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galaxy.model.migrate.versions package¶
Submodules¶
galaxy.model.migrate.versions.0001_initial_tables module¶
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galaxy.model.migrate.versions.0001_initial_tables.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0002_metadata_file_table module¶
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galaxy.model.migrate.versions.0002_metadata_file_table.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0003_security_and_libraries module¶
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galaxy.model.migrate.versions.0003_security_and_libraries.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0004_indexes_and_defaults module¶
galaxy.model.migrate.versions.0005_cleanup_datasets_fix module¶
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galaxy.model.migrate.versions.0005_cleanup_datasets_fix.now()¶ Return a new datetime representing UTC day and time.
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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>¶
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permitted_actions= <galaxy.util.bunch.Bunch object>¶
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file_path= '/tmp/'¶
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engine= None¶
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__init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True)¶
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id¶
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state¶
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deleted¶
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purged¶
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purgable¶
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external_filename¶
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file_size¶
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file_name¶
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extra_files_path¶
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active_history_associations¶
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active_library_associations¶
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create_time¶
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history_associations¶
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library_associations¶
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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)¶
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update_time¶
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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:
objectA base class for all ‘dataset instances’, HDAs, LDAs, etc
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states= <galaxy.util.bunch.Bunch object>¶
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permitted_actions= <galaxy.util.bunch.Bunch object>¶
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__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]¶
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ext¶
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state¶
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file_name¶
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extra_files_path¶
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metadata¶
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dbkey¶
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get_raw_data()[source]¶ Returns the full data. To stream it open the file_name and read/write as needed
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source_library_dataset¶
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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)¶
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hid¶
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to_library_dataset_dataset_association(target_folder, replace_dataset=None, parent_id=None)[source]¶
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blurb¶
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children¶
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copied_from_history_dataset_association_id¶
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copied_from_library_dataset_dataset_association_id¶
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copied_to_history_dataset_associations¶
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copied_to_library_dataset_dataset_associations¶
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create_time¶
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dataset¶
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dataset_id¶
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deleted¶
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designation¶
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extension¶
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id¶
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info¶
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name¶
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parent_id¶
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peek¶
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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)¶
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update_time¶
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visible¶
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visible_children¶
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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)¶
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library_dataset¶
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blurb¶
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children¶
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copied_from_history_dataset_association_id¶
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copied_from_library_dataset_dataset_association_id¶
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copied_to_history_dataset_associations¶
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copied_to_library_dataset_dataset_associations¶
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create_time¶
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dataset¶
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dataset_id¶
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deleted¶
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designation¶
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extension¶
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id¶
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info¶
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library_dataset_id¶
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message¶
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name¶
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parent_id¶
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peek¶
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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)¶
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update_time¶
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visible¶
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visible_children¶
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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)¶
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order_id¶
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library_dataset_dataset_association¶
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info¶
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name¶
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create_time¶
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deleted¶
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expired_datasets¶
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id¶
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library_dataset_dataset_association_id¶
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purged¶
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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)¶
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update_time¶
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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.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.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
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galaxy.model.migrate.versions.0008_galaxy_forms.now()¶ Return a new datetime representing UTC day and time.
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.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
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galaxy.model.migrate.versions.0010_hda_display_at_authz_table.now()¶ Return a new datetime representing UTC day and time.
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.
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galaxy.model.migrate.versions.0011_v0010_mysql_index_fix.now()¶ Return a new datetime representing UTC day and time.
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.
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galaxy.model.migrate.versions.0012_user_address.now()¶ Return a new datetime representing UTC day and time.
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.0014_pages module¶
- Migration script to add support for “Pages”.
- Creates Page and PageRevision tables
- Adds username column to User table
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galaxy.model.migrate.versions.0014_pages.now()¶ Return a new datetime representing UTC day and time.
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.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.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.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.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.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.0021_user_prefs module¶
This migration script adds a user preferences table to Galaxy.
galaxy.model.migrate.versions.0022_visualization_tables module¶
- Migration script to add support for storing visualizations.
