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galaxy.model.migrate.versions package

Submodules

galaxy.model.migrate.versions.0001_initial_tables module

galaxy.model.migrate.versions.0001_initial_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0001_initial_tables.upgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0002_metadata_file_table module

galaxy.model.migrate.versions.0002_metadata_file_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0002_metadata_file_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0002_metadata_file_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0003_security_and_libraries module

galaxy.model.migrate.versions.0003_security_and_libraries.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0003_security_and_libraries.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0003_security_and_libraries.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0004_indexes_and_defaults module

galaxy.model.migrate.versions.0004_indexes_and_defaults.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0004_indexes_and_defaults.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0005_cleanup_datasets_fix module

galaxy.model.migrate.versions.0005_cleanup_datasets_fix.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0005_cleanup_datasets_fix.get_permitted_actions(**kwds)[source]
galaxy.model.migrate.versions.0005_cleanup_datasets_fix.directory_hash_id(id)[source]
class galaxy.model.migrate.versions.0005_cleanup_datasets_fix.Dataset(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True)[source]

Bases: object

states = <galaxy.util.bunch.Bunch object>
permitted_actions = <galaxy.util.bunch.Bunch object>
file_path = '/tmp/'
engine = None
__init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True)
id
state
deleted
purged
purgable
external_filename
file_size
get_file_name()[source]
set_file_name(filename)[source]
file_name
extra_files_path
get_size()[source]

Returns the size of the data on disk

set_size()[source]

Returns the size of the data on disk

has_data()[source]

Detects whether there is any data

mark_deleted(include_children=True)[source]
active_history_associations
active_library_associations
create_time
history_associations
library_associations
table = Table('dataset', MetaData(bind=None), Column('id', Integer(), table=<dataset>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('state', TrimmedString(length=64), table=<dataset>), Column('deleted', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purgable', Boolean(), table=<dataset>, default=ColumnDefault(True)), Column('external_filename', TEXT(), table=<dataset>), Column('_extra_files_path', TEXT(), table=<dataset>), Column('file_size', Numeric(precision=15, scale=0), table=<dataset>), schema=None)
update_time
class galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance(id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validation_errors=None, visible=True, create_dataset=False)[source]

Bases: object

A base class for all ‘dataset instances’, HDAs, LDAs, etc

states = <galaxy.util.bunch.Bunch object>
permitted_actions = <galaxy.util.bunch.Bunch object>
__init__(id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validation_errors=None, visible=True, create_dataset=False)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

ext
get_dataset_state()[source]
set_dataset_state(state)[source]
state
get_file_name()[source]
set_file_name(filename)[source]
file_name
extra_files_path
get_metadata()[source]
set_metadata(bunch)[source]
metadata
get_dbkey()[source]
set_dbkey(value)[source]
dbkey
get_size()[source]

Returns the size of the data on disk

set_size()[source]

Returns the size of the data on disk

has_data()[source]

Detects whether there is any data

get_raw_data()[source]

Returns the full data. To stream it open the file_name and read/write as needed

set_peek()[source]
init_meta(copy_from=None)[source]
set_meta(**kwd)[source]
missing_meta(**kwd)[source]
as_display_type(type, **kwd)[source]
display_peek()[source]
display_name()[source]
display_info()[source]
get_converted_files_by_type(file_type)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
get_child_by_designation(designation)[source]
add_validation_error(validation_error)[source]
extend_validation_errors(validation_errors)[source]
mark_deleted(include_children=True)[source]
mark_undeleted(include_children=True)[source]
undeletable()[source]
source_library_dataset
class galaxy.model.migrate.versions.0005_cleanup_datasets_fix.HistoryDatasetAssociation(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, **kwd)[source]

Bases: galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance

__init__(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, **kwd)
hid
copy(copy_children=False, parent_id=None, target_history=None)[source]
to_library_dataset_dataset_association(target_folder, replace_dataset=None, parent_id=None)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
blurb
children
copied_from_history_dataset_association_id
copied_from_library_dataset_dataset_association_id
copied_to_history_dataset_associations
copied_to_library_dataset_dataset_associations
create_time
dataset
dataset_id
deleted
designation
extension
id
info
name
parent_id
peek
table = Table('history_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<history_dataset_association>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<history_dataset_association>), Column('create_time', DateTime(), table=<history_dataset_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<history_dataset_association>), Column('hid', Integer(), table=<history_dataset_association>), Column('name', TrimmedString(length=255), table=<history_dataset_association>), Column('info', TrimmedString(length=255), table=<history_dataset_association>), Column('blurb', TrimmedString(length=255), table=<history_dataset_association>), Column('peek', TEXT(), table=<history_dataset_association>), Column('extension', TrimmedString(length=64), table=<history_dataset_association>), Column('metadata', MetadataType(), table=<history_dataset_association>, key='_metadata'), Column('parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('designation', TrimmedString(length=255), table=<history_dataset_association>), Column('deleted', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('visible', Boolean(), table=<history_dataset_association>), schema=None)
update_time
visible
visible_children
class galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDatasetDatasetAssociation(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, **kwd)[source]

