[2] | 1 | from sqlalchemy import * |
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| 2 | from migrate import * |
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| 3 | |
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| 4 | import datetime |
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| 5 | now = datetime.datetime.utcnow |
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| 6 | |
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| 7 | # Need our custom types, but don't import anything else from model |
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| 8 | from galaxy.model.custom_types import * |
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| 9 | |
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| 10 | import logging |
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| 11 | log = logging.getLogger( __name__ ) |
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| 12 | |
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| 13 | metadata = MetaData( migrate_engine ) |
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| 14 | |
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| 15 | # Tables as of changeset 1464:c7acaa1bb88f |
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| 16 | User_table = Table( "galaxy_user", metadata, |
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| 17 | Column( "id", Integer, primary_key=True), |
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| 18 | Column( "create_time", DateTime, default=now ), |
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| 19 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 20 | Column( "email", TrimmedString( 255 ), nullable=False ), |
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| 21 | Column( "password", TrimmedString( 40 ), nullable=False ), |
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| 22 | Column( "external", Boolean, default=False ) ) |
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| 23 | |
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| 24 | History_table = Table( "history", metadata, |
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| 25 | Column( "id", Integer, primary_key=True), |
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| 26 | Column( "create_time", DateTime, default=now ), |
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| 27 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
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| 28 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 29 | Column( "name", TrimmedString( 255 ) ), |
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| 30 | Column( "hid_counter", Integer, default=1 ), |
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| 31 | Column( "deleted", Boolean, index=True, default=False ), |
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| 32 | Column( "purged", Boolean, index=True, default=False ), |
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| 33 | Column( "genome_build", TrimmedString( 40 ) ) ) |
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| 34 | |
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| 35 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, |
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| 36 | Column( "id", Integer, primary_key=True ), |
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| 37 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 38 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
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| 39 | Column( "create_time", DateTime, default=now ), |
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| 40 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 41 | Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), |
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| 42 | Column( "hid", Integer ), |
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| 43 | Column( "name", TrimmedString( 255 ) ), |
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| 44 | Column( "info", TrimmedString( 255 ) ), |
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| 45 | Column( "blurb", TrimmedString( 255 ) ), |
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| 46 | Column( "peek" , TEXT ), |
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| 47 | Column( "extension", TrimmedString( 64 ) ), |
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| 48 | Column( "metadata", MetadataType(), key="_metadata" ), |
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| 49 | Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), |
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| 50 | Column( "designation", TrimmedString( 255 ) ), |
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| 51 | Column( "deleted", Boolean, index=True, default=False ), |
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| 52 | Column( "visible", Boolean ) ) |
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| 53 | |
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| 54 | Dataset_table = Table( "dataset", metadata, |
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| 55 | Column( "id", Integer, primary_key=True ), |
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| 56 | Column( "create_time", DateTime, default=now ), |
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| 57 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
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| 58 | Column( "state", TrimmedString( 64 ) ), |
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| 59 | Column( "deleted", Boolean, index=True, default=False ), |
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| 60 | Column( "purged", Boolean, index=True, default=False ), |
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| 61 | Column( "purgable", Boolean, default=True ), |
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| 62 | Column( "external_filename" , TEXT ), |
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| 63 | Column( "_extra_files_path", TEXT ), |
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| 64 | Column( 'file_size', Numeric( 15, 0 ) ) ) |
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| 65 | |
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| 66 | ImplicitlyConvertedDatasetAssociation_table = Table( "implicitly_converted_dataset_association", metadata, |
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| 67 | Column( "id", Integer, primary_key=True ), |
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| 68 | Column( "create_time", DateTime, default=now ), |
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| 69 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 70 | Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), |
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| 71 | Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 72 | Column( "deleted", Boolean, index=True, default=False ), |
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| 73 | Column( "metadata_safe", Boolean, index=True, default=True ), |
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| 74 | Column( "type", TrimmedString( 255 ) ) ) |
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| 75 | |
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| 76 | ValidationError_table = Table( "validation_error", metadata, |
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| 77 | Column( "id", Integer, primary_key=True ), |
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| 78 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 79 | Column( "message", TrimmedString( 255 ) ), |
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| 80 | Column( "err_type", TrimmedString( 64 ) ), |
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| 81 | Column( "attributes", TEXT ) ) |
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| 82 | |
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| 83 | Job_table = Table( "job", metadata, |
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| 84 | Column( "id", Integer, primary_key=True ), |
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| 85 | Column( "create_time", DateTime, default=now ), |
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| 86 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 87 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 88 | Column( "tool_id", String( 255 ) ), |
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| 89 | Column( "tool_version", TEXT, default="1.0.0" ), |
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| 90 | Column( "state", String( 64 ) ), |
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| 91 | Column( "info", TrimmedString( 255 ) ), |
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| 92 | Column( "command_line", TEXT ), |
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| 93 | Column( "param_filename", String( 1024 ) ), |
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| 94 | Column( "runner_name", String( 255 ) ), |
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| 95 | Column( "stdout", TEXT ), |
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| 96 | Column( "stderr", TEXT ), |
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| 97 | Column( "traceback", TEXT ), |
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| 98 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), |
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| 99 | Column( "job_runner_name", String( 255 ) ), |
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| 100 | Column( "job_runner_external_id", String( 255 ) ) ) |
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| 101 | |
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| 102 | JobParameter_table = Table( "job_parameter", metadata, |
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| 103 | Column( "id", Integer, primary_key=True ), |
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| 104 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
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| 105 | Column( "name", String(255) ), |
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| 106 | Column( "value", TEXT ) ) |