- Creates Visualization and VisualizationRevision tables
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galaxy.model.migrate.versions.0022_visualization_tables.now()¶ Return a new datetime representing UTC day and time.
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.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.0025_user_info module¶
This script adds a foreign key to the form_values table in the galaxy_user table
galaxy.model.migrate.versions.0026_cloud_tables module¶
This script adds tables needed for Galaxy cloud functionality.
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galaxy.model.migrate.versions.0026_cloud_tables.now()¶ Return a new datetime representing UTC day and time.
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<cloud_image>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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.0027_request_events module¶
This migration script adds the request_event table and removes the state field in the request table
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galaxy.model.migrate.versions.0027_request_events.now()¶ Return a new datetime representing UTC day and time.
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.0029_user_actions module¶
This migration script adds a user actions table to Galaxy.
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galaxy.model.migrate.versions.0029_user_actions.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0030_history_slug_column module¶
Migration script to add column for a history slug.
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.0032_stored_workflow_slug_column module¶
Migration script to add slug column for stored workflow.
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.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.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.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.
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galaxy.model.migrate.versions.0037_samples_library.now()¶ Return a new datetime representing UTC day and time.
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.
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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.0039_add_synopsis_column_to_library_table module¶
Migration script to add a synopsis column to the library table.
galaxy.model.migrate.versions.0040_page_annotations module¶
Migration script to (a) create tables for annotating pages.
galaxy.model.migrate.versions.0041_workflow_invocation module¶
Migration script to create tables for tracking workflow invocations.
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galaxy.model.migrate.versions.0041_workflow_invocation.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0042_workflow_invocation_fix module¶
Drop and readd workflow invocation tables, allowing null jobs
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galaxy.model.migrate.versions.0042_workflow_invocation_fix.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module¶
Migration script to create tables and columns for sharing visualizations.
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.0045_request_type_permissions_table module¶
Migration script to add the request_type_permissions table.
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galaxy.model.migrate.versions.0045_request_type_permissions_table.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0046_post_job_actions module¶
Migration script to create tables for handling post-job actions.
galaxy.model.migrate.versions.0047_job_table_user_id_column module¶
Add a user_id column to the job table.
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.0049_api_keys_table module¶
Migration script to add the api_keys table.
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galaxy.model.migrate.versions.0049_api_keys_table.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0050_drop_cloud_tables module¶
This script drops tables that were associated with the old Galaxy Cloud functionality.
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galaxy.model.migrate.versions.0050_drop_cloud_tables.now()¶ Return a new datetime representing UTC day and time.
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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 datetime.utcnow>)), Column('update_time', DateTime(), table=<cloud_image>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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.0051_imported_col_for_jobs_table module¶
Migration script to add imported column for jobs table.
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
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galaxy.model.migrate.versions.0052_sample_dataset_table.now()¶ Return a new datetime representing UTC day and time.
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.0054_visualization_dbkey module¶
Migration script to add dbkey column for visualization.
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.0056_workflow_outputs module¶
Migration script to create tables for adding explicit workflow outputs.
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.0058_history_import_export module¶
Migration script to create table for exporting histories to archives.
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.0060_history_archive_import module¶
Migration script to create column and table for importing histories from file archives.
galaxy.model.migrate.versions.0061_tasks module¶
Migration script to create tables task management.
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galaxy.model.migrate.versions.0061_tasks.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0062_user_openid_table module¶
Migration script to create table for associating sessions and users with OpenIDs.
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galaxy.model.migrate.versions.0062_user_openid_table.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0063_sequencer_table module¶
Migration script to create a new ‘sequencer’ table
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galaxy.model.migrate.versions.0063_sequencer_table.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module¶
Migration script to add the run and sample_run_association tables.
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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.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.0066_deferred_job_and_transfer_job_tables module¶
Migration script to create table for storing deferred job and managed transfer information.
