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Merge pull request #4333 from VJalili/patch-1

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Some formatting
This commit is contained in:
Marius van den Beek
2017-07-23 20:36:50 +02:00
committed by GitHub
parent fe038dcb4e 08fec8770a
commit e43a12ad3e
1 changed files with 101 additions and 101 deletions
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lib/galaxy/model/mapping.py
+101 -101
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@@ -47,7 +47,7 @@ metadata = MetaData()
model.User.table = Table(
"galaxy_user", metadata,
Column( "id", Integer, primary_key=True),
Column( "id", Integer, primary_key=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "email", TrimmedString( 255 ), index=True, nullable=False ),
@@ -64,19 +64,19 @@ model.User.table = Table(
model.UserAddress.table = Table(
"user_address", metadata,
Column( "id", Integer, primary_key=True),
Column( "id", Integer, primary_key=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "desc", TrimmedString( 255 )),
Column( "name", TrimmedString( 255 ), nullable=False),
Column( "institution", TrimmedString( 255 )),
Column( "address", TrimmedString( 255 ), nullable=False),
Column( "city", TrimmedString( 255 ), nullable=False),
Column( "state", TrimmedString( 255 ), nullable=False),
Column( "postal_code", TrimmedString( 255 ), nullable=False),
Column( "country", TrimmedString( 255 ), nullable=False),
Column( "phone", TrimmedString( 255 )),
Column( "desc", TrimmedString( 255 ) ),
Column( "name", TrimmedString( 255 ), nullable=False ),
Column( "institution", TrimmedString( 255 ) ),
Column( "address", TrimmedString( 255 ), nullable=False ),
Column( "city", TrimmedString( 255 ), nullable=False ),
Column( "state", TrimmedString( 255 ), nullable=False ),
Column( "postal_code", TrimmedString( 255 ), nullable=False ),
Column( "country", TrimmedString( 255 ), nullable=False ),
Column( "phone", TrimmedString( 255 ) ),
Column( "deleted", Boolean, index=True, default=False ),
Column( "purged", Boolean, index=True, default=False ) )
@@ -98,7 +98,7 @@ model.PasswordResetToken.table = Table(
model.History.table = Table(
"history", metadata,
Column( "id", Integer, primary_key=True),
Column( "id", Integer, primary_key=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
@@ -178,7 +178,7 @@ model.HistoryDatasetAssociationSubset.table = Table(
Column( "id", Integer, primary_key=True ),
Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
Column( "history_dataset_association_subset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
Column( "location", Unicode(255), index=True) )
Column( "location", Unicode( 255 ), index=True ) )
model.ImplicitlyConvertedDatasetAssociation.table = Table(
"implicitly_converted_dataset_association", metadata,
@@ -397,8 +397,8 @@ model.ExtendedMetadataIndex.table = Table(
Column( "id", Integer, primary_key=True ),
Column( "extended_metadata_id", Integer,
ForeignKey("extended_metadata.id", onupdate="CASCADE", ondelete="CASCADE" ), index=True ),
Column( "path", String( 255 )),
Column( "value", TEXT))
Column( "path", String( 255 ) ),
Column( "value", TEXT ) )
model.Library.table = Table(
"library", metadata,
@@ -480,7 +480,7 @@ model.Job.table = Table(
Column( "destination_params", JSONType, nullable=True ),
Column( "object_store_id", TrimmedString( 255 ), index=True ),
Column( "imported", Boolean, default=False, index=True ),
Column( "params", TrimmedString(255), index=True ),
Column( "params", TrimmedString( 255 ), index=True ),
Column( "handler", TrimmedString( 255 ), index=True ) )
model.JobStateHistory.table = Table(
@@ -496,7 +496,7 @@ model.JobParameter.table = Table(
"job_parameter", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "name", String(255) ),
Column( "name", String( 255 ) ),
Column( "value", TEXT ) )
model.JobToInputDatasetAssociation.table = Table(
@@ -504,49 +504,49 @@ model.JobToInputDatasetAssociation.table = Table(
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
Column( "name", String(255) ) )
Column( "name", String( 255 ) ) )
model.JobToOutputDatasetAssociation.table = Table(
"job_to_output_dataset", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
Column( "name", String(255) ) )
Column( "name", String( 255 ) ) )
model.JobToInputDatasetCollectionAssociation.table = Table(
"job_to_input_dataset_collection", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ),
Column( "name", Unicode(255) ) )
Column( "name", Unicode( 255 ) ) )
model.JobToImplicitOutputDatasetCollectionAssociation.table = Table(