Bases: galaxy.model.migrate.versions.0005_cleanup_datasets_fix.DatasetInstance

__init__(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, **kwd)
library_dataset
to_history_dataset_association(target_history, parent_id=None)[source]
copy(copy_children=False, parent_id=None, target_folder=None)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
get_library_item_info_templates(template_list=[], restrict=False)[source]
blurb
children
copied_from_history_dataset_association_id
copied_from_library_dataset_dataset_association_id
copied_to_history_dataset_associations
copied_to_library_dataset_dataset_associations
create_time
dataset
dataset_id
deleted
designation
extension
id
info
library_dataset_id
message
name
parent_id
peek
table = Table('library_dataset_dataset_association', MetaData(bind=None), Column('id', Integer(), table=<library_dataset_dataset_association>, primary_key=True, nullable=False), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<library_dataset_dataset_association>), Column('create_time', DateTime(), table=<library_dataset_dataset_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<library_dataset_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('name', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('info', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('blurb', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('peek', TEXT(), table=<library_dataset_dataset_association>), Column('extension', TrimmedString(length=64), table=<library_dataset_dataset_association>), Column('metadata', MetadataType(), table=<library_dataset_dataset_association>, key='_metadata'), Column('parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('designation', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_association>, default=ColumnDefault(False)), Column('visible', Boolean(), table=<library_dataset_dataset_association>), Column('message', TrimmedString(length=255), table=<library_dataset_dataset_association>), schema=None)
update_time
visible
visible_children
class galaxy.model.migrate.versions.0005_cleanup_datasets_fix.LibraryDataset(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)[source]

Bases: object

__init__(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)
order_id
library_dataset_dataset_association
set_library_dataset_dataset_association(ldda)[source]
get_info()[source]
set_info(info)[source]
info
get_name()[source]
set_name(name)[source]
name
display_name()[source]
get_purged()[source]
set_purged(purged)[source]
purged
create_time
deleted
expired_datasets
get_library_item_info_templates(template_list=[], restrict=False)[source]
id
library_dataset_dataset_association_id
table = Table('library_dataset', MetaData(bind=None), Column('id', Integer(), table=<library_dataset>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset>), Column('order_id', Integer(), table=<library_dataset>), Column('create_time', DateTime(), table=<library_dataset>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('name', TrimmedString(length=255), table=<library_dataset>, key='_name'), Column('info', TrimmedString(length=255), table=<library_dataset>, key='_info'), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)
update_time
galaxy.model.migrate.versions.0005_cleanup_datasets_fix.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0005_cleanup_datasets_fix.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0006_change_qual_datatype module

This migration script changes certain values in the history_dataset_association.extension column, specifically ‘qual’ is changed to be ‘qual454’.

galaxy.model.migrate.versions.0006_change_qual_datatype.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0006_change_qual_datatype.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0007_sharing_histories module

This migration script creates the new history_user_share_association table, and adds a new boolean type column to the history table. This provides support for sharing histories in the same way that workflows are shared.

galaxy.model.migrate.versions.0007_sharing_histories.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0007_sharing_histories.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0008_galaxy_forms module

This migration script adds the following new tables for supporting Galaxy forms: 1) form_definition_current 2) form_definition 3) form_values 4) request_type 5) request 6) sample 7) sample_state 8) sample_event

galaxy.model.migrate.versions.0008_galaxy_forms.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0008_galaxy_forms.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0008_galaxy_forms.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0009_request_table module

This migration script adds a new column to 2 tables: 1) a new boolean type column named ‘submitted’ to the ‘request’ table 2) a new string type column named ‘bar_code’ to the ‘sample’ table

galaxy.model.migrate.versions.0009_request_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0009_request_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0010_hda_display_at_authz_table module

This migration script adds the history_dataset_association_display_at_authorization table, which allows ‘private’ datasets to be displayed at external sites without making them public.

If using mysql, this script will display the following error, which is corrected in the next migration script: history_dataset_association_display_at_authorization table failed: (OperationalError) (1059, “Identifier name ‘ix_history_dataset_association_display_at_authorization_update_time’ is too long

galaxy.model.migrate.versions.0010_hda_display_at_authz_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0010_hda_display_at_authz_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0010_hda_display_at_authz_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module

This script fixes a problem introduced in the previous migration script 0010_hda_display_at_authz_table.py . MySQL has a name length limit and thus the index “ix_hdadaa_history_dataset_association_id” has to be manually created.

galaxy.model.migrate.versions.0011_v0010_mysql_index_fix.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0011_v0010_mysql_index_fix.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0011_v0010_mysql_index_fix.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0012_user_address module

This script adds a new user_address table that is currently only used with sample requests, where a user can select from a list of his addresses to associate with the request. This script also drops the request.submitted column which was boolean and replaces it with a request.state column which is a string, allowing for more flexibility with request states.

galaxy.model.migrate.versions.0012_user_address.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0012_user_address.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0012_user_address.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module

This migration script eliminates all of the tables that were used for the 1st version of the library templates where template fields and contents were each stored as a separate table row in various library item tables. All of these tables are dropped in this script, eliminating all existing template data. A total of 14 existing tables are dropped.

