diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt index 976e71e8bd9..21759162474 100644 --- a/.ci/py3_sources.txt +++ b/.ci/py3_sources.txt @@ -32,6 +32,14 @@ lib/galaxy/forms/ lib/galaxy/jobs/ lib/galaxy/managers/ lib/galaxy/model/__init__.py +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 lib/galaxy/objectstore/ lib/galaxy/openid/ lib/galaxy/quota/ diff --git a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py index de3733670f7..4d0cf1104e1 100644 --- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py @@ -20,10 +20,10 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script changes certain values in the history_dataset_association.extension" - print "column, specifically 'qual' is chaged to be 'qual454'." - print "========================================" + print("========================================") + print("This migration script changes certain values in the history_dataset_association.extension") + print("column, specifically 'qual' is chaged to be 'qual454'.") + print("========================================") def upgrade(migrate_engine): diff --git a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py index 3f959c7463c..599717e60a1 100644 --- a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py +++ b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py @@ -21,11 +21,11 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script creates the new history_user_share_association table, and adds" - print "a new boolean type column to the history table. This provides support for sharing" - print "histories in the same way that workflows are shared." - print "========================================" + print("========================================") + print("This migration script creates the new history_user_share_association table, and adds") + print("a new boolean type column to the history table. This provides support for sharing") + print("histories in the same way that workflows are shared.") + print("========================================") HistoryUserShareAssociation_table = Table( "history_user_share_association", metadata, Column( "id", Integer, primary_key=True ), diff --git a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py index b3adfd8370d..9c0912e1fae 100644 --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py @@ -31,17 +31,17 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script adds the following new tables for supporting Galaxy forms:" - print "1) form_definition_current" - print "2) form_definition" - print "3) form_values" - print "4) request_type" - print "5) request" - print "6) sample" - print "7) sample_state" - print "8) sample_event" - print "========================================" + print("========================================") + print("This migration script adds the following new tables for supporting Galaxy forms:") + print("1) form_definition_current") + print("2) form_definition") + print("3) form_values") + print("4) request_type") + print("5) request") + print("6) sample") + print("7) sample_state") + print("8) sample_event") + print("========================================") FormDefinitionCurrent_table = Table('form_definition_current', metadata, Column( "id", Integer, primary_key=True), diff --git a/lib/galaxy/model/migrate/versions/0009_request_table.py b/lib/galaxy/model/migrate/versions/0009_request_table.py index 72476ec5bf7..da2b21d71c6 100644 --- a/lib/galaxy/model/migrate/versions/0009_request_table.py +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py @@ -22,11 +22,11 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script adds a new column to 2 tables:" - print "1) a new boolean type column named 'submitted' to the 'request' table" - print "2) a new string type column named 'bar_code' to the 'sample' table" - print "========================================" + print("========================================") + print("This migration script adds a new column to 2 tables:") + print("1) a new boolean type column named 'submitted' to the 'request' table") + print("2) a new string type column named 'bar_code' to the 'sample' table") + print("========================================") def upgrade(migrate_engine): diff --git a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py index 059013e550c..ca86235123d 100644 --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py @@ -29,15 +29,15 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script adds the history_dataset_association_display_at_authorization table, which" - print "allows 'private' datasets to be displayed at external sites without making them public." - print "" - print "If using mysql, this script will display the following error, which is corrected in the next migration" - print "script: history_dataset_association_display_at_authorization table failed: (OperationalError)" - print "(1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time'" - print "is too long." - print "========================================" + print("========================================") + print("This migration script adds the history_dataset_association_display_at_authorization table, which") + print("allows 'private' datasets to be displayed at external sites without making them public.") + print("") + print("If using mysql, this script will display the following error, which is corrected in the next migration") + print("script: history_dataset_association_display_at_authorization table failed: (OperationalError)") + print("(1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time'") + print("is too long.") + print("========================================") HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), diff --git a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py index 8e69bd7d144..5fcf1e6dff2 100644 --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py @@ -24,11 +24,11 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL" - print "has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has" - print "to be manually created." - print "========================================" + print("========================================") + print("This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL") + print("has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has") + print("to be manually created.") + print("========================================") HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), diff --git a/lib/galaxy/model/migrate/versions/0012_user_address.py b/lib/galaxy/model/migrate/versions/0012_user_address.py index 89beaf65e03..de22c8b162b 100644 --- a/lib/galaxy/model/migrate/versions/0012_user_address.py +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py @@ -26,12 +26,12 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This script adds a new user_address table that is currently only used with sample requests, where" - print "a user can select from a list of his addresses to associate with the request. This script also" - print "drops the request.submitted column which was boolean and replaces it with a request.state column" - print "which is a string, allowing for more flexibility with request states." - print "========================================" + print("========================================") + print("This script adds a new user_address table that is currently only used with sample requests, where") + print("a user can select from a list of his addresses to associate with the request. This script also") + print("drops the request.submitted column which was boolean and replaces it with a request.state column") + print("which is a string, allowing for more flexibility with request states.") + print("========================================") UserAddress_table = Table( "user_address", metadata, Column( "id", Integer, primary_key=True), diff --git a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py index a7884890d24..f781ddde61c 100644 --- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py @@ -32,22 +32,22 @@ metadata = MetaData() def display_migration_details(): - print "========================================" - print "This migration script eliminates all of the tables that were used for the 1st version of the" - print "library templates where template fields and contents were each stored as a separate table row" - print "in various library item tables. All of these tables are dropped in this script, eliminating all" - print "existing template data. A total of 14 existing tables are dropped." - print "" - print "We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified" - print "list in the form_values table. This script introduces the following 3 new association tables:" - print "1) library_info_association" - print "2) library_folder_info_association" - print "3) library_dataset_dataset_info_association" - print "" - print "If using mysql, this script will throw an (OperationalError) exception due to a long index name" - print "on the library_dataset_dataset_info_association table, which is OK because the script creates" - print "an index with a shortened name." - print "========================================" + print("========================================") + print("This migration script eliminates all of the tables that were used for the 1st version of the") + print("library templates where template fields and contents were each stored as a separate table row") + print("in various library item tables. All of these tables are dropped in this script, eliminating all") + print("existing template data. A total of 14 existing tables are dropped.") + print("") + print("We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified") + print("list in the form_values table. This script introduces the following 3 new association tables:") + print("1) library_info_association") + print("2) library_folder_info_association") + print("3) library_dataset_dataset_info_association") + print("") + print("If using mysql, this script will throw an (OperationalError) exception due to a long index name") + print("on the library_dataset_dataset_info_association table, which is OK because the script creates") + print("an index with a shortened name.") + print("========================================") LibraryInfoAssociation_table = Table( 'library_info_association', metadata, Column( "id", Integer, primary_key=True),