteractiveToolEntryPoint.host
InteractiveToolEntryPoint.port
InteractiveToolEntryPoint.protocol
InteractiveToolEntryPoint.entry_url
InteractiveToolEntryPoint.created_time
InteractiveToolEntryPoint.modified_time
InteractiveToolEntryPoint.job
InteractiveToolEntryPoint.dict_collection_visible_keys
InteractiveToolEntryPoint.dict_element_visible_keys
InteractiveToolEntryPoint.__init__()
InteractiveToolEntryPoint.requires_domain
InteractiveToolEntryPoint.configured
InteractiveToolEntryPoint.deleted
InteractiveToolEntryPoint.token
InteractiveToolEntryPoint.info
InteractiveToolEntryPoint.active
InteractiveToolEntryPoint.output_datasets_ids
InteractiveToolEntryPoint.table
GenomeIndexToolData
GenomeIndexToolData.id
GenomeIndexToolData.job_id
GenomeIndexToolData.dataset_id
GenomeIndexToolData.fasta_path
GenomeIndexToolData.created_time
GenomeIndexToolData.modified_time
GenomeIndexToolData.indexer
GenomeIndexToolData.user_id
GenomeIndexToolData.job
GenomeIndexToolData.dataset
GenomeIndexToolData.user
GenomeIndexToolData.__init__()
GenomeIndexToolData.table
Group
UserGroupAssociation
Notification
UserNotificationAssociation
UserNotificationAssociation.id
UserNotificationAssociation.user_id
UserNotificationAssociation.notification_id
UserNotificationAssociation.seen_time
UserNotificationAssociation.deleted
UserNotificationAssociation.update_time
UserNotificationAssociation.__init__()
UserNotificationAssociation.user
UserNotificationAssociation.notification
UserNotificationAssociation.table
is_hda()
HistoryAudit
History
History.create_time
History.user_id
History.hid_counter
History.genome_build
History.importable
History.slug
History.preferred_object_store_id
History.archived
History.archive_export_id
History.datasets
History.exports
History.active_datasets
History.dataset_collections
History.active_dataset_collections
History.visible_datasets
History.visible_dataset_collections
History.tags
History.annotations
History.ratings
History.default_permissions
History.users_shared_with
History.galaxy_sessions
History.workflow_invocations
History.jobs
History.update_time
History.users_shared_with_count
History.average_rating
History.users_shared_with_dot_users
History.dict_collection_visible_keys
History.dict_element_visible_keys
History.default_name
History.__init__()
History.id
History.name
History.deleted
History.purged
History.importing
History.published
History.user
History.init_on_load()
History.stage_addition()
History.empty
History.count
History.add_pending_items()
History.add_galaxy_session()
History.add_dataset()
History.add_datasets()
History.add_dataset_collection()
History.copy()
History.get_dataset_by_hid()
History.has_possible_members
History.activatable_datasets
History.to_dict()
History.latest_export
History.unhide_datasets()
History.resume_paused_jobs()
History.paused_jobs
History.disk_size
History.disk_nice_size
History.active_dataset_and_roles_query
History.active_datasets_and_roles
History.active_visible_datasets_and_roles
History.active_visible_dataset_collections
History.active_contents
History.contents_iter()
History.table
UserShareAssociation
HistoryUserShareAssociation
UserRoleAssociation
GroupRoleAssociation
Role
UserQuotaSourceUsage
UserQuotaAssociation
UserQuotaAssociation.id
UserQuotaAssociation.user_id
UserQuotaAssociation.quota_id
UserQuotaAssociation.create_time
UserQuotaAssociation.update_time
UserQuotaAssociation.dict_element_visible_keys
UserQuotaAssociation.__init__()
UserQuotaAssociation.user
UserQuotaAssociation.quota
UserQuotaAssociation.table
GroupQuotaAssociation
GroupQuotaAssociation.id
GroupQuotaAssociation.group_id
GroupQuotaAssociation.quota_id
GroupQuotaAssociation.create_time
GroupQuotaAssociation.update_time
GroupQuotaAssociation.dict_element_visible_keys
GroupQuotaAssociation.__init__()
GroupQuotaAssociation.group
GroupQuotaAssociation.quota
GroupQuotaAssociation.table
Quota
Quota.id
Quota.create_time
Quota.update_time
Quota.deleted
Quota.default
Quota.groups
Quota.users
Quota.dict_collection_visible_keys
Quota.dict_element_visible_keys
Quota.valid_operations
Quota.__init__()
Quota.name
Quota.description
Quota.bytes
Quota.operation
Quota.quota_source_label
Quota.get_amount()
Quota.set_amount()
Quota.amount
Quota.display_amount
Quota.table
DefaultQuotaAssociation
DefaultQuotaAssociation.id
DefaultQuotaAssociation.create_time
DefaultQuotaAssociation.update_time
DefaultQuotaAssociation.quota_id
DefaultQuotaAssociation.dict_element_visible_keys
DefaultQuotaAssociation.types
DefaultQuotaAssociation.__init__()
DefaultQuotaAssociation.type
DefaultQuotaAssociation.quota
DefaultQuotaAssociation.table
DatasetPermissions
LibraryPermissions
LibraryFolderPermissions
LibraryFolderPermissions.id
LibraryFolderPermissions.create_time
LibraryFolderPermissions.update_time
LibraryFolderPermissions.library_folder_id
LibraryFolderPermissions.role_id
LibraryFolderPermissions.__init__()
LibraryFolderPermissions.action
LibraryFolderPermissions.folder
LibraryFolderPermissions.role
LibraryFolderPermissions.table
LibraryDatasetPermissions
LibraryDatasetPermissions.id
LibraryDatasetPermissions.create_time
LibraryDatasetPermissions.update_time
LibraryDatasetPermissions.library_dataset_id
LibraryDatasetPermissions.role_id
LibraryDatasetPermissions.__init__()
LibraryDatasetPermissions.action
LibraryDatasetPermissions.library_dataset
LibraryDatasetPermissions.role
LibraryDatasetPermissions.table
LibraryDatasetDatasetAssociationPermissions
LibraryDatasetDatasetAssociationPermissions.id
LibraryDatasetDatasetAssociationPermissions.create_time
LibraryDatasetDatasetAssociationPermissions.update_time
LibraryDatasetDatasetAssociationPermissions.library_dataset_dataset_association_id
LibraryDatasetDatasetAssociationPermissions.role_id
LibraryDatasetDatasetAssociationPermissions.__init__()
LibraryDatasetDatasetAssociationPermissions.action
LibraryDatasetDatasetAssociationPermissions.library_dataset_dataset_association
LibraryDatasetDatasetAssociationPermissions.role
LibraryDatasetDatasetAssociationPermissions.table
DefaultUserPermissions
DefaultHistoryPermissions
StorableObject
Dataset
Dataset.job_id
Dataset.create_time
Dataset.update_time
Dataset.object_store_id
Dataset.created_from_basename
Dataset.total_size
Dataset.actions
Dataset.job
Dataset.active_history_associations
Dataset.purged_history_associations
Dataset.active_library_associations
Dataset.history_associations
Dataset.library_associations
Dataset.states
Dataset.non_ready_states
Dataset.ready_states
Dataset.valid_input_states
Dataset.no_data_states
Dataset.terminal_states
Dataset.conversion_messages
Dataset.permitted_actions
Dataset.file_path
Dataset.object_store
Dataset.engine
Dataset.__init__()
Dataset.id
Dataset.uuid
Dataset.state
Dataset.deleted
Dataset.purged
Dataset.purgable
Dataset.external_filename
Dataset.file_size
Dataset.sources
Dataset.hashes
Dataset.is_new
Dataset.in_ready_state()
Dataset.shareable
Dataset.ensure_shareable()
Dataset.get_file_name()
Dataset.quota_source_label
Dataset.quota_source_info
Dataset.set_file_name()
Dataset.file_name
Dataset.get_extra_files_path()
Dataset.create_extra_files_path()
Dataset.set_extra_files_path()
Dataset.extra_files_path
Dataset.extra_files_path_exists()
Dataset.store_by
Dataset.extra_files_path_name_from()
Dataset.extra_files_path_name
Dataset.get_size()
Dataset.set_size()
Dataset.get_total_size()
Dataset.set_total_size()
Dataset.has_data()
Dataset.mark_deleted()
Dataset.user_can_purge
Dataset.full_delete()
Dataset.get_access_roles()
Dataset.get_manage_permissions_roles()
Dataset.has_manage_permissions_roles()
Dataset.table
DatasetSource
DatasetSource.id
DatasetSource.dataset_id
DatasetSource.source_uri
DatasetSource.extra_files_path
DatasetSource.transform
DatasetSource.dataset
DatasetSource.hashes
DatasetSource.dict_collection_visible_keys
DatasetSource.dict_element_visible_keys
DatasetSource.copy()
DatasetSource.__init__()
DatasetSource.table
DatasetSourceHash
DatasetHash
datatype_for_extension()
DatasetInstance
DatasetInstance.states
DatasetInstance.conversion_messages
DatasetInstance.conversion_messages.PENDING
DatasetInstance.conversion_messages.NO_DATA
DatasetInstance.conversion_messages.NO_CHROMOSOME
DatasetInstance.conversion_messages.NO_CONVERTER
DatasetInstance.conversion_messages.NO_TOOL
DatasetInstance.conversion_messages.DATA
DatasetInstance.conversion_messages.ERROR
DatasetInstance.conversion_messages.OK
DatasetInstance.permitted_actions
DatasetInstance.purged
DatasetInstance.creating_job_associations
DatasetInstance.validated_states
DatasetInstance.__init__()
DatasetInstance.peek
DatasetInstance.ext
DatasetInstance.has_deferred_data
DatasetInstance.get_dataset_state()
DatasetInstance.raw_set_dataset_state()
DatasetInstance.set_dataset_state()
DatasetInstance.state
DatasetInstance.get_file_name()
DatasetInstance.set_file_name()
DatasetInstance.file_name
DatasetInstance.link_to()
DatasetInstance.extra_files_path
DatasetInstance.extra_files_path_exists()
DatasetInstance.datatype
DatasetInstance.get_metadata()
DatasetInstance.set_metadata_requires_flush
DatasetInstance.set_metadata()
DatasetInstance.metadata
DatasetInstance.has_metadata_files
DatasetInstance.metadata_file_types
DatasetInstance.get_metadata_file_paths_and_extensions()
DatasetInstance.get_dbkey()
DatasetInstance.set_dbkey()
DatasetInstance.dbkey
DatasetInstance.ok_to_edit_metadata()
DatasetInstance.change_datatype()
DatasetInstance.get_size()
DatasetInstance.set_size()
DatasetInstance.get_total_size()
DatasetInstance.set_total_size()
DatasetInstance.has_data()
DatasetInstance.get_created_from_basename()
DatasetInstance.set_created_from_basename()
DatasetInstance.created_from_basename
DatasetInstance.sources
DatasetInstance.hashes
DatasetInstance.get_mime()
DatasetInstance.set_peek()
DatasetInstance.init_meta()
DatasetInstance.set_meta()
DatasetInstance.missing_meta()
DatasetInstance.as_display_type()
DatasetInstance.display_peek()
DatasetInstance.display_name()
DatasetInstance.display_info()
DatasetInstance.get_converted_files_by_type()
DatasetInstance.get_converted_dataset_deps()
DatasetInstance.get_converted_dataset()
DatasetInstance.copy_attributes()
DatasetInstance.get_metadata_dataset()
DatasetInstance.clear_associated_files()
DatasetInstance.get_converter_types()
DatasetInstance.can_convert_to()
DatasetInstance.find_conversion_destination()
DatasetInstance.add_validation_error()
DatasetInstance.extend_validation_errors()
DatasetInstance.mark_deleted()
DatasetInstance.mark_undeleted()
DatasetInstance.mark_unhidden()
DatasetInstance.undeletable()
DatasetInstance.is_ok
DatasetInstance.is_pending
DatasetInstance.source_library_dataset
DatasetInstance.source_dataset_chain
DatasetInstance.creating_job
DatasetInstance.get_display_applications()
DatasetInstance.get_datasources()
DatasetInstance.convert_dataset()
HistoryDatasetAssociation
HistoryDatasetAssociation.__init__()
HistoryDatasetAssociation.hid
HistoryDatasetAssociation.history
HistoryDatasetAssociation.copied_from_history_dataset_association
HistoryDatasetAssociation.copied_from_library_dataset_dataset_association
HistoryDatasetAssociation.user
HistoryDatasetAssociation.copy_from()
HistoryDatasetAssociation.copy()
HistoryDatasetAssociation.copy_tags_to()
HistoryDatasetAssociation.copy_attributes()
HistoryDatasetAssociation.to_library_dataset_dataset_association()
HistoryDatasetAssociation.clear_associated_files()
HistoryDatasetAssociation.get_access_roles()
HistoryDatasetAssociation.purge_usage_from_quota()
HistoryDatasetAssociation.quota_amount()
HistoryDatasetAssociation.to_dict()
HistoryDatasetAssociation.unpause_dependent_jobs()
HistoryDatasetAssociation.history_content_type
HistoryDatasetAssociation.content_type
HistoryDatasetAssociation.type_id
HistoryDatasetAssociation.annotations
HistoryDatasetAssociation.blurb
HistoryDatasetAssociation.copied_from_history_dataset_association_id
HistoryDatasetAssociation.copied_from_library_dataset_dataset_association_id
HistoryDatasetAssociation.copied_to_history_dataset_associations
HistoryDatasetAssociation.copied_to_library_dataset_dataset_associations
HistoryDatasetAssociation.create_time
HistoryDatasetAssociation.creating_job_associations
HistoryDatasetAssociation.dataset
HistoryDatasetAssociation.dataset_id
HistoryDatasetAssociation.deleted
HistoryDatasetAssociation.dependent_jobs
HistoryDatasetAssociation.designation
HistoryDatasetAssociation.extended_metadata
HistoryDatasetAssociation.extended_metadata_id
HistoryDatasetAssociation.extension
HistoryDatasetAssociation.hidden_beneath_collection_instance
HistoryDatasetAssociation.hidden_beneath_collection_instance_id
HistoryDatasetAssociation.history_id
HistoryDatasetAssociation.id
HistoryDatasetAssociation.implicitly_converted_datasets
HistoryDatasetAssociation.implicitly_converted_parent_datasets
HistoryDatasetAssociation.info
HistoryDatasetAssociation.metadata_deferred
HistoryDatasetAssociation.name
HistoryDatasetAssociation.parent_id
HistoryDatasetAssociation.purged
HistoryDatasetAssociation.ratings
HistoryDatasetAssociation.table
HistoryDatasetAssociation.tags
HistoryDatasetAssociation.tool_version
HistoryDatasetAssociation.update_time
HistoryDatasetAssociation.validated_state
HistoryDatasetAssociation.validated_state_message
HistoryDatasetAssociation.version
HistoryDatasetAssociation.visible
HistoryDatasetAssociationHistory
HistoryDatasetAssociationHistory.id
HistoryDatasetAssociationHistory.__init__()
HistoryDatasetAssociationHistory.history_dataset_association_id
HistoryDatasetAssociationHistory.name
HistoryDatasetAssociationHistory.update_time
HistoryDatasetAssociationHistory.version
HistoryDatasetAssociationHistory.extension
HistoryDatasetAssociationHistory.extended_metadata_id
HistoryDatasetAssociationHistory.table
HistoryDatasetAssociationDisplayAtAuthorization
HistoryDatasetAssociationDisplayAtAuthorization.id
HistoryDatasetAssociationDisplayAtAuthorization.create_time
HistoryDatasetAssociationDisplayAtAuthorization.update_time
HistoryDatasetAssociationDisplayAtAuthorization.history_dataset_association_id
HistoryDatasetAssociationDisplayAtAuthorization.user_id
HistoryDatasetAssociationDisplayAtAuthorization.__init__()
HistoryDatasetAssociationDisplayAtAuthorization.history_dataset_association
HistoryDatasetAssociationDisplayAtAuthorization.user
HistoryDatasetAssociationDisplayAtAuthorization.site
HistoryDatasetAssociationDisplayAtAuthorization.table
HistoryDatasetAssociationSubset
HistoryDatasetAssociationSubset.id
HistoryDatasetAssociationSubset.history_dataset_association_id
HistoryDatasetAssociationSubset.history_dataset_association_subset_id
HistoryDatasetAssociationSubset.__init__()
HistoryDatasetAssociationSubset.hda
HistoryDatasetAssociationSubset.subset
HistoryDatasetAssociationSubset.location
HistoryDatasetAssociationSubset.table
Library
Library.id
Library.root_folder_id
Library.create_time
Library.update_time
Library.deleted
Library.purged
Library.actions
Library.permitted_actions
Library.dict_collection_visible_keys
Library.dict_element_visible_keys
Library.__init__()
Library.name
Library.description
Library.synopsis
Library.root_folder
Library.to_dict()
Library.get_active_folders()
Library.get_access_roles()
Library.table
LibraryFolder
LibraryFolder.id
LibraryFolder.parent_id
LibraryFolder.create_time
LibraryFolder.update_time
LibraryFolder.deleted
LibraryFolder.purged
LibraryFolder.folders
LibraryFolder.parent
LibraryFolder.active_folders
LibraryFolder.datasets
LibraryFolder.active_datasets
LibraryFolder.library_root
LibraryFolder.actions
LibraryFolder.dict_element_visible_keys
LibraryFolder.__init__()
LibraryFolder.name
LibraryFolder.description
LibraryFolder.item_count
LibraryFolder.order_id
LibraryFolder.genome_build
LibraryFolder.add_library_dataset()
LibraryFolder.add_folder()
LibraryFolder.activatable_library_datasets
LibraryFolder.to_dict()
LibraryFolder.library_path
LibraryFolder.parent_library
LibraryFolder.table
LibraryDataset
LibraryDataset.id
LibraryDataset.library_dataset_dataset_association_id
LibraryDataset.folder_id
LibraryDataset.order_id
LibraryDataset.create_time
LibraryDataset.update_time
LibraryDataset.deleted
LibraryDataset.purged
LibraryDataset.folder
LibraryDataset.library_dataset_dataset_association
LibraryDataset.expired_datasets
LibraryDataset.actions
LibraryDataset.upload_options
LibraryDataset.get_info()
LibraryDataset.set_info()
LibraryDataset.info
LibraryDataset.get_name()
LibraryDataset.set_name()
LibraryDataset.name
LibraryDataset.display_name()
LibraryDataset.to_dict()
LibraryDataset.__init__()
LibraryDataset.table
LibraryDatasetDatasetAssociation
LibraryDatasetDatasetAssociation.__init__()
LibraryDatasetDatasetAssociation.copied_from_history_dataset_association_id
LibraryDatasetDatasetAssociation.copied_from_library_dataset_dataset_association_id
LibraryDatasetDatasetAssociation.library_dataset
LibraryDatasetDatasetAssociation.user
LibraryDatasetDatasetAssociation.to_history_dataset_association()
LibraryDatasetDatasetAssociation.copy()
LibraryDatasetDatasetAssociation.clear_associated_files()
LibraryDatasetDatasetAssociation.get_access_roles()
LibraryDatasetDatasetAssociation.get_manage_permissions_roles()
LibraryDatasetDatasetAssociation.has_manage_permissions_roles()
LibraryDatasetDatasetAssociation.to_dict()
LibraryDatasetDatasetAssociation.update_parent_folder_update_times()
LibraryDatasetDatasetAssociation.actions
LibraryDatasetDatasetAssociation.blurb
LibraryDatasetDatasetAssociation.copied_from_history_dataset_association
LibraryDatasetDatasetAssociation.copied_from_library_dataset_dataset_association
LibraryDatasetDatasetAssociation.copied_to_history_dataset_associations
LibraryDatasetDatasetAssociation.copied_to_library_dataset_dataset_associations
LibraryDatasetDatasetAssociation.create_time
LibraryDatasetDatasetAssociation.creating_job_associations
LibraryDatasetDatasetAssociation.dataset
LibraryDatasetDatasetAssociation.dataset_id
LibraryDatasetDatasetAssociation.deleted
LibraryDatasetDatasetAssociation.dependent_jobs
LibraryDatasetDatasetAssociation.designation
LibraryDatasetDatasetAssociation.extended_metadata
LibraryDatasetDatasetAssociation.extended_metadata_id
LibraryDatasetDatasetAssociation.extension
LibraryDatasetDatasetAssociation.id
LibraryDatasetDatasetAssociation.implicitly_converted_datasets
LibraryDatasetDatasetAssociation.implicitly_converted_parent_datasets
LibraryDatasetDatasetAssociation.info
LibraryDatasetDatasetAssociation.library_dataset_id
LibraryDatasetDatasetAssociation.message
LibraryDatasetDatasetAssociation.metadata_deferred