We’re now basing library templates on forms, so field contents are stored as a jsonified list in the form_values table. This script introduces the following 3 new association tables: 1) library_info_association 2) library_folder_info_association 3) library_dataset_dataset_info_association

galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0014_pages module

Migration script to add support for “Pages”.
  1. Creates Page and PageRevision tables
  2. Adds username column to User table
galaxy.model.migrate.versions.0014_pages.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0014_pages.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0014_pages.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0015_tagging module

This migration script adds the tables necessary to support tagging of histories, datasets, and history-dataset associations (user views of datasets).

galaxy.model.migrate.versions.0015_tagging.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0015_tagging.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module

This script was used to fix a problem introduced in 0015_tagging.py. MySQL has a name length limit and thus the index “ix_hda_ta_history_dataset_association_id” had to be manually created.

This is now fixed in SQLAlchemy Migrate.

galaxy.model.migrate.versions.0016_v0015_mysql_index_fix.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0016_v0015_mysql_index_fix.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0017_library_item_indexes module

This script adds 3 indexes to table columns: library_folder.name, library_dataset.name, library_dataset_dataset_association.name.

galaxy.model.migrate.versions.0017_library_item_indexes.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0017_library_item_indexes.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module

This migration script provides support for (a) ordering tags by recency and (b) tagging pages. This script deletes all existing tags.

galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0019_request_library_folder module

This script creates a request.folder_id column which is a foreign key to the library_folder table. This also adds a ‘type’ and ‘layout’ column to the form_definition table.

galaxy.model.migrate.versions.0019_request_library_folder.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0019_request_library_folder.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0020_library_upload_job module

This script creates a job_to_output_library_dataset table for allowing library uploads to run as regular jobs. To support this, a library_folder_id column is added to the job table, and library_folder/output_library_datasets relations are added to the Job object. An index is also added to the dataset.state column.

galaxy.model.migrate.versions.0020_library_upload_job.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0020_library_upload_job.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0021_user_prefs module

This migration script adds a user preferences table to Galaxy.

galaxy.model.migrate.versions.0021_user_prefs.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0021_user_prefs.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0022_visualization_tables module

Migration script to add support for storing visualizations.
  1. Creates Visualization and VisualizationRevision tables
galaxy.model.migrate.versions.0022_visualization_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0022_visualization_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0022_visualization_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module

Migration script to add columns for tracking whether pages are deleted and publicly accessible.

galaxy.model.migrate.versions.0023_page_published_and_deleted_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0023_page_published_and_deleted_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0024_page_slug_unique_constraint module

Remove unique constraint from page slugs to allow creating a page with the same slug as a deleted page.

galaxy.model.migrate.versions.0024_page_slug_unique_constraint.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0024_page_slug_unique_constraint.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0025_user_info module

This script adds a foreign key to the form_values table in the galaxy_user table

galaxy.model.migrate.versions.0025_user_info.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0025_user_info.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0026_cloud_tables module

This script adds tables needed for Galaxy cloud functionality.

galaxy.model.migrate.versions.0026_cloud_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0026_cloud_tables.CloudImage_table = Table('cloud_image', MetaData(bind=None), Column('id', Integer(), table=<cloud_image>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cloud_image>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<cloud_image>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('provider_type', TEXT(), table=<cloud_image>), Column('image_id', TEXT(), table=<cloud_image>, nullable=False), Column('manifest', TEXT(), table=<cloud_image>), Column('state', TEXT(), table=<cloud_image>), Column('architecture', TEXT(), table=<cloud_image>), Column('deleted', Boolean(), table=<cloud_image>, default=ColumnDefault(False)), schema=None)

UserConfiguredInstance (UCI) table

galaxy.model.migrate.versions.0026_cloud_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0026_cloud_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0027_request_events module

This migration script adds the request_event table and removes the state field in the request table

galaxy.model.migrate.versions.0027_request_events.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0027_request_events.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0027_request_events.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0028_external_metadata_file_override module

This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, allowing existing metadata files to be written when using external metadata and a cluster set up with read-only access to database/files

galaxy.model.migrate.versions.0028_external_metadata_file_override.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0028_external_metadata_file_override.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0029_user_actions module

This migration script adds a user actions table to Galaxy.

galaxy.model.migrate.versions.0029_user_actions.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0029_user_actions.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0029_user_actions.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0030_history_slug_column module

Migration script to add column for a history slug.