"job_to_implicit_output_dataset_collection", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "dataset_collection_id", Integer, ForeignKey( "dataset_collection.id" ), index=True ),
Column( "name", Unicode(255) ) )
Column( "name", Unicode( 255 ) ) )
model.JobToOutputDatasetCollectionAssociation.table = Table(
"job_to_output_dataset_collection", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ),
Column( "name", Unicode(255) ) )
Column( "name", Unicode( 255 ) ) )
model.JobToInputLibraryDatasetAssociation.table = Table(
"job_to_input_library_dataset", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
Column( "name", String(255) ) )
Column( "name", String( 255 ) ) )
model.JobToOutputLibraryDatasetAssociation.table = Table(
"job_to_output_library_dataset", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
Column( "name", String(255) ) )
Column( "name", String( 255 ) ) )
model.ImplicitlyCreatedDatasetCollectionInput.table = Table(
"implicitly_created_dataset_collection_inputs", metadata,
@@ -555,7 +555,7 @@ model.ImplicitlyCreatedDatasetCollectionInput.table = Table(
ForeignKey( "history_dataset_collection_association.id" ), index=True ),
Column( "input_dataset_collection_id", Integer,
ForeignKey( "history_dataset_collection_association.id" ), index=True ),
Column( "name", Unicode(255) ) )
Column( "name", Unicode( 255 ) ) )
model.JobExternalOutputMetadata.table = Table(
"job_external_output_metadata", metadata,
@@ -598,24 +598,24 @@ model.JobMetricText.table = Table(
"job_metric_text", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "plugin", Unicode(255) ),
Column( "metric_name", Unicode(255) ),
Column( "metric_value", Unicode(JOB_METRIC_MAX_LENGTH) ) )
Column( "plugin", Unicode( 255 ) ),
Column( "metric_name", Unicode( 255 ) ),
Column( "metric_value", Unicode( JOB_METRIC_MAX_LENGTH ) ) )
model.TaskMetricText.table = Table(
"task_metric_text", metadata,
Column( "id", Integer, primary_key=True ),
Column( "task_id", Integer, ForeignKey( "task.id" ), index=True ),
Column( "plugin", Unicode(255) ),
Column( "metric_name", Unicode(255) ),
Column( "metric_value", Unicode(JOB_METRIC_MAX_LENGTH) ) )
Column( "plugin", Unicode( 255 ) ),
Column( "metric_name", Unicode( 255 ) ),
Column( "metric_value", Unicode( JOB_METRIC_MAX_LENGTH ) ) )
model.JobMetricNumeric.table = Table(
"job_metric_numeric", metadata,
Column( "id", Integer, primary_key=True ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
Column( "plugin", Unicode(255) ),
Column( "metric_name", Unicode(255) ),
Column( "plugin", Unicode( 255 ) ),
Column( "metric_name", Unicode( 255 ) ),
Column( "metric_value", Numeric( 22, 7 ) ) )
model.TaskMetricNumeric.table = Table(
@@ -623,7 +623,7 @@ model.TaskMetricNumeric.table = Table(
Column( "id", Integer, primary_key=True ),
Column( "task_id", Integer, ForeignKey( "task.id" ), index=True ),
Column( "plugin", Unicode(255) ),
Column( "metric_name", Unicode(255) ),
Column( "metric_name", Unicode( 255 ) ),
Column( "metric_value", Numeric( 22, 7 ) ) )
@@ -656,7 +656,7 @@ model.Task.table = Table(
Column( "info", TrimmedString( 255 ) ),
Column( "traceback", TEXT ),
Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ),
Column( "working_directory", String(1024)),
Column( "working_directory", String( 1024 )),
Column( "task_runner_name", String( 255 ) ),
Column( "task_runner_external_id", String( 255 ) ),
Column( "prepare_input_files_cmd", TEXT ) )
@@ -665,8 +665,8 @@ model.PostJobAction.table = Table(
"post_job_action", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
Column( "action_type", String(255), nullable=False ),
Column( "output_name", String(255), nullable=True ),
Column( "action_type", String( 255 ), nullable=False ),
Column( "output_name", String( 255 ), nullable=True ),
Column( "action_arguments", JSONType, nullable=True ) )
model.PostJobActionAssociation.table = Table(
@@ -716,7 +716,7 @@ model.HistoryDatasetCollectionAssociation.table = Table(
Column( "deleted", Boolean, default=False ),
Column( "copied_from_history_dataset_collection_association_id", Integer,
ForeignKey( "history_dataset_collection_association.id" ), nullable=True ),
Column( "implicit_output_name", Unicode(255), nullable=True ) )
Column( "implicit_output_name", Unicode( 255 ), nullable=True ) )
model.LibraryDatasetCollectionAssociation.table = Table(
"library_dataset_collection_association", metadata,
@@ -737,7 +737,7 @@ model.DatasetCollectionElement.table = Table(
Column( "child_collection_id", Integer, ForeignKey( "dataset_collection.id" ), index=True, nullable=True ),