LibraryDatasetDatasetAssociation.name
LibraryDatasetDatasetAssociation.parent_id
LibraryDatasetDatasetAssociation.table
LibraryDatasetDatasetAssociation.tags
LibraryDatasetDatasetAssociation.tool_version
LibraryDatasetDatasetAssociation.update_time
LibraryDatasetDatasetAssociation.user_id
LibraryDatasetDatasetAssociation.validated_state
LibraryDatasetDatasetAssociation.validated_state_message
LibraryDatasetDatasetAssociation.visible
LibraryDatasetDatasetAssociation.purged
ExtendedMetadata
ExtendedMetadataIndex
LibraryInfoAssociation
LibraryInfoAssociation.id
LibraryInfoAssociation.library_id
LibraryInfoAssociation.form_definition_id
LibraryInfoAssociation.form_values_id
LibraryInfoAssociation.deleted
LibraryInfoAssociation.__init__()
LibraryInfoAssociation.library
LibraryInfoAssociation.template
LibraryInfoAssociation.info
LibraryInfoAssociation.inheritable
LibraryInfoAssociation.table
LibraryFolderInfoAssociation
LibraryFolderInfoAssociation.id
LibraryFolderInfoAssociation.library_folder_id
LibraryFolderInfoAssociation.form_definition_id
LibraryFolderInfoAssociation.form_values_id
LibraryFolderInfoAssociation.deleted
LibraryFolderInfoAssociation.__init__()
LibraryFolderInfoAssociation.folder
LibraryFolderInfoAssociation.template
LibraryFolderInfoAssociation.info
LibraryFolderInfoAssociation.inheritable
LibraryFolderInfoAssociation.table
LibraryDatasetDatasetInfoAssociation
LibraryDatasetDatasetInfoAssociation.id
LibraryDatasetDatasetInfoAssociation.library_dataset_dataset_association_id
LibraryDatasetDatasetInfoAssociation.form_definition_id
LibraryDatasetDatasetInfoAssociation.form_values_id
LibraryDatasetDatasetInfoAssociation.deleted
LibraryDatasetDatasetInfoAssociation.__init__()
LibraryDatasetDatasetInfoAssociation.library_dataset_dataset_association
LibraryDatasetDatasetInfoAssociation.template
LibraryDatasetDatasetInfoAssociation.info
LibraryDatasetDatasetInfoAssociation.inheritable
LibraryDatasetDatasetInfoAssociation.table
ImplicitlyConvertedDatasetAssociation
ImplicitlyConvertedDatasetAssociation.create_time
ImplicitlyConvertedDatasetAssociation.update_time
ImplicitlyConvertedDatasetAssociation.hda_id
ImplicitlyConvertedDatasetAssociation.ldda_id
ImplicitlyConvertedDatasetAssociation.hda_parent_id
ImplicitlyConvertedDatasetAssociation.ldda_parent_id
ImplicitlyConvertedDatasetAssociation.__init__()
ImplicitlyConvertedDatasetAssociation.id
ImplicitlyConvertedDatasetAssociation.dataset
ImplicitlyConvertedDatasetAssociation.dataset_ldda
ImplicitlyConvertedDatasetAssociation.parent_hda
ImplicitlyConvertedDatasetAssociation.parent_ldda
ImplicitlyConvertedDatasetAssociation.type
ImplicitlyConvertedDatasetAssociation.deleted
ImplicitlyConvertedDatasetAssociation.metadata_safe
ImplicitlyConvertedDatasetAssociation.clear()
ImplicitlyConvertedDatasetAssociation.table
InnerCollectionFilter
DatasetCollection
DatasetCollection.populated_state_message
DatasetCollection.create_time
DatasetCollection.update_time
DatasetCollection.elements
DatasetCollection.dict_collection_visible_keys
DatasetCollection.dict_element_visible_keys
DatasetCollection.populated_states
DatasetCollection.__init__()
DatasetCollection.id
DatasetCollection.collection_type
DatasetCollection.populated_state
DatasetCollection.element_count
DatasetCollection.dataset_states_and_extensions_summary
DatasetCollection.has_deferred_data
DatasetCollection.populated_optimized
DatasetCollection.populated
DatasetCollection.dataset_action_tuples
DatasetCollection.element_identifiers_extensions_and_paths
DatasetCollection.element_identifiers_extensions_paths_and_metadata_files
DatasetCollection.waiting_for_elements
DatasetCollection.mark_as_populated()
DatasetCollection.handle_population_failed()
DatasetCollection.finalize()
DatasetCollection.dataset_instances
DatasetCollection.dataset_elements
DatasetCollection.dataset_elements_and_identifiers()
DatasetCollection.first_dataset_element
DatasetCollection.state
DatasetCollection.validate()
DatasetCollection.copy()
DatasetCollection.replace_failed_elements()
DatasetCollection.set_from_dict()
DatasetCollection.has_subcollections
DatasetCollection.table
DatasetCollectionInstance
HistoryDatasetCollectionAssociation
HistoryDatasetCollectionAssociation.id
HistoryDatasetCollectionAssociation.collection_id
HistoryDatasetCollectionAssociation.history_id
HistoryDatasetCollectionAssociation.name
HistoryDatasetCollectionAssociation.hid
HistoryDatasetCollectionAssociation.copied_from_history_dataset_collection_association_id
HistoryDatasetCollectionAssociation.implicit_output_name
HistoryDatasetCollectionAssociation.job_id
HistoryDatasetCollectionAssociation.implicit_collection_jobs_id
HistoryDatasetCollectionAssociation.create_time
HistoryDatasetCollectionAssociation.update_time
HistoryDatasetCollectionAssociation.collection
HistoryDatasetCollectionAssociation.history
HistoryDatasetCollectionAssociation.copied_from_history_dataset_collection_association
HistoryDatasetCollectionAssociation.copied_to_history_dataset_collection_association
HistoryDatasetCollectionAssociation.implicit_collection_jobs
HistoryDatasetCollectionAssociation.job
HistoryDatasetCollectionAssociation.tags
HistoryDatasetCollectionAssociation.annotations
HistoryDatasetCollectionAssociation.ratings
HistoryDatasetCollectionAssociation.creating_job_associations
HistoryDatasetCollectionAssociation.dict_dbkeysandextensions_visible_keys
HistoryDatasetCollectionAssociation.editable_keys
HistoryDatasetCollectionAssociation.__init__()
HistoryDatasetCollectionAssociation.deleted
HistoryDatasetCollectionAssociation.visible
HistoryDatasetCollectionAssociation.implicit_input_collections
HistoryDatasetCollectionAssociation.history_content_type
HistoryDatasetCollectionAssociation.content_type
HistoryDatasetCollectionAssociation.type_id
HistoryDatasetCollectionAssociation.job_source_type
HistoryDatasetCollectionAssociation.job_state_summary
HistoryDatasetCollectionAssociation.job_state_summary_dict
HistoryDatasetCollectionAssociation.dataset_dbkeys_and_extensions_summary
HistoryDatasetCollectionAssociation.job_source_id
HistoryDatasetCollectionAssociation.touch()
HistoryDatasetCollectionAssociation.to_hda_representative()
HistoryDatasetCollectionAssociation.to_dict()
HistoryDatasetCollectionAssociation.add_implicit_input_collection()
HistoryDatasetCollectionAssociation.find_implicit_input_collection()
HistoryDatasetCollectionAssociation.copy()
HistoryDatasetCollectionAssociation.waiting_for_elements
HistoryDatasetCollectionAssociation.contains_collection()
HistoryDatasetCollectionAssociation.table
LibraryDatasetCollectionAssociation
LibraryDatasetCollectionAssociation.id
LibraryDatasetCollectionAssociation.collection_id
LibraryDatasetCollectionAssociation.folder_id
LibraryDatasetCollectionAssociation.name
LibraryDatasetCollectionAssociation.collection
LibraryDatasetCollectionAssociation.folder
LibraryDatasetCollectionAssociation.tags
LibraryDatasetCollectionAssociation.annotations
LibraryDatasetCollectionAssociation.ratings
LibraryDatasetCollectionAssociation.editable_keys
LibraryDatasetCollectionAssociation.__init__()
LibraryDatasetCollectionAssociation.deleted
LibraryDatasetCollectionAssociation.to_dict()
LibraryDatasetCollectionAssociation.table
DatasetCollectionElement
DatasetCollectionElement.dataset_collection_id
DatasetCollectionElement.hda_id
DatasetCollectionElement.ldda_id
DatasetCollectionElement.child_collection_id
DatasetCollectionElement.dict_collection_visible_keys
DatasetCollectionElement.dict_element_visible_keys
DatasetCollectionElement.UNINITIALIZED_ELEMENT
DatasetCollectionElement.__init__()
DatasetCollectionElement.hda
DatasetCollectionElement.ldda
DatasetCollectionElement.child_collection
DatasetCollectionElement.id
DatasetCollectionElement.collection
DatasetCollectionElement.element_index
DatasetCollectionElement.element_identifier
DatasetCollectionElement.element_type
DatasetCollectionElement.is_collection
DatasetCollectionElement.element_object
DatasetCollectionElement.dataset_instance
DatasetCollectionElement.dataset
DatasetCollectionElement.first_dataset_instance()
DatasetCollectionElement.dataset_instances
DatasetCollectionElement.has_deferred_data
DatasetCollectionElement.copy_to_collection()
DatasetCollectionElement.table
Event
GalaxySession
GalaxySession.id
GalaxySession.create_time
GalaxySession.update_time
GalaxySession.user_id
GalaxySession.remote_host
GalaxySession.remote_addr
GalaxySession.referer
GalaxySession.current_history_id
GalaxySession.session_key
GalaxySession.prev_session_id
GalaxySession.disk_usage
GalaxySession.current_history
GalaxySession.histories
GalaxySession.user
GalaxySession.__init__()
GalaxySession.is_valid
GalaxySession.last_action
GalaxySession.add_history()
GalaxySession.get_disk_usage()
GalaxySession.set_disk_usage()
GalaxySession.total_disk_usage
GalaxySession.table
GalaxySessionToHistoryAssociation
GalaxySessionToHistoryAssociation.id
GalaxySessionToHistoryAssociation.create_time
GalaxySessionToHistoryAssociation.session_id
GalaxySessionToHistoryAssociation.history_id
GalaxySessionToHistoryAssociation.__init__()
GalaxySessionToHistoryAssociation.galaxy_session
GalaxySessionToHistoryAssociation.history
GalaxySessionToHistoryAssociation.table
UCI
StoredWorkflow
StoredWorkflow.id
StoredWorkflow.user_id
StoredWorkflow.latest_workflow_id
StoredWorkflow.deleted
StoredWorkflow.importable
StoredWorkflow.from_path
StoredWorkflow.tags
StoredWorkflow.owner_tags
StoredWorkflow.annotations
StoredWorkflow.ratings
StoredWorkflow.users_shared_with
StoredWorkflow.average_rating
StoredWorkflow.users_shared_with_dot_users
StoredWorkflow.dict_collection_visible_keys
StoredWorkflow.dict_element_visible_keys
StoredWorkflow.__init__()
StoredWorkflow.user
StoredWorkflow.name
StoredWorkflow.slug
StoredWorkflow.create_time
StoredWorkflow.update_time
StoredWorkflow.published
StoredWorkflow.latest_workflow
StoredWorkflow.workflows
StoredWorkflow.hidden
StoredWorkflow.get_internal_version()
StoredWorkflow.show_in_tool_panel()
StoredWorkflow.copy_tags_from()
StoredWorkflow.to_dict()
StoredWorkflow.table
Workflow
Workflow.id
Workflow.create_time
Workflow.update_time
Workflow.stored_workflow_id
Workflow.parent_workflow_id
Workflow.name
Workflow.has_cycles
Workflow.has_errors
Workflow.reports_config
Workflow.creator_metadata
Workflow.license
Workflow.source_metadata
Workflow.steps
Workflow.parent_workflow_steps
Workflow.stored_workflow
Workflow.step_count
Workflow.dict_collection_visible_keys
Workflow.dict_element_visible_keys
Workflow.input_step_types
Workflow.__init__()
Workflow.uuid
Workflow.has_outputs_defined()
Workflow.to_dict()
Workflow.steps_by_id
Workflow.step_by_index()
Workflow.step_by_label()
Workflow.input_steps
Workflow.workflow_outputs
Workflow.workflow_output_for()
Workflow.workflow_output_labels
Workflow.top_level_workflow
Workflow.top_level_stored_workflow
Workflow.copy()
Workflow.log_str()
Workflow.table
WorkflowStep
WorkflowStep.id
WorkflowStep.create_time
WorkflowStep.update_time
WorkflowStep.workflow_id
WorkflowStep.subworkflow_id
WorkflowStep.dynamic_tool_id
WorkflowStep.type
WorkflowStep.tool_id
WorkflowStep.tool_version
WorkflowStep.tool_inputs
WorkflowStep.tool_errors
WorkflowStep.position
WorkflowStep.config
WorkflowStep.order_index
WorkflowStep.when_expression
WorkflowStep.label
WorkflowStep.temp_input_connections
WorkflowStep.subworkflow
WorkflowStep.dynamic_tool
WorkflowStep.tags
WorkflowStep.annotations
WorkflowStep.post_job_actions
WorkflowStep.inputs
WorkflowStep.workflow_outputs
WorkflowStep.output_connections
WorkflowStep.workflow
WorkflowStep.module
WorkflowStep.state
WorkflowStep.upgrade_messages
WorkflowStep.STEP_TYPE_TO_INPUT_TYPE
WorkflowStep.DEFAULT_POSITION
WorkflowStep.__init__()
WorkflowStep.uuid
WorkflowStep.init_on_load()
WorkflowStep.tool_uuid
WorkflowStep.input_type
WorkflowStep.input_default_value
WorkflowStep.input_optional
WorkflowStep.setup_inputs_by_name()
WorkflowStep.inputs_by_name
WorkflowStep.get_input()
WorkflowStep.get_or_add_input()
WorkflowStep.add_connection()
WorkflowStep.input_connections
WorkflowStep.unique_workflow_outputs
WorkflowStep.content_id
WorkflowStep.input_connections_by_name
WorkflowStep.setup_input_connections_by_name()
WorkflowStep.create_or_update_workflow_output()
WorkflowStep.workflow_output_for()
WorkflowStep.copy_to()
WorkflowStep.log_str()
WorkflowStep.clear_module_extras()
WorkflowStep.table
WorkflowStepInput
WorkflowStepInput.id
WorkflowStepInput.workflow_step_id
WorkflowStepInput.name
WorkflowStepInput.merge_type
WorkflowStepInput.scatter_type
WorkflowStepInput.value_from
WorkflowStepInput.value_from_type
WorkflowStepInput.default_value
WorkflowStepInput.runtime_value
WorkflowStepInput.connections
WorkflowStepInput.__init__()
WorkflowStepInput.workflow_step
WorkflowStepInput.default_value_set
WorkflowStepInput.copy()
WorkflowStepInput.table
WorkflowStepConnection
WorkflowStepConnection.id
WorkflowStepConnection.output_step_id
WorkflowStepConnection.input_step_input_id
WorkflowStepConnection.output_name
WorkflowStepConnection.input_subworkflow_step_id
WorkflowStepConnection.input_step_input
WorkflowStepConnection.input_subworkflow_step
WorkflowStepConnection.output_step
WorkflowStepConnection.NON_DATA_CONNECTION
WorkflowStepConnection.non_data_connection
WorkflowStepConnection.input_name
WorkflowStepConnection.input_step
WorkflowStepConnection.input_step_id
WorkflowStepConnection.copy()
WorkflowStepConnection.__init__()
WorkflowStepConnection.table
WorkflowOutput
StoredWorkflowUserShareAssociation
StoredWorkflowUserShareAssociation.id
StoredWorkflowUserShareAssociation.stored_workflow_id
StoredWorkflowUserShareAssociation.user_id
StoredWorkflowUserShareAssociation.user
StoredWorkflowUserShareAssociation.stored_workflow
StoredWorkflowUserShareAssociation.__init__()
StoredWorkflowUserShareAssociation.table
StoredWorkflowMenuEntry
WorkflowInvocation
WorkflowInvocation.id
WorkflowInvocation.create_time
WorkflowInvocation.update_time
WorkflowInvocation.workflow_id
WorkflowInvocation.state
WorkflowInvocation.scheduler
WorkflowInvocation.handler
WorkflowInvocation.uuid
WorkflowInvocation.history_id
WorkflowInvocation.history
WorkflowInvocation.input_parameters
WorkflowInvocation.step_states
WorkflowInvocation.input_step_parameters
WorkflowInvocation.input_datasets
WorkflowInvocation.input_dataset_collections
WorkflowInvocation.subworkflow_invocations
WorkflowInvocation.steps
WorkflowInvocation.workflow
WorkflowInvocation.output_dataset_collections
WorkflowInvocation.output_datasets
WorkflowInvocation.output_values
WorkflowInvocation.messages
WorkflowInvocation.dict_collection_visible_keys
WorkflowInvocation.dict_element_visible_keys
WorkflowInvocation.states
WorkflowInvocation.non_terminal_states
WorkflowInvocation.create_subworkflow_invocation_for_step()
WorkflowInvocation.attach_subworkflow_invocation_for_step()
WorkflowInvocation.get_subworkflow_invocation_for_step()
WorkflowInvocation.get_subworkflow_invocation_association_for_step()
WorkflowInvocation.active
WorkflowInvocation.cancel()
WorkflowInvocation.fail()
WorkflowInvocation.step_states_by_step_id()
WorkflowInvocation.step_invocations_by_step_id()
WorkflowInvocation.step_invocation_for_step_id()
WorkflowInvocation.step_invocation_for_label()
WorkflowInvocation.poll_unhandled_workflow_ids()
WorkflowInvocation.poll_active_workflow_ids()
WorkflowInvocation.add_output()
WorkflowInvocation.get_output_object()
WorkflowInvocation.get_input_object()
WorkflowInvocation.output_associations
WorkflowInvocation.input_associations
WorkflowInvocation.to_dict()
WorkflowInvocation.add_input()
WorkflowInvocation.add_message()
WorkflowInvocation.resource_parameters
WorkflowInvocation.has_input_for_step()
WorkflowInvocation.set_handler()
WorkflowInvocation.log_str()
WorkflowInvocation.__init__()
WorkflowInvocation.table
WorkflowInvocationToSubworkflowInvocationAssociation
WorkflowInvocationToSubworkflowInvocationAssociation.id
WorkflowInvocationToSubworkflowInvocationAssociation.workflow_invocation_id
WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id
WorkflowInvocationToSubworkflowInvocationAssociation.workflow_step_id
WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation
WorkflowInvocationToSubworkflowInvocationAssociation.workflow_step
WorkflowInvocationToSubworkflowInvocationAssociation.parent_workflow_invocation
WorkflowInvocationToSubworkflowInvocationAssociation.dict_collection_visible_keys
WorkflowInvocationToSubworkflowInvocationAssociation.dict_element_visible_keys
WorkflowInvocationToSubworkflowInvocationAssociation.__init__()
WorkflowInvocationToSubworkflowInvocationAssociation.table
WorkflowInvocationMessage
WorkflowInvocationMessage.id
WorkflowInvocationMessage.workflow_invocation_id
WorkflowInvocationMessage.reason
WorkflowInvocationMessage.details
WorkflowInvocationMessage.output_name
WorkflowInvocationMessage.workflow_step_id
WorkflowInvocationMessage.dependent_workflow_step_id
WorkflowInvocationMessage.job_id
WorkflowInvocationMessage.hda_id
WorkflowInvocationMessage.hdca_id
WorkflowInvocationMessage.workflow_invocation
WorkflowInvocationMessage.workflow_step
WorkflowInvocationMessage.dependent_workflow_step
WorkflowInvocationMessage.workflow_step_index
WorkflowInvocationMessage.dependent_workflow_step_index
WorkflowInvocationMessage.history_id
WorkflowInvocationMessage.__init__()
WorkflowInvocationMessage.table
EffectiveOutput
WorkflowInvocationStepObjectStores
WorkflowInvocationStepObjectStores.preferred_object_store_id
WorkflowInvocationStepObjectStores.preferred_outputs_object_store_id
WorkflowInvocationStepObjectStores.preferred_intermediate_object_store_id
WorkflowInvocationStepObjectStores.step_effective_outputs
WorkflowInvocationStepObjectStores.is_output_name_an_effective_output()
WorkflowInvocationStepObjectStores.is_split_configuration
WorkflowInvocationStep
WorkflowInvocationStep.id
WorkflowInvocationStep.create_time
WorkflowInvocationStep.update_time
WorkflowInvocationStep.workflow_invocation_id
WorkflowInvocationStep.workflow_step_id
WorkflowInvocationStep.state
WorkflowInvocationStep.job_id
WorkflowInvocationStep.implicit_collection_jobs_id
WorkflowInvocationStep.action
WorkflowInvocationStep.workflow_step
WorkflowInvocationStep.job
WorkflowInvocationStep.implicit_collection_jobs
WorkflowInvocationStep.output_dataset_collections
WorkflowInvocationStep.output_datasets
WorkflowInvocationStep.workflow_invocation
WorkflowInvocationStep.output_value
WorkflowInvocationStep.order_index