galaxy.model.migrate.versions.0030_history_slug_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0030_history_slug_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0031_community_and_workflow_tags module

Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows.

galaxy.model.migrate.versions.0031_community_and_workflow_tags.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0031_community_and_workflow_tags.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0032_stored_workflow_slug_column module

Migration script to add slug column for stored workflow.

galaxy.model.migrate.versions.0032_stored_workflow_slug_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0032_stored_workflow_slug_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module

Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages.

galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0034_page_user_share_association module

Migration script to create a table for page-user share association.

galaxy.model.migrate.versions.0034_page_user_share_association.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0034_page_user_share_association.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module

Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps.

galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module

Migration script to add a deleted column to the following tables: library_info_association, library_folder_info_association, library_dataset_dataset_info_association.

galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0037_samples_library module

This migration script removes the library_id & folder_id fields in the ‘request’ table and adds the same to the ‘sample’ table. This also adds a ‘datatx’ column to request_type table to store the sequencer login information. Finally, this adds a ‘dataset_files’ column to the sample table.

galaxy.model.migrate.versions.0037_samples_library.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0037_samples_library.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0037_samples_library.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module

Migration script to add an inheritable column to the following tables: library_info_association, library_folder_info_association. Also, in case of sqlite check if the previous migration script deleted the request table and if so, restore the table.

galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module

Migration script to add a synopsis column to the library table.

galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0040_page_annotations module

Migration script to (a) create tables for annotating pages.

galaxy.model.migrate.versions.0040_page_annotations.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0040_page_annotations.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0041_workflow_invocation module

Migration script to create tables for tracking workflow invocations.

galaxy.model.migrate.versions.0041_workflow_invocation.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0041_workflow_invocation.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0041_workflow_invocation.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0042_workflow_invocation_fix module

Drop and readd workflow invocation tables, allowing null jobs

galaxy.model.migrate.versions.0042_workflow_invocation_fix.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0042_workflow_invocation_fix.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0042_workflow_invocation_fix.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module

Migration script to create tables and columns for sharing visualizations.

galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module

Migration script to add a notify column to the request table.

galaxy.model.migrate.versions.0044_add_notify_column_to_request_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0044_add_notify_column_to_request_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0045_request_type_permissions_table module

Migration script to add the request_type_permissions table.

galaxy.model.migrate.versions.0045_request_type_permissions_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0045_request_type_permissions_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0045_request_type_permissions_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0046_post_job_actions module

Migration script to create tables for handling post-job actions.

galaxy.model.migrate.versions.0046_post_job_actions.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0046_post_job_actions.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0047_job_table_user_id_column module

Add a user_id column to the job table.

galaxy.model.migrate.versions.0047_job_table_user_id_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0047_job_table_user_id_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0048_dataset_instance_state_column module

Add a state column to the history_dataset_association and library_dataset_dataset_association table.

galaxy.model.migrate.versions.0048_dataset_instance_state_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0048_dataset_instance_state_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0049_api_keys_table module

Migration script to add the api_keys table.

galaxy.model.migrate.versions.0049_api_keys_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0049_api_keys_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0049_api_keys_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0050_drop_cloud_tables module

This script drops tables that were associated with the old Galaxy Cloud functionality.

galaxy.model.migrate.versions.0050_drop_cloud_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0050_drop_cloud_tables.CloudImage_table = Table('cloud_image', MetaData(bind=None), Column('id', Integer(), table=<cloud_image>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cloud_image>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<cloud_image>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('provider_type', TEXT(), table=<cloud_image>), Column('image_id', TEXT(), table=<cloud_image>, nullable=False), Column('manifest', TEXT(), table=<cloud_image>), Column('state', TEXT(), table=<cloud_image>), Column('architecture', TEXT(), table=<cloud_image>), Column('deleted', Boolean(), table=<cloud_image>, default=ColumnDefault(False)), schema=None)

UserConfiguredInstance (UCI) table

galaxy.model.migrate.versions.0050_drop_cloud_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0050_drop_cloud_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module

Migration script to add imported column for jobs table.

galaxy.model.migrate.versions.0051_imported_col_for_jobs_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0051_imported_col_for_jobs_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0052_sample_dataset_table module

Migration script to add the sample_dataset table and remove the ‘dataset_files’ column from the ‘sample’ table

galaxy.model.migrate.versions.0052_sample_dataset_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0052_sample_dataset_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0052_sample_dataset_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0053_item_ratings module

Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations.

galaxy.model.migrate.versions.0053_item_ratings.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0053_item_ratings.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0054_visualization_dbkey module

Migration script to add dbkey column for visualization.

galaxy.model.migrate.versions.0054_visualization_dbkey.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0054_visualization_dbkey.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module

Migration script to add the post_job_action_association table.

galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0056_workflow_outputs module

Migration script to create tables for adding explicit workflow outputs.

galaxy.model.migrate.versions.0056_workflow_outputs.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0056_workflow_outputs.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0057_request_notify module

Migration script to modify the ‘notify’ field in the ‘request’ table from a boolean to a JSONType

galaxy.model.migrate.versions.0057_request_notify.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0057_request_notify.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0058_history_import_export module

Migration script to create table for exporting histories to archives.

galaxy.model.migrate.versions.0058_history_import_export.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0058_history_import_export.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0059_sample_dataset_file_path module

Migration script to modify the ‘file_path’ field type in ‘sample_dataset’ table to ‘TEXT’ so that it can support large file paths exceeding 255 characters

galaxy.model.migrate.versions.0059_sample_dataset_file_path.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0059_sample_dataset_file_path.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0060_history_archive_import module

Migration script to create column and table for importing histories from file archives.

galaxy.model.migrate.versions.0060_history_archive_import.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0060_history_archive_import.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0061_tasks module

Migration script to create tables task management.

galaxy.model.migrate.versions.0061_tasks.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0061_tasks.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0061_tasks.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0062_user_openid_table module

Migration script to create table for associating sessions and users with OpenIDs.

galaxy.model.migrate.versions.0062_user_openid_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0062_user_openid_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0062_user_openid_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0063_sequencer_table module

Migration script to create a new ‘sequencer’ table

galaxy.model.migrate.versions.0063_sequencer_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0063_sequencer_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0063_sequencer_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module

Migration script to add the run and sample_run_association tables.

galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module

Migration script to add ‘name’ attribute to the JSON dict which describes a form definition field and the form values in the database. In the ‘form_values’ table, the ‘content’ column is now a JSON dict instead of a list.

galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module

Migration script to create table for storing deferred job and managed transfer information.

galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0067_populate_sequencer_table module

Migration script to populate the ‘sequencer’ table and it is populated using unique entries in the ‘datatx_info’ column in the ‘request_type’ table. It also deletes the ‘datatx_info’ column in the ‘request_type’ table and adds a foreign key to the ‘sequencer’ table. The actual contents of the datatx_info column are stored as form_values.

galaxy.model.migrate.versions.0067_populate_sequencer_table.get_latest_id(migrate_engine, table)[source]
galaxy.model.migrate.versions.0067_populate_sequencer_table.create_sequencer_form_definition(migrate_engine)[source]

Create a new form_definition containing 5 fields (host, username, password, data_dir & rename_datasets) which described the existing datatx_info json dict in the request_type table

galaxy.model.migrate.versions.0067_populate_sequencer_table.get_sequencer_id(migrate_engine, sequencer_info)[source]

Get the sequencer id corresponding to the sequencer information

galaxy.model.migrate.versions.0067_populate_sequencer_table.add_sequencer(migrate_engine, sequencer_index, sequencer_form_definition_id, sequencer_info)[source]

Adds a new sequencer to the sequencer table along with its form values.

galaxy.model.migrate.versions.0067_populate_sequencer_table.update_sequencer_id_in_request_type(migrate_engine, request_type_id, sequencer_id)[source]

Update the foreign key to the sequencer table in the request_type table

galaxy.model.migrate.versions.0067_populate_sequencer_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0067_populate_sequencer_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module

This migration script renames the sequencer table to ‘external_service’ table and creates a association table, ‘request_type_external_service_association’ and populates it. The ‘sequencer_id’ foreign_key from the ‘request_type’ table is removed. The ‘sequencer_type_id’ column is renamed to ‘external_service_type_id’ in the renamed table ‘external_service’. Finally, adds a foreign key to the external_service table in the sample_dataset table and populates it.

galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0069_rename_sequencer_form_type module

Migration script to rename the sequencer information form type to external service information form

galaxy.model.migrate.versions.0069_rename_sequencer_form_type.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0069_rename_sequencer_form_type.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module

Migration script to add ‘info’ column to the transfer_job table.

galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module

Migration script to add ‘workflow’ and ‘history’ columns for a sample.

galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module

Migration script to add ‘pid’ and ‘socket’ columns to the transfer_job table.

galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module

Migration script to add ‘ldda_parent_id’ column to the implicitly_converted_dataset_association table.

galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module

Migration script to add ‘purged’ column to the library_dataset table.

galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module

Migration script to add a ‘subindex’ column to the run table.

galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module

This migration script fixes the data corruption caused in the form_values table (content json field) by migrate script 65.

galaxy.model.migrate.versions.0076_fix_form_values_data_corruption.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0076_fix_form_values_data_corruption.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0077_create_tool_tag_association_table module

Migration script to create table for storing tool tag associations.

galaxy.model.migrate.versions.0077_create_tool_tag_association_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0077_create_tool_tag_association_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module

Migration script to add ‘total_size’ column to the dataset table, ‘purged’ column to the HDA table, and ‘disk_usage’ column to the User and GalaxySession tables.

galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0079_input_library_to_job_table module