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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.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.
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galaxy.model.migrate.versions.0067_populate_sequencer_table.get_latest_id(migrate_engine, table)[source]¶
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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
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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
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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.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.
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galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services.now()¶ Return a new datetime representing UTC day and time.
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.0070_add_info_column_to_deferred_job_table module¶
Migration script to add ‘info’ column to the transfer_job table.
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.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.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.0074_add_purged_column_to_library_dataset_table module¶
Migration script to add ‘purged’ column to the library_dataset table.
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.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.0077_create_tool_tag_association_table module¶
Migration script to create table for storing tool tag associations.
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.0079_input_library_to_job_table module¶
Migration script to add the job_to_input_library_dataset table.
galaxy.model.migrate.versions.0080_quota_tables module¶
Migration script to create tables for disk quotas.
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galaxy.model.migrate.versions.0080_quota_tables.now()¶ Return a new datetime representing UTC day and time.
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.0082_add_tool_shed_repository_table module¶
Migration script to add the tool_shed_repository table.
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galaxy.model.migrate.versions.0082_add_tool_shed_repository_table.now()¶ Return a new datetime representing UTC day and time.
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.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.0085_add_task_info module¶
Migration script to add ‘info’ column to the task table.
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.0087_tool_id_guid_map_table module¶
Migration script to create the tool_id_guid_map table.
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galaxy.model.migrate.versions.0087_tool_id_guid_map_table.now()¶ Return a new datetime representing UTC day and time.
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.0089_add_object_store_id_columns module¶
Migration script to add ‘object_store_id’ column to various tables
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.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.
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galaxy.model.migrate.versions.0091_add_tool_version_tables.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0092_add_migrate_tools_table module¶
Migration script to create the migrate_tools table.
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.0094_add_job_handler_col module¶
Migration script to add a ‘handler’ column to the ‘job’ table.
galaxy.model.migrate.versions.0095_hda_subsets module¶
Migration script to create table for tracking history_dataset_association subsets.
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.0097_add_ctx_rev_column module¶
Migration script to add the ctx_rev column to the tool_shed_repository table.
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.0099_add_tool_dependency_table module¶
Migration script to add the tool_dependency table.
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galaxy.model.migrate.versions.0099_add_tool_dependency_table.now()¶ Return a new datetime representing UTC day and time.
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.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.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.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.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 datetime.utcnow>)), Column('update_time', DateTime(), table=<deferred_job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.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.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.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.0107_add_exit_code_to_job_and_task module¶
Add the exit_code column to the Job and Task tables.
galaxy.model.migrate.versions.0108_add_extended_metadata module¶
Add the ExtendedMetadata and ExtendedMetadataIndex tables
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.0110_add_dataset_uuid module¶
Add UUID column to dataset table
galaxy.model.migrate.versions.0111_add_job_destinations module¶
Add support for job destinations to the job table
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.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.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.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.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.0117_add_user_activation module¶
Adds ‘active’ and ‘activation_token’ columns to the galaxy_user table.
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.0119_job_metrics module¶
Migration script for job metric plugins.
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.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.0122_grow_mysql_blobs module¶
Migration script to grow MySQL blobs.
galaxy.model.migrate.versions.0123_add_workflow_request_tables module¶
Migration script for workflow request tables.
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.0125_workflow_step_tracking module¶
Migration script to enhance workflow step usability by adding labels and UUIDs.
galaxy.model.migrate.versions.0126_password_reset module¶
Migration script for the password reset table
galaxy.model.migrate.versions.0127_output_collection_adjustments module¶
Migration script updating collections tables for output collections.
galaxy.model.migrate.versions.0128_session_timeout module¶
Migration script to add session update time (used for timeouts)
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.0130_change_pref_datatype module¶
Migration script to change the ‘value’ column of ‘user_preference’ table from varchar to text.