WorkflowInvocationStep.subworkflow_invocation_id
WorkflowInvocationStep.dict_collection_visible_keys
WorkflowInvocationStep.dict_element_visible_keys
WorkflowInvocationStep.states
WorkflowInvocationStep.is_new
WorkflowInvocationStep.add_output()
WorkflowInvocationStep.jobs
WorkflowInvocationStep.preferred_object_stores
WorkflowInvocationStep.to_dict()
WorkflowInvocationStep.__init__()
WorkflowInvocationStep.table
WorkflowRequestInputParameter
WorkflowRequestInputParameter.id
WorkflowRequestInputParameter.workflow_invocation_id
WorkflowRequestInputParameter.name
WorkflowRequestInputParameter.value
WorkflowRequestInputParameter.type
WorkflowRequestInputParameter.workflow_invocation
WorkflowRequestInputParameter.dict_collection_visible_keys
WorkflowRequestInputParameter.types
WorkflowRequestInputParameter.__init__()
WorkflowRequestInputParameter.table
WorkflowRequestStepState
WorkflowRequestStepState.id
WorkflowRequestStepState.workflow_invocation_id
WorkflowRequestStepState.workflow_step_id
WorkflowRequestStepState.value
WorkflowRequestStepState.workflow_step
WorkflowRequestStepState.workflow_invocation
WorkflowRequestStepState.dict_collection_visible_keys
WorkflowRequestStepState.__init__()
WorkflowRequestStepState.table
WorkflowRequestToInputDatasetAssociation
WorkflowRequestToInputDatasetAssociation.id
WorkflowRequestToInputDatasetAssociation.name
WorkflowRequestToInputDatasetAssociation.workflow_invocation_id
WorkflowRequestToInputDatasetAssociation.workflow_step_id
WorkflowRequestToInputDatasetAssociation.dataset_id
WorkflowRequestToInputDatasetAssociation.workflow_step
WorkflowRequestToInputDatasetAssociation.dataset
WorkflowRequestToInputDatasetAssociation.workflow_invocation
WorkflowRequestToInputDatasetAssociation.history_content_type
WorkflowRequestToInputDatasetAssociation.dict_collection_visible_keys
WorkflowRequestToInputDatasetAssociation.__init__()
WorkflowRequestToInputDatasetAssociation.table
WorkflowRequestToInputDatasetCollectionAssociation
WorkflowRequestToInputDatasetCollectionAssociation.id
WorkflowRequestToInputDatasetCollectionAssociation.name
WorkflowRequestToInputDatasetCollectionAssociation.workflow_invocation_id
WorkflowRequestToInputDatasetCollectionAssociation.workflow_step_id
WorkflowRequestToInputDatasetCollectionAssociation.dataset_collection_id
WorkflowRequestToInputDatasetCollectionAssociation.workflow_step
WorkflowRequestToInputDatasetCollectionAssociation.dataset_collection
WorkflowRequestToInputDatasetCollectionAssociation.workflow_invocation
WorkflowRequestToInputDatasetCollectionAssociation.history_content_type
WorkflowRequestToInputDatasetCollectionAssociation.dict_collection_visible_keys
WorkflowRequestToInputDatasetCollectionAssociation.__init__()
WorkflowRequestToInputDatasetCollectionAssociation.table
WorkflowRequestInputStepParameter
WorkflowRequestInputStepParameter.id
WorkflowRequestInputStepParameter.workflow_invocation_id
WorkflowRequestInputStepParameter.workflow_step_id
WorkflowRequestInputStepParameter.parameter_value
WorkflowRequestInputStepParameter.workflow_step
WorkflowRequestInputStepParameter.workflow_invocation
WorkflowRequestInputStepParameter.dict_collection_visible_keys
WorkflowRequestInputStepParameter.__init__()
WorkflowRequestInputStepParameter.table
WorkflowInvocationOutputDatasetAssociation
WorkflowInvocationOutputDatasetAssociation.id
WorkflowInvocationOutputDatasetAssociation.workflow_invocation_id
WorkflowInvocationOutputDatasetAssociation.workflow_step_id
WorkflowInvocationOutputDatasetAssociation.dataset_id
WorkflowInvocationOutputDatasetAssociation.workflow_output_id
WorkflowInvocationOutputDatasetAssociation.workflow_invocation
WorkflowInvocationOutputDatasetAssociation.workflow_step
WorkflowInvocationOutputDatasetAssociation.dataset
WorkflowInvocationOutputDatasetAssociation.workflow_output
WorkflowInvocationOutputDatasetAssociation.history_content_type
WorkflowInvocationOutputDatasetAssociation.dict_collection_visible_keys
WorkflowInvocationOutputDatasetAssociation.__init__()
WorkflowInvocationOutputDatasetAssociation.table
WorkflowInvocationOutputDatasetCollectionAssociation
WorkflowInvocationOutputDatasetCollectionAssociation.id
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_invocation_id
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_step_id
WorkflowInvocationOutputDatasetCollectionAssociation.dataset_collection_id
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_output_id
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_invocation
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_step
WorkflowInvocationOutputDatasetCollectionAssociation.dataset_collection
WorkflowInvocationOutputDatasetCollectionAssociation.workflow_output
WorkflowInvocationOutputDatasetCollectionAssociation.history_content_type
WorkflowInvocationOutputDatasetCollectionAssociation.dict_collection_visible_keys
WorkflowInvocationOutputDatasetCollectionAssociation.__init__()
WorkflowInvocationOutputDatasetCollectionAssociation.table
WorkflowInvocationOutputValue
WorkflowInvocationOutputValue.id
WorkflowInvocationOutputValue.workflow_invocation_id
WorkflowInvocationOutputValue.workflow_step_id
WorkflowInvocationOutputValue.workflow_output_id
WorkflowInvocationOutputValue.value
WorkflowInvocationOutputValue.workflow_invocation
WorkflowInvocationOutputValue.workflow_invocation_step
WorkflowInvocationOutputValue.workflow_step
WorkflowInvocationOutputValue.workflow_output
WorkflowInvocationOutputValue.dict_collection_visible_keys
WorkflowInvocationOutputValue.__init__()
WorkflowInvocationOutputValue.table
WorkflowInvocationStepOutputDatasetAssociation
WorkflowInvocationStepOutputDatasetAssociation.id
WorkflowInvocationStepOutputDatasetAssociation.workflow_invocation_step_id
WorkflowInvocationStepOutputDatasetAssociation.dataset_id
WorkflowInvocationStepOutputDatasetAssociation.output_name
WorkflowInvocationStepOutputDatasetAssociation.workflow_invocation_step
WorkflowInvocationStepOutputDatasetAssociation.dataset
WorkflowInvocationStepOutputDatasetAssociation.dict_collection_visible_keys
WorkflowInvocationStepOutputDatasetAssociation.__init__()
WorkflowInvocationStepOutputDatasetAssociation.table
WorkflowInvocationStepOutputDatasetCollectionAssociation
WorkflowInvocationStepOutputDatasetCollectionAssociation.id
WorkflowInvocationStepOutputDatasetCollectionAssociation.workflow_invocation_step_id
WorkflowInvocationStepOutputDatasetCollectionAssociation.workflow_step_id
WorkflowInvocationStepOutputDatasetCollectionAssociation.dataset_collection_id
WorkflowInvocationStepOutputDatasetCollectionAssociation.output_name
WorkflowInvocationStepOutputDatasetCollectionAssociation.workflow_invocation_step
WorkflowInvocationStepOutputDatasetCollectionAssociation.dataset_collection
WorkflowInvocationStepOutputDatasetCollectionAssociation.dict_collection_visible_keys
WorkflowInvocationStepOutputDatasetCollectionAssociation.__init__()
WorkflowInvocationStepOutputDatasetCollectionAssociation.table
MetadataFile
MetadataFile.id
MetadataFile.hda_id
MetadataFile.lda_id
MetadataFile.create_time
MetadataFile.update_time
MetadataFile.object_store_id
MetadataFile.deleted
MetadataFile.purged
MetadataFile.__init__()
MetadataFile.uuid
MetadataFile.history_dataset
MetadataFile.library_dataset
MetadataFile.name
MetadataFile.dataset
MetadataFile.update_from_file()
MetadataFile.file_name
MetadataFile.table
FormDefinition
FormDefinition.id
FormDefinition.create_time
FormDefinition.update_time
FormDefinition.name
FormDefinition.desc
FormDefinition.form_definition_current_id
FormDefinition.fields
FormDefinition.type
FormDefinition.layout
FormDefinition.form_definition_current
FormDefinition.supported_field_types
FormDefinition.types
FormDefinition.dict_collection_visible_keys
FormDefinition.dict_element_visible_keys
FormDefinition.to_dict()
FormDefinition.grid_fields()
FormDefinition.__init__()
FormDefinition.table
FormDefinitionCurrent
FormValues
UserAddress
UserAddress.id
UserAddress.create_time
UserAddress.update_time
UserAddress.user_id
UserAddress.desc
UserAddress.name
UserAddress.institution
UserAddress.address
UserAddress.city
UserAddress.state
UserAddress.postal_code
UserAddress.country
UserAddress.phone
UserAddress.deleted
UserAddress.purged
UserAddress.user
UserAddress.to_dict()
UserAddress.__init__()
UserAddress.table
PSAAssociation
PSAAssociation.id
PSAAssociation.server_url
PSAAssociation.handle
PSAAssociation.secret
PSAAssociation.issued
PSAAssociation.lifetime
PSAAssociation.assoc_type
PSAAssociation.sa_session
PSAAssociation.save()
PSAAssociation.store()
PSAAssociation.get()
PSAAssociation.remove()
PSAAssociation.__init__()
PSAAssociation.table
PSACode
PSANonce
PSAPartial
UserAuthnzToken
UserAuthnzToken.id
UserAuthnzToken.user
UserAuthnzToken.sa_session
UserAuthnzToken.__init__()
UserAuthnzToken.provider
UserAuthnzToken.uid
UserAuthnzToken.user_id
UserAuthnzToken.extra_data
UserAuthnzToken.lifetime
UserAuthnzToken.assoc_type
UserAuthnzToken.get_id_token()
UserAuthnzToken.set_extra_data()
UserAuthnzToken.save()
UserAuthnzToken.username_max_length()
UserAuthnzToken.user_model()
UserAuthnzToken.changed()
UserAuthnzToken.user_query()
UserAuthnzToken.user_exists()
UserAuthnzToken.get_username()
UserAuthnzToken.create_user()
UserAuthnzToken.get_user()
UserAuthnzToken.get_users_by_email()
UserAuthnzToken.get_social_auth()
UserAuthnzToken.get_social_auth_for_user()
UserAuthnzToken.create_social_auth()
UserAuthnzToken.table
CustosAuthnzToken
CustosAuthnzToken.id
CustosAuthnzToken.user_id
CustosAuthnzToken.external_user_id
CustosAuthnzToken.provider
CustosAuthnzToken.access_token
CustosAuthnzToken.id_token
CustosAuthnzToken.refresh_token
CustosAuthnzToken.expiration_time
CustosAuthnzToken.refresh_expiration_time
CustosAuthnzToken.user
CustosAuthnzToken.__init__()
CustosAuthnzToken.table
CloudAuthz
Page
Page.id
Page.create_time
Page.update_time
Page.user_id
Page.latest_revision_id
Page.title
Page.deleted
Page.importable
Page.slug
Page.published
Page.user
Page.revisions
Page.latest_revision
Page.tags
Page.annotations
Page.ratings
Page.users_shared_with
Page.average_rating
Page.users_shared_with_dot_users
Page.dict_element_visible_keys
Page.to_dict()
Page.username
Page.email_hash
Page.__init__()
Page.table
PageRevision
PageRevision.id
PageRevision.create_time
PageRevision.update_time
PageRevision.page_id
PageRevision.title
PageRevision.content
PageRevision.page
PageRevision.DEFAULT_CONTENT_FORMAT
PageRevision.dict_element_visible_keys
PageRevision.__init__()
PageRevision.content_format
PageRevision.to_dict()
PageRevision.table
PageUserShareAssociation
Visualization
Visualization.id
Visualization.create_time
Visualization.update_time
Visualization.user_id
Visualization.latest_revision_id
Visualization.title
Visualization.type
Visualization.dbkey
Visualization.deleted
Visualization.importable
Visualization.slug
Visualization.published
Visualization.user
Visualization.revisions
Visualization.latest_revision
Visualization.tags
Visualization.annotations
Visualization.ratings
Visualization.users_shared_with
Visualization.average_rating
Visualization.users_shared_with_dot_users
Visualization.__init__()
Visualization.copy()
Visualization.table
VisualizationRevision
VisualizationRevision.id
VisualizationRevision.create_time
VisualizationRevision.update_time
VisualizationRevision.visualization_id
VisualizationRevision.title
VisualizationRevision.dbkey
VisualizationRevision.config
VisualizationRevision.visualization
VisualizationRevision.copy()
VisualizationRevision.__init__()
VisualizationRevision.table
VisualizationUserShareAssociation
VisualizationUserShareAssociation.id
VisualizationUserShareAssociation.visualization_id
VisualizationUserShareAssociation.user_id
VisualizationUserShareAssociation.user
VisualizationUserShareAssociation.visualization
VisualizationUserShareAssociation.__init__()
VisualizationUserShareAssociation.table
Tag
ItemTagAssociation
HistoryTagAssociation
HistoryTagAssociation.id
HistoryTagAssociation.history_id
HistoryTagAssociation.tag_id
HistoryTagAssociation.user_id
HistoryTagAssociation.user_tname
HistoryTagAssociation.value
HistoryTagAssociation.history
HistoryTagAssociation.tag
HistoryTagAssociation.user
HistoryTagAssociation.__init__()
HistoryTagAssociation.table
HistoryTagAssociation.user_value
HistoryDatasetAssociationTagAssociation
HistoryDatasetAssociationTagAssociation.id
HistoryDatasetAssociationTagAssociation.history_dataset_association_id
HistoryDatasetAssociationTagAssociation.tag_id
HistoryDatasetAssociationTagAssociation.user_id
HistoryDatasetAssociationTagAssociation.user_tname
HistoryDatasetAssociationTagAssociation.value
HistoryDatasetAssociationTagAssociation.history_dataset_association
HistoryDatasetAssociationTagAssociation.tag
HistoryDatasetAssociationTagAssociation.user
HistoryDatasetAssociationTagAssociation.__init__()
HistoryDatasetAssociationTagAssociation.table
HistoryDatasetAssociationTagAssociation.user_value
LibraryDatasetDatasetAssociationTagAssociation
LibraryDatasetDatasetAssociationTagAssociation.id
LibraryDatasetDatasetAssociationTagAssociation.library_dataset_dataset_association_id
LibraryDatasetDatasetAssociationTagAssociation.tag_id
LibraryDatasetDatasetAssociationTagAssociation.user_id
LibraryDatasetDatasetAssociationTagAssociation.user_tname
LibraryDatasetDatasetAssociationTagAssociation.value
LibraryDatasetDatasetAssociationTagAssociation.library_dataset_dataset_association
LibraryDatasetDatasetAssociationTagAssociation.tag
LibraryDatasetDatasetAssociationTagAssociation.user
LibraryDatasetDatasetAssociationTagAssociation.__init__()
LibraryDatasetDatasetAssociationTagAssociation.table
LibraryDatasetDatasetAssociationTagAssociation.user_value
PageTagAssociation
PageTagAssociation.id
PageTagAssociation.page_id
PageTagAssociation.tag_id
PageTagAssociation.user_id
PageTagAssociation.user_tname
PageTagAssociation.value
PageTagAssociation.page
PageTagAssociation.tag
PageTagAssociation.user
PageTagAssociation.__init__()
PageTagAssociation.table
PageTagAssociation.user_value
WorkflowStepTagAssociation
WorkflowStepTagAssociation.id
WorkflowStepTagAssociation.workflow_step_id
WorkflowStepTagAssociation.tag_id
WorkflowStepTagAssociation.user_id
WorkflowStepTagAssociation.user_tname
WorkflowStepTagAssociation.value
WorkflowStepTagAssociation.workflow_step
WorkflowStepTagAssociation.tag
WorkflowStepTagAssociation.user
WorkflowStepTagAssociation.__init__()
WorkflowStepTagAssociation.table
WorkflowStepTagAssociation.user_value
StoredWorkflowTagAssociation
StoredWorkflowTagAssociation.id
StoredWorkflowTagAssociation.stored_workflow_id
StoredWorkflowTagAssociation.tag_id
StoredWorkflowTagAssociation.user_id
StoredWorkflowTagAssociation.user_tname
StoredWorkflowTagAssociation.value
StoredWorkflowTagAssociation.stored_workflow
StoredWorkflowTagAssociation.tag
StoredWorkflowTagAssociation.user
StoredWorkflowTagAssociation.__init__()
StoredWorkflowTagAssociation.table
StoredWorkflowTagAssociation.user_value
VisualizationTagAssociation
VisualizationTagAssociation.id
VisualizationTagAssociation.visualization_id
VisualizationTagAssociation.tag_id
VisualizationTagAssociation.user_id
VisualizationTagAssociation.user_tname
VisualizationTagAssociation.value
VisualizationTagAssociation.visualization
VisualizationTagAssociation.tag
VisualizationTagAssociation.user
VisualizationTagAssociation.__init__()
VisualizationTagAssociation.table
VisualizationTagAssociation.user_value
HistoryDatasetCollectionTagAssociation
HistoryDatasetCollectionTagAssociation.id
HistoryDatasetCollectionTagAssociation.history_dataset_collection_id
HistoryDatasetCollectionTagAssociation.tag_id
HistoryDatasetCollectionTagAssociation.user_id
HistoryDatasetCollectionTagAssociation.user_tname
HistoryDatasetCollectionTagAssociation.value
HistoryDatasetCollectionTagAssociation.dataset_collection
HistoryDatasetCollectionTagAssociation.tag
HistoryDatasetCollectionTagAssociation.user
HistoryDatasetCollectionTagAssociation.__init__()
HistoryDatasetCollectionTagAssociation.table
HistoryDatasetCollectionTagAssociation.user_value
LibraryDatasetCollectionTagAssociation
LibraryDatasetCollectionTagAssociation.id
LibraryDatasetCollectionTagAssociation.library_dataset_collection_id
LibraryDatasetCollectionTagAssociation.tag_id
LibraryDatasetCollectionTagAssociation.user_id
LibraryDatasetCollectionTagAssociation.user_tname
LibraryDatasetCollectionTagAssociation.value
LibraryDatasetCollectionTagAssociation.dataset_collection
LibraryDatasetCollectionTagAssociation.tag
LibraryDatasetCollectionTagAssociation.user
LibraryDatasetCollectionTagAssociation.__init__()
LibraryDatasetCollectionTagAssociation.table
LibraryDatasetCollectionTagAssociation.user_value
ToolTagAssociation
HistoryAnnotationAssociation
HistoryDatasetAssociationAnnotationAssociation
HistoryDatasetAssociationAnnotationAssociation.__init__()
HistoryDatasetAssociationAnnotationAssociation.table
HistoryDatasetAssociationAnnotationAssociation.id
HistoryDatasetAssociationAnnotationAssociation.history_dataset_association_id
HistoryDatasetAssociationAnnotationAssociation.user_id
HistoryDatasetAssociationAnnotationAssociation.annotation
HistoryDatasetAssociationAnnotationAssociation.hda
HistoryDatasetAssociationAnnotationAssociation.user
StoredWorkflowAnnotationAssociation
StoredWorkflowAnnotationAssociation.__init__()
StoredWorkflowAnnotationAssociation.table
StoredWorkflowAnnotationAssociation.id
StoredWorkflowAnnotationAssociation.stored_workflow_id
StoredWorkflowAnnotationAssociation.user_id
StoredWorkflowAnnotationAssociation.annotation
StoredWorkflowAnnotationAssociation.stored_workflow
StoredWorkflowAnnotationAssociation.user
WorkflowStepAnnotationAssociation
WorkflowStepAnnotationAssociation.__init__()
WorkflowStepAnnotationAssociation.table
WorkflowStepAnnotationAssociation.id
WorkflowStepAnnotationAssociation.workflow_step_id
WorkflowStepAnnotationAssociation.user_id
WorkflowStepAnnotationAssociation.annotation
WorkflowStepAnnotationAssociation.workflow_step
WorkflowStepAnnotationAssociation.user
PageAnnotationAssociation
VisualizationAnnotationAssociation
VisualizationAnnotationAssociation.__init__()
VisualizationAnnotationAssociation.table
VisualizationAnnotationAssociation.id
VisualizationAnnotationAssociation.visualization_id
VisualizationAnnotationAssociation.user_id
VisualizationAnnotationAssociation.annotation
VisualizationAnnotationAssociation.visualization
VisualizationAnnotationAssociation.user
HistoryDatasetCollectionAssociationAnnotationAssociation