Migration script to add the job_to_input_library_dataset table.

galaxy.model.migrate.versions.0079_input_library_to_job_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0079_input_library_to_job_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0080_quota_tables module

Migration script to create tables for disk quotas.

galaxy.model.migrate.versions.0080_quota_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0080_quota_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0080_quota_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module

Migration script to add a ‘tool_version’ column to the hda/ldda tables.

galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module

Migration script to add the tool_shed_repository table.

galaxy.model.migrate.versions.0082_add_tool_shed_repository_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0082_add_tool_shed_repository_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0082_add_tool_shed_repository_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0083_add_prepare_files_to_task module

Migration script to add ‘prepare_input_files_cmd’ column to the task table and to rename a column.

galaxy.model.migrate.versions.0083_add_prepare_files_to_task.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0083_add_prepare_files_to_task.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module

Migration script to add ‘ldda_id’ column to the implicitly_converted_dataset_association table.

galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0085_add_task_info module

Migration script to add ‘info’ column to the task table.

galaxy.model.migrate.versions.0085_add_task_info.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0085_add_task_info.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module

Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table.

galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0087_tool_id_guid_map_table module

Migration script to create the tool_id_guid_map table.

galaxy.model.migrate.versions.0087_tool_id_guid_map_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0087_tool_id_guid_map_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0087_tool_id_guid_map_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module

Migration script to add the installed_changeset_revision column to the tool_shed_repository table.

galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0089_add_object_store_id_columns module

Migration script to add ‘object_store_id’ column to various tables

galaxy.model.migrate.versions.0089_add_object_store_id_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0089_add_object_store_id_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module

Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table.

galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0091_add_tool_version_tables module

Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.

galaxy.model.migrate.versions.0091_add_tool_version_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0091_add_tool_version_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0091_add_tool_version_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0092_add_migrate_tools_table module

Migration script to create the migrate_tools table.

galaxy.model.migrate.versions.0092_add_migrate_tools_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0092_add_migrate_tools_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0093_add_job_params_col module

Migration script to add a ‘params’ column to the ‘job’ table.

galaxy.model.migrate.versions.0093_add_job_params_col.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0093_add_job_params_col.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0094_add_job_handler_col module

Migration script to add a ‘handler’ column to the ‘job’ table.

galaxy.model.migrate.versions.0094_add_job_handler_col.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0094_add_job_handler_col.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0095_hda_subsets module

Migration script to create table for tracking history_dataset_association subsets.

galaxy.model.migrate.versions.0095_hda_subsets.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0095_hda_subsets.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0096_openid_provider module

Migration script to add column to openid table for provider. Remove any OpenID entries with nonunique GenomeSpace Identifier

galaxy.model.migrate.versions.0096_openid_provider.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0096_openid_provider.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0097_add_ctx_rev_column module

Migration script to add the ctx_rev column to the tool_shed_repository table.

galaxy.model.migrate.versions.0097_add_ctx_rev_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0097_add_ctx_rev_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0098_genome_index_tool_data_table module

Migration script to create the genome_index_tool_data table.

galaxy.model.migrate.versions.0098_genome_index_tool_data_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0098_genome_index_tool_data_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0098_genome_index_tool_data_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0099_add_tool_dependency_table module

Migration script to add the tool_dependency table.

galaxy.model.migrate.versions.0099_add_tool_dependency_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0099_add_tool_dependency_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0099_add_tool_dependency_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module

Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text.

galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column module

Migration script to drop the installed_changeset_revision column from the tool_dependency table.

galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns module

Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table.

galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns module

Migration script to add status and error_message columns to the tool_shed_repository table.

galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters module

Migration script to update the deferred job parameters for liftover transfer jobs.

galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.now()

Return a new datetime representing UTC day and time.

class galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.DeferredJob(state=None, plugin=None, params=None)[source]

Bases: object

states = <galaxy.util.bunch.Bunch object>
__init__(state=None, plugin=None, params=None)
state
plugin
params
create_time
id
table = Table('deferred_job', MetaData(bind=None), Column('id', Integer(), table=<deferred_job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<deferred_job>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<deferred_job>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('state', String(length=64), table=<deferred_job>), Column('plugin', String(length=128), table=<deferred_job>), Column('params', JSONType(), table=<deferred_job>), schema=None)
update_time
galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0105_add_cleanup_event_table module

Migration script to add the cleanup_event* tables.

galaxy.model.migrate.versions.0105_add_cleanup_event_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0105_add_cleanup_event_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0105_add_cleanup_event_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0106_add_missing_indexes module

Migration script to create missing indexes. Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.

galaxy.model.migrate.versions.0106_add_missing_indexes.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0106_add_missing_indexes.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task module

Add the exit_code column to the Job and Task tables.

galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0108_add_extended_metadata module

Add the ExtendedMetadata and ExtendedMetadataIndex tables

galaxy.model.migrate.versions.0108_add_extended_metadata.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0108_add_extended_metadata.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0109_add_repository_dependency_tables module

Migration script to add the repository_dependency and repository_repository_dependency_association tables.

galaxy.model.migrate.versions.0109_add_repository_dependency_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0109_add_repository_dependency_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0109_add_repository_dependency_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0110_add_dataset_uuid module

Add UUID column to dataset table

galaxy.model.migrate.versions.0110_add_dataset_uuid.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0110_add_dataset_uuid.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0111_add_job_destinations module

Add support for job destinations to the job table

galaxy.model.migrate.versions.0111_add_job_destinations.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0111_add_job_destinations.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables module

Migration script to add the data_manager_history_association table and data_manager_job_association.

galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0113_update_migrate_tools_table module

Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.

galaxy.model.migrate.versions.0113_update_migrate_tools_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0113_update_migrate_tools_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0114_update_migrate_tools_table_again module

Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.

galaxy.model.migrate.versions.0114_update_migrate_tools_table_again.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0114_update_migrate_tools_table_again.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0115_longer_user_password_field module

Expand the length of the password fields in the galaxy_user table to allow for other hasing schemes

galaxy.model.migrate.versions.0115_longer_user_password_field.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0115_longer_user_password_field.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col module

Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table.

galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0117_add_user_activation module

Adds ‘active’ and ‘activation_token’ columns to the galaxy_user table.

galaxy.model.migrate.versions.0117_add_user_activation.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0117_add_user_activation.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0118_add_hda_extended_metadata module

Add link from history_dataset_association to the extended_metadata table

galaxy.model.migrate.versions.0118_add_hda_extended_metadata.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0118_add_hda_extended_metadata.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0119_job_metrics module

Migration script for job metric plugins.

galaxy.model.migrate.versions.0119_job_metrics.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0119_job_metrics.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0120_dataset_collections module

Migration script for tables related to dataset collections.

galaxy.model.migrate.versions.0120_dataset_collections.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0120_dataset_collections.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0120_dataset_collections.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0121_workflow_uuids module

Add UUIDs to workflows

galaxy.model.migrate.versions.0121_workflow_uuids.metadata = MetaData(bind=None)

Because both workflow and job requests can be determined based the a fixed data structure, their IDs are based on hashing the data structure

galaxy.model.migrate.versions.0121_workflow_uuids.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0121_workflow_uuids.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0122_grow_mysql_blobs module

Migration script to grow MySQL blobs.

galaxy.model.migrate.versions.0122_grow_mysql_blobs.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0122_grow_mysql_blobs.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0123_add_workflow_request_tables module

Migration script for workflow request tables.

galaxy.model.migrate.versions.0123_add_workflow_request_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0123_add_workflow_request_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0124_job_state_history module

Migration script for the job state history table

galaxy.model.migrate.versions.0124_job_state_history.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0124_job_state_history.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0124_job_state_history.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0125_workflow_step_tracking module

Migration script to enhance workflow step usability by adding labels and UUIDs.

galaxy.model.migrate.versions.0125_workflow_step_tracking.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0125_workflow_step_tracking.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0126_password_reset module

Migration script for the password reset table

galaxy.model.migrate.versions.0126_password_reset.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0126_password_reset.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0127_output_collection_adjustments module

Migration script updating collections tables for output collections.

galaxy.model.migrate.versions.0127_output_collection_adjustments.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0127_output_collection_adjustments.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0128_session_timeout module

Migration script to add session update time (used for timeouts)

galaxy.model.migrate.versions.0128_session_timeout.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0128_session_timeout.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0129_job_external_output_metadata_validity module

Migration script to allow invalidation of job external output metadata temp files

galaxy.model.migrate.versions.0129_job_external_output_metadata_validity.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0129_job_external_output_metadata_validity.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0130_change_pref_datatype module

Migration script to change the ‘value’ column of ‘user_preference’ table from varchar to text.

galaxy.model.migrate.versions.0130_change_pref_datatype.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0130_change_pref_datatype.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules module

Migration script to support subworkflows and workflow request input parameters

galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user module

Migration script to add a last_password_change field to the user table

galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0133_add_dependency_column_to_job module

Add dependencies column to jobs table

galaxy.model.migrate.versions.0133_add_dependency_column_to_job.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0133_add_dependency_column_to_job.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module

Postponed to migration 160.

galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0135_add_library_tags module

This migration script adds support for storing tags in the context of a dataset in a library

galaxy.model.migrate.versions.0135_add_library_tags.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0135_add_library_tags.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0136_collection_and_workflow_state module

Migration script for collections and workflows connections.

galaxy.model.migrate.versions.0136_collection_and_workflow_state.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0136_collection_and_workflow_state.get_new_tables()[source]
galaxy.model.migrate.versions.0136_collection_and_workflow_state.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0136_collection_and_workflow_state.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0137_add_copied_from_job_id_column module

Add copied_from_job_id column to jobs table

galaxy.model.migrate.versions.0137_add_copied_from_job_id_column.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0137_add_copied_from_job_id_column.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0138_add_hda_version module

Add version column to history_dataset_association table

galaxy.model.migrate.versions.0138_add_hda_version.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0138_add_hda_version.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table module

Migration script to add the history_dataset_association_history table.

galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table module

Add dataset_version column to job_to_input_dataset table

galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0141_add_oidc_tables module

Migration script to add a new tables for an OpenID Connect authentication and authorization.

galaxy.model.migrate.versions.0141_add_oidc_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0141_add_oidc_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0142_change_numeric_metric_precision module

Migration script to change the ‘value’ column of ‘user_preference’ table from numeric(22, 7) to numeric(26, 7)

galaxy.model.migrate.versions.0142_change_numeric_metric_precision.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0142_change_numeric_metric_precision.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0143_add_cloudauthz_tables module

Migration script to add a new tables for CloudAuthz (tokens required to access cloud-based resources).

galaxy.model.migrate.versions.0143_add_cloudauthz_tables.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0143_add_cloudauthz_tables.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0144_add_cleanup_event_user_table module

Migration script to add the cleanup_event_user_association table.

galaxy.model.migrate.versions.0144_add_cleanup_event_user_table.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0144_add_cleanup_event_user_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0144_add_cleanup_event_user_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0145_add_workflow_step_input module

Migration script for workflow step input table.

galaxy.model.migrate.versions.0145_add_workflow_step_input.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0145_add_workflow_step_input.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0146_workflow_paths module

Migration script for workflow paths.

galaxy.model.migrate.versions.0146_workflow_paths.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0146_workflow_paths.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0147_job_messages module

Add structured failure reason column to jobs table

galaxy.model.migrate.versions.0147_job_messages.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0147_job_messages.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0148_add_checksum_table module

Migration script to add dataset source and hash tables.

galaxy.model.migrate.versions.0148_add_checksum_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0148_add_checksum_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0149_dynamic_tools module

Migration script to add the dynamic_tool table.

galaxy.model.migrate.versions.0149_dynamic_tools.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0149_dynamic_tools.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0149_dynamic_tools.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz module

Adds create_time columns to cloudauthz table.

galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0151_add_worker_process module

Add table for worker processes

galaxy.model.migrate.versions.0151_add_worker_process.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0151_add_worker_process.downgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0151_add_worker_process.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0152_add_metadata_file_uuid module

Adds uuid column to MetadataFile table.

galaxy.model.migrate.versions.0152_add_metadata_file_uuid.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0152_add_metadata_file_uuid.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0153_add_custos_authnz_token_table module

Migration for adding custos_authnz_token table.

galaxy.model.migrate.versions.0153_add_custos_authnz_token_table.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0153_add_custos_authnz_token_table.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.0154_created_from_basename module

Adds created_from_basename to dataset.

galaxy.model.migrate.versions.0154_created_from_basename.now()

Return a new datetime representing UTC day and time.

galaxy.model.migrate.versions.0154_created_from_basename.upgrade(migrate_engine)[source]
galaxy.model.migrate.versions.0154_created_from_basename.downgrade(migrate_engine)[source]

galaxy.model.migrate.versions.util module

galaxy.model.migrate.versions.util.engine_false(migrate_engine)[source]
galaxy.model.migrate.versions.util.engine_true(migrate_engine)[source]
galaxy.model.migrate.versions.util.nextval(migrate_engine, table, col='id')[source]
galaxy.model.migrate.versions.util.localtimestamp(migrate_engine)[source]
galaxy.model.migrate.versions.util.create_table(table)[source]
galaxy.model.migrate.versions.util.drop_table(table, metadata=None)[source]
Parameters:table (Table or str) – Table to drop
galaxy.model.migrate.versions.util.add_column(column, table, metadata, **kwds)[source]
Parameters:table (Table or str) – Table to add the column to
galaxy.model.migrate.versions.util.alter_column(column_name, table, metadata=None, **kwds)[source]
Parameters:
  • table (Table or str) – Table to alter
  • metadata (Metadata) – Needed only if table is a table name
galaxy.model.migrate.versions.util.drop_column(column_name, table, metadata=None)[source]
Parameters:
  • table (Table or str) – Table to drop the column from
  • metadata (Metadata) – Needed only if table is a table name
galaxy.model.migrate.versions.util.add_index(index_name, table, column_name, metadata=None, **kwds)[source]
Parameters:
  • table (Table or str) – Table to add the index to
  • metadata (Metadata) – Needed only if table is a table name
galaxy.model.migrate.versions.util.drop_index(index, table, column_name=None, metadata=None)[source]
Parameters:
  • index (Index or str) – Index to drop
  • table (Table or str) – Table to drop the index from
  • metadata (Metadata) – Needed only if table is a table name