# Element index and identifier to define this parent-child relationship.
Column( "element_index", Integer ),
Column( "element_identifier", Unicode(255), ) )
Column( "element_identifier", Unicode( 255 ), ) )
model.Event.table = Table(
"event", metadata,
@@ -766,7 +766,7 @@ model.GalaxySession.table = Table(
# saves a reference to the previous session so we have a way to chain them together
Column( "prev_session_id", Integer ),
Column( "disk_usage", Numeric( 15, 0 ), index=True ),
Column( "last_action", DateTime) )
Column( "last_action", DateTime ) )
model.GalaxySessionToHistoryAssociation.table = Table(
"galaxy_session_to_history", metadata,
@@ -809,7 +809,7 @@ model.WorkflowStep.table = Table(
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
Column( "subworkflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=True ),
Column( "type", String(64) ),
Column( "type", String( 64 ) ),
Column( "tool_id", TEXT ),
# Reserved for future
Column( "tool_version", TEXT ),
@@ -820,24 +820,24 @@ model.WorkflowStep.table = Table(
Column( "order_index", Integer ),
Column( "uuid", UUIDType ),
# Column( "input_connections", JSONType ),
Column( "label", Unicode(255) ) )
Column( "label", Unicode( 255 ) ) )
model.WorkflowRequestStepState.table = Table(
"workflow_request_step_states", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_invocation_id", Integer,
ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id" )),
ForeignKey( "workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" ) ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
Column( "value", JSONType ) )
model.WorkflowRequestInputParameter.table = Table(
"workflow_request_input_parameters", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_invocation_id", Integer,
ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
Column( "name", Unicode(255) ),
ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" ) ),
Column( "name", Unicode( 255 ) ),
Column( "value", TEXT ),
Column( "type", Unicode(255) ) )
Column( "type", Unicode( 255 ) ) )
model.WorkflowRequestInputStepParmeter.table = Table(
"workflow_request_input_step_parameter", metadata,
@@ -850,17 +850,17 @@ model.WorkflowRequestInputStepParmeter.table = Table(
model.WorkflowRequestToInputDatasetAssociation.table = Table(
"workflow_request_to_input_dataset", metadata,
Column( "id", Integer, primary_key=True ),
Column( "name", String(255) ),
Column( "name", String( 255 ) ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ) )
model.WorkflowRequestToInputDatasetCollectionAssociation.table = Table(
"workflow_request_to_input_collection_dataset", metadata,
Column( "id", Integer, primary_key=True ),
Column( "name", String(255) ),
Column( "name", String( 255 ) ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ) )
model.WorkflowStepConnection.table = Table(
@@ -876,9 +876,9 @@ model.WorkflowStepConnection.table = Table(
model.WorkflowOutput.table = Table(
"workflow_output", metadata,
Column( "id", Integer, primary_key=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False ),
Column( "output_name", String(255), nullable=True ),
Column( "label", Unicode(255) ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
Column( "output_name", String( 255 ), nullable=True ),
Column( "label", Unicode( 255 ) ),
Column( "uuid", UUIDType ),
)
@@ -909,7 +909,7 @@ model.WorkflowInvocationToSubworkflowInvocationAssociation.table = Table(
Column( "id", Integer, primary_key=True ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "subworkflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
)
model.StoredWorkflowUserShareAssociation.table = Table(
@@ -1003,7 +1003,7 @@ model.FormValues.table = Table(
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
Column( "content", JSONType()) )
Column( "content", JSONType() ) )
model.Request.table = Table(
"request", metadata,
@@ -1189,9 +1189,9 @@ model.HistoryTagAssociation.table = Table(
Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.DatasetTagAssociation.table = Table(
"dataset_tag_association", metadata,
@@ -1199,9 +1199,9 @@ model.DatasetTagAssociation.table = Table(
Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.HistoryDatasetAssociationTagAssociation.table = Table(
"history_dataset_association_tag_association", metadata,
