diff --git a/doc/source/admin/config.rst b/doc/source/admin/config.rst index 0d95c1595a2..a2ffed2b8af 100644 --- a/doc/source/admin/config.rst +++ b/doc/source/admin/config.rst @@ -93,7 +93,7 @@ Configuration Basics ---------------------------- - Edit ``config/galaxy.yml`` (copy it from ``config/galaxy.yml.sample`` if it does not exist) to make configuration - changes. This is a `YAML configuration file`_ and should contain one or two sections, one named ``gravity`` for + changes. This is a YAML configuration file and should contain one or two sections, one named ``gravity`` for process management via `Gravity`_ (optional) and one named ``galaxy`` for Galaxy (required). - The `gravity` section contain several important options about how to diff --git a/doc/source/admin/config_logging.rst b/doc/source/admin/config_logging.rst index cd6e4460a9a..33348695a9a 100644 --- a/doc/source/admin/config_logging.rst +++ b/doc/source/admin/config_logging.rst @@ -9,22 +9,19 @@ There are two ways in which you can configure logging for Galaxy servers: 1. Basic/automatic configuration with control over log level and log destination (standard output or a named log file). 2. More complex configuration using the Python :mod:`logging` module's :func:`logging.config.dictConfig` or :func:`logging.config.fileConfig`. -By default, Galaxy logs all messages to standard output at the ``DEBUG`` logging level, unless the ``--daemon`` argument -is passed to ``run.sh``, in which case, output is logged to a location configured in `gravity`_. - -Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing ` documentation. - Basic Configuration ---------------------------- -Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs. The level -is controlled by the ``log_level`` configuration option. +Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs. -If not set, Galaxy logs all messages at the ``DEBUG`` level (versions prior to 18.01 defaulted to ``INFO`` if unset, but -the default config file shipped with ``log_level`` explicitly set to ``DEBUG`` for development purposes). +The logging level is controlled by the ``log_level`` configuration option. By default, Galaxy logs all messages at the +``DEBUG`` level. -Galaxy logs all messages to standard output by default if running in the foreground. If running in the background, the -log is written to a location configured in `gravity`_. +Galaxy logs all messages to standard output by default if running in the foreground. If running in the background (e.g. +by passing the ``--daemon`` argument to ``run.sh``), the log is written to a location configured in +`gravity `_. + +Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing ` documentation. **Setting the log level:** diff --git a/doc/source/lib/galaxy.app_unittest_utils.rst b/doc/source/lib/galaxy.app_unittest_utils.rst index b7102289a47..03d8255bcae 100644 --- a/doc/source/lib/galaxy.app_unittest_utils.rst +++ b/doc/source/lib/galaxy.app_unittest_utils.rst @@ -9,14 +9,6 @@ galaxy.app\_unittest\_utils package Submodules ---------- -galaxy.app\_unittest\_utils.celery\_helper module -------------------------------------------------- - -.. automodule:: galaxy.app_unittest_utils.celery_helper - :members: - :undoc-members: - :show-inheritance: - galaxy.app\_unittest\_utils.galaxy\_mock module ----------------------------------------------- diff --git a/doc/source/lib/galaxy.containers.rst b/doc/source/lib/galaxy.containers.rst deleted file mode 100644 index 6a1a6952015..00000000000 --- a/doc/source/lib/galaxy.containers.rst +++ /dev/null @@ -1,42 +0,0 @@ -galaxy.containers package -========================= - -.. automodule:: galaxy.containers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.containers.docker module -------------------------------- - -.. automodule:: galaxy.containers.docker - :members: - :undoc-members: - :show-inheritance: - -galaxy.containers.docker\_decorators module -------------------------------------------- - -.. automodule:: galaxy.containers.docker_decorators - :members: - :undoc-members: - :show-inheritance: - -galaxy.containers.docker\_model module --------------------------------------- - -.. automodule:: galaxy.containers.docker_model - :members: - :undoc-members: - :show-inheritance: - -galaxy.containers.docker\_swarm module --------------------------------------- - -.. automodule:: galaxy.containers.docker_swarm - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index ba4f5c2ed25..6975459123f 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -268,6 +268,14 @@ galaxy.datatypes.proteomics module :undoc-members: :show-inheritance: +galaxy.datatypes.qiime2 module +------------------------------ + +.. automodule:: galaxy.datatypes.qiime2 + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.qualityscore module ------------------------------------ diff --git a/doc/source/lib/galaxy.files.rst b/doc/source/lib/galaxy.files.rst index 47b7e4bf13d..8d98f0d70b8 100644 --- a/doc/source/lib/galaxy.files.rst +++ b/doc/source/lib/galaxy.files.rst @@ -14,3 +14,14 @@ Subpackages galaxy.files.sources galaxy.files.unittest_utils + +Submodules +---------- + +galaxy.files.uris module +------------------------ + +.. automodule:: galaxy.files.uris + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_metrics.instrumenters.rst b/doc/source/lib/galaxy.job_metrics.instrumenters.rst index 54615895b99..c6312d28484 100644 --- a/doc/source/lib/galaxy.job_metrics.instrumenters.rst +++ b/doc/source/lib/galaxy.job_metrics.instrumenters.rst @@ -17,14 +17,6 @@ galaxy.job\_metrics.instrumenters.cgroup module :undoc-members: :show-inheritance: -galaxy.job\_metrics.instrumenters.collectl module -------------------------------------------------- - -.. automodule:: galaxy.job_metrics.instrumenters.collectl - :members: - :undoc-members: - :show-inheritance: - galaxy.job\_metrics.instrumenters.core module --------------------------------------------- diff --git a/doc/source/lib/galaxy.job_metrics.rst b/doc/source/lib/galaxy.job_metrics.rst index f8c01bd1cb5..73af55fcaf0 100644 --- a/doc/source/lib/galaxy.job_metrics.rst +++ b/doc/source/lib/galaxy.job_metrics.rst @@ -24,3 +24,11 @@ galaxy.job\_metrics.formatting module :members: :undoc-members: :show-inheritance: + +galaxy.job\_metrics.safety module +--------------------------------- + +.. automodule:: galaxy.job_metrics.safety + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index 0a1c0bebbc1..426630b05c1 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -273,6 +273,14 @@ galaxy.managers.metrics module :undoc-members: :show-inheritance: +galaxy.managers.model\_stores module +------------------------------------ + +.. automodule:: galaxy.managers.model_stores + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.pages module ---------------------------- diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst deleted file mode 100644 index 7f78af9078c..00000000000 --- a/doc/source/lib/galaxy.model.migrate.rst +++ /dev/null @@ -1,27 +0,0 @@ -galaxy.model.migrate package -============================ - -.. automodule:: galaxy.model.migrate - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - galaxy.model.migrate.triggers - galaxy.model.migrate.versions - -Submodules ----------- - -galaxy.model.migrate.check module ---------------------------------- - -.. automodule:: galaxy.model.migrate.check - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrate.triggers.rst b/doc/source/lib/galaxy.model.migrate.triggers.rst deleted file mode 100644 index 7297f66154f..00000000000 --- a/doc/source/lib/galaxy.model.migrate.triggers.