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Python3: lib/galaxy/model/migrate/versions/0006..0013
lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py lib/galaxy/model/migrate/versions/0007_sharing_histories.py lib/galaxy/model/migrate/versions/0008_galaxy_forms.py lib/galaxy/model/migrate/versions/0009_request_table.py lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py lib/galaxy/model/migrate/versions/0012_user_address.py lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
This commit is contained in:
Timur Shtatland
@@ -32,6 +32,14 @@ lib/galaxy/forms/
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lib/galaxy/jobs/
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lib/galaxy/managers/
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lib/galaxy/model/__init__.py
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lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
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lib/galaxy/model/migrate/versions/0007_sharing_histories.py
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lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
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lib/galaxy/model/migrate/versions/0009_request_table.py
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lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
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lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
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lib/galaxy/model/migrate/versions/0012_user_address.py
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lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
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lib/galaxy/objectstore/
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lib/galaxy/openid/
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lib/galaxy/quota/
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@@ -20,10 +20,10 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script changes certain values in the history_dataset_association.extension"
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print "column, specifically 'qual' is chaged to be 'qual454'."
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print "========================================"
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print("========================================")
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print("This migration script changes certain values in the history_dataset_association.extension")
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print("column, specifically 'qual' is chaged to be 'qual454'.")
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print("========================================")
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def upgrade(migrate_engine):
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@@ -21,11 +21,11 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script creates the new history_user_share_association table, and adds"
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print "a new boolean type column to the history table. This provides support for sharing"
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print "histories in the same way that workflows are shared."
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print "========================================"
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print("========================================")
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print("This migration script creates the new history_user_share_association table, and adds")
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print("a new boolean type column to the history table. This provides support for sharing")
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print("histories in the same way that workflows are shared.")
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print("========================================")
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HistoryUserShareAssociation_table = Table( "history_user_share_association", metadata,
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Column( "id", Integer, primary_key=True ),
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@@ -31,17 +31,17 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script adds the following new tables for supporting Galaxy forms:"
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print "1) form_definition_current"
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print "2) form_definition"
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print "3) form_values"
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print "4) request_type"
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print "5) request"
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print "6) sample"
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print "7) sample_state"
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print "8) sample_event"
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print "========================================"
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print("========================================")
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print("This migration script adds the following new tables for supporting Galaxy forms:")
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print("1) form_definition_current")
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print("2) form_definition")
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print("3) form_values")
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print("4) request_type")
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print("5) request")
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print("6) sample")
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print("7) sample_state")
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print("8) sample_event")
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print("========================================")
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FormDefinitionCurrent_table = Table('form_definition_current', metadata,
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Column( "id", Integer, primary_key=True),
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@@ -22,11 +22,11 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script adds a new column to 2 tables:"
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print "1) a new boolean type column named 'submitted' to the 'request' table"
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print "2) a new string type column named 'bar_code' to the 'sample' table"
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print "========================================"
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print("========================================")
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print("This migration script adds a new column to 2 tables:")
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print("1) a new boolean type column named 'submitted' to the 'request' table")
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print("2) a new string type column named 'bar_code' to the 'sample' table")
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print("========================================")
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def upgrade(migrate_engine):
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@@ -29,15 +29,15 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script adds the history_dataset_association_display_at_authorization table, which"
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print "allows 'private' datasets to be displayed at external sites without making them public."
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print ""
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print "If using mysql, this script will display the following error, which is corrected in the next migration"
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print "script: history_dataset_association_display_at_authorization table failed: (OperationalError)"
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print "(1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time'"
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print "is too long."
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print "========================================"
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print("========================================")
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print("This migration script adds the history_dataset_association_display_at_authorization table, which")
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print("allows 'private' datasets to be displayed at external sites without making them public.")
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print("")
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print("If using mysql, this script will display the following error, which is corrected in the next migration")
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print("script: history_dataset_association_display_at_authorization table failed: (OperationalError)")
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print("(1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time'")
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print("is too long.")
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print("========================================")
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HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata,
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Column( "id", Integer, primary_key=True ),
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@@ -24,11 +24,11 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL"
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print "has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has"
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print "to be manually created."
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print "========================================"
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print("========================================")
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print("This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL")
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print("has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has")
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print("to be manually created.")
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print("========================================")
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HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata,
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Column( "id", Integer, primary_key=True ),
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@@ -26,12 +26,12 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This script adds a new user_address table that is currently only used with sample requests, where"
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print "a user can select from a list of his addresses to associate with the request. This script also"
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print "drops the request.submitted column which was boolean and replaces it with a request.state column"
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print "which is a string, allowing for more flexibility with request states."
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print "========================================"
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print("========================================")
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print("This script adds a new user_address table that is currently only used with sample requests, where")
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print("a user can select from a list of his addresses to associate with the request. This script also")
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print("drops the request.submitted column which was boolean and replaces it with a request.state column")
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print("which is a string, allowing for more flexibility with request states.")
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print("========================================")
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UserAddress_table = Table( "user_address", metadata,
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Column( "id", Integer, primary_key=True),
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@@ -32,22 +32,22 @@ metadata = MetaData()
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def display_migration_details():
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print "========================================"
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print "This migration script eliminates all of the tables that were used for the 1st version of the"
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print "library templates where template fields and contents were each stored as a separate table row"
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print "in various library item tables. All of these tables are dropped in this script, eliminating all"
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print "existing template data. A total of 14 existing tables are dropped."
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print ""
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print "We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified"
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print "list in the form_values table. This script introduces the following 3 new association tables:"
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print "1) library_info_association"
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print "2) library_folder_info_association"
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print "3) library_dataset_dataset_info_association"
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print ""
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print "If using mysql, this script will throw an (OperationalError) exception due to a long index name"
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print "on the library_dataset_dataset_info_association table, which is OK because the script creates"
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print "an index with a shortened name."
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print "========================================"
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print("========================================")
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print("This migration script eliminates all of the tables that were used for the 1st version of the")
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print("library templates where template fields and contents were each stored as a separate table row")
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print("in various library item tables. All of these tables are dropped in this script, eliminating all")
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print("existing template data. A total of 14 existing tables are dropped.")
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print("")
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print("We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified")
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print("list in the form_values table. This script introduces the following 3 new association tables:")
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print("1) library_info_association")
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print("2) library_folder_info_association")
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print("3) library_dataset_dataset_info_association")
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print("")
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print("If using mysql, this script will throw an (OperationalError) exception due to a long index name")
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print("on the library_dataset_dataset_info_association table, which is OK because the script creates")
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print("an index with a shortened name.")
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print("========================================")
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LibraryInfoAssociation_table = Table( 'library_info_association', metadata,
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Column( "id", Integer, primary_key=True),
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