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| 107 | |
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| 108 | JobToInputDatasetAssociation_table = Table( "job_to_input_dataset", metadata, |
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| 109 | Column( "id", Integer, primary_key=True ), |
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| 110 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
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| 111 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 112 | Column( "name", String(255) ) ) |
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| 113 | |
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| 114 | JobToOutputDatasetAssociation_table = Table( "job_to_output_dataset", metadata, |
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| 115 | Column( "id", Integer, primary_key=True ), |
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| 116 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
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| 117 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 118 | Column( "name", String(255) ) ) |
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| 119 | |
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| 120 | Event_table = Table( "event", metadata, |
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| 121 | Column( "id", Integer, primary_key=True ), |
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| 122 | Column( "create_time", DateTime, default=now ), |
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| 123 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 124 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True, nullable=True ), |
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| 125 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), |
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| 126 | Column( "message", TrimmedString( 1024 ) ), |
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| 127 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), |
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| 128 | Column( "tool_id", String( 255 ) ) ) |
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| 129 | |
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| 130 | GalaxySession_table = Table( "galaxy_session", metadata, |
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| 131 | Column( "id", Integer, primary_key=True ), |
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| 132 | Column( "create_time", DateTime, default=now ), |
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| 133 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 134 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), |
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| 135 | Column( "remote_host", String( 255 ) ), |
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| 136 | Column( "remote_addr", String( 255 ) ), |
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| 137 | Column( "referer", TEXT ), |
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| 138 | Column( "current_history_id", Integer, ForeignKey( "history.id" ), nullable=True ), |
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| 139 | Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), |
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| 140 | Column( "is_valid", Boolean, default=False ), |
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| 141 | Column( "prev_session_id", Integer ) |
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| 142 | ) |
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| 143 | |
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| 144 | GalaxySessionToHistoryAssociation_table = Table( "galaxy_session_to_history", metadata, |
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| 145 | Column( "id", Integer, primary_key=True ), |
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| 146 | Column( "create_time", DateTime, default=now ), |
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| 147 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), |
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| 148 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) ) |
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| 149 | |
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| 150 | StoredWorkflow_table = Table( "stored_workflow", metadata, |
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| 151 | Column( "id", Integer, primary_key=True ), |
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| 152 | Column( "create_time", DateTime, default=now ), |
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| 153 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 154 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), |
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| 155 | Column( "latest_workflow_id", Integer, |
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| 156 | ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ), |
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| 157 | Column( "name", TEXT ), |
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| 158 | Column( "deleted", Boolean, default=False ), |
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| 159 | ) |
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| 160 | |
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| 161 | Workflow_table = Table( "workflow", metadata, |
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| 162 | Column( "id", Integer, primary_key=True ), |
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| 163 | Column( "create_time", DateTime, default=now ), |
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| 164 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 165 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ), |
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| 166 | Column( "name", TEXT ), |
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| 167 | Column( "has_cycles", Boolean ), |
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| 168 | Column( "has_errors", Boolean ) |
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| 169 | ) |
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| 170 | |
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| 171 | WorkflowStep_table = Table( "workflow_step", metadata, |
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| 172 | Column( "id", Integer, primary_key=True ), |
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| 173 | Column( "create_time", DateTime, default=now ), |
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| 174 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 175 | Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ), |
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| 176 | Column( "type", String(64) ), |
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| 177 | Column( "tool_id", TEXT ), |
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| 178 | Column( "tool_version", TEXT ), |
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| 179 | Column( "tool_inputs", JSONType ), |
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| 180 | Column( "tool_errors", JSONType ), |
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| 181 | Column( "position", JSONType ), |
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| 182 | Column( "config", JSONType ), |
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| 183 | Column( "order_index", Integer ) |
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| 184 | ) |
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| 185 | |
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| 186 | WorkflowStepConnection_table = Table( "workflow_step_connection", metadata, |
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| 187 | Column( "id", Integer, primary_key=True ), |
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| 188 | Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
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| 189 | Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
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| 190 | Column( "output_name", TEXT ), |
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| 191 | Column( "input_name", TEXT) |
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| 192 | ) |
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| 193 | |
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| 194 | StoredWorkflowUserShareAssociation_table = Table( "stored_workflow_user_share_connection", metadata, |
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| 195 | Column( "id", Integer, primary_key=True ), |
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| 196 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
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| 197 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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| 198 | ) |
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| 199 | |
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| 200 | StoredWorkflowMenuEntry_table = Table( "stored_workflow_menu_entry", metadata, |
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| 201 | Column( "id", Integer, primary_key=True ), |
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| 202 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
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| 203 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 204 | Column( "order_index", Integer ) ) |
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| 205 | |
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| 206 | def upgrade(): |
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| 207 | metadata.create_all() |
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| 208 | |
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| 209 | ## def downgrade(): |
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| 210 | ## # Operations to reverse the above upgrade go here. |
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| 211 | ## pass |
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