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.model.migrate.triggers package -===================================== - -.. automodule:: galaxy.model.migrate.triggers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.model.migrate.triggers.history\_update\_time\_field module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.triggers.history_update_time_field - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.triggers.update\_audit\_table module ---------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.triggers.update_audit_table - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrate.versions.rst b/doc/source/lib/galaxy.model.migrate.versions.rst deleted file mode 100644 index 07d2348277c..00000000000 --- a/doc/source/lib/galaxy.model.migrate.versions.rst +++ /dev/null @@ -1,1458 +0,0 @@ -galaxy.model.migrate.versions package -===================================== - -.. automodule:: galaxy.model.migrate.versions - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.model.migrate.versions.0001\_initial\_tables module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0001_initial_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0002\_metadata\_file\_table module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0002_metadata_file_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0003\_security\_and\_libraries module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0003_security_and_libraries - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0004\_indexes\_and\_defaults module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0004_indexes_and_defaults - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0005\_cleanup\_datasets\_fix module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0005_cleanup_datasets_fix - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0006\_change\_qual\_datatype module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0006_change_qual_datatype - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0007\_sharing\_histories module -------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0007_sharing_histories - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0008\_galaxy\_forms module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0008_galaxy_forms - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0009\_request\_table module ---------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0009_request_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0010\_hda\_display\_at\_authz\_table module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0010_hda_display_at_authz_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0011\_v0010\_mysql\_index\_fix module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0011_v0010_mysql_index_fix - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0012\_user\_address module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0012_user_address - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0013\_change\_lib\_item\_templates\_to\_forms module ----------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0014\_pages module ------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0014_pages - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0015\_tagging module --------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0015_tagging - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0016\_v0015\_mysql\_index\_fix module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0016_v0015_mysql_index_fix - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0017\_library\_item\_indexes module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0017_library_item_indexes - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0018\_ordered\_tags\_and\_page\_tags module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0019\_request\_library\_folder module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0019_request_library_folder - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0020\_library\_upload\_job module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0020_library_upload_job - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0021\_user\_prefs module ------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0021_user_prefs - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0022\_visualization\_tables module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0022_visualization_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0023\_page\_published\_and\_deleted\_columns module ---------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0023_page_published_and_deleted_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0024\_page\_slug\_unique\_constraint module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0024_page_slug_unique_constraint - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0025\_user\_info module ------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0025_user_info - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0026\_cloud\_tables module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0026_cloud_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0027\_request\_events module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0027_request_events - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0028\_external\_metadata\_file\_override module ------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0028_external_metadata_file_override - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0029\_user\_actions module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0029_user_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0030\_history\_slug\_column module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0030_history_slug_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0031\_community\_and\_workflow\_tags module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0031_community_and_workflow_tags - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0032\_stored\_workflow\_slug\_column module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0032_stored_workflow_slug_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0033\_published\_cols\_for\_histories\_and\_workflows module ------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0034\_page\_user\_share\_association module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0034_page_user_share_association - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0035\_item\_annotations\_and\_workflow\_step\_tags module ---------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0036\_add\_deleted\_column\_to\_library\_template\_assoc\_tables module ------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0037\_samples\_library module ------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0037_samples_library - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0038\_add\_inheritable\_column\_to\_library\_template\_assoc\_tables module ---------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0039\_add\_synopsis\_column\_to\_library\_table module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0040\_page\_annotations module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0040_page_annotations - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0041\_workflow\_invocation module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0041_workflow_invocation - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0042\_workflow\_invocation\_fix module --------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0042_workflow_invocation_fix - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0043\_visualization\_sharing\_tagging\_annotating module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0044\_add\_notify\_column\_to\_request\_table module ----------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0044_add_notify_column_to_request_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0045\_request\_type\_permissions\_table module ----------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0045_request_type_permissions_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0046\_post\_job\_actions module -------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0046_post_job_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0047\_job\_table\_user\_id\_column module ------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0047_job_table_user_id_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0048\_dataset\_instance\_state\_column module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0048_dataset_instance_state_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0049\_api\_keys\_table