HistoryDatasetCollectionAssociationAnnotationAssociation.__init__()
HistoryDatasetCollectionAssociationAnnotationAssociation.table
HistoryDatasetCollectionAssociationAnnotationAssociation.id
HistoryDatasetCollectionAssociationAnnotationAssociation.history_dataset_collection_id
HistoryDatasetCollectionAssociationAnnotationAssociation.user_id
HistoryDatasetCollectionAssociationAnnotationAssociation.annotation
HistoryDatasetCollectionAssociationAnnotationAssociation.history_dataset_collection
HistoryDatasetCollectionAssociationAnnotationAssociation.user
LibraryDatasetCollectionAnnotationAssociation
LibraryDatasetCollectionAnnotationAssociation.__init__()
LibraryDatasetCollectionAnnotationAssociation.table
LibraryDatasetCollectionAnnotationAssociation.id
LibraryDatasetCollectionAnnotationAssociation.library_dataset_collection_id
LibraryDatasetCollectionAnnotationAssociation.user_id
LibraryDatasetCollectionAnnotationAssociation.annotation
LibraryDatasetCollectionAnnotationAssociation.dataset_collection
LibraryDatasetCollectionAnnotationAssociation.user
Vault
ItemRatingAssociation
HistoryRatingAssociation
HistoryDatasetAssociationRatingAssociation
HistoryDatasetAssociationRatingAssociation.__init__()
HistoryDatasetAssociationRatingAssociation.table
HistoryDatasetAssociationRatingAssociation.id
HistoryDatasetAssociationRatingAssociation.history_dataset_association_id
HistoryDatasetAssociationRatingAssociation.user_id
HistoryDatasetAssociationRatingAssociation.rating
HistoryDatasetAssociationRatingAssociation.history_dataset_association
HistoryDatasetAssociationRatingAssociation.user
StoredWorkflowRatingAssociation
StoredWorkflowRatingAssociation.__init__()
StoredWorkflowRatingAssociation.table
StoredWorkflowRatingAssociation.id
StoredWorkflowRatingAssociation.stored_workflow_id
StoredWorkflowRatingAssociation.user_id
StoredWorkflowRatingAssociation.rating
StoredWorkflowRatingAssociation.stored_workflow
StoredWorkflowRatingAssociation.user
PageRatingAssociation
VisualizationRatingAssociation
VisualizationRatingAssociation.__init__()
VisualizationRatingAssociation.table
VisualizationRatingAssociation.id
VisualizationRatingAssociation.visualization_id
VisualizationRatingAssociation.user_id
VisualizationRatingAssociation.rating
VisualizationRatingAssociation.visualization
VisualizationRatingAssociation.user
HistoryDatasetCollectionRatingAssociation
HistoryDatasetCollectionRatingAssociation.__init__()
HistoryDatasetCollectionRatingAssociation.table
HistoryDatasetCollectionRatingAssociation.id
HistoryDatasetCollectionRatingAssociation.history_dataset_collection_id
HistoryDatasetCollectionRatingAssociation.user_id
HistoryDatasetCollectionRatingAssociation.rating
HistoryDatasetCollectionRatingAssociation.dataset_collection
HistoryDatasetCollectionRatingAssociation.user
LibraryDatasetCollectionRatingAssociation
LibraryDatasetCollectionRatingAssociation.__init__()
LibraryDatasetCollectionRatingAssociation.table
LibraryDatasetCollectionRatingAssociation.id
LibraryDatasetCollectionRatingAssociation.library_dataset_collection_id
LibraryDatasetCollectionRatingAssociation.user_id
LibraryDatasetCollectionRatingAssociation.rating
LibraryDatasetCollectionRatingAssociation.dataset_collection
LibraryDatasetCollectionRatingAssociation.user
DataManagerHistoryAssociation
DataManagerHistoryAssociation.__init__()
DataManagerHistoryAssociation.table
DataManagerHistoryAssociation.id
DataManagerHistoryAssociation.create_time
DataManagerHistoryAssociation.update_time
DataManagerHistoryAssociation.history_id
DataManagerHistoryAssociation.user_id
DataManagerHistoryAssociation.history
DataManagerHistoryAssociation.user
DataManagerJobAssociation
UserPreference
UserAction
APIKeys
copy_list()
CleanupEvent
CleanupEventDatasetAssociation
CleanupEventMetadataFileAssociation
CleanupEventHistoryAssociation
CleanupEventHistoryDatasetAssociationAssociation
CleanupEventHistoryDatasetAssociationAssociation.__init__()
CleanupEventHistoryDatasetAssociationAssociation.table
CleanupEventHistoryDatasetAssociationAssociation.id
CleanupEventHistoryDatasetAssociationAssociation.create_time
CleanupEventHistoryDatasetAssociationAssociation.cleanup_event_id
CleanupEventHistoryDatasetAssociationAssociation.hda_id
CleanupEventLibraryAssociation
CleanupEventLibraryFolderAssociation
CleanupEventLibraryDatasetAssociation
CleanupEventLibraryDatasetDatasetAssociationAssociation
CleanupEventLibraryDatasetDatasetAssociationAssociation.__init__()
CleanupEventLibraryDatasetDatasetAssociationAssociation.table
CleanupEventLibraryDatasetDatasetAssociationAssociation.id
CleanupEventLibraryDatasetDatasetAssociationAssociation.create_time
CleanupEventLibraryDatasetDatasetAssociationAssociation.cleanup_event_id
CleanupEventLibraryDatasetDatasetAssociationAssociation.ldda_id
CleanupEventImplicitlyConvertedDatasetAssociationAssociation
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.__init__()
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.table
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.id
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.create_time
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.cleanup_event_id
CleanupEventImplicitlyConvertedDatasetAssociationAssociation.icda_id
receive_init()
JobStateSummary
JobStateSummary.all_jobs
JobStateSummary.deleted
JobStateSummary.deleting
JobStateSummary.error
JobStateSummary.failed
JobStateSummary.new
JobStateSummary.ok
JobStateSummary.paused
JobStateSummary.queued
JobStateSummary.resubmitted
JobStateSummary.running
JobStateSummary.skipped
JobStateSummary.stop
JobStateSummary.stopped
JobStateSummary.upload
JobStateSummary.waiting
- Subpackages
- galaxy.model.dataset_collections package
- Subpackages
- Submodules
- galaxy.model.dataset_collections.builder module
- galaxy.model.dataset_collections.matching module
- galaxy.model.dataset_collections.registry module
- galaxy.model.dataset_collections.structure module
- galaxy.model.dataset_collections.subcollections module
- galaxy.model.dataset_collections.type_description module
- galaxy.model.migrations package
DatabaseConfig
InvalidModelIdError
AlembicManager
verify_databases_via_script()
verify_databases()
DatabaseStateVerifier
get_last_sqlalchemymigrate_version()
get_alembic_manager()
get_metadata()
get_gxy_metadata()
get_tsi_metadata()
- Submodules
- galaxy.model.migrations.scripts module
- galaxy.model.migrations.util module
- galaxy.model.orm package
- galaxy.model.store package
StoreAppProtocol
ImportDiscardedDataType
ImportOptions
SessionlessContext
replace_metadata_file()
ModelImportStore
ObjectImportTracker
FileTracebackException
get_import_model_store_for_directory()
DictImportModelStore
get_import_model_store_for_dict()
BaseDirectoryImportModelStore
restore_times()
DirectoryImportModelStore1901
DirectoryImportModelStoreLatest
BagArchiveImportModelStore
ModelExportStore
DirectoryModelExportStore
WriteCrates
WorkflowInvocationOnlyExportStore
BcoExportOptions
BcoModelExportStore
ROCrateModelExportStore
ROCrateArchiveModelExportStore
TarModelExportStore
BagDirectoryModelExportStore
BagArchiveModelExportStore
get_export_store_factory()
tar_export_directory()
get_export_dataset_filename()
imported_store_for_metadata()
source_to_import_store()
payload_to_source_uri()
- Submodules
- galaxy.model.store.build_objects module
- galaxy.model.store.discover module
- galaxy.model.store.load_objects module
- galaxy.model.tool_shed_install package
- galaxy.model.triggers package
- galaxy.model.unittest_utils package
- galaxy.model.view package
- galaxy.model.dataset_collections package
- Submodules
- galaxy.model.base module
- galaxy.model.custom_types module
- galaxy.model.database_heartbeat module
now()
DatabaseHeartbeat
DatabaseHeartbeat.__init__()
DatabaseHeartbeat.sa_session
DatabaseHeartbeat.server_name
DatabaseHeartbeat.start()
DatabaseHeartbeat.shutdown()
DatabaseHeartbeat.get_active_processes()
DatabaseHeartbeat.add_change_callback()
DatabaseHeartbeat.is_config_watcher
DatabaseHeartbeat.update_watcher_designation()
DatabaseHeartbeat.send_database_heartbeat()
- galaxy.model.database_utils module
- galaxy.model.deferred module
- galaxy.model.index_filter_util module
- galaxy.model.item_attrs module
- galaxy.model.mapping module
- galaxy.model.metadata module
Statement
MetadataElement
MetadataCollection
MetadataCollection.__init__()
MetadataCollection.get_parent()
MetadataCollection.set_parent()
MetadataCollection.parent
MetadataCollection.spec
MetadataCollection.remove_key()
MetadataCollection.element_is_set()
MetadataCollection.get_metadata_parameter()
MetadataCollection.make_dict_copy()
MetadataCollection.requires_dataset_id
MetadataCollection.from_JSON_dict()
MetadataCollection.to_JSON_dict()
MetadataSpecCollection
MetadataParameter
MetadataParameter.__init__()
MetadataParameter.get_field()
MetadataParameter.to_string()
MetadataParameter.to_safe_string()
MetadataParameter.make_copy()
MetadataParameter.marshal()
MetadataParameter.validate()
MetadataParameter.unwrap()
MetadataParameter.wrap()
MetadataParameter.from_external_value()
MetadataParameter.to_external_value()
MetadataElementSpec
SelectParameter
DBKeyParameter
RangeParameter
ColumnParameter
ColumnTypesParameter
ListParameter
DictParameter
PythonObjectParameter
FileParameter
MetadataTempFile
- galaxy.model.none_like module
- galaxy.model.scoped_session module
- galaxy.model.search module
ViewField
ViewQueryBaseClass
library_extended_metadata_filter()
ldda_parent_library_filter()
LibraryDatasetDatasetView
LibraryView
library_folder_parent_library_id_filter()
library_path_filter()
LibraryFolderView
library_dataset_name_filter()
LibraryDatasetView
ToolView
history_dataset_handle_tag()
history_dataset_extended_metadata_filter()
HistoryDatasetView
history_handle_tag()
history_handle_annotation()
HistoryView
workflow_tag_handler()
WorkflowView
job_param_filter()
job_input_hda_filter()
job_input_ldda_filter()
job_output_hda_filter()
JobView
PageView
PageRevisionView
GalaxyQuery
GalaxyQueryComparison
GalaxyQueryAnd
GalaxyParseError
SearchQuery
GalaxySearchEngine
- galaxy.model.security module
GalaxyRBACAgent
GalaxyRBACAgent.__init__()
GalaxyRBACAgent.sa_session
GalaxyRBACAgent.sort_by_attr()
GalaxyRBACAgent.get_all_roles()
GalaxyRBACAgent.get_roles_for_action()
GalaxyRBACAgent.get_valid_roles()
GalaxyRBACAgent.get_legitimate_roles()
GalaxyRBACAgent.ok_to_display()
GalaxyRBACAgent.allow_action()
GalaxyRBACAgent.get_actions_for_items()
GalaxyRBACAgent.allow_action_on_libitems()
GalaxyRBACAgent.dataset_access_mapping()
GalaxyRBACAgent.dataset_permission_map_for_access()
GalaxyRBACAgent.item_permission_map_for_modify()
GalaxyRBACAgent.item_permission_map_for_manage()
GalaxyRBACAgent.item_permission_map_for_add()
GalaxyRBACAgent.can_access_dataset()
GalaxyRBACAgent.can_access_datasets()
GalaxyRBACAgent.can_access_collection()
GalaxyRBACAgent.can_manage_dataset()
GalaxyRBACAgent.can_access_library()
GalaxyRBACAgent.get_accessible_libraries()
GalaxyRBACAgent.has_accessible_folders()
GalaxyRBACAgent.has_accessible_library_datasets()
GalaxyRBACAgent.can_access_library_item()
GalaxyRBACAgent.can_add_library_item()
GalaxyRBACAgent.can_modify_library_item()
GalaxyRBACAgent.can_manage_library_item()
GalaxyRBACAgent.get_item_actions()
GalaxyRBACAgent.guess_derived_permissions_for_datasets()
GalaxyRBACAgent.guess_derived_permissions()
GalaxyRBACAgent.associate_components()
GalaxyRBACAgent.associate_user_group()
GalaxyRBACAgent.associate_user_role()
GalaxyRBACAgent.associate_group_role()
GalaxyRBACAgent.associate_action_dataset_role()
GalaxyRBACAgent.create_user_role()
GalaxyRBACAgent.create_private_user_role()
GalaxyRBACAgent.get_private_user_role()
GalaxyRBACAgent.get_role()
GalaxyRBACAgent.create_role()
GalaxyRBACAgent.get_sharing_roles()
GalaxyRBACAgent.user_set_default_permissions()
GalaxyRBACAgent.user_get_default_permissions()
GalaxyRBACAgent.history_set_default_permissions()
GalaxyRBACAgent.history_get_default_permissions()
GalaxyRBACAgent.set_all_dataset_permissions()
GalaxyRBACAgent.set_dataset_permission()
GalaxyRBACAgent.get_permissions()
GalaxyRBACAgent.copy_dataset_permissions()
GalaxyRBACAgent.privately_share_dataset()
GalaxyRBACAgent.set_all_library_permissions()
GalaxyRBACAgent.set_library_item_permission()
GalaxyRBACAgent.library_is_public()
GalaxyRBACAgent.library_is_unrestricted()
GalaxyRBACAgent.make_library_public()
GalaxyRBACAgent.folder_is_public()
GalaxyRBACAgent.folder_is_unrestricted()
GalaxyRBACAgent.make_folder_public()
GalaxyRBACAgent.dataset_is_public()
GalaxyRBACAgent.dataset_is_unrestricted()
GalaxyRBACAgent.dataset_is_private_to_user()
GalaxyRBACAgent.dataset_is_private_to_a_user()
GalaxyRBACAgent.datasets_are_public()
GalaxyRBACAgent.make_dataset_public()
GalaxyRBACAgent.derive_roles_from_access()
GalaxyRBACAgent.copy_library_permissions()
GalaxyRBACAgent.get_permitted_libraries()
GalaxyRBACAgent.show_library_item()
GalaxyRBACAgent.get_showable_folders()
GalaxyRBACAgent.set_entity_user_associations()
GalaxyRBACAgent.set_entity_group_associations()
GalaxyRBACAgent.set_entity_role_associations()
GalaxyRBACAgent.get_component_associations()
GalaxyRBACAgent.check_folder_contents()
HostAgent
- galaxy.model.tags module
ItemTagAssocInfo
TagHandler
TagHandler.__init__()
TagHandler.create_tag_handler_session()
TagHandler.add_tags_from_list()
TagHandler.remove_tags_from_list()
TagHandler.set_tags_from_list()
TagHandler.get_tag_assoc_class()
TagHandler.get_id_col_in_item_tag_assoc_table()
TagHandler.get_community_tags()
TagHandler.get_tool_tags()
TagHandler.remove_item_tag()
TagHandler.delete_item_tags()
TagHandler.item_has_tag()
TagHandler.apply_item_tag()
TagHandler.apply_item_tags()
TagHandler.get_tags_list()
TagHandler.get_tags_str()
TagHandler.get_tag_by_id()
TagHandler.get_tag_by_name()
TagHandler.parse_tags()
TagHandler.parse_tags_list()
GalaxyTagHandler
GalaxyTagHandlerSession
GalaxySessionlessTagHandler
CommunityTagHandler
- galaxy.objectstore package
ObjectStore
ObjectStore.exists()
ObjectStore.construct_path()
ObjectStore.create()
ObjectStore.empty()
ObjectStore.size()
ObjectStore.delete()
ObjectStore.get_data()
ObjectStore.get_filename()
ObjectStore.update_from_file()
ObjectStore.get_object_url()
ObjectStore.get_concrete_store_name()
ObjectStore.get_concrete_store_description_markdown()
ObjectStore.get_concrete_store_badges()
ObjectStore.is_private()
ObjectStore.object_store_ids()
ObjectStore.object_store_allows_id_selection()
ObjectStore.object_store_ids_allowing_selection()
ObjectStore.get_concrete_store_by_object_store_id()
ObjectStore.get_store_usage_percent()
ObjectStore.get_store_by()
ObjectStore.cache_targets()
ObjectStore.to_dict()
ObjectStore.get_quota_source_map()
BaseObjectStore
BaseObjectStore.store_by
BaseObjectStore.store_type
BaseObjectStore.__init__()
BaseObjectStore.start()
BaseObjectStore.shutdown()
BaseObjectStore.file_ready()
BaseObjectStore.parse_xml()
BaseObjectStore.from_xml()
BaseObjectStore.to_dict()
BaseObjectStore.exists()
BaseObjectStore.construct_path()
BaseObjectStore.create()
BaseObjectStore.empty()
BaseObjectStore.size()
BaseObjectStore.delete()
BaseObjectStore.get_data()
BaseObjectStore.get_filename()
BaseObjectStore.update_from_file()
BaseObjectStore.get_object_url()
BaseObjectStore.get_concrete_store_name()
BaseObjectStore.get_concrete_store_description_markdown()
BaseObjectStore.get_concrete_store_badges()
BaseObjectStore.get_store_usage_percent()
BaseObjectStore.get_store_by()
BaseObjectStore.is_private()
BaseObjectStore.cache_targets()
BaseObjectStore.parse_private_from_config_xml()
BaseObjectStore.parse_badges_from_config_xml()
BaseObjectStore.get_quota_source_map()
ConcreteObjectStore
DiskObjectStore
NestedObjectStore
DistributedObjectStore
DistributedObjectStore.store_type
DistributedObjectStore.__init__()
DistributedObjectStore.parse_xml()
DistributedObjectStore.from_xml()
DistributedObjectStore.to_dict()
DistributedObjectStore.shutdown()
DistributedObjectStore.get_quota_source_map()
DistributedObjectStore.object_store_ids()
DistributedObjectStore.object_store_allows_id_selection()
DistributedObjectStore.object_store_ids_allowing_selection()
DistributedObjectStore.get_concrete_store_by_object_store_id()
DistributedObjectStore.store_by
HierarchicalObjectStore
QuotaModel
ConcreteObjectStoreModel
type_to_object_store_class()
build_object_store_from_config()
local_extra_dirs()
config_to_dict()
QuotaSourceInfo
QuotaSourceMap
ObjectStorePopulator
- Subpackages
- Submodules
- galaxy.objectstore.azure_blob module
- galaxy.objectstore.cloud module
- galaxy.objectstore.irods module
- galaxy.objectstore.pithos module
- galaxy.objectstore.pulsar module
- galaxy.objectstore.s3 module
- galaxy.objectstore.s3_multipart_upload module
- galaxy.quota package
- galaxy.schema package
BootstrapAdminUser
ValueFilterQueryParams
PaginationQueryParams
FilterQueryParams
SerializationParams
PdfDocumentType
APIKeyModel
- Submodules
- galaxy.schema.fetch_data module
FetchBaseModel
ElementsFromType
BaseFetchDataTarget
ItemsFromSrc
Src
DestinationType
HdaDestination
HdcaDestination
LibraryFolderDestination
BaseCollectionTarget
LibraryDestination
ExtraFiles
BaseDataElement
BaseDataElement.name
BaseDataElement.dbkey
BaseDataElement.info
BaseDataElement.ext
BaseDataElement.space_to_tab
BaseDataElement.to_posix_lines
BaseDataElement.deferred
BaseDataElement.tags
BaseDataElement.created_from_basename
BaseDataElement.extra_files
BaseDataElement.auto_decompress
BaseDataElement.items_from
BaseDataElement.collection_type
BaseDataElement.MD5
BaseDataElement.description
BaseDataElement.Config
FileDataElement
PastedDataElement
UrlDataElement
ServerDirElement
FtpImportElement
ItemsFromModel
FtpImportTarget
PathDataElement
CompositeDataElement
CompositeItems
NestedElement
BaseDataTarget
DataElementsTarget
DataElementsFromTarget
HdcaDataItemsTarget
HdcaDataItemsFromTarget
FilesPayload
BaseDataPayload
FetchDataPayload
FetchDataFormPayload
- galaxy.schema.fields module
- galaxy.schema.remote_files module
- galaxy.schema.schema module
DatasetState
JobState
DatasetCollectionPopulatedState
Model
UserModel
GroupModel
JobSourceType
HistoryContentType
HistoryImportArchiveSourceType
DCEType
DatasetSourceType
ColletionSourceType
HistoryContentSource
TagItem
TagCollection
MetadataFile
DatasetPermissions
Hyperlink
DisplayApp
Visualization
HistoryItemBase
HistoryItemCommon
HDASummary
HDAInaccessible
DatasetValidatedState
HDADetailed
HDADetailed.model_class
HDADetailed.hda_ldda
HDADetailed.accessible
HDADetailed.genome_build
HDADetailed.misc_info
HDADetailed.misc_blurb
HDADetailed.file_ext
HDADetailed.file_size
HDADetailed.resubmitted
HDADetailed.metadata
HDADetailed.metadata_dbkey
HDADetailed.metadata_data_lines
HDADetailed.meta_files
HDADetailed.data_type
HDADetailed.peek
HDADetailed.creating_job
HDADetailed.rerunnable
HDADetailed.uuid
HDADetailed.permissions
HDADetailed.file_name
HDADetailed.display_apps
HDADetailed.display_types
HDADetailed.visualizations
HDADetailed.validated_state
HDADetailed.validated_state_message
HDADetailed.annotation
HDADetailed.download_url
HDADetailed.type
HDADetailed.api_type
HDADetailed.created_from_basename
HDAExtended
DCSummary
HDAObject
DCObject
DCESummary
DCDetailed
HDCJobStateSummary
HDCJobStateSummary.all_jobs
HDCJobStateSummary.new
HDCJobStateSummary.waiting
HDCJobStateSummary.running
HDCJobStateSummary.error
HDCJobStateSummary.paused
HDCJobStateSummary.skipped
HDCJobStateSummary.deleted_new
HDCJobStateSummary.resubmitted
HDCJobStateSummary.queued
HDCJobStateSummary.ok
HDCJobStateSummary.failed
HDCJobStateSummary.deleted
HDCJobStateSummary.upload
HDCASummary
HDCADetailed
HistoryBase
HistoryContentItemBase
HistoryContentItem
EncodedHistoryContentItem
UpdateContentItem
UpdateHistoryContentsBatchPayload
HistoryContentItemOperation
HistoryContentItemOperation.hide
HistoryContentItemOperation.unhide
HistoryContentItemOperation.delete
HistoryContentItemOperation.undelete
HistoryContentItemOperation.purge
HistoryContentItemOperation.change_datatype
HistoryContentItemOperation.change_dbkey
HistoryContentItemOperation.add_tags
HistoryContentItemOperation.remove_tags
BulkOperationParams
ChangeDatatypeOperationParams
ChangeDbkeyOperationParams
TagOperationParams
HistoryContentBulkOperationPayload
BulkOperationItemError
HistoryContentBulkOperationResult
UpdateHistoryContentsPayload
HistorySummary
HistorySummary.model_class
HistorySummary.id
HistorySummary.name
HistorySummary.deleted
HistorySummary.purged
HistorySummary.archived
HistorySummary.url
HistorySummary.published
HistorySummary.count
HistorySummary.annotation
HistorySummary.tags
HistorySummary.update_time
HistorySummary.preferred_object_store_id
HistoryActiveContentCounts
HistoryDetailed
ExportHistoryArchivePayload
WorkflowIndexQueryPayload
WorkflowIndexQueryPayload.show_deleted
WorkflowIndexQueryPayload.show_hidden
WorkflowIndexQueryPayload.show_published
WorkflowIndexQueryPayload.show_shared
WorkflowIndexQueryPayload.sort_by
WorkflowIndexQueryPayload.sort_desc
WorkflowIndexQueryPayload.limit
WorkflowIndexQueryPayload.offset
WorkflowIndexQueryPayload.search
WorkflowIndexQueryPayload.skip_step_counts
JobIndexSortByEnum
JobIndexQueryPayload
JobIndexQueryPayload.states
JobIndexQueryPayload.user_details
JobIndexQueryPayload.user_id
JobIndexQueryPayload.tool_ids
JobIndexQueryPayload.tool_ids_like
JobIndexQueryPayload.date_range_min
JobIndexQueryPayload.date_range_max
JobIndexQueryPayload.history_id
JobIndexQueryPayload.workflow_id
JobIndexQueryPayload.invocation_id
JobIndexQueryPayload.order_by
JobIndexQueryPayload.search
JobIndexQueryPayload.limit
JobIndexQueryPayload.offset
InvocationSortByEnum
InvocationIndexQueryPayload
InvocationIndexQueryPayload.workflow_id
InvocationIndexQueryPayload.history_id
InvocationIndexQueryPayload.job_id
InvocationIndexQueryPayload.user_id
InvocationIndexQueryPayload.sort_by
InvocationIndexQueryPayload.sort_desc
InvocationIndexQueryPayload.include_terminal
InvocationIndexQueryPayload.limit
InvocationIndexQueryPayload.offset
PageIndexQueryPayload
CreateHistoryPayload
CollectionElementIdentifier
CreateNewCollectionPayload
CreateNewCollectionPayload.collection_type
CreateNewCollectionPayload.element_identifiers
CreateNewCollectionPayload.name
CreateNewCollectionPayload.hide_source_items
CreateNewCollectionPayload.copy_elements
CreateNewCollectionPayload.instance_type
CreateNewCollectionPayload.history_id
CreateNewCollectionPayload.folder_id
ModelStoreFormat
StoreContentSource
CreateHistoryFromStore
StoreExportPayload
ShortTermStoreExportPayload
BcoGenerationParametersMixin
WriteStoreToPayload
ObjectExportResponseBase
JobExportHistoryArchiveModel
ExportObjectType
ExportObjectRequestMetadata
ExportObjectResultMetadata
ExportObjectMetadata
ObjectExportTaskResponse
JobExportHistoryArchiveListResponse
ExportTaskListResponse
ArchiveHistoryRequestPayload
ExportRecordData
ExportAssociationData
ArchivedHistorySummary
ArchivedHistorySummary.model_class
ArchivedHistorySummary.id
ArchivedHistorySummary.name
ArchivedHistorySummary.deleted
ArchivedHistorySummary.purged
ArchivedHistorySummary.archived
ArchivedHistorySummary.url
ArchivedHistorySummary.published
ArchivedHistorySummary.count
ArchivedHistorySummary.annotation
ArchivedHistorySummary.tags
ArchivedHistorySummary.update_time
ArchivedHistorySummary.preferred_object_store_id
ArchivedHistoryDetailed
ArchivedHistoryDetailed.contents_url
ArchivedHistoryDetailed.size
ArchivedHistoryDetailed.user_id
ArchivedHistoryDetailed.create_time
ArchivedHistoryDetailed.importable
ArchivedHistoryDetailed.slug
ArchivedHistoryDetailed.username_and_slug
ArchivedHistoryDetailed.genome_build
ArchivedHistoryDetailed.state
ArchivedHistoryDetailed.state_ids
ArchivedHistoryDetailed.state_details
ArchivedHistoryDetailed.model_class
ArchivedHistoryDetailed.id
ArchivedHistoryDetailed.name
ArchivedHistoryDetailed.deleted
ArchivedHistoryDetailed.purged
ArchivedHistoryDetailed.archived
ArchivedHistoryDetailed.url
ArchivedHistoryDetailed.published
ArchivedHistoryDetailed.count
ArchivedHistoryDetailed.annotation
ArchivedHistoryDetailed.tags
ArchivedHistoryDetailed.update_time
ArchivedHistoryDetailed.preferred_object_store_id
LabelValuePair
CustomBuildsMetadataResponse
JobIdResponse
JobBaseModel
JobImportHistoryResponse
ItemStateSummary
JobStateSummary
ImplicitCollectionJobsStateSummary
WorkflowInvocationStateSummary
JobSummary
DatasetSourceIdBase
DatasetSourceId
EncodedDatasetSourceId
DatasetJobInfo
JobDetails
JobMetric
JobMetricCollection
JobFullDetails
StoredWorkflowSummary
StoredWorkflowSummary.id
StoredWorkflowSummary.model_class
StoredWorkflowSummary.create_time
StoredWorkflowSummary.update_time
StoredWorkflowSummary.name
StoredWorkflowSummary.url
StoredWorkflowSummary.published
StoredWorkflowSummary.annotations
StoredWorkflowSummary.tags
StoredWorkflowSummary.deleted
StoredWorkflowSummary.hidden
StoredWorkflowSummary.owner
StoredWorkflowSummary.latest_workflow_uuid
StoredWorkflowSummary.number_of_steps
StoredWorkflowSummary.show_in_tool_panel
WorkflowInput
WorkflowOutput
InputStep
WorkflowModuleType
WorkflowStepBase
ToolBasedWorkflowStep
InputDataStep
InputDataCollectionStep
InputParameterStep
PauseStep
ToolStep
SubworkflowStep
Creator
Organization
Person
StoredWorkflowDetailed
Input
Output
InputConnection
WorkflowStepLayoutPosition
WorkflowStepToExportBase
WorkflowStepToExportBase.id
WorkflowStepToExportBase.type
WorkflowStepToExportBase.name
WorkflowStepToExportBase.annotation
WorkflowStepToExportBase.tool_id
WorkflowStepToExportBase.uuid
WorkflowStepToExportBase.label
WorkflowStepToExportBase.inputs
WorkflowStepToExportBase.outputs
WorkflowStepToExportBase.input_connections
WorkflowStepToExportBase.position
WorkflowStepToExportBase.workflow_outputs
WorkflowStepToExport
ToolShedRepositorySummary
PostJobAction
WorkflowToolStepToExport
SubworkflowStepToExport
WorkflowToExport
BasicRoleModel
RoleModelResponse
RoleDefinitionModel
RoleListResponse
GroupRoleResponse
GroupRoleListResponse
GroupUserResponse
GroupUserListResponse
ImportToolDataBundleUriSource
ImportToolDataBundleDatasetSource
ToolShedRepository
ToolShedRepositoryChangeset
InstalledRepositoryToolShedStatus
InstalledToolShedRepository
InstalledToolShedRepository.model_class
InstalledToolShedRepository.id
InstalledToolShedRepository.status
InstalledToolShedRepository.name
InstalledToolShedRepository.owner
InstalledToolShedRepository.deleted
InstalledToolShedRepository.ctx_rev
InstalledToolShedRepository.error_message
InstalledToolShedRepository.installed_changeset_revision
InstalledToolShedRepository.tool_shed
InstalledToolShedRepository.dist_to_shed
InstalledToolShedRepository.uninstalled
InstalledToolShedRepository.changeset_revision
InstalledToolShedRepository.tool_shed_status
InstalledToolShedRepositories
CheckForUpdatesResponse
LibraryPermissionScope
LibraryLegacySummary
LibrarySummary
LibrarySummaryList
CreateLibraryPayload
CreateLibrariesFromStore
UpdateLibraryPayload
DeleteLibraryPayload
LibraryCurrentPermissions
LegacyLibraryPermissionsPayload
LibraryPermissionAction
DatasetPermissionAction
LibraryPermissionsPayloadBase
LibraryPermissionsPayload
LibraryFolderPermissionAction
LibraryFolderPermissionsPayload
LibraryFolderDetails
LibraryFolderDetails.model_class
LibraryFolderDetails.id
LibraryFolderDetails.name
LibraryFolderDetails.description
LibraryFolderDetails.item_count
LibraryFolderDetails.parent_library_id
LibraryFolderDetails.parent_id
LibraryFolderDetails.genome_build
LibraryFolderDetails.update_time
LibraryFolderDetails.deleted
LibraryFolderDetails.library_path
CreateLibraryFolderPayload
UpdateLibraryFolderPayload
LibraryAvailablePermissions
LibraryFolderCurrentPermissions
LibraryFolderContentsIndexQueryPayload
LibraryFolderItemBase
FolderLibraryFolderItem
FileLibraryFolderItem
FileLibraryFolderItem.id
FileLibraryFolderItem.type
FileLibraryFolderItem.file_ext
FileLibraryFolderItem.date_uploaded
FileLibraryFolderItem.is_unrestricted
FileLibraryFolderItem.is_private
FileLibraryFolderItem.state
FileLibraryFolderItem.file_size
FileLibraryFolderItem.raw_size
FileLibraryFolderItem.ldda_id
FileLibraryFolderItem.tags
FileLibraryFolderItem.message
LibraryFolderMetadata
LibraryFolderContentsIndexResult
CreateLibraryFilePayload
DatasetAssociationRoles
UpdateDatasetPermissionsPayload
CustomHistoryItem
DeleteHistoryContentPayload
DeleteHistoryContentResult
HistoryContentsArchiveDryRunResult
HistoryContentStats
HistoryContentsResult
HistoryContentsWithStatsResult
SharingOptions
ShareWithExtra
ShareWithPayload
SetSlugPayload
UserEmail
UserBeaconSetting
SharingStatus
ShareWithStatus
HDABasicInfo
ShareHistoryExtra
PageContentFormat
PageSummaryBase
MaterializeDatasetInstanceAPIRequest
MaterializeDatasetInstanceRequest
CreatePagePayload
AsyncTaskResultSummary
AsyncFile
PageSummary
PageDetails
PageSummaryList
- galaxy.schema.tasks module
SetupHistoryExportJob
PrepareDatasetCollectionDownload
GeneratePdfDownload
RequestUser
GenerateHistoryDownload
GenerateHistoryContentDownload
BcoGenerationTaskParametersMixin
GenerateInvocationDownload
WriteInvocationTo
WriteHistoryContentTo
WriteHistoryTo
ImportModelStoreTaskRequest
MaterializeDatasetInstanceTaskRequest
ComputeDatasetHashTaskRequest
PurgeDatasetsTaskRequest
- galaxy.schema.types module
- galaxy.security package
Action
RBACAgent
RBACAgent.permitted_actions
RBACAgent.get_action()
RBACAgent.get_actions()
RBACAgent.get_item_actions()
RBACAgent.guess_derived_permissions_for_datasets()
RBACAgent.can_access_dataset()
RBACAgent.can_manage_dataset()
RBACAgent.can_access_library()
RBACAgent.can_add_library_item()
RBACAgent.can_modify_library_item()
RBACAgent.can_manage_library_item()
RBACAgent.associate_components()
RBACAgent.create_private_user_role()
RBACAgent.get_private_user_role()
RBACAgent.user_set_default_permissions()
RBACAgent.history_set_default_permissions()
RBACAgent.set_all_dataset_permissions()
RBACAgent.set_dataset_permission()
RBACAgent.set_all_library_permissions()
RBACAgent.set_library_item_permission()
RBACAgent.library_is_public()
RBACAgent.make_library_public()
RBACAgent.get_accessible_libraries()
RBACAgent.get_permitted_libraries()
RBACAgent.folder_is_public()
RBACAgent.make_folder_public()
RBACAgent.dataset_is_public()
RBACAgent.make_dataset_public()
RBACAgent.get_permissions()
RBACAgent.get_all_roles()
RBACAgent.get_legitimate_roles()
RBACAgent.derive_roles_from_access()
RBACAgent.get_component_associations()
RBACAgent.components_are_associated()
RBACAgent.convert_permitted_action_strings()
get_permitted_actions()
- Submodules
- galaxy.security.idencoding module
- galaxy.security.object_wrapper module
- galaxy.security.passwords module
- galaxy.security.ssh_util module
- galaxy.security.validate_user_input module
- galaxy.security.vault module
- galaxy.selenium package
- Subpackages
- Submodules
- galaxy.selenium.cli module
- galaxy.selenium.components module
- galaxy.selenium.context module
- galaxy.selenium.data module
- galaxy.selenium.driver_factory module
- galaxy.selenium.has_driver module
exception_indicates_click_intercepted()
exception_indicates_not_clickable()
exception_indicates_stale_element()
HasDriver
HasDriver.by
HasDriver.keys
HasDriver.driver
HasDriver.axe_script_url
HasDriver.axe_skip
HasDriver.re_get_with_query_params()
HasDriver.assert_xpath()
HasDriver.assert_selector()
HasDriver.assert_selector_absent_or_hidden()
HasDriver.assert_absent_or_hidden()
HasDriver.assert_disabled()
HasDriver.selector_is_displayed()
HasDriver.is_displayed()
HasDriver.assert_selector_absent()
HasDriver.find_elements()
HasDriver.assert_absent()
HasDriver.element_absent()
HasDriver.wait_for_xpath()
HasDriver.wait_for_xpath_visible()
HasDriver.wait_for_selector()
HasDriver.wait_for_present()
HasDriver.wait_for_visible()
HasDriver.wait_for_selector_visible()
HasDriver.wait_for_selector_clickable()
HasDriver.wait_for_clickable()
HasDriver.wait_for_selector_absent_or_hidden()
HasDriver.wait_for_selector_absent()
HasDriver.wait_for_element_count_of_at_least()
HasDriver.wait_for_absent()
HasDriver.wait_for_absent_or_hidden()
HasDriver.wait_for_id()
HasDriver.click()
HasDriver.action_chains()
HasDriver.send_enter()
HasDriver.send_escape()
HasDriver.send_backspace()
HasDriver.timeout_for()
HasDriver.wait()
HasDriver.click_xpath()
HasDriver.click_label()
HasDriver.click_selector()
HasDriver.fill()
HasDriver.click_submit()
HasDriver.prepend_timeout_message()
HasDriver.accept_alert()
HasDriver.find_element_by_link_text()
HasDriver.find_element_by_xpath()
HasDriver.find_element_by_id()
HasDriver.find_element_by_selector()
HasDriver.axe_eval()
SeleniumTimeoutException
- galaxy.selenium.jupyter_context module
- galaxy.selenium.navigates_galaxy module
WaitType
HistoryEntry
WAIT_TYPES
NullTourCallback
exception_seems_to_indicate_transition()
retry_call_during_transitions()
retry_during_transitions()
edit_details()
NavigatesGalaxy
NavigatesGalaxy.timeout_multiplier
NavigatesGalaxy.driver
NavigatesGalaxy.build_url()
NavigatesGalaxy.screenshot()
NavigatesGalaxy.screenshot_if()
NavigatesGalaxy.default_password
NavigatesGalaxy.wait_types
NavigatesGalaxy.get()
NavigatesGalaxy.navigation
NavigatesGalaxy.components
NavigatesGalaxy.wait_length()
NavigatesGalaxy.sleep_for()
NavigatesGalaxy.sleep_for_seconds()
NavigatesGalaxy.timeout_for()
NavigatesGalaxy.home()
NavigatesGalaxy.go_to_trs_search()
NavigatesGalaxy.go_to_trs_by_id()
NavigatesGalaxy.go_to_workflow_sharing()
NavigatesGalaxy.go_to_workflow_export()
NavigatesGalaxy.go_to_history_sharing()
NavigatesGalaxy.switch_to_main_panel()
NavigatesGalaxy.local_storage()
NavigatesGalaxy.main_panel()
NavigatesGalaxy.api_get()
NavigatesGalaxy.api_post()
NavigatesGalaxy.api_delete()
NavigatesGalaxy.get_galaxy_session()
NavigatesGalaxy.selenium_to_requests_cookies()
NavigatesGalaxy.history_panel_name_element()
NavigatesGalaxy.history_panel_name()
NavigatesGalaxy.history_panel_collection_rename()
NavigatesGalaxy.history_panel_expand_collection()
NavigatesGalaxy.history_panel_collection_name_element()
NavigatesGalaxy.make_accessible_and_publishable()
NavigatesGalaxy.history_contents()
NavigatesGalaxy.current_history()
NavigatesGalaxy.current_history_id()
NavigatesGalaxy.current_history_publish()
NavigatesGalaxy.latest_history_entry()
NavigatesGalaxy.latest_history_item()
NavigatesGalaxy.wait_for_history()
NavigatesGalaxy.history_panel_create_new_with_name()
NavigatesGalaxy.history_panel_create_new()
NavigatesGalaxy.history_panel_wait_for_hid_ok()
NavigatesGalaxy.history_panel_wait_for_hid_deferred()
NavigatesGalaxy.wait_for_hid_ok_and_open_details()
NavigatesGalaxy.history_panel_item_component()
NavigatesGalaxy.wait_for_history_to_have_hid()
NavigatesGalaxy.history_panel_wait_for_hid_visible()
NavigatesGalaxy.hid_to_history_item()
NavigatesGalaxy.history_item_wait_for()
NavigatesGalaxy.history_panel_wait_for_history_loaded()
NavigatesGalaxy.history_panel_wait_for_hid_hidden()
NavigatesGalaxy.history_panel_wait_for_hid_state()
NavigatesGalaxy.click_grid_popup_option()
NavigatesGalaxy.published_grid_search_for()
NavigatesGalaxy.get_logged_in_user()
NavigatesGalaxy.get_api_key()
NavigatesGalaxy.get_user_id()
NavigatesGalaxy.get_user_email()
NavigatesGalaxy.is_logged_in()
NavigatesGalaxy.submit_login()
NavigatesGalaxy.fill_login_and_submit()
NavigatesGalaxy.register()
NavigatesGalaxy.wait_for_logged_in()
NavigatesGalaxy.click_center()
NavigatesGalaxy.hover_over()
NavigatesGalaxy.perform_single_upload()
NavigatesGalaxy.perform_upload()
NavigatesGalaxy.perform_upload_of_pasted_content()
NavigatesGalaxy.perform_upload_of_composite_dataset_pasted_data()
NavigatesGalaxy.upload_list()
NavigatesGalaxy.upload_pair()
NavigatesGalaxy.upload_paired_list()
NavigatesGalaxy.upload_tab_click()
NavigatesGalaxy.upload_start_click()
NavigatesGalaxy.upload_set_footer_extension()
NavigatesGalaxy.upload_set_footer_genome()
NavigatesGalaxy.upload_set_collection_type()
NavigatesGalaxy.upload_start()
NavigatesGalaxy.upload_build()
NavigatesGalaxy.upload_queue_local_file()
NavigatesGalaxy.upload_paste_data()
NavigatesGalaxy.upload_rule_start()
NavigatesGalaxy.upload_rule_build()
NavigatesGalaxy.upload_rule_set_data_type()
NavigatesGalaxy.upload_rule_set_input_type()
NavigatesGalaxy.upload_rule_set_dataset()
NavigatesGalaxy.rule_builder_set_collection_name()
NavigatesGalaxy.rule_builder_set_extension()
NavigatesGalaxy.rule_builder_filter_count()
NavigatesGalaxy.rule_builder_sort()
NavigatesGalaxy.rule_builder_add_regex_groups()
NavigatesGalaxy.rule_builder_add_regex_replacement()
NavigatesGalaxy.rule_builder_add_value()
NavigatesGalaxy.rule_builder_remove_columns()
NavigatesGalaxy.rule_builder_concatenate_columns()
NavigatesGalaxy.rule_builder_split_columns()
NavigatesGalaxy.rule_builder_swap_columns()
NavigatesGalaxy.rule_builder_rule_editor()
NavigatesGalaxy.rule_builder_set_mapping()
NavigatesGalaxy.rule_builder_set_source()
NavigatesGalaxy.rule_builder_enter_source_text()
NavigatesGalaxy.workflow_editor_set_license()
NavigatesGalaxy.workflow_editor_click_option()
NavigatesGalaxy.workflow_editor_click_options()
NavigatesGalaxy.workflow_editor_options_menu_element()
NavigatesGalaxy.workflow_editor_click_run()
NavigatesGalaxy.workflow_editor_click_save()
NavigatesGalaxy.navigate_to_histories_page()
NavigatesGalaxy.navigate_to_histories_shared_with_me_page()
NavigatesGalaxy.navigate_to_user_preferences()
NavigatesGalaxy.navigate_to_invocations()
NavigatesGalaxy.navigate_to_pages()
NavigatesGalaxy.navigate_to_published_workflows()
NavigatesGalaxy.navigate_to_published_histories_page()
NavigatesGalaxy.navigate_to_published_pages()
NavigatesGalaxy.admin_open()
NavigatesGalaxy.create_quota()
NavigatesGalaxy.select_dataset_from_lib_import_modal()
NavigatesGalaxy.create_new_library()
NavigatesGalaxy.libraries_open()
NavigatesGalaxy.libraries_open_with_name()
NavigatesGalaxy.page_open_and_screenshot()
NavigatesGalaxy.libraries_index_table_elements()
NavigatesGalaxy.libraries_index_create()
NavigatesGalaxy.libraries_index_click_search()
NavigatesGalaxy.libraries_index_sort_selector()
NavigatesGalaxy.libraries_index_sort_click()
NavigatesGalaxy.libraries_index_search_for()
NavigatesGalaxy.libraries_folder_create()
NavigatesGalaxy.libraries_click_dataset_import()
NavigatesGalaxy.libraries_dataset_import()
NavigatesGalaxy.libraries_dataset_import_from_history_select()
NavigatesGalaxy.libraries_dataset_import_from_history_click_ok()
NavigatesGalaxy.libraries_table_elements()
NavigatesGalaxy.populate_library_folder_from_import_dir()
NavigatesGalaxy.navigate_to_new_library()
NavigatesGalaxy.wait_for_overlays_cleared()
NavigatesGalaxy.clear_tooltips()
NavigatesGalaxy.pages_index_table_elements()
NavigatesGalaxy.page_index_click_option()
NavigatesGalaxy.workflow_index_open()
NavigatesGalaxy.workflow_index_table_elements()
NavigatesGalaxy.workflow_index_table_row()
NavigatesGalaxy.workflow_index_column_text()
NavigatesGalaxy.workflow_index_click_search()
NavigatesGalaxy.workflow_index_search_for()
NavigatesGalaxy.workflow_index_click_import()
NavigatesGalaxy.workflow_index_rename()
NavigatesGalaxy.workflow_index_name()
NavigatesGalaxy.workflow_click_option()
NavigatesGalaxy.select_dropdown_item()
NavigatesGalaxy.workflow_index_click_option()
NavigatesGalaxy.workflow_index_click_tag_display()
NavigatesGalaxy.workflow_index_add_tag()
NavigatesGalaxy.workflow_index_tags()
NavigatesGalaxy.workflow_index_tag_elements()
NavigatesGalaxy.workflow_index_click_tag()
NavigatesGalaxy.workflow_import_submit_url()
NavigatesGalaxy.workflow_sharing_click_publish()
NavigatesGalaxy.tagging_add()
NavigatesGalaxy.workflow_run_with_name()
NavigatesGalaxy.workflow_run_specify_inputs()
NavigatesGalaxy.workflow_run_submit()
NavigatesGalaxy.workflow_run_ensure_expanded()
NavigatesGalaxy.workflow_create_new()
NavigatesGalaxy.invocation_index_table_elements()
NavigatesGalaxy.tool_open()
NavigatesGalaxy.datasource_tool_open()
NavigatesGalaxy.run_environment_test_tool()
NavigatesGalaxy.select_storage()
NavigatesGalaxy.create_page_and_edit()
NavigatesGalaxy.create_page()
NavigatesGalaxy.tool_parameter_div()
NavigatesGalaxy.tool_parameter_edit_rules()
NavigatesGalaxy.tool_set_value()
NavigatesGalaxy.tool_form_generate_tour()
NavigatesGalaxy.tool_form_execute()
NavigatesGalaxy.click_masthead_user()
NavigatesGalaxy.click_masthead_shared_data()
NavigatesGalaxy.click_masthead_workflow()
NavigatesGalaxy.click_button_new_workflow()
NavigatesGalaxy.wait_for_sizzle_selector_clickable()
NavigatesGalaxy.click_history_options()
NavigatesGalaxy.click_history_option_export_to_file()
NavigatesGalaxy.click_history_option_sharing()
NavigatesGalaxy.click_history_option()
NavigatesGalaxy.history_element()
NavigatesGalaxy.content_item_by_attributes()
NavigatesGalaxy.history_click_create_new()
NavigatesGalaxy.history_click_editor_save()
NavigatesGalaxy.history_panel_click_copy_elements()
NavigatesGalaxy.use_bootstrap_dropdown()
NavigatesGalaxy.histories_click_advanced_search()
NavigatesGalaxy.histories_get_history_names()
NavigatesGalaxy.history_panel_add_tags()
NavigatesGalaxy.history_panel_rename()
NavigatesGalaxy.history_panel_name_input()
NavigatesGalaxy.history_panel_click_to_rename()
NavigatesGalaxy.history_panel_refresh_click()
NavigatesGalaxy.history_panel_multi_operations_show()
NavigatesGalaxy.history_panel_muli_operation_select_hid()
NavigatesGalaxy.history_panel_multi_operation_action_click()
NavigatesGalaxy.open_history_multi_view()
NavigatesGalaxy.history_multi_view_display_collection_contents()
NavigatesGalaxy.history_panel_item_edit()
NavigatesGalaxy.history_panel_item_view_dataset_details()
NavigatesGalaxy.history_panel_item_click_visualization_menu()
NavigatesGalaxy.history_panel_item_available_visualizations_elements()
NavigatesGalaxy.history_panel_item_get_tags()
NavigatesGalaxy.history_panel_item_available_visualizations()
NavigatesGalaxy.history_panel_item_click_visualization()
NavigatesGalaxy.history_panel_item_selector()
NavigatesGalaxy.modal_body_selector()
NavigatesGalaxy.history_panel_item_body_component()
NavigatesGalaxy.hda_click_primary_action_button()
NavigatesGalaxy.hda_click_details()
NavigatesGalaxy.history_panel_click_item_title()
NavigatesGalaxy.history_panel_ensure_showing_item_details()
NavigatesGalaxy.history_panel_item_showing_details()
NavigatesGalaxy.collection_builder_set_name()
NavigatesGalaxy.collection_builder_hide_originals()
NavigatesGalaxy.collection_builder_create()
NavigatesGalaxy.collection_builder_clear_filters()
NavigatesGalaxy.collection_builder_click_paired_item()
NavigatesGalaxy.logout_if_needed()
NavigatesGalaxy.logout()
NavigatesGalaxy.run_tour()
NavigatesGalaxy.tour_wait_for_clickable_element()
NavigatesGalaxy.tour_wait_for_element_present()
NavigatesGalaxy.get_tooltip_text()
NavigatesGalaxy.assert_selector_absent_or_hidden_after_transitions()
NavigatesGalaxy.assert_absent_or_hidden_after_transitions()
NavigatesGalaxy.assert_tooltip_text()
NavigatesGalaxy.assert_tooltip_text_contains()
NavigatesGalaxy.assert_error_message()
NavigatesGalaxy.assert_warning_message()
NavigatesGalaxy.assert_success_message()
NavigatesGalaxy.assert_message()
NavigatesGalaxy.assert_no_error_message()
NavigatesGalaxy.run_tour_step()
NavigatesGalaxy.wait_for_and_click_selector()
NavigatesGalaxy.wait_for_and_click()
NavigatesGalaxy.set_history_annotation()
NavigatesGalaxy.ensure_history_annotation_area_displayed()
NavigatesGalaxy.select_set_value()
NavigatesGalaxy.select2_set_value()
NavigatesGalaxy.snapshot()
NavigatesGalaxy.open_history_editor()
NavigatesGalaxy.close_history_editor()
NavigatesGalaxy.share_ensure_by_user_available()
NavigatesGalaxy.share_unshare_with_user()
NavigatesGalaxy.share_with_user()
NavigatesGalaxy.tutorial_mode_activate()
NotLoggedInException
ClientBuildException
- galaxy.selenium.sizzle module
- galaxy.selenium.smart_components module
SmartComponent
SmartTarget
SmartTarget.__init__()
SmartTarget.all()
SmartTarget.wait_for_element_count_of_at_least()
SmartTarget.wait_for_and_click()
SmartTarget.wait_for_visible()
SmartTarget.wait_for_select()
SmartTarget.wait_for_clickable()
SmartTarget.wait_for_text()
SmartTarget.wait_for_value()
SmartTarget.is_displayed
SmartTarget.is_absent
SmartTarget.wait_for_absent_or_hidden()
SmartTarget.wait_for_absent()
SmartTarget.wait_for_present()
SmartTarget.assert_absent()
SmartTarget.assert_absent_or_hidden()
SmartTarget.assert_absent_or_hidden_after_transitions()
SmartTarget.assert_disabled()
SmartTarget.data_value()
SmartTarget.assert_data_value()
SmartTarget.has_class()
SmartTarget.wait_for_and_send_keys()
SmartTarget.wait_for_and_clear_and_send_keys()
SmartTarget.axe_eval()
SmartTarget.assert_no_axe_violations_with_impact_of_at_least()
- galaxy.tool_shed package
- Subpackages
- galaxy.tool_shed.galaxy_install package
- galaxy.tool_shed.metadata package
- galaxy.tool_shed.tools package
- galaxy.tool_shed.util package
- Submodules
- galaxy.tool_shed.util.basic_util module
- galaxy.tool_shed.util.container_util module
- galaxy.tool_shed.util.hg_util module
- galaxy.tool_shed.util.metadata_util module
- galaxy.tool_shed.util.repository_util module
- galaxy.tool_shed.util.shed_util_common module
- galaxy.tool_shed.util.tool_dependency_util module
- galaxy.tool_shed.util.tool_util module
- Submodules
- galaxy.tool_shed.repository_type module
- galaxy.tool_shed.tool_shed_registry module
- Subpackages
- galaxy.tool_util package
- Subpackages
- galaxy.tool_util.biotools package
- galaxy.tool_util.client package
- galaxy.tool_util.cwl package
tool_proxy()
tool_proxy_from_persistent_representation()
workflow_proxy()
handle_outputs()
to_cwl_job()
to_galaxy_parameters()
needs_shell_quoting()
- Submodules
- galaxy.tool_util.cwl.cwltool_deps module
- galaxy.tool_util.cwl.parser module
- galaxy.tool_util.cwl.representation module
- galaxy.tool_util.cwl.runnable module
- galaxy.tool_util.cwl.runtime_actions module
- galaxy.tool_util.cwl.schema module
- galaxy.tool_util.cwl.util module
- galaxy.tool_util.deps package
build_dependency_manager()
DependencyManager
CachedDependencyManager
NullDependencyManager
- Subpackages
- Submodules
- galaxy.tool_util.deps.brew_exts module
- galaxy.tool_util.deps.brew_util module
- galaxy.tool_util.deps.commands module
- galaxy.tool_util.deps.conda_compat module
- galaxy.tool_util.deps.conda_util module
- galaxy.tool_util.deps.container_classes module
- galaxy.tool_util.deps.container_volumes module
- galaxy.tool_util.deps.containers module
- galaxy.tool_util.deps.dependencies module
- galaxy.tool_util.deps.docker_util module
- galaxy.tool_util.deps.dockerfiles module
- galaxy.tool_util.deps.installable module
- galaxy.tool_util.deps.requirements module
- galaxy.tool_util.deps.singularity_util module
- galaxy.tool_util.deps.views module
- galaxy.tool_util.linters package
- Submodules
- galaxy.tool_util.linters.citations module
- galaxy.tool_util.linters.command module
- galaxy.tool_util.linters.cwl module
- galaxy.tool_util.linters.general module
- galaxy.tool_util.linters.help module
- galaxy.tool_util.linters.inputs module
- galaxy.tool_util.linters.outputs module
- galaxy.tool_util.linters.stdio module
- galaxy.tool_util.linters.tests module
- galaxy.tool_util.linters.xml_order module
- galaxy.tool_util.locations package
- galaxy.tool_util.ontologies package
- galaxy.tool_util.parser package
get_input_source()
get_tool_source()
get_tool_source_from_representation()
RequiredFiles
ToolOutputCollectionPart
ToolSource
- Submodules
- galaxy.tool_util.parser.cwl module
- galaxy.tool_util.parser.factory module
- galaxy.tool_util.parser.interface module
- galaxy.tool_util.parser.output_actions module
- galaxy.tool_util.parser.output_collection_def module
- galaxy.tool_util.parser.output_objects module
- galaxy.tool_util.parser.stdio module
- galaxy.tool_util.parser.util module
- galaxy.tool_util.parser.xml module
- galaxy.tool_util.parser.yaml module
- galaxy.tool_util.toolbox package
AbstractToolBox
AbstractToolTagManager
panel_item_types
ToolSection
ToolSectionLabel
- Subpackages
- Submodules
- galaxy.tool_util.toolbox.base module
- galaxy.tool_util.toolbox.integrated_panel module
- galaxy.tool_util.toolbox.panel module
- galaxy.tool_util.toolbox.parser module
- galaxy.tool_util.toolbox.tags module
- galaxy.tool_util.toolbox.watcher module
- galaxy.tool_util.unittest_utils package
- galaxy.tool_util.verify package
verify()
make_temp_fname()
files_delta()
get_compressed_formats()
files_diff()
files_re_match()
files_re_match_multiline()
files_contains()
- Subpackages
- Submodules
- galaxy.tool_util.verify.interactor module
- galaxy.tool_util.verify.script module
- galaxy.tool_util.verify.test_data module
- galaxy.tool_util.verify.wait module
- Submodules
- galaxy.tool_util.edam_util module
- galaxy.tool_util.fetcher module
- galaxy.tool_util.lint module
LintLevel
LintMessage
XMLLintMessageLine
XMLLintMessageXPath
LintContext
LintContext.__init__()
LintContext.skip_types
LintContext.level
LintContext.lint_message_class
LintContext.object_name
LintContext.message_list
LintContext.found_errors
LintContext.found_warns
LintContext.lint()
LintContext.valid_messages
LintContext.info_messages
LintContext.warn_messages
LintContext.error_messages
LintContext.valid()
LintContext.info()
LintContext.error()
LintContext.warn()
LintContext.failed()
lint_tool_source()
get_lint_context_for_tool_source()
lint_xml()
lint_tool_source_with()
lint_xml_with()
- galaxy.tool_util.loader module
- galaxy.tool_util.loader_directory module
- galaxy.tool_util.output_checker module
- galaxy.tool_util.provided_metadata module
parse_tool_provided_metadata()
BaseToolProvidedMetadata
BaseToolProvidedMetadata.get_new_datasets()
BaseToolProvidedMetadata.has_failed_outputs()
BaseToolProvidedMetadata.get_new_dataset_meta_by_basename()
BaseToolProvidedMetadata.get_unnamed_outputs()
BaseToolProvidedMetadata.get_dataset_meta()
BaseToolProvidedMetadata.rewrite()
BaseToolProvidedMetadata.get_new_datasets_for_metadata_collection()
NullToolProvidedMetadata
LegacyToolProvidedMetadata
LegacyToolProvidedMetadata.__init__()
LegacyToolProvidedMetadata.get_dataset_meta()
LegacyToolProvidedMetadata.get_new_dataset_meta_by_basename()
LegacyToolProvidedMetadata.get_new_datasets()
LegacyToolProvidedMetadata.has_failed_outputs()
LegacyToolProvidedMetadata.get_unnamed_outputs()
LegacyToolProvidedMetadata.rewrite()
LegacyToolProvidedMetadata.get_new_datasets_for_metadata_collection()
ToolProvidedMetadata
- Subpackages
- galaxy.tools package
safe_update
get_safe_version()
ToolNotFoundException
create_tool_from_source()
create_tool_from_representation()
NullToolTagManager
PersistentToolTagManager
ToolBox
ToolBox.__init__()
ToolBox.tool_tag_manager()
ToolBox.sa_session
ToolBox.reload_dependency_manager()
ToolBox.load_builtin_converters()
ToolBox.persist_cache()
ToolBox.can_load_config_file()
ToolBox.has_reloaded()
ToolBox.all_requirements
ToolBox.tools_by_id
ToolBox.get_cache_region()
ToolBox.create_tool()
ToolBox.get_expanded_tool_source()
ToolBox.create_dynamic_tool()
ToolBox.get_tool_components()
DefaultToolState
Tool
Tool.job_tool_configurations
Tool.tool_type
Tool.requires_setting_metadata
Tool.produces_entry_points
Tool.default_tool_action
Tool.tool_action
Tool.tool_type_local
Tool.dict_collection_visible_keys
Tool.version
Tool.__init__()
Tool.job_search
Tool.remove_from_cache()
Tool.history_manager
Tool.version_object
Tool.sa_session
Tool.lineage
Tool.tool_versions
Tool.is_latest_version
Tool.latest_version
Tool.is_datatype_converter
Tool.tool_shed_repository
Tool.produces_collections_with_unknown_structure
Tool.valid_input_states
Tool.requires_galaxy_python_environment
Tool.get_configured_job_handler()
Tool.get_job_destination()
Tool.get_panel_section()
Tool.allow_user_access()
Tool.parse()
Tool.parse_tests()
Tool.tests
Tool.test_data_path()
Tool.tool_provided_metadata()
Tool.parse_command()
Tool.parse_environment_variables()
Tool.parse_inputs()
Tool.parse_outputs()
Tool.parse_stdio()
Tool.parse_input_elem()
Tool.parse_param_elem()
Tool.populate_resource_parameters()
Tool.populate_tool_shed_info()
Tool.help
Tool.biotools_reference
Tool.find_output_def()
Tool.is_workflow_compatible
Tool.check_workflow_compatible()
Tool.new_state()
Tool.get_param()
Tool.get_hook()
Tool.visit_inputs()
Tool.expand_incoming()
Tool.handle_input()
Tool.handle_incoming_errors()
Tool.handle_single_execution()
Tool.params_with_missing_data_table_entry
Tool.params_with_missing_index_file
Tool.get_static_param_values()
Tool.execute()
Tool.params_to_strings()
Tool.params_from_strings()
Tool.check_and_update_param_values()
Tool.build_dependency_cache()
Tool.build_dependency_shell_commands()
Tool.installed_tool_dependencies
Tool.tool_requirements
Tool.tool_requirements_status
Tool.output_discover_patterns
Tool.build_redirect_url_params()
Tool.parse_redirect_url()
Tool.call_hook()
Tool.exec_before_job()
Tool.exec_after_process()
Tool.job_failed()
Tool.discover_outputs()
Tool.to_archive()
Tool.to_dict()
Tool.to_json()
Tool.populate_model()
Tool.get_default_history_by_trans()
Tool.get_externally_referenced_paths()
OutputParameterJSONTool
OutputParameterJSONTool.tool_type
OutputParameterJSONTool.exec_before_job()
OutputParameterJSONTool.job_tool_configurations
OutputParameterJSONTool.tool_action
OutputParameterJSONTool.job_search
OutputParameterJSONTool.version
OutputParameterJSONTool.stdio_exit_codes
OutputParameterJSONTool.stdio_regexes
OutputParameterJSONTool.inputs_by_page
OutputParameterJSONTool.display_by_page
OutputParameterJSONTool.action
OutputParameterJSONTool.labels
OutputParameterJSONTool.input_params
OutputParameterJSONTool.old_id
OutputParameterJSONTool.python_template_version
OutputParameterJSONTool.dependencies
ExpressionTool
ExpressionTool.requires_js_runtime
ExpressionTool.tool_type
ExpressionTool.tool_type_local
ExpressionTool.EXPRESSION_INPUTS_NAME
ExpressionTool.parse_command()
ExpressionTool.parse_outputs()
ExpressionTool.exec_before_job()
ExpressionTool.exec_after_process()
ExpressionTool.parse_environment_variables()
ExpressionTool.job_tool_configurations
ExpressionTool.tool_action
ExpressionTool.job_search
ExpressionTool.version
ExpressionTool.stdio_exit_codes
ExpressionTool.stdio_regexes
ExpressionTool.inputs_by_page
ExpressionTool.display_by_page
ExpressionTool.action
ExpressionTool.labels
ExpressionTool.input_params
ExpressionTool.old_id
ExpressionTool.python_template_version
ExpressionTool.dependencies
DataSourceTool
DataSourceTool.tool_type
DataSourceTool.default_tool_action
DataSourceTool.parse_inputs()
DataSourceTool.exec_before_job()
DataSourceTool.job_tool_configurations
DataSourceTool.tool_action
DataSourceTool.job_search
DataSourceTool.version
DataSourceTool.stdio_exit_codes
DataSourceTool.stdio_regexes
DataSourceTool.inputs_by_page
DataSourceTool.display_by_page
DataSourceTool.action
DataSourceTool.labels
DataSourceTool.input_params
DataSourceTool.old_id
DataSourceTool.python_template_version
DataSourceTool.dependencies
AsyncDataSourceTool
AsyncDataSourceTool.tool_type
AsyncDataSourceTool.job_tool_configurations
AsyncDataSourceTool.tool_action
AsyncDataSourceTool.job_search
AsyncDataSourceTool.version
AsyncDataSourceTool.stdio_exit_codes
AsyncDataSourceTool.stdio_regexes
AsyncDataSourceTool.inputs_by_page
AsyncDataSourceTool.display_by_page
AsyncDataSourceTool.action
AsyncDataSourceTool.labels
AsyncDataSourceTool.input_params
AsyncDataSourceTool.old_id
AsyncDataSourceTool.python_template_version
AsyncDataSourceTool.dependencies
DataDestinationTool
DataDestinationTool.tool_type
DataDestinationTool.job_tool_configurations
DataDestinationTool.tool_action
DataDestinationTool.job_search