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.0132_add_lastpasswordchange_to_user module¶
Migration script to add a last_password_change field to the user table
galaxy.model.migrate.versions.0133_add_dependency_column_to_job module¶
Add dependencies column to jobs table
galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module¶
Postponed to migration 160.
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.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.0137_add_copied_from_job_id_column module¶
Add copied_from_job_id column to jobs table
galaxy.model.migrate.versions.0138_add_hda_version module¶
Add version column to history_dataset_association table
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.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.0141_add_oidc_tables module¶
Migration script to add a new tables for an OpenID Connect authentication and authorization.
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.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.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.0145_add_workflow_step_input module¶
Migration script for workflow step input table.
galaxy.model.migrate.versions.0146_workflow_paths module¶
Migration script for workflow paths.
galaxy.model.migrate.versions.0147_job_messages module¶
Add structured failure reason column to jobs table
galaxy.model.migrate.versions.0148_add_checksum_table module¶
Migration script to add dataset source and hash tables.
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.0150_add_create_time_field_for_cloudauthz module¶
Adds create_time columns to cloudauthz table.
galaxy.model.migrate.versions.0151_add_worker_process module¶
Add table for worker processes
-
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.0153_add_custos_authnz_token_table module¶
Migration for adding custos_authnz_token table.
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.0155_job_galaxy_version module¶
Add ‘galaxy_version’ attribute to Job table.
-
galaxy.model.migrate.versions.0155_job_galaxy_version.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0156_add_interactivetools module¶
Migration script to add new tables for InteractiveTools.
-
galaxy.model.migrate.versions.0156_add_interactivetools.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0157_rework_dataset_validation module¶
Rework dataset validation in database.
galaxy.model.migrate.versions.0158_workflow_reports module¶
Adds reports_config to workflow.
-
galaxy.model.migrate.versions.0158_workflow_reports.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0159_add_job_external_id_index module¶
Add index for job runner external ID.
galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again module¶
Migration script to set the ‘deleted’ column of the ‘history_dataset_association’ table to True if ‘purged’ is True.
galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table module¶
Migration script to add a new workflow_invocation_output_parameter table to track output parameters.
galaxy.model.migrate.versions.0162_job_only_pjas module¶
Migration script to allow null workflow_step for PostJobActions. This enables using PJAs with individual job executions.
galaxy.model.migrate.versions.0163_worker_process_pid module¶
Adds pid column to worker_process table.
galaxy.model.migrate.versions.0164_page_format module¶
Adds page content format.
-
galaxy.model.migrate.versions.0164_page_format.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.0165_add_content_update_time module¶
Adds timestamps to hdca table. Adds triggers to dataset, hda, hdca tables to update history.update_time when contents are changed.
-
galaxy.model.migrate.versions.0165_add_content_update_time.create_timestamps(metadata, table_name)[source]¶
-
galaxy.model.migrate.versions.0165_add_content_update_time.drop_timestamps(metadata, table_name)[source]¶
-
galaxy.model.migrate.versions.0165_add_content_update_time.now()¶ Return a new datetime representing UTC day and time.
galaxy.model.migrate.versions.util module¶
-
galaxy.model.migrate.versions.util.drop_table(table, metadata=None)[source]¶ Parameters: table ( Tableor str) – Table to drop
-
galaxy.model.migrate.versions.util.add_column(column, table, metadata, **kwds)[source]¶ Parameters: table ( Tableor str) – Table to add the column to
-
galaxy.model.migrate.versions.util.alter_column(column_name, table, metadata=None, **kwds)[source]¶ Parameters: - table (
Tableor str) – Table to alter - metadata (
Metadata) – Needed only iftableis a table name
- table (
-
galaxy.model.migrate.versions.util.drop_column(column_name, table, metadata=None)[source]¶ Parameters: - table (
Tableor str) – Table to drop the column from - metadata (
Metadata) – Needed only iftableis a table name
- table (