module ------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0049_api_keys_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0050\_drop\_cloud\_tables module --------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0050_drop_cloud_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0051\_imported\_col\_for\_jobs\_table module --------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0051_imported_col_for_jobs_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0052\_sample\_dataset\_table module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0052_sample_dataset_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0053\_item\_ratings module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0053_item_ratings - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0054\_visualization\_dbkey module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0054_visualization_dbkey - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0055\_add\_pja\_assoc\_for\_jobs module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0056\_workflow\_outputs module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0056_workflow_outputs - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0057\_request\_notify module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0057_request_notify - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0058\_history\_import\_export module ------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0058_history_import_export - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0059\_sample\_dataset\_file\_path module ----------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0059_sample_dataset_file_path - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0060\_history\_archive\_import module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0060_history_archive_import - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0061\_tasks module ------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0061_tasks - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0062\_user\_openid\_table module --------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0062_user_openid_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0063\_sequencer\_table module ------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0063_sequencer_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0064\_add\_run\_and\_sample\_run\_association\_tables module ------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0065\_add\_name\_to\_form\_fields\_and\_values module ------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0066\_deferred\_job\_and\_transfer\_job\_tables module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0067\_populate\_sequencer\_table module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0067_populate_sequencer_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0068\_rename\_sequencer\_to\_external\_services module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0069\_rename\_sequencer\_form\_type module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0069_rename_sequencer_form_type - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0070\_add\_info\_column\_to\_deferred\_job\_table module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0071\_add\_history\_and\_workflow\_to\_sample module ----------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0072\_add\_pid\_and\_socket\_columns\_to\_transfer\_job\_table module ---------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0073\_add\_ldda\_to\_implicit\_conversion\_table module -------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0074\_add\_purged\_column\_to\_library\_dataset\_table module -------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0075\_add\_subindex\_column\_to\_run\_table module --------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0076\_fix\_form\_values\_data\_corruption module ------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0076_fix_form_values_data_corruption - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0077\_create\_tool\_tag\_association\_table module --------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0077_create_tool_tag_association_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0078\_add\_columns\_for\_disk\_usage\_accounting module -------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0079\_input\_library\_to\_job\_table module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0079_input_library_to_job_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0080\_quota\_tables module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0080_quota_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0081\_add\_tool\_version\_to\_hda\_ldda module ----------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0082\_add\_tool\_shed\_repository\_table module ------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0082_add_tool_shed_repository_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0083\_add\_prepare\_files\_to\_task module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0083_add_prepare_files_to_task - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0084\_add\_ldda\_id\_to\_implicit\_conversion\_table module ------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0085\_add\_task\_info module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0085_add_task_info - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0086\_add\_tool\_shed\_repository\_table\_columns module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0087\_tool\_id\_guid\_map\_table module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0087_tool_id_guid_map_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0088\_add\_installed\_changeset\_revison\_column module -------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0089\_add\_object\_store\_id\_columns module --------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0089_add_object_store_id_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0090\_add\_tool\_shed\_repository\_table\_columns module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0091\_add\_tool\_version\_tables module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0091_add_tool_version_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0092\_add\_migrate\_tools\_table module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0092_add_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0093\_add\_job\_params\_col module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0093_add_job_params_col - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0094\_add\_job\_handler\_col module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0094_add_job_handler_col - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0095\_hda\_subsets module -------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0095_hda_subsets - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0096\_openid\_provider module ------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0096_openid_provider - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0097\_add\_ctx\_rev\_column module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0097_add_ctx_rev_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0098\_genome\_index\_tool\_data\_table module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0098_genome_index_tool_data_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0099\_add\_tool\_dependency\_table module ------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0099_add_tool_dependency_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0100\_alter\_tool\_dependency\_table\_version\_column module ------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0101\_drop\_installed\_changeset\_revision\_column module ---------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0102\_add\_tool\_dependency\_status\_columns module ---------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0103\_add\_tool\_shed\_repository\_status\_columns module ---------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0104\_update\_genome\_downloader\_job\_parameters module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0105\_add\_cleanup\_event\_table module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0105_add_cleanup_event_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0106\_add\_missing\_indexes module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0106_add_missing_indexes - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0107\_add\_exit\_code\_to\_job\_and\_task module ------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0108\_add\_extended\_metadata module ------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0108_add_extended_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0109\_add\_repository\_dependency\_tables module ------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0109_add_repository_dependency_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0110\_add\_dataset\_uuid module -------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0110_add_dataset_uuid - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0111\_add\_job\_destinations module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0111_add_job_destinations - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0112\_add\_data\_manager\_history\_association\_and\_data\_manager\_job\_association\_tables module ---------------------------------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0113\_update\_migrate\_tools\_table module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0113_update_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0114\_update\_migrate\_tools\_table\_again module -------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0114_update_migrate_tools_table_again - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0115\_longer\_user\_password\_field module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0115_longer_user_password_field - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0116\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module ------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0117\_add\_user\_activation module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0117_add_user_activation - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0118\_add\_hda\_extended\_metadata module ------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0118_add_hda_extended_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0119\_job\_metrics module -------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0119_job_metrics - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0120\_dataset\_collections module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0120_dataset_collections - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0121\_workflow\_uuids module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0121_workflow_uuids - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0122\_grow\_mysql\_blobs module -------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0122_grow_mysql_blobs - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0123\_add\_workflow\_request\_tables module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0123_add_workflow_request_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0124\_job\_state\_history module --------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0124_job_state_history - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0125\_workflow\_step\_tracking module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0125_workflow_step_tracking - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0126\_password\_reset module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0126_password_reset - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0127\_output\_collection\_adjustments module --------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0127_output_collection_adjustments - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0128\_session\_timeout module ------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0128_session_timeout - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0129\_job\_external\_output\_metadata\_validity module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0129_job_external_output_metadata_validity - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0130\_change\_pref\_datatype module ------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0130_change_pref_datatype - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0131\_subworkflow\_and\_input\_parameter\_modules module --------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0132\_add\_lastpasswordchange\_to\_user module ----------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0133\_add\_dependency\_column\_to\_job module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0133_add_dependency_column_to_job - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0134\_hda\_set\_deleted\_if\_purged module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0135\_add\_library\_tags module -------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0135_add_library_tags - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0136\_collection\_and\_workflow\_state module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0136_collection_and_workflow_state - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0137\_add\_copied\_from\_job\_id\_column module ------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0137_add_copied_from_job_id_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0138\_add\_hda\_version module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0138_add_hda_version - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0139\_add\_history\_dataset\_association\_history\_table module ---------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0140\_add\_dataset\_version\_to\_job\_to\_input\_dataset\_association\_table module ------------------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0141\_add\_oidc\_tables module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0141_add_oidc_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0142\_change\_numeric\_metric\_precision module ------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0142_change_numeric_metric_precision - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0143\_add\_cloudauthz\_tables module ------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0143_add_cloudauthz_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0144\_add\_cleanup\_event\_user\_table module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0144_add_cleanup_event_user_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0145\_add\_workflow\_step\_input module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0145_add_workflow_step_input - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0146\_workflow\_paths module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0146_workflow_paths - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0147\_job\_messages module --------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0147_job_messages - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0148\_add\_checksum\_table module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0148_add_checksum_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0149\_dynamic\_tools module ---------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0149_dynamic_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0150\_add\_create\_time\_field\_for\_cloudauthz module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0151\_add\_worker\_process module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0151_add_worker_process - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0152\_add\_metadata\_file\_uuid module --------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0152_add_metadata_file_uuid - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0153\_add\_custos\_authnz\_token\_table module ----------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0153_add_custos_authnz_token_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0154\_created\_from\_basename module ------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0154_created_from_basename - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0155\_job\_galaxy\_version module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0155_job_galaxy_version - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0156\_add\_interactivetools module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0156_add_interactivetools - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0157\_rework\_dataset\_validation module ----------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0157_rework_dataset_validation - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0158\_workflow\_reports module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0158_workflow_reports - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0159\_add\_job\_external\_id\_index module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0159_add_job_external_id_index - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0160\_hda\_set\_deleted\_if\_purged\_again module -------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0161\_add\_workflow\_invocation\_output\_table module ------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0162\_job\_only\_pjas module ----------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0162_job_only_pjas - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0163\_worker\_process\_pid module ---------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0163_worker_process_pid - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0164\_page\_format module -------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0164_page_format - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0165\_add\_content\_update\_time module ---------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0165_add_content_update_time - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0166\_job\_state\_summary\_view module --------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0166_job_state_summary_view - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0167\_add\_job\_to\_input\_dataset\_collection\_element\_association module ---------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0168\_stored\_workflow\_hidden\_col module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0168_stored_workflow_hidden_col - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0169\_add\_missing\_indexes module ----------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0169_add_missing_indexes - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0170\_add\_more\_missing\_indexes module ----------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0170_add_more_missing_indexes - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0171\_schemaorg\_metadata module --------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0171_schemaorg_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0172\_it\_entrypoint\_requires\_domain module ---------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0173\_add\_job\_id\_to\_dataset module --------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0173_add_job_id_to_dataset - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0174\_readd\_update\_time\_triggers module ------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0174_readd_update_time_triggers - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0175\_history\_audit module ---------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0175_history_audit - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0176\_add\_indexes\_on\_update\_time module -------------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0176_add_indexes_on_update_time - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0177\_update\_job\_state\_summary module ----------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0177_update_job_state_summary - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0178\_drop\_deferredjob\_table module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0178_drop_deferredjob_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0179\_drop\_transferjob\_table module -------------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0179_drop_transferjob_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.0180\_add\_vault\_table module ------------------------------------------------------------- - -.. automodule:: galaxy.model.migrate.versions.0180_add_vault_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.migrate.versions.util module ------------------------------------------ - -.. automodule:: galaxy.model.migrate.versions.util - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrations.rst b/doc/source/lib/galaxy.model.migrations.rst new file mode 100644 index 00000000000..4212e1dc003 --- /dev/null +++ b/doc/source/lib/galaxy.model.migrations.rst @@ -0,0 +1,26 @@ +galaxy.model.migrations package +=============================== + +.. automodule:: galaxy.model.migrations + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrations.scripts module +-------------------------------------- + +.. automodule:: galaxy.model.migrations.scripts + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrations.util module +----------------------------------- + +.. automodule:: galaxy.model.migrations.util + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 726abd3e20a..d5d891d5614 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -32,3 +32,11 @@ galaxy.model.orm.scripts module :members: :undoc-members: :show-inheritance: + +galaxy.model.orm.util module +---------------------------- + +.. automodule:: galaxy.model.orm.util + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index 5805dce314f..a99d4400332 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -13,10 +13,11 @@ Subpackages :maxdepth: 4 galaxy.model.dataset_collections - galaxy.model.migrate + galaxy.model.migrations galaxy.model.orm galaxy.model.store galaxy.model.tool_shed_install + galaxy.model.triggers galaxy.model.unittest_utils galaxy.model.view @@ -55,6 +56,22 @@ galaxy.model.database\_utils module :undoc-members: :show-inheritance: +galaxy.model.deferred module +---------------------------- + +.. automodule:: galaxy.model.deferred + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.index\_filter\_util module +--------------------------------------- + +.. automodule:: galaxy.model.index_filter_util + :members: + :undoc-members: + :show-inheritance: + galaxy.model.item\_attrs module ------------------------------- diff --git a/doc/source/lib/galaxy.model.store.rst b/doc/source/lib/galaxy.model.store.rst index 84e3b2fcb3f..6a7baa50222 100644 --- a/doc/source/lib/galaxy.model.store.rst +++ b/doc/source/lib/galaxy.model.store.rst @@ -24,3 +24,11 @@ galaxy.model.store.discover module :members: :undoc-members: :show-inheritance: + +galaxy.model.store.load\_objects module +--------------------------------------- + +.. automodule:: galaxy.model.store.load_objects + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst deleted file mode 100644 index 6fbecd637b3..00000000000 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.model.tool\_shed\_install.migrate package -================================================ - -.. automodule:: galaxy.model.tool_shed_install.migrate - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - galaxy.model.tool_shed_install.migrate.versions - -Submodules ----------- - -galaxy.model.tool\_shed\_install.migrate.check module ------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.check - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst deleted file mode 100644 index 9c39abe91a3..00000000000 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst +++ /dev/null @@ -1,146 +0,0 @@ -galaxy.model.tool\_shed\_install.migrate.versions package -========================================================= - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.model.tool\_shed\_install.migrate.versions.0001\_add\_tool\_shed\_repository\_table module -------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0001_add_tool_shed_repository_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0002\_add\_tool\_shed\_repository\_table\_columns module ----------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0002_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0003\_tool\_id\_guid\_map\_table module ------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0003_tool_id_guid_map_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0004\_add\_installed\_changeset\_revison\_column module ---------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0005\_add\_tool\_shed\_repository\_table\_columns module ----------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0005_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0006\_add\_tool\_version\_tables module ------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0006_add_tool_version_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0007\_add\_migrate\_tools\_table module ------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0007_add_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0008\_add\_ctx\_rev\_column module ------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0008_add_ctx_rev_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0009\_add\_tool\_dependency\_table module -------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0009_add_tool_dependency_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0010\_alter\_tool\_dependency\_table\_version\_column module --------------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0011\_drop\_installed\_changeset\_revision\_column module ------------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0011_drop_installed_changeset_revision_column - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0012\_add\_tool\_dependency\_status\_columns module ------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0012_add_tool_dependency_status_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0013\_add\_tool\_shed\_repository\_status\_columns module ------------------------------------------------------------------------------------------------------------ - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0013_add_tool_shed_repository_status_columns - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0014\_add\_repository\_dependency\_tables module --------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0014_add_repository_dependency_tables - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0015\_update\_migrate\_tools\_table module --------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0015_update_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0016\_update\_migrate\_tools\_table\_again module ---------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0016_update_migrate_tools_table_again - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.tool\_shed\_install.migrate.versions.0017\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module -------------------------------------------------------------------------------------------------------------------------- - -.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0017_drop_update_available_col_add_tool_shed_status_col - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index 464c6ec817e..310da54edfa 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -6,14 +6,6 @@ galaxy.model.tool\_shed\_install package :undoc-members: :show-inheritance: -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - galaxy.model.tool_shed_install.migrate - Submodules ---------- diff --git a/doc/source/lib/galaxy.model.triggers.rst b/doc/source/lib/galaxy.model.triggers.rst new file mode 100644 index 00000000000..8b533245807 --- /dev/null +++ b/doc/source/lib/galaxy.model.triggers.rst @@ -0,0 +1,34 @@ +galaxy.model.triggers package +============================= + +.. automodule:: galaxy.model.triggers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.triggers.history\_update\_time\_field module +--------------------------------------------------------- + +.. automodule:: galaxy.model.triggers.history_update_time_field + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.triggers.update\_audit\_table module +------------------------------------------------- + +.. automodule:: galaxy.model.triggers.update_audit_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.triggers.utils module +---------------------------------- + +.. automodule:: galaxy.model.triggers.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.unittest_utils.rst b/doc/source/lib/galaxy.model.unittest_utils.rst index b6b8fc19959..b99b4ecfeaf 100644 --- a/doc/source/lib/galaxy.model.unittest_utils.rst +++ b/doc/source/lib/galaxy.model.unittest_utils.rst @@ -16,3 +16,11 @@ galaxy.model.unittest\_utils.data\_app module :members: :undoc-members: :show-inheritance: + +galaxy.model.unittest\_utils.store\_fixtures module +--------------------------------------------------- + +.. automodule:: galaxy.model.unittest_utils.store_fixtures + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index 5220a7fd12b..29c593de677 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -18,7 +18,6 @@ Subpackages galaxy.authnz galaxy.celery galaxy.config - galaxy.containers galaxy.datatypes galaxy.dependencies galaxy.exceptions diff --git a/doc/source/lib/galaxy.schema.rst b/doc/source/lib/galaxy.schema.rst index 0e245468d5d..3f1420b256b 100644 --- a/doc/source/lib/galaxy.schema.rst +++ b/doc/source/lib/galaxy.schema.rst @@ -9,6 +9,14 @@ galaxy.schema package Submodules ---------- +galaxy.schema.fetch\_data module +-------------------------------- + +.. automodule:: galaxy.schema.fetch_data + :members: + :undoc-members: + :show-inheritance: + galaxy.schema.fields module --------------------------- @@ -33,6 +41,14 @@ galaxy.schema.schema module :undoc-members: :show-inheritance: +galaxy.schema.tasks module +-------------------------- + +.. automodule:: galaxy.schema.tasks + :members: + :undoc-members: + :show-inheritance: + galaxy.schema.types module -------------------------- diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst index bc765a12beb..63b17d56508 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst @@ -15,7 +15,6 @@ Subpackages galaxy.tool_shed.galaxy_install.datatypes galaxy.tool_shed.galaxy_install.metadata galaxy.tool_shed.galaxy_install.repository_dependencies - galaxy.tool_shed.galaxy_install.tool_dependencies galaxy.tool_shed.galaxy_install.tools Submodules diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst deleted file mode 100644 index 78eb081a3cd..00000000000 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst +++ /dev/null @@ -1,58 +0,0 @@ -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe package -=================================================================== - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader module ---------------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module -------------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module ---------------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module ----------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module --------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module -------------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst deleted file mode 100644 index f577255f4ea..00000000000 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.tool\_shed.galaxy\_install.tool\_dependencies package -============================================================ - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - galaxy.tool_shed.galaxy_install.tool_dependencies.recipe - -Submodules ----------- - -galaxy.tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module ------------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.rst b/doc/source/lib/galaxy.tool_util.deps.rst index 947dddb4f28..11b9620b43a 100644 --- a/doc/source/lib/galaxy.tool_util.deps.rst +++ b/doc/source/lib/galaxy.tool_util.deps.rst @@ -67,6 +67,14 @@ galaxy.tool\_util.deps.container\_classes module :undoc-members: :show-inheritance: +galaxy.tool\_util.deps.container\_volumes module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.container_volumes + :members: + :undoc-members: + :show-inheritance: + galaxy.tool\_util.deps.containers module ---------------------------------------- diff --git a/doc/source/lib/galaxy.tool_util.ontologies.rst b/doc/source/lib/galaxy.tool_util.ontologies.rst new file mode 100644 index 00000000000..a637bad8e76 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.ontologies.rst @@ -0,0 +1,18 @@ +galaxy.tool\_util.ontologies package +==================================== + +.. automodule:: galaxy.tool_util.ontologies + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.ontologies.ontology\_data module +-------------------------------------------------- + +.. automodule:: galaxy.tool_util.ontologies.ontology_data + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst index e8150cd1d9c..c0ae09c08dc 100644 --- a/doc/source/lib/galaxy.tool_util.rst +++ b/doc/source/lib/galaxy.tool_util.rst @@ -18,6 +18,7 @@ Subpackages galaxy.tool_util.deps galaxy.tool_util.linters galaxy.tool_util.locations + galaxy.tool_util.ontologies galaxy.tool_util.parser galaxy.tool_util.toolbox galaxy.tool_util.unittest_utils diff --git a/doc/source/lib/galaxy.tours.rst b/doc/source/lib/galaxy.tours.rst index 56232296de6..6acee82e903 100644 --- a/doc/source/lib/galaxy.tours.rst +++ b/doc/source/lib/galaxy.tours.rst @@ -5,3 +5,14 @@ galaxy.tours package :members: :undoc-members: :show-inheritance: + +Submodules +---------- + +galaxy.tours.validate module +---------------------------- + +.. automodule:: galaxy.tours.validate + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst deleted file mode 100644 index 1eabd88f0c9..00000000000 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.util.pastescript package -=============================== - -.. automodule:: galaxy.util.pastescript - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.util.pastescript.loadwsgi module ---------------------------------------- - -.. automodule:: galaxy.util.pastescript.loadwsgi - :members: - :undoc-members: - :show-inheritance: - -galaxy.util.pastescript.serve module ------------------------------------- - -.. automodule:: galaxy.util.pastescript.serve - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 8a7703a412d..c685d84751c 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -13,7 +13,6 @@ Subpackages :maxdepth: 4 galaxy.util.custom_logging - galaxy.util.pastescript galaxy.util.path galaxy.util.tool_shed @@ -388,14 +387,6 @@ galaxy.util.watcher module :undoc-members: :show-inheritance: -galaxy.util.web\_compat module ------------------------------- - -.. automodule:: galaxy.util.web_compat - :members: - :undoc-members: - :show-inheritance: - galaxy.util.xml\_macros module ------------------------------ diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst index 6209b4d1398..2910013437e 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -17,14 +17,6 @@ galaxy.visualization.plugins.config\_parser module :undoc-members: :show-inheritance: -galaxy.visualization.plugins.interactive\_environments module -------------------------------------------------------------- - -.. automodule:: galaxy.visualization.plugins.interactive_environments - :members: - :undoc-members: - :show-inheritance: - galaxy.visualization.plugins.plugin module ------------------------------------------ diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index f86afbd143d..7eccd1d39b3 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -9,14 +9,6 @@ galaxy.web.framework.middleware package Submodules ---------- -galaxy.web.framework.middleware.batch module --------------------------------------------- - -.. automodule:: galaxy.web.framework.middleware.batch - :members: - :undoc-members: - :show-inheritance: - galaxy.web.framework.middleware.error module -------------------------------------------- diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index d32dba66462..0fa754d7f88 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -15,18 +15,11 @@ Subpackages galaxy.web.framework galaxy.web.legacy_framework galaxy.web.proxy + galaxy.web.short_term_storage Submodules ---------- -galaxy.web.buildapp module --------------------------- - -.. automodule:: galaxy.web.buildapp - :members: - :undoc-members: - :show-inheritance: - galaxy.web.form\_builder module ------------------------------- diff --git a/doc/source/lib/galaxy.web.short_term_storage.rst b/doc/source/lib/galaxy.web.short_term_storage.rst new file mode 100644 index 00000000000..576245fa1c4 --- /dev/null +++ b/doc/source/lib/galaxy.web.short_term_storage.rst @@ -0,0 +1,7 @@ +galaxy.web.short\_term\_storage package +======================================= + +.. automodule:: galaxy.web.short_term_storage + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 54995bc1dd9..8682f4468c5 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -337,6 +337,14 @@ galaxy.webapps.galaxy.api.search module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.api.short\_term\_storage module +----------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.short_term_storage + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.api.tags module ------------------------------------- @@ -345,6 +353,14 @@ galaxy.webapps.galaxy.api.tags module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.api.tasks module +-------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tasks + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.api.tool\_data module ------------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index d60ce2330bd..f3fe0a6ca33 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -81,14 +81,6 @@ galaxy.webapps.galaxy.controllers.history module :undoc-members: :show-inheritance: -galaxy.webapps.galaxy.controllers.interactive\_environments module ------------------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.controllers.interactive_environments - :members: - :undoc-members: - :show-inheritance: - galaxy.webapps.galaxy.controllers.library module ------------------------------------------------ diff --git a/doc/source/lib/galaxy.webapps.galaxy.services.rst b/doc/source/lib/galaxy.webapps.galaxy.services.rst index 871a56dad7e..b784e52d468 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.services.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.services.rst @@ -9,6 +9,14 @@ galaxy.webapps.galaxy.services package Submodules ---------- +galaxy.webapps.galaxy.services.authenticate module +-------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.authenticate + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.services.base module ------------------------------------------ @@ -49,6 +57,22 @@ galaxy.webapps.galaxy.services.history\_contents module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.services.invocations module +------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.invocations + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.jobs module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.services.jobs + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.services.libraries module ----------------------------------------------- @@ -97,6 +121,22 @@ galaxy.webapps.galaxy.services.sharable module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.services.tools module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.tools + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.users module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.users + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.services.visualizations module ---------------------------------------------------- @@ -104,3 +144,11 @@ galaxy.webapps.galaxy.services.visualizations module :members: :undoc-members: :show-inheritance: + +galaxy.webapps.galaxy.services.workflows module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.workflows + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.openapi.rst b/doc/source/lib/galaxy.webapps.openapi.rst new file mode 100644 index 00000000000..7af8dd005b7 --- /dev/null +++ b/doc/source/lib/galaxy.webapps.openapi.rst @@ -0,0 +1,18 @@ +galaxy.webapps.openapi package +============================== + +.. automodule:: galaxy.webapps.openapi + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.openapi.utils module +----------------------------------- + +.. automodule:: galaxy.webapps.openapi.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index e8f02a396c3..df681fd888a 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -14,6 +14,7 @@ Subpackages galaxy.webapps.base galaxy.webapps.galaxy + galaxy.webapps.openapi galaxy.webapps.reports Submodules diff --git a/doc/source/lib/galaxy_ext.container_monitor.rst b/doc/source/lib/galaxy_ext.container_monitor.rst new file mode 100644 index 00000000000..16c2596f199 --- /dev/null +++ b/doc/source/lib/galaxy_ext.container_monitor.rst @@ -0,0 +1,18 @@ +galaxy\_ext.container\_monitor package +====================================== + +.. automodule:: galaxy_ext.container_monitor + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy\_ext.container\_monitor.monitor module +--------------------------------------------- + +.. automodule:: galaxy_ext.container_monitor.monitor + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index 22bf2e82487..fbc02806749 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -12,5 +12,6 @@ Subpackages .. toctree:: :maxdepth: 4 + galaxy_ext.container_monitor galaxy_ext.expressions galaxy_ext.metadata diff --git a/doc/source/lib/galaxy_test.api.rst b/doc/source/lib/galaxy_test.api.rst index 12049df9da5..0486930b82e 100644 --- a/doc/source/lib/galaxy_test.api.rst +++ b/doc/source/lib/galaxy_test.api.rst @@ -17,14 +17,6 @@ Subpackages Submodules ---------- -galaxy\_test.api.conftest module --------------------------------- - -.. automodule:: galaxy_test.api.conftest - :members: - :undoc-members: - :show-inheritance: - galaxy\_test.api.sharable module -------------------------------- @@ -33,14 +25,6 @@ galaxy\_test.api.sharable module :undoc-members: :show-inheritance: -galaxy\_test.api.test\_api\_batch module ----------------------------------------- - -.. automodule:: galaxy_test.api.test_api_batch - :members: - :undoc-members: - :show-inheritance: - galaxy\_test.api.test\_authenticate module ------------------------------------------ diff --git a/doc/source/lib/galaxy_test.performance.rst b/doc/source/lib/galaxy_test.performance.rst index 5930228cd0b..11d091b4191 100644 --- a/doc/source/lib/galaxy_test.performance.rst +++ b/doc/source/lib/galaxy_test.performance.rst @@ -9,14 +9,6 @@ galaxy\_test.performance package Submodules ---------- -galaxy\_test.performance.conftest module ----------------------------------------- - -.. automodule:: galaxy_test.performance.conftest - :members: - :undoc-members: - :show-inheritance: - galaxy\_test.performance.test\_workflow\_framework\_performance module ---------------------------------------------------------------------- diff --git a/doc/source/lib/galaxy_test.rst b/doc/source/lib/galaxy_test.rst index 00eb52df606..00fa7466c4c 100644 --- a/doc/source/lib/galaxy_test.rst +++ b/doc/source/lib/galaxy_test.rst @@ -17,3 +17,14 @@ Subpackages galaxy_test.driver galaxy_test.performance galaxy_test.selenium + +Submodules +---------- + +galaxy\_test.conftest module +---------------------------- + +.. automodule:: galaxy_test.conftest + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.selenium.rst b/doc/source/lib/galaxy_test.selenium.rst index fbfa28b243c..85de6c7db3b 100644 --- a/doc/source/lib/galaxy_test.selenium.rst +++ b/doc/source/lib/galaxy_test.selenium.rst @@ -97,6 +97,14 @@ galaxy\_test.selenium.test\_data\_source\_tools module :undoc-members: :show-inheritance: +galaxy\_test.selenium.test\_dataset\_metadata\_download module +-------------------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_dataset_metadata_download + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.test\_histories\_list module -------------------------------------------------- @@ -185,6 +193,14 @@ galaxy\_test.selenium.test\_history\_structure module :undoc-members: :show-inheritance: +galaxy\_test.selenium.test\_invocation\_grid module +--------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_invocation_grid + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.test\_jupyter module ------------------------------------------ diff --git a/doc/source/lib/tool_shed.test.functional.rst b/doc/source/lib/tool_shed.test.functional.rst index 557c9a025f0..3bbb84a4631 100644 --- a/doc/source/lib/tool_shed.test.functional.rst +++ b/doc/source/lib/tool_shed.test.functional.rst @@ -441,14 +441,6 @@ tool\_shed.test.functional.test\_1410\_update\_manager module :undoc-members: :show-inheritance: -tool\_shed.test.functional.test\_1420\_tool\_dependency\_environment\_inheritance module ----------------------------------------------------------------------------------------- - -.. automodule:: tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance - :members: - :undoc-members: - :show-inheritance: - tool\_shed.test.functional.test\_1430\_repair\_installed\_repository module --------------------------------------------------------------------------- @@ -457,14 +449,6 @@ tool\_shed.test.functional.test\_1430\_repair\_installed\_repository module :undoc-members: :show-inheritance: -tool\_shed.test.functional.test\_1440\_missing\_env\_sh\_files module ---------------------------------------------------------------------- - -.. automodule:: tool_shed.test.functional.test_1440_missing_env_sh_files - :members: - :undoc-members: - :show-inheritance: - tool\_shed.test.functional.test\_1450\_installing\_datatypes\_sniffers module ----------------------------------------------------------------------------- diff --git a/lib/galaxy/model/orm/util.py b/lib/galaxy/model/orm/util.py index f8b064a9ba9..795af1616fb 100644 --- a/lib/galaxy/model/orm/util.py +++ b/lib/galaxy/model/orm/util.py @@ -8,12 +8,13 @@ def add_object_to_object_session(object, object_with_session): https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0 This function preserves SQLAlchemy's pre-2.0 logic and should be used when: + 1. foo and bar are model instances, that are associated (via SQLAlchemy's relationship), AND 2. bar is assigned to foo's bar relationship (e.g. foo.bar = bar), AND 3. bar is in a session and foo is not, AND 4. foo is implicitly added to bar's session upon assignment(2), as indicated - by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session - along the backref cascade path...' + by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session + along the backref cascade path...' """ if object_with_session: session = get_object_session(object_with_session) diff --git a/lib/galaxy/webapps/galaxy/api/common.py b/lib/galaxy/webapps/galaxy/api/common.py index 063d9a6d56d..b74daf0d70c 100644 --- a/lib/galaxy/webapps/galaxy/api/common.py +++ b/lib/galaxy/webapps/galaxy/api/common.py @@ -149,10 +149,10 @@ def query_parameter_as_list(query): """Used as FastAPI dependable for query parameters that need to behave as a list of values separated by comma or as multiple instances of the same parameter. - **Important**: the `query` annotation provided must define the `alias` exactly as the name of the actual parameter name. + .. important:: the ``query`` annotation provided must define the ``alias`` exactly as the name of the actual parameter name. + + Usage example:: - Usage example: - ```python ValueQueryParam = Query( default=None, alias="value", # Important! this is the parameter name that will be displayed in the API docs @@ -166,11 +166,11 @@ def query_parameter_as_list(query): values: Optional[List[str]] = Depends(query_parameter_as_list(ValueQueryParam)), ): ... - ``` This will render in the API docs as a single string query parameter but will make the following requests equivalent: - - `api/my_route?value=val1,val2,val3` - - `api/my_route?value=val1&value=val2&value=val3` + + - ``api/my_route?value=val1,val2,val3`` + - ``api/my_route?value=val1&value=val2&value=val3`` """ def parse_elements(