@@ -1209,9 +1209,9 @@ model.HistoryDatasetAssociationTagAssociation.table = Table(
Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.StoredWorkflowTagAssociation.table = Table(
"stored_workflow_tag_association", metadata,
@@ -1219,9 +1219,9 @@ model.StoredWorkflowTagAssociation.table = Table(
Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", Unicode(255), index=True ),
Column( "value", Unicode(255), index=True ),
Column( "user_value", Unicode(255), index=True ) )
Column( "user_tname", Unicode( 255 ), index=True ),
Column( "value", Unicode( 255 ), index=True ),
Column( "user_value", Unicode( 255 ), index=True ) )
model.PageTagAssociation.table = Table(
"page_tag_association", metadata,
@@ -1229,9 +1229,9 @@ model.PageTagAssociation.table = Table(
Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.WorkflowStepTagAssociation.table = Table(
"workflow_step_tag_association", metadata,
@@ -1239,9 +1239,9 @@ model.WorkflowStepTagAssociation.table = Table(
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", Unicode(255), index=True ),
Column( "value", Unicode(255), index=True ),
Column( "user_value", Unicode(255), index=True ) )
Column( "user_tname", Unicode( 255 ), index=True ),
Column( "value", Unicode( 255 ), index=True ),
Column( "user_value", Unicode( 255 ), index=True ) )
model.VisualizationTagAssociation.table = Table(
"visualization_tag_association", metadata,
@@ -1249,9 +1249,9 @@ model.VisualizationTagAssociation.table = Table(
Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.HistoryDatasetCollectionTagAssociation.table = Table(
"history_dataset_collection_tag_association", metadata,
@@ -1260,9 +1260,9 @@ model.HistoryDatasetCollectionTagAssociation.table = Table(
ForeignKey( "history_dataset_collection_association.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.LibraryDatasetCollectionTagAssociation.table = Table(
"library_dataset_collection_tag_association", metadata,
@@ -1271,9 +1271,9 @@ model.LibraryDatasetCollectionTagAssociation.table = Table(
ForeignKey( "library_dataset_collection_association.id" ), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
model.ToolTagAssociation.table = Table(
"tool_tag_association", metadata,
@@ -1281,9 +1281,9 @@ model.ToolTagAssociation.table = Table(
Column( "tool_id", TrimmedString(255), index=True ),
Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "user_tname", TrimmedString(255), index=True ),
Column( "value", TrimmedString(255), index=True ),
Column( "user_value", TrimmedString(255), index=True ) )
Column( "user_tname", TrimmedString( 255 ), index=True ),
Column( "value", TrimmedString( 255 ), index=True ),
Column( "user_value", TrimmedString( 255 ), index=True ) )
# Annotation tables.
@@ -1456,7 +1456,7 @@ mapper( model.FormValues, model.FormValues.table, properties=dict(
mapper( model.Request, model.Request.table, properties=dict(
values=relation( model.FormValues,
primaryjoin=( model.Request.table.c.form_values_id == model.FormValues.table.c.id )),
primaryjoin=( model.Request.table.c.form_values_id == model.FormValues.table.c.id ) ),
type=relation( model.RequestType,
primaryjoin=( model.Request.table.c.request_type_id == model.RequestType.table.c.id ) ),
user=relation( model.User,
@@ -1683,7 +1683,7 @@ mapper( model.History, model.History.table, properties=dict(
galaxy_sessions=relation( model.GalaxySessionToHistoryAssociation ),
datasets=relation( model.HistoryDatasetAssociation,
backref="history",
order_by=asc(model.HistoryDatasetAssociation.table.c.hid) ),
order_by=asc( model.HistoryDatasetAssociation.table.c.hid ) ),
exports=relation( model.JobExportHistoryArchive,
primaryjoin=( model.JobExportHistoryArchive.table.c.history_id == model.History.table.c.id ),
order_by=desc( model.JobExportHistoryArchive.table.c.id ) ),
@@ -1741,7 +1741,7 @@ mapper( model.HistoryUserShareAssociation, model.HistoryUserShareAssociation.tab
mapper( model.User, model.User.table, properties=dict(
histories=relation( model.History,
backref="user",
order_by=desc(model.History.table.c.update_time ) ),
order_by=desc( model.History.table.c.update_time ) ),
active_histories=relation( model.History,
primaryjoin=(
( model.History.table.c.user_id == model.User.table.c.id ) &
@@ -1757,7 +1757,7 @@ mapper( model.User, model.User.table, properties=dict(