DataDestinationTool.version
DataDestinationTool.stdio_exit_codes
DataDestinationTool.stdio_regexes
DataDestinationTool.inputs_by_page
DataDestinationTool.display_by_page
DataDestinationTool.action
DataDestinationTool.labels
DataDestinationTool.input_params
DataDestinationTool.old_id
DataDestinationTool.python_template_version
DataDestinationTool.dependencies
SetMetadataTool
ExportHistoryTool
ExportHistoryTool.tool_type
ExportHistoryTool.job_tool_configurations
ExportHistoryTool.tool_action
ExportHistoryTool.job_search
ExportHistoryTool.version
ExportHistoryTool.stdio_exit_codes
ExportHistoryTool.stdio_regexes
ExportHistoryTool.inputs_by_page
ExportHistoryTool.display_by_page
ExportHistoryTool.action
ExportHistoryTool.labels
ExportHistoryTool.input_params
ExportHistoryTool.old_id
ExportHistoryTool.python_template_version
ExportHistoryTool.dependencies
ImportHistoryTool
ImportHistoryTool.tool_type
ImportHistoryTool.exec_after_process()
ImportHistoryTool.job_tool_configurations
ImportHistoryTool.tool_action
ImportHistoryTool.job_search
ImportHistoryTool.version
ImportHistoryTool.stdio_exit_codes
ImportHistoryTool.stdio_regexes
ImportHistoryTool.inputs_by_page
ImportHistoryTool.display_by_page
ImportHistoryTool.action
ImportHistoryTool.labels
ImportHistoryTool.input_params
ImportHistoryTool.old_id
ImportHistoryTool.python_template_version
ImportHistoryTool.dependencies
InteractiveTool
InteractiveTool.tool_type
InteractiveTool.produces_entry_points
InteractiveTool.__init__()
InteractiveTool.exec_after_process()
InteractiveTool.job_failed()
InteractiveTool.job_tool_configurations
InteractiveTool.tool_action
InteractiveTool.job_search
InteractiveTool.version
InteractiveTool.stdio_exit_codes
InteractiveTool.stdio_regexes
InteractiveTool.inputs_by_page
InteractiveTool.display_by_page
InteractiveTool.action
InteractiveTool.labels
InteractiveTool.input_params
InteractiveTool.old_id
InteractiveTool.python_template_version
InteractiveTool.dependencies
DataManagerTool
DataManagerTool.tool_type
DataManagerTool.default_tool_action
DataManagerTool.__init__()
DataManagerTool.exec_after_process()
DataManagerTool.get_default_history_by_trans()
DataManagerTool.allow_user_access()
DataManagerTool.job_tool_configurations
DataManagerTool.tool_action
DataManagerTool.job_search
DataManagerTool.version
DataManagerTool.stdio_exit_codes
DataManagerTool.stdio_regexes
DataManagerTool.inputs_by_page
DataManagerTool.display_by_page
DataManagerTool.action
DataManagerTool.labels
DataManagerTool.input_params
DataManagerTool.old_id
DataManagerTool.python_template_version
DataManagerTool.dependencies
DatabaseOperationTool
DatabaseOperationTool.default_tool_action
DatabaseOperationTool.require_terminal_states
DatabaseOperationTool.require_dataset_ok
DatabaseOperationTool.tool_type_local
DatabaseOperationTool.valid_input_states
DatabaseOperationTool.allow_errored_inputs
DatabaseOperationTool.check_inputs_ready()
DatabaseOperationTool.produce_outputs()
DatabaseOperationTool.job_tool_configurations
DatabaseOperationTool.tool_action
DatabaseOperationTool.job_search
DatabaseOperationTool.version
DatabaseOperationTool.stdio_exit_codes
DatabaseOperationTool.stdio_regexes
DatabaseOperationTool.inputs_by_page
DatabaseOperationTool.display_by_page
DatabaseOperationTool.action
DatabaseOperationTool.labels
DatabaseOperationTool.input_params
DatabaseOperationTool.old_id
DatabaseOperationTool.python_template_version
DatabaseOperationTool.dependencies
UnzipCollectionTool
UnzipCollectionTool.tool_type
UnzipCollectionTool.require_terminal_states
UnzipCollectionTool.require_dataset_ok
UnzipCollectionTool.produce_outputs()
UnzipCollectionTool.job_tool_configurations
UnzipCollectionTool.tool_action
UnzipCollectionTool.job_search
UnzipCollectionTool.version
UnzipCollectionTool.stdio_exit_codes
UnzipCollectionTool.stdio_regexes
UnzipCollectionTool.inputs_by_page
UnzipCollectionTool.display_by_page
UnzipCollectionTool.action
UnzipCollectionTool.labels
UnzipCollectionTool.input_params
UnzipCollectionTool.old_id
UnzipCollectionTool.python_template_version
UnzipCollectionTool.dependencies
ZipCollectionTool
ZipCollectionTool.tool_type
ZipCollectionTool.require_terminal_states
ZipCollectionTool.require_dataset_ok
ZipCollectionTool.produce_outputs()
ZipCollectionTool.job_tool_configurations
ZipCollectionTool.tool_action
ZipCollectionTool.job_search
ZipCollectionTool.version
ZipCollectionTool.stdio_exit_codes
ZipCollectionTool.stdio_regexes
ZipCollectionTool.inputs_by_page
ZipCollectionTool.display_by_page
ZipCollectionTool.action
ZipCollectionTool.labels
ZipCollectionTool.input_params
ZipCollectionTool.old_id
ZipCollectionTool.python_template_version
ZipCollectionTool.dependencies
BuildListCollectionTool
BuildListCollectionTool.tool_type
BuildListCollectionTool.require_terminal_states
BuildListCollectionTool.require_dataset_ok
BuildListCollectionTool.produce_outputs()
BuildListCollectionTool.job_tool_configurations
BuildListCollectionTool.tool_action
BuildListCollectionTool.job_search
BuildListCollectionTool.version
BuildListCollectionTool.stdio_exit_codes
BuildListCollectionTool.stdio_regexes
BuildListCollectionTool.inputs_by_page
BuildListCollectionTool.display_by_page
BuildListCollectionTool.action
BuildListCollectionTool.labels
BuildListCollectionTool.input_params
BuildListCollectionTool.old_id
BuildListCollectionTool.python_template_version
BuildListCollectionTool.dependencies
ExtractDatasetCollectionTool
ExtractDatasetCollectionTool.tool_type
ExtractDatasetCollectionTool.require_terminal_states
ExtractDatasetCollectionTool.require_dataset_ok
ExtractDatasetCollectionTool.produce_outputs()
ExtractDatasetCollectionTool.job_tool_configurations
ExtractDatasetCollectionTool.tool_action
ExtractDatasetCollectionTool.job_search
ExtractDatasetCollectionTool.version
ExtractDatasetCollectionTool.stdio_exit_codes
ExtractDatasetCollectionTool.stdio_regexes
ExtractDatasetCollectionTool.inputs_by_page
ExtractDatasetCollectionTool.display_by_page
ExtractDatasetCollectionTool.action
ExtractDatasetCollectionTool.labels
ExtractDatasetCollectionTool.input_params
ExtractDatasetCollectionTool.old_id
ExtractDatasetCollectionTool.python_template_version
ExtractDatasetCollectionTool.dependencies
MergeCollectionTool
MergeCollectionTool.tool_type
MergeCollectionTool.require_terminal_states
MergeCollectionTool.require_dataset_ok
MergeCollectionTool.produce_outputs()
MergeCollectionTool.job_tool_configurations
MergeCollectionTool.tool_action
MergeCollectionTool.job_search
MergeCollectionTool.version
MergeCollectionTool.stdio_exit_codes
MergeCollectionTool.stdio_regexes
MergeCollectionTool.inputs_by_page
MergeCollectionTool.display_by_page
MergeCollectionTool.action
MergeCollectionTool.labels
MergeCollectionTool.input_params
MergeCollectionTool.old_id
MergeCollectionTool.python_template_version
MergeCollectionTool.dependencies
FilterDatasetsTool
FilterDatasetsTool.require_terminal_states
FilterDatasetsTool.require_dataset_ok
FilterDatasetsTool.element_is_valid()
FilterDatasetsTool.produce_outputs()
FilterDatasetsTool.job_tool_configurations
FilterDatasetsTool.tool_action
FilterDatasetsTool.job_search
FilterDatasetsTool.version
FilterDatasetsTool.stdio_exit_codes
FilterDatasetsTool.stdio_regexes
FilterDatasetsTool.inputs_by_page
FilterDatasetsTool.display_by_page
FilterDatasetsTool.action
FilterDatasetsTool.labels
FilterDatasetsTool.input_params
FilterDatasetsTool.old_id
FilterDatasetsTool.python_template_version
FilterDatasetsTool.dependencies
FilterFailedDatasetsTool
FilterFailedDatasetsTool.tool_type
FilterFailedDatasetsTool.require_dataset_ok
FilterFailedDatasetsTool.element_is_valid()
FilterFailedDatasetsTool.job_tool_configurations
FilterFailedDatasetsTool.tool_action
FilterFailedDatasetsTool.job_search
FilterFailedDatasetsTool.version
FilterFailedDatasetsTool.stdio_exit_codes
FilterFailedDatasetsTool.stdio_regexes
FilterFailedDatasetsTool.inputs_by_page
FilterFailedDatasetsTool.display_by_page
FilterFailedDatasetsTool.action
FilterFailedDatasetsTool.labels
FilterFailedDatasetsTool.input_params
FilterFailedDatasetsTool.old_id
FilterFailedDatasetsTool.python_template_version
FilterFailedDatasetsTool.dependencies
FilterEmptyDatasetsTool
FilterEmptyDatasetsTool.tool_type
FilterEmptyDatasetsTool.require_dataset_ok
FilterEmptyDatasetsTool.element_is_valid()
FilterEmptyDatasetsTool.job_tool_configurations
FilterEmptyDatasetsTool.tool_action
FilterEmptyDatasetsTool.job_search
FilterEmptyDatasetsTool.version
FilterEmptyDatasetsTool.stdio_exit_codes
FilterEmptyDatasetsTool.stdio_regexes
FilterEmptyDatasetsTool.inputs_by_page
FilterEmptyDatasetsTool.display_by_page
FilterEmptyDatasetsTool.action
FilterEmptyDatasetsTool.labels
FilterEmptyDatasetsTool.input_params
FilterEmptyDatasetsTool.old_id
FilterEmptyDatasetsTool.python_template_version
FilterEmptyDatasetsTool.dependencies
FlattenTool
FlattenTool.tool_type
FlattenTool.require_terminal_states
FlattenTool.require_dataset_ok
FlattenTool.produce_outputs()
FlattenTool.job_tool_configurations
FlattenTool.tool_action
FlattenTool.job_search
FlattenTool.version
FlattenTool.stdio_exit_codes
FlattenTool.stdio_regexes
FlattenTool.inputs_by_page
FlattenTool.display_by_page
FlattenTool.action
FlattenTool.labels
FlattenTool.input_params
FlattenTool.old_id
FlattenTool.python_template_version
FlattenTool.dependencies
SortTool
SortTool.tool_type
SortTool.require_terminal_states
SortTool.require_dataset_ok
SortTool.produce_outputs()
SortTool.job_tool_configurations
SortTool.tool_action
SortTool.job_search
SortTool.version
SortTool.stdio_exit_codes
SortTool.stdio_regexes
SortTool.inputs_by_page
SortTool.display_by_page
SortTool.action
SortTool.labels
SortTool.input_params
SortTool.old_id
SortTool.python_template_version
SortTool.dependencies
RelabelFromFileTool
RelabelFromFileTool.tool_type
RelabelFromFileTool.produce_outputs()
RelabelFromFileTool.job_tool_configurations
RelabelFromFileTool.tool_action
RelabelFromFileTool.job_search
RelabelFromFileTool.version
RelabelFromFileTool.stdio_exit_codes
RelabelFromFileTool.stdio_regexes
RelabelFromFileTool.inputs_by_page
RelabelFromFileTool.display_by_page
RelabelFromFileTool.action
RelabelFromFileTool.labels
RelabelFromFileTool.input_params
RelabelFromFileTool.old_id
RelabelFromFileTool.python_template_version
RelabelFromFileTool.dependencies
ApplyRulesTool
ApplyRulesTool.tool_type
ApplyRulesTool.produce_outputs()
ApplyRulesTool.job_tool_configurations
ApplyRulesTool.tool_action
ApplyRulesTool.job_search
ApplyRulesTool.version
ApplyRulesTool.stdio_exit_codes
ApplyRulesTool.stdio_regexes
ApplyRulesTool.inputs_by_page
ApplyRulesTool.display_by_page
ApplyRulesTool.action
ApplyRulesTool.labels
ApplyRulesTool.input_params
ApplyRulesTool.old_id
ApplyRulesTool.python_template_version
ApplyRulesTool.dependencies
TagFromFileTool
TagFromFileTool.tool_type
TagFromFileTool.produce_outputs()
TagFromFileTool.job_tool_configurations
TagFromFileTool.tool_action
TagFromFileTool.job_search
TagFromFileTool.version
TagFromFileTool.stdio_exit_codes
TagFromFileTool.stdio_regexes
TagFromFileTool.inputs_by_page
TagFromFileTool.display_by_page
TagFromFileTool.action
TagFromFileTool.labels
TagFromFileTool.input_params
TagFromFileTool.old_id
TagFromFileTool.python_template_version
TagFromFileTool.dependencies
FilterFromFileTool
FilterFromFileTool.tool_type
FilterFromFileTool.produce_outputs()
FilterFromFileTool.job_tool_configurations
FilterFromFileTool.tool_action
FilterFromFileTool.job_search
FilterFromFileTool.version
FilterFromFileTool.stdio_exit_codes
FilterFromFileTool.stdio_regexes
FilterFromFileTool.inputs_by_page
FilterFromFileTool.display_by_page
FilterFromFileTool.action
FilterFromFileTool.labels
FilterFromFileTool.input_params
FilterFromFileTool.old_id
FilterFromFileTool.python_template_version
FilterFromFileTool.dependencies
DuplicateFileToCollectionTool
DuplicateFileToCollectionTool.tool_type
DuplicateFileToCollectionTool.require_terminal_states
DuplicateFileToCollectionTool.require_dataset_ok
DuplicateFileToCollectionTool.produce_outputs()
DuplicateFileToCollectionTool.job_tool_configurations
DuplicateFileToCollectionTool.tool_action
DuplicateFileToCollectionTool.job_search
DuplicateFileToCollectionTool.version
DuplicateFileToCollectionTool.stdio_exit_codes
DuplicateFileToCollectionTool.stdio_regexes
DuplicateFileToCollectionTool.inputs_by_page
DuplicateFileToCollectionTool.display_by_page
DuplicateFileToCollectionTool.action
DuplicateFileToCollectionTool.labels
DuplicateFileToCollectionTool.input_params
DuplicateFileToCollectionTool.old_id
DuplicateFileToCollectionTool.python_template_version
DuplicateFileToCollectionTool.dependencies
TracksterConfig
SetParamAction
tool_class
BadValue
InterruptedUpload
- Subpackages
- galaxy.tools.actions package
ToolExecutionCache
ToolAction
DefaultToolAction
OutputCollections
on_text_for_names()
filter_output()
get_ext_or_implicit_ext()
determine_output_format()
- Submodules
- galaxy.tools.actions.data_manager module
- galaxy.tools.actions.data_source module
- galaxy.tools.actions.history_imp_exp module
- galaxy.tools.actions.metadata module
- galaxy.tools.actions.model_operations module
- galaxy.tools.actions.upload module
- galaxy.tools.actions.upload_common module
- galaxy.tools.data package
- galaxy.tools.data_manager package
- galaxy.tools.error_reports package
- galaxy.tools.expressions package
- galaxy.tools.filters package
- galaxy.tools.imp_exp package
- galaxy.tools.parameters package
DataCollectionToolParameter
DataToolParameter
SelectToolParameter
- Submodules
- galaxy.tools.parameters.basic module
- galaxy.tools.parameters.dataset_matcher module
- galaxy.tools.parameters.dynamic_options module
- galaxy.tools.parameters.grouping module
- galaxy.tools.parameters.history_query module
- galaxy.tools.parameters.input_translation module
- galaxy.tools.parameters.meta module
- galaxy.tools.parameters.sanitize module
- galaxy.tools.parameters.validation module
- galaxy.tools.parameters.wrapped module
- galaxy.tools.parameters.wrapped_json module
- galaxy.tools.search package
- galaxy.tools.util package
- galaxy.tools.actions package
- Submodules
- galaxy.tools.biotools module
- galaxy.tools.cache module
- galaxy.tools.data_fetch module
- galaxy.tools.errors module
- galaxy.tools.evaluation module
ToolErrorLog
global_tool_logs()
ToolEvaluator
PartialToolEvaluator
PartialToolEvaluator.materialize_datasets
PartialToolEvaluator.build()
PartialToolEvaluator.app
PartialToolEvaluator.job
PartialToolEvaluator.file_sources_dict
PartialToolEvaluator.param_dict
PartialToolEvaluator.extra_filenames
PartialToolEvaluator.environment_variables
PartialToolEvaluator.version_command_line
PartialToolEvaluator.command_line
RemoteToolEvaluator
RemoteToolEvaluator.materialize_datasets
RemoteToolEvaluator.execute_tool_hooks()
RemoteToolEvaluator.app
RemoteToolEvaluator.job
RemoteToolEvaluator.file_sources_dict
RemoteToolEvaluator.param_dict
RemoteToolEvaluator.extra_filenames
RemoteToolEvaluator.environment_variables
RemoteToolEvaluator.version_command_line
RemoteToolEvaluator.command_line
RemoteToolEvaluator.build()
- galaxy.tools.exception_handling module
- galaxy.tools.execute module
- galaxy.tools.recommendations module
- galaxy.tools.remote_tool_eval module
- galaxy.tools.repositories module
- galaxy.tools.special_tools module
- galaxy.tools.test module
- galaxy.tools.wrappers module
ToolParameterValueWrapper
RawObjectWrapper
InputValueWrapper
SelectToolParameterWrapper
DatasetFilenameWrapper
DatasetFilenameWrapper.MetadataWrapper
DatasetFilenameWrapper.__init__()
DatasetFilenameWrapper.false_path
DatasetFilenameWrapper.element_identifier
DatasetFilenameWrapper.file_ext
DatasetFilenameWrapper.name_and_ext
DatasetFilenameWrapper.get_staging_path()
DatasetFilenameWrapper.all_metadata_files
DatasetFilenameWrapper.serialize()
DatasetFilenameWrapper.is_collection
DatasetFilenameWrapper.is_of_type()
HasDatasets
DatasetListWrapper
DatasetCollectionWrapper
DatasetCollectionWrapper.__init__()
DatasetCollectionWrapper.name
DatasetCollectionWrapper.collection
DatasetCollectionWrapper.get_datasets_for_group()
DatasetCollectionWrapper.keys()
DatasetCollectionWrapper.is_collection
DatasetCollectionWrapper.element_identifier
DatasetCollectionWrapper.all_paths
DatasetCollectionWrapper.all_metadata_files
DatasetCollectionWrapper.element_identifiers_extensions_paths_and_metadata_files
DatasetCollectionWrapper.get_all_staging_paths()
DatasetCollectionWrapper.serialize()
DatasetCollectionWrapper.is_input_supplied
ElementIdentifierMapper
- galaxy.tours package
- galaxy.util package
ElementTree
shlex_join()
str_removeprefix()
remove_protocol_from_url()
is_binary()
is_uuid()
directory_hash_id()
get_charset_from_http_headers()
synchronized()
iter_start_of_line()
file_reader()
chunk_iterable()
unique_id()
parse_xml()
parse_xml_string()
parse_xml_string_to_etree()
xml_to_string()
xml_element_compare()
xml_element_list_compare()
xml_element_to_dict()
pretty_print_xml()
get_file_size()
shrink_stream_by_size()
shrink_and_unicodify()
shrink_string_by_size()
pretty_print_time_interval()
pretty_print_json()
restore_text()
sanitize_text()
sanitize_lists_to_string()
sanitize_param()
sanitize_for_filename()
find_instance_nested()
mask_password_from_url()
ready_name_for_url()
which()
in_directory()
merge_sorted_iterables()
Params
xml_text()
parse_resource_parameters()
asbool()
string_as_bool()
string_as_bool_or_none()
listify()
commaify()
roundify()
unicodify()
filesystem_safe_string()
smart_str()
strip_control_characters()
object_to_string()
string_to_object()
clean_multiline_string()
ParamsWithSpecs
compare_urls()
read_build_sites()
relativize_symlinks()
stringify_dictionary_keys()
mkstemp_ln()
umask_fix_perms()
docstring_trim()
nice_size()
size_to_bytes()
send_mail()
force_symlink()
unlink()
move_merge()
safe_str_cmp()
galaxy_directory()
in_packages()
galaxy_samples_directory()
config_directories_from_setting()
parse_int()
parse_non_hex_float()
build_url()
url_get()
is_url()
check_github_api_response_rate_limit()
download_to_file()
stream_to_open_named_file()
classproperty
ExecutionTimer
StructuredExecutionTimer
enum_values()
- Subpackages
- Submodules
- galaxy.util.aliaspickler module
- galaxy.util.bool_expressions module
- galaxy.util.bunch module
- galaxy.util.bytesize module
- galaxy.util.checkers module
- galaxy.util.commands module
- galaxy.util.compression_utils module
get_fileobj()
get_fileobj_raw()
file_iter()
decompress_bytes_to_directory()
decompress_path_to_directory()
CompressedFile
CompressedFile.can_decompress()
CompressedFile.__init__()
CompressedFile.archive
CompressedFile.common_prefix_dir
CompressedFile.extract()
CompressedFile.safemembers()
CompressedFile.getmembers_tar()
CompressedFile.getmembers_zip()
CompressedFile.getname_tar()
CompressedFile.getname_zip()
CompressedFile.getmember()
CompressedFile.getmembers()
CompressedFile.getname()
CompressedFile.isdir()
CompressedFile.isdir_tar()
CompressedFile.isdir_zip()
CompressedFile.isfile()
CompressedFile.open_tar()
CompressedFile.open_zip()
CompressedFile.zipfile_ok()
- galaxy.util.dbkeys module
- galaxy.util.dictifiable module
- galaxy.util.dynamic module
- galaxy.util.expressions module
- galaxy.util.facts module
- galaxy.util.filelock module
- galaxy.util.form_builder module
- galaxy.util.hash_util module
- galaxy.util.heartbeat module
- galaxy.util.image_util module
- galaxy.util.inflection module
- galaxy.util.json module
- galaxy.util.jstree module
- galaxy.util.lazy_process module
- galaxy.util.monitors module
- galaxy.util.odict module
- galaxy.util.oset module
- galaxy.util.permutations module
- galaxy.util.plugin_config module
- galaxy.util.properties module
- galaxy.util.renamed_temporary_file module
- galaxy.util.resources module
- galaxy.util.rules_dsl module
get_rules_specification()
apply_regex()
BaseRuleDefinition
AddColumnMetadataRuleDefinition
AddColumnGroupTagValueRuleDefinition
AddColumnConcatenateRuleDefinition
AddColumnBasenameRuleDefinition
AddColumnRegexRuleDefinition
AddColumnRownumRuleDefinition
AddColumnValueRuleDefinition
AddColumnSubstrRuleDefinition
RemoveColumnsRuleDefinition
AddFilterRegexRuleDefinition
AddFilterCountRuleDefinition
AddFilterEmptyRuleDefinition
AddFilterMatchesRuleDefinition
AddFilterCompareRuleDefinition
SortRuleDefinition
SwapColumnsRuleDefinition
SplitColumnsRuleDefinition
flat_map()
RuleSet
rule_class
- galaxy.util.sanitize_html module
- galaxy.util.script module
- galaxy.util.search module
- galaxy.util.simplegraph module
- galaxy.util.sleeper module
- galaxy.util.sockets module
- galaxy.util.specs module
- galaxy.util.sqlite module
- galaxy.util.submodules module
- galaxy.util.task module
- galaxy.util.template module
- galaxy.util.tool_version module
- galaxy.util.topsort module
- galaxy.util.ucsc module
- galaxy.util.validation module
- galaxy.util.watcher module
- galaxy.util.xml_macros module
- galaxy.util.yaml_util module
- galaxy.util.zipstream module
- galaxy.visualization package
- galaxy.web package
do_not_cache()
error()
expose()
expose_api()
expose_api_anonymous()
expose_api_anonymous_and_sessionless()
expose_api_raw()
expose_api_raw_anonymous()
expose_api_raw_anonymous_and_sessionless()
format_return_as_json()
json()
json_pretty()
legacy_expose_api()
legacy_expose_api_anonymous()
legacy_expose_api_raw()
legacy_expose_api_raw_anonymous()
require_admin()
require_login()
legacy_url_for()
url_for()
- Subpackages
- Submodules
- galaxy.web.form_builder module
- galaxy.web.statsd_client module
- galaxy.web_stack package
ApplicationStackLogFilter
ApplicationStack
ApplicationStack.name
ApplicationStack.prohibited_middleware
ApplicationStack.log_filter_class
ApplicationStack.log_format
ApplicationStack.server_name_template
ApplicationStack.default_app_name
ApplicationStack.log_filter()
ApplicationStack.get_app_kwds()
ApplicationStack.register_postfork_function()
ApplicationStack.__init__()
ApplicationStack.supports_returning()
ApplicationStack.supports_skip_locked()
ApplicationStack.get_preferred_handler_assignment_method()
ApplicationStack.init_job_handling()
ApplicationStack.init_late_prefork()
ApplicationStack.log_startup()
ApplicationStack.start()
ApplicationStack.allowed_middleware()
ApplicationStack.workers()
ApplicationStack.pool_name
ApplicationStack.configured_pools
ApplicationStack.has_base_pool()
ApplicationStack.has_pool()
ApplicationStack.in_pool()
ApplicationStack.pool_members()
ApplicationStack.facts
ApplicationStack.set_postfork_server_name()
ApplicationStack.shutdown()
WebApplicationStack
GunicornApplicationStack
GunicornApplicationStack.name
GunicornApplicationStack.do_post_fork
GunicornApplicationStack.postfork_functions
GunicornApplicationStack.late_postfork_event
GunicornApplicationStack.late_postfork_thread
GunicornApplicationStack.register_postfork_function()
GunicornApplicationStack.run_postfork()
GunicornApplicationStack.late_postfork()
GunicornApplicationStack.log_startup()
WeblessApplicationStack
application_stack_class()
application_stack_instance()
application_stack_log_filter()
application_stack_log_formatter()
register_postfork_function()
get_app_kwds()
- Submodules
- galaxy.web_stack.gunicorn_config module
- galaxy.web_stack.handlers module
HANDLER_ASSIGNMENT_METHODS
HandlerAssignmentSkip
ConfiguresHandlers
ConfiguresHandlers.DEFAULT_HANDLER_TAG
ConfiguresHandlers.DEFAULT_BASE_HANDLER_POOLS
ConfiguresHandlers.add_handler()
ConfiguresHandlers.xml_to_dict()
ConfiguresHandlers.get_xml_default()
ConfiguresHandlers.deterministic_handler_assignment
ConfiguresHandlers.is_handler
ConfiguresHandlers.handler_tags
ConfiguresHandlers.self_handler_tags
ConfiguresHandlers.assign_handler()
- galaxy.web_stack.message module
- galaxy.web_stack.transport module
ApplicationStackTransport
ApplicationStackTransport.SHUTDOWN_MSG
ApplicationStackTransport.__init__()
ApplicationStackTransport.init_late_prefork()
ApplicationStackTransport.start_if_needed()
ApplicationStackTransport.stop_if_unneeded()
ApplicationStackTransport.start()
ApplicationStackTransport.send_message()
ApplicationStackTransport.shutdown()
- galaxy.webapps package
- galaxy.webhooks package
- galaxy.work package
- galaxy.workflow package
- Subpackages
- Submodules
- galaxy.workflow.extract module
- galaxy.workflow.modules module
NoReplacement
ConditionalStepWhen
to_cwl()
from_cwl()
evaluate_value_from_expressions()
WorkflowModule
WorkflowModule.label
WorkflowModule.type
WorkflowModule.name
WorkflowModule.__init__()
WorkflowModule.from_dict()
WorkflowModule.from_workflow_step()
WorkflowModule.save_to_step()
WorkflowModule.get_type()
WorkflowModule.get_name()
WorkflowModule.get_version()
WorkflowModule.get_content_id()
WorkflowModule.get_tooltip()
WorkflowModule.get_state()
WorkflowModule.get_export_state()
WorkflowModule.get_tool_state()
WorkflowModule.recover_state()
WorkflowModule.step_state_to_tool_state()
WorkflowModule.get_errors()
WorkflowModule.get_inputs()
WorkflowModule.get_all_inputs()
WorkflowModule.get_data_inputs()
WorkflowModule.get_all_outputs()
WorkflowModule.get_data_outputs()
WorkflowModule.get_post_job_actions()
WorkflowModule.check_and_update_state()
WorkflowModule.add_dummy_datasets()
WorkflowModule.get_config_form()
WorkflowModule.get_runtime_state()
WorkflowModule.get_runtime_inputs()
WorkflowModule.compute_runtime_state()
WorkflowModule.encode_runtime_state()
WorkflowModule.decode_runtime_state()
WorkflowModule.execute()
WorkflowModule.do_invocation_step_action()
WorkflowModule.recover_mapping()
WorkflowModule.get_informal_replacement_parameters()
WorkflowModule.compute_collection_info()
SubWorkflowModule
SubWorkflowModule.type
SubWorkflowModule.name
SubWorkflowModule.subworkflow
SubWorkflowModule.__init__()
SubWorkflowModule.from_dict()
SubWorkflowModule.from_workflow_step()
SubWorkflowModule.save_to_step()
SubWorkflowModule.get_name()
SubWorkflowModule.get_all_inputs()
SubWorkflowModule.get_modules()
SubWorkflowModule.version_changes
SubWorkflowModule.check_and_update_state()
SubWorkflowModule.get_errors()
SubWorkflowModule.get_all_outputs()
SubWorkflowModule.get_post_job_actions()
SubWorkflowModule.get_content_id()
SubWorkflowModule.execute()
SubWorkflowModule.get_runtime_state()
SubWorkflowModule.get_runtime_inputs()
SubWorkflowModule.get_informal_replacement_parameters()
InputProxy
optional_param()
format_param()
InputModuleState
InputModule
InputDataModule
InputDataCollectionModule
InputDataCollectionModule.type
InputDataCollectionModule.name
InputDataCollectionModule.default_collection_type
InputDataCollectionModule.collection_type
InputDataCollectionModule.get_inputs()
InputDataCollectionModule.get_runtime_inputs()
InputDataCollectionModule.get_all_outputs()
InputDataCollectionModule.label
InputParameterModule
InputParameterModule.POSSIBLE_PARAMETER_TYPES
InputParameterModule.type
InputParameterModule.name
InputParameterModule.default_parameter_type
InputParameterModule.default_optional
InputParameterModule.default_default_value
InputParameterModule.parameter_type
InputParameterModule.optional
InputParameterModule.default_value
InputParameterModule.get_inputs()
InputParameterModule.restrict_options()
InputParameterModule.get_runtime_inputs()
InputParameterModule.get_runtime_state()
InputParameterModule.get_all_outputs()
InputParameterModule.execute()
InputParameterModule.step_state_to_tool_state()
InputParameterModule.get_export_state()
InputParameterModule.save_to_step()
InputParameterModule.label
PauseModule
ToolModule
ToolModule.type
ToolModule.name
ToolModule.__init__()
ToolModule.from_dict()
ToolModule.from_workflow_step()
ToolModule.save_to_step()
ToolModule.get_name()
ToolModule.get_content_id()
ToolModule.get_version()
ToolModule.get_tooltip()
ToolModule.get_errors()
ToolModule.get_inputs()
ToolModule.get_all_inputs()
ToolModule.get_all_outputs()
ToolModule.get_config_form()
ToolModule.check_and_update_state()
ToolModule.add_dummy_datasets()
ToolModule.get_post_job_actions()
ToolModule.recover_state()
ToolModule.augment_tool_state_for_input_connections()
ToolModule.get_runtime_state()
ToolModule.get_runtime_inputs()
ToolModule.compute_runtime_state()
ToolModule.decode_runtime_state()
ToolModule.execute()
ToolModule.get_informal_replacement_parameters()
ToolModule.label
WorkflowModuleFactory
load_module_sections()
DelayedWorkflowEvaluation
CancelWorkflowEvaluation
FailWorkflowEvaluation
SkipWorkflowStepEvaluation
WorkflowModuleInjector
populate_module_and_state()
- galaxy.workflow.render module
- galaxy.workflow.run module
- galaxy.workflow.run_request module
- galaxy.workflow.scheduling_manager module
- galaxy.workflow.steps module
- galaxy.workflow.trs_proxy module
Submodules¶
galaxy.app module¶
- class galaxy.app.SentryClientMixin[source]¶
Bases:
object
- config: GalaxyAppConfiguration¶
- application_stack: ApplicationStack¶
- class galaxy.app.MinimalGalaxyApplication(fsmon=False, **kwargs)[source]¶
Bases:
BasicSharedApp
,HaltableContainer
,SentryClientMixin
Encapsulates the state of a minimal Galaxy application
- model: GalaxyModelMapping¶
- job_config: JobConfiguration¶
- toolbox_search: ToolBoxSearch¶
- container_finder: ContainerFinder¶
- install_model: ModelMapping¶
- object_store: BaseObjectStore¶
- config: GalaxyAppConfiguration¶
- property tool_dependency_dir¶
- class galaxy.app.GalaxyManagerApplication(configure_logging=True, use_converters=True, use_display_applications=True, **kwargs)[source]¶
Bases:
MinimalManagerApp
,MinimalGalaxyApplication
Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context.
- model: GalaxyModelMapping¶
- class galaxy.app.UniverseApplication(**kwargs)[source]¶
Bases:
StructuredApp
,GalaxyManagerApplication
Encapsulates the state of a Universe application
- model: GalaxyModelMapping¶
- class galaxy.app.StatsdStructuredExecutionTimer(galaxy_statsd_client, *args, **kwds)[source]¶
Bases:
StructuredExecutionTimer
galaxy.config_watchers module¶
- class galaxy.config_watchers.ConfigWatchers(app: StructuredApp)[source]¶
Bases:
object
Contains ToolConfWatcher, ToolWatcher and ToolDataWatcher objects.
- __init__(app: StructuredApp)[source]¶
- property watchers¶
- property data_manager_configs¶
- property tool_data_paths¶
- property tool_config_paths¶
- property job_rules_paths¶
galaxy.di module¶
Dependency injection framework for Galaxy-type apps.
- class galaxy.di.Container[source]¶
Bases:
Container
Abstraction around lagom to provide a dependency injection context.
Abstractions used by Galaxy should come through this interface so we can swap out the backend as needed. For instance https://punq.readthedocs.io/en/latest/ containers look very nice and would allow us to also inject by name (e.g. for config variables for instance).
- resolve_or_none(dep_type: Type[T]) Optional[T] [source]¶
Resolve the dependent type or just return None.
If resolution is impossible assume caller has a backup plan for constructing the desired object. Used to construct controllers that may or may not be resolvable (some have upgraded but legacy framework still works).
galaxy.main module¶
Entry point for starting Galaxy without starting as part of a web server.
Example Usage: Start a job/workflow handler without a web server and with a given name using.
galaxy-main –server-name handler0
Start as a daemon with (requires daemonized - install with ‘pip install daemonize’):
galaxy-main -d –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –server-name handler0
In daemon mode logging of Galaxy (as opposed to this script) is configured via a loggers section in Galaxy’s ini file - this can be overridden with sensible defaults logging to a single file with the following:
galaxy-main -d –server-name handler0 –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –log-file handler0.log
- galaxy.main.load_galaxy_app(config_builder, config_env=False, log=None, attach_to_pools=None, **kwds)[source]¶
galaxy.main_config module¶
Utilities for finding Galaxy’s configuration file.
This is for use by web framework code and scripts (e.g. scripts/galaxy_main.py).
- galaxy.main_config.find_config(supplied_config: Optional[str], galaxy_root: Optional[str], app_name: str = 'galaxy') Optional[str] [source]¶
- class galaxy.main_config.WebappSetupProps(app_name: str, default_section_name: str, env_config_file: str, env_config_section: Optional[str] = None, check_galaxy_root: bool = False)[source]¶
Bases:
tuple
Basic properties to provide information about the App and the environment variables used to resolve the App configuration.
- property app_name¶
Alias for field number 0
- property default_section_name¶
Alias for field number 1
- property env_config_file¶
Alias for field number 2
- property env_config_section¶
Alias for field number 3
- property check_galaxy_root¶
Alias for field number 4
- class galaxy.main_config.WebappConfig(global_conf: dict, load_app_kwds: dict, wsgi_preflight: bool = False)[source]¶
Bases:
tuple
The resolved configuration values for a Webapp.
- property global_conf¶
Alias for field number 0
- property load_app_kwds¶
Alias for field number 1
- property wsgi_preflight¶
Alias for field number 2
- class galaxy.main_config.WebappConfigResolver(props: WebappSetupProps)[source]¶
Bases:
object
- __init__(props: WebappSetupProps) None [source]¶
- resolve_config() WebappConfig [source]¶
galaxy.queue_worker module¶
Galaxy control queue and worker. This is used to handle ‘app’ control like reloading the toolbox, etc., across multiple processes.
- galaxy.queue_worker.send_local_control_task(app, task, get_response=False, kwargs=None)[source]¶
This sends a message to the process-local control worker, which is useful for one-time asynchronous tasks like recalculating user disk usage.
- galaxy.queue_worker.send_control_task(app, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]¶
This sends a control task out to all processes, useful for things like reloading a data table, which needs to happen individually in all processes. Set noop_self to True to not run task for current process. Set get_response to True to wait for and return the task results as a list.
- class galaxy.queue_worker.ControlTask(queue_worker)[source]¶
Bases:
object
- property connection¶
- property control_queues¶
- property exchange¶
- property declare_queues¶
- galaxy.queue_worker.create_panel_section(app, **kwargs)[source]¶
Updates in memory toolbox dictionary.
- class galaxy.queue_worker.GalaxyQueueWorker(app, task_mapping=None)[source]¶
Bases:
ConsumerProducerMixin
,Thread
This is a flexible worker for galaxy’s queues. Each process, web or handler, will have one of these used for dispatching so called ‘control’ tasks.
- send_control_task(task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]¶
- property declare_queues¶
galaxy.queues module¶
All message queues used by Galaxy
- galaxy.queues.all_control_queues_for_declare(application_stack)[source]¶
For in-memory routing (used by sqlalchemy-based transports), we need to be able to build the entire routing table in producers.
galaxy.structured_app module¶
Typed description of Galaxy’s app object.
Bases:
Container
Stripped down version of the
app
shared between Galaxy and ToolShed.Code that is shared between Galaxy and the Tool Shed should be annotated as using BasicSharedApp instead of StructuredApp below.
- class galaxy.structured_app.MinimalToolApp(*args, **kwds)[source]¶
Bases:
Protocol
- object_store: BaseObjectStore¶
- tool_data_tables: ToolDataTableManager¶
- file_sources: ConfiguredFileSources¶
- security: IdEncodingHelper¶
- __init__(*args, **kwargs)¶
- class galaxy.structured_app.MinimalApp[source]¶
Bases:
BasicSharedApp
- tag_handler: GalaxyTagHandler¶
- model: GalaxyModelMapping¶
- install_model: ModelMapping¶
- security_agent: GalaxyRBACAgent¶
- class galaxy.structured_app.MinimalManagerApp[source]¶
Bases:
MinimalApp
- file_sources: ConfiguredFileSources¶
- genome_builds: GenomeBuilds¶
- dataset_collection_manager: DatasetCollectionManager¶
- tool_data_tables: ToolDataTableManager¶
- history_manager: HistoryManager¶
- hda_manager: HDAManager¶
- workflow_manager: WorkflowsManager¶
- installed_repository_manager: InstalledRepositoryManager¶
- job_config: JobConfiguration¶
- job_metrics: JobMetrics¶
- error_reports: ErrorReports¶
- object_store: BaseObjectStore¶
- tool_shed_registry: Registry¶
- class galaxy.structured_app.StructuredApp[source]¶
Bases:
MinimalManagerApp
Interface defining typed description of the Galaxy UniverseApplication.
Ideally nothing that depends on StructuredApp should require StructuredApp so we can have a clean import dag. This will require setting up a lot more distinction between interfaces and implementations in Galaxy though. In the meantime, for imports that would bring in StructuredApp if properly type (cyclical imports), we’re just setting the class attributes to Any.
- dependency_resolvers_view: DependencyResolversView¶
- container_finder: ContainerFinder¶
- test_data_resolver: TestDataResolver¶
- webhooks_registry: WebhooksRegistry¶
- tool_data_tables: ToolDataTableManager¶
- watchers: ConfigWatchers¶