collection_class=ordering_list( 'order_index' ) ),
_preferences=relation( model.UserPreference,
backref="user",
collection_class=attribute_mapped_collection('name')),
collection_class=attribute_mapped_collection( 'name' ) ),
# addresses=relation( UserAddress,
# primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) ),
values=relation( model.FormValues,
@@ -1993,7 +1993,7 @@ mapper( model.LibraryDatasetDatasetAssociation, model.LibraryDatasetDatasetAssoc
extended_metadata=relation( model.ExtendedMetadata,
primaryjoin=( ( model.LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id ) )
),
_metadata=deferred(model.LibraryDatasetDatasetAssociation.table.c._metadata)
_metadata=deferred( model.LibraryDatasetDatasetAssociation.table.c._metadata )
) )
mapper( model.LibraryDatasetDatasetInfoAssociation, model.LibraryDatasetDatasetInfoAssociation.table, properties=dict(
@@ -2108,7 +2108,7 @@ mapper( model.GenomeIndexToolData, model.GenomeIndexToolData.table, properties=d
mapper(model.PostJobAction, model.PostJobAction.table, properties=dict(
workflow_step=relation( model.WorkflowStep,
backref='post_job_actions',
primaryjoin=(model.WorkflowStep.table.c.id == model.PostJobAction.table.c.workflow_step_id ) )
primaryjoin=( model.WorkflowStep.table.c.id == model.PostJobAction.table.c.workflow_step_id ) )
) )
mapper( model.PostJobActionAssociation, model.PostJobActionAssociation.table, properties=dict(
@@ -2309,7 +2309,7 @@ mapper( model.StoredWorkflowMenuEntry, model.StoredWorkflowMenuEntry.table, prop
) )
mapper( model.WorkflowInvocation, model.WorkflowInvocation.table, properties=dict(
history=relation( model.History, backref=backref('workflow_invocations', uselist=True )),
history=relation( model.History, backref=backref('workflow_invocations', uselist=True ) ),
input_parameters=relation( model.WorkflowRequestInputParameter ),
step_states=relation( model.WorkflowRequestStepState ),
input_step_parameters=relation( model.WorkflowRequestInputStepParmeter ),
@@ -2442,7 +2442,7 @@ simple_mapping( model.Tag,
def tag_mapping( tag_association_class, backref_name ):
simple_mapping( tag_association_class, tag=relation( model.Tag, backref=backref_name), user=relation( model.User ) )
simple_mapping( tag_association_class, tag=relation( model.Tag, backref=backref_name ), user=relation( model.User ) )
tag_mapping( model.HistoryTagAssociation, "tagged_histories" )
@@ -2459,7 +2459,7 @@ tag_mapping( model.ToolTagAssociation, "tagged_tools" )
# Annotation tables.
def annotation_mapping( annotation_class, **kwds ):
kwds = dict( (key, relation( value ) ) for key, value in kwds.items() )
kwds = dict( ( key, relation( value ) ) for key, value in kwds.items() )
simple_mapping( annotation_class, **dict(user=relation( model.User ), **kwds ) )
@@ -2477,8 +2477,8 @@ annotation_mapping( model.LibraryDatasetCollectionAnnotationAssociation,
# Rating tables.
def rating_mapping( rating_class, **kwds ):
kwds = dict( (key, relation( value ) ) for key, value in kwds.items() )
simple_mapping( rating_class, **dict(user=relation( model.User ), **kwds ) )
kwds = dict( ( key, relation( value ) ) for key, value in kwds.items() )
simple_mapping( rating_class, **dict( user=relation( model.User ), **kwds ) )
rating_mapping( model.HistoryRatingAssociation, history=model.History )
@@ -2556,8 +2556,8 @@ def _workflow_invocation_update( self ):
conn = object_session( self ).connection()
table = self.table
now_val = now()
stmt = table.update().values(update_time=now_val).where(and_(table.c.id == self.id, table.c.update_time < now_val))
conn.execute(stmt)
stmt = table.update().values( update_time=now_val ).where( and_( table.c.id == self.id, table.c.update_time < now_val ) )
conn.execute( stmt )
model.WorkflowInvocation.update = _workflow_invocation_update
@@ -2583,9 +2583,9 @@ def init( file_path, url, engine_options={}, create_tables=False, map_install_mo
if map_install_models:
import galaxy.model.tool_shed_install.mapping # noqa: F401
from galaxy.model import tool_shed_install
model_modules.append(tool_shed_install)
model_modules.append( tool_shed_install )
result = ModelMapping(model_modules, engine=engine)
result = ModelMapping( model_modules, engine=engine )
# Create tables if needed
if create_tables: