mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Make _metadata regular JSONType field
This commit is contained in:
mvdbeek
@@ -113,6 +113,10 @@ class JSONType(sqlalchemy.types.TypeDecorator):
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return (x == y)
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class MutableJSONType(JSONType):
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"""Associated with MutationObj"""
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class MutationObj(Mutable):
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"""
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Mutable JSONType for SQLAlchemy from original gist:
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@@ -269,7 +273,8 @@ class MutationList(MutationObj, list):
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self.changed()
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MutationObj.associate_with(JSONType)
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MutationObj.associate_with(MutableJSONType)
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metadata_pickler = AliasPickleModule({
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("cookbook.patterns", "Bunch"): ("galaxy.util.bunch", "Bunch")
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+35
-35
@@ -42,7 +42,7 @@ from galaxy import model
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from galaxy.model.base import SharedModelMapping
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from galaxy.model.custom_types import (
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JSONType,
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MetadataType,
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MutableJSONType,
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TrimmedString,
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UUIDType,
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)
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@@ -142,7 +142,7 @@ model.UserAuthnzToken.table = Table(
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Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True),
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Column('uid', VARCHAR(255)),
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Column('provider', VARCHAR(32)),
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Column('extra_data', JSONType, nullable=True),
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Column('extra_data', MutableJSONType, nullable=True),
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Column('lifetime', Integer),
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Column('assoc_type', VARCHAR(64)))
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@@ -166,9 +166,9 @@ model.CloudAuthz.table = Table(
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Column('id', Integer, primary_key=True),
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Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True),
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Column('provider', String(255)),
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Column('config', JSONType),
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Column('config', MutableJSONType),
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Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True),
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Column('tokens', JSONType),
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Column('tokens', MutableJSONType),
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Column('last_update', DateTime),
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Column('last_activity', DateTime),
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Column('description', TEXT),
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@@ -194,7 +194,7 @@ model.DynamicTool.table = Table(
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Column("tool_directory", Unicode(255)),
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Column("hidden", Boolean, default=True),
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Column("active", Boolean, default=True),
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Column("value", JSONType),
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Column("value", MutableJSONType),
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)
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@@ -240,7 +240,7 @@ model.HistoryDatasetAssociation.table = Table(
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Column("peek", TEXT, key="_peek"),
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Column("tool_version", TEXT),
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Column("extension", TrimmedString(64)),
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Column("metadata", MetadataType, key="_metadata"),
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Column("metadata", JSONType, key="_metadata"),
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Column("parent_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
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Column("designation", TrimmedString(255)),
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Column("deleted", Boolean, index=True, default=False),
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@@ -263,7 +263,7 @@ model.HistoryDatasetAssociationHistory.table = Table(
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Column("version", Integer),
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Column("name", TrimmedString(255)),
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Column("extension", TrimmedString(64)),
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Column("metadata", MetadataType, key="_metadata"),
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Column("metadata", JSONType, key="_metadata"),
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Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
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)
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@@ -292,7 +292,7 @@ model.DatasetSource.table = Table(
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Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
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Column("source_uri", TEXT),
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Column("extra_files_path", TEXT),
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Column("transform", JSONType)
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Column("transform", MutableJSONType)
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)
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model.DatasetHash.table = Table(
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@@ -519,7 +519,7 @@ model.LibraryDatasetDatasetAssociation.table = Table(
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Column("peek", TEXT, key="_peek"),
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Column("tool_version", TEXT),
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Column("extension", TrimmedString(64)),
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Column("metadata", MetadataType, key="_metadata"),
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Column("metadata", JSONType, key="_metadata"),
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Column("parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
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Column("designation", TrimmedString(255)),
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Column("deleted", Boolean, index=True, default=False),
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@@ -533,7 +533,7 @@ model.LibraryDatasetDatasetAssociation.table = Table(
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model.ExtendedMetadata.table = Table(
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"extended_metadata", metadata,
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Column("id", Integer, primary_key=True),
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Column("data", JSONType))
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Column("data", MutableJSONType))
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model.ExtendedMetadataIndex.table = Table(
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"extended_metadata_index", metadata,
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@@ -613,8 +613,8 @@ model.Job.table = Table(
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Column("info", TrimmedString(255)),
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Column("copied_from_job_id", Integer, nullable=True),
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Column("command_line", TEXT),
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Column("dependencies", JSONType, nullable=True),
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Column("job_messages", JSONType, nullable=True),
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Column("dependencies", MutableJSONType, nullable=True),
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Column("job_messages", MutableJSONType, nullable=True),
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Column("param_filename", String(1024)),
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Column("runner_name", String(255)),
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Column("job_stdout", TEXT),
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@@ -628,7 +628,7 @@ model.Job.table = Table(
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Column("job_runner_name", String(255)),
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Column("job_runner_external_id", String(255), index=True),
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Column("destination_id", String(255), nullable=True),
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Column("destination_params", JSONType, nullable=True),
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Column("destination_params", MutableJSONType, nullable=True),
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Column("object_store_id", TrimmedString(255), index=True),
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Column("imported", Boolean, default=False, index=True),
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Column("params", TrimmedString(255), index=True),
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@@ -820,7 +820,7 @@ model.InteractiveToolEntryPoint.table = Table(
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Column("protocol", TEXT),
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Column("entry_url", TEXT),
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Column("requires_domain", Boolean, default=True),
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Column("info", JSONType, nullable=True),
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Column("info", MutableJSONType, nullable=True),
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Column("configured", Boolean, default=False),
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Column("deleted", Boolean, default=False),
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Column("created_time", DateTime, default=now),
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@@ -832,7 +832,7 @@ model.JobContainerAssociation.table = Table(
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Column("job_id", Integer, ForeignKey("job.id"), index=True),
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Column("container_type", TEXT),
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Column("container_name", TEXT),
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Column("container_info", JSONType, nullable=True),
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Column("container_info", MutableJSONType, nullable=True),
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Column("created_time", DateTime, default=now),
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Column("modified_time", DateTime, default=now, onupdate=now))
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@@ -851,7 +851,7 @@ model.Task.table = Table(
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Column("tool_stdout", TEXT),
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Column("tool_stderr", TEXT),
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Column("exit_code", Integer, nullable=True),
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Column("job_messages", JSONType, nullable=True),
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Column("job_messages", MutableJSONType, nullable=True),
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Column("info", TrimmedString(255)),
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Column("traceback", TEXT),
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Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
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@@ -866,7 +866,7 @@ model.PostJobAction.table = Table(
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Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=True),
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Column("action_type", String(255), nullable=False),
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Column("output_name", String(255), nullable=True),
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Column("action_arguments", JSONType, nullable=True))
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Column("action_arguments", MutableJSONType, nullable=True))
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model.PostJobActionAssociation.table = Table(
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"post_job_action_association", metadata,
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@@ -881,7 +881,7 @@ model.DeferredJob.table = Table(
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Column("update_time", DateTime, default=now, onupdate=now),
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Column("state", String(64), index=True),
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Column("plugin", String(128), index=True),
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Column("params", JSONType))
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Column("params", MutableJSONType))
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model.TransferJob.table = Table(
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"transfer_job", metadata,
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@@ -893,7 +893,7 @@ model.TransferJob.table = Table(
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Column("info", TEXT),
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Column("pid", Integer),
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Column("socket", Integer),
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Column("params", JSONType))
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Column("params", MutableJSONType))
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model.DatasetCollection.table = Table(
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"dataset_collection", metadata,
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@@ -1008,8 +1008,8 @@ model.Workflow.table = Table(
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Column("name", TEXT),
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Column("has_cycles", Boolean),
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Column("has_errors", Boolean),
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Column("reports_config", JSONType),
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Column("creator_metadata", JSONType),
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Column("reports_config", MutableJSONType),
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Column("creator_metadata", MutableJSONType),
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Column("license", TEXT),
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Column("uuid", UUIDType, nullable=True))
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@@ -1024,10 +1024,10 @@ model.WorkflowStep.table = Table(
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Column("type", String(64)),
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Column("tool_id", TEXT),
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Column("tool_version", TEXT),
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Column("tool_inputs", JSONType),
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Column("tool_errors", JSONType),
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Column("position", JSONType),
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Column("config", JSONType),
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Column("tool_inputs", MutableJSONType),
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Column("tool_errors", MutableJSONType),
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Column("position", MutableJSONType),
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Column("config", MutableJSONType),
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Column("order_index", Integer),
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Column("uuid", UUIDType),
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# Column( "input_connections", JSONType ),
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@@ -1041,9 +1041,9 @@ model.WorkflowStepInput.table = Table(
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Column("name", TEXT),
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Column("merge_type", TEXT),
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Column("scatter_type", TEXT),
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Column("value_from", JSONType),
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Column("value_from", MutableJSONType),
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Column("value_from_type", TEXT),
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Column("default_value", JSONType),
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Column("default_value", MutableJSONType),
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Column("default_value_set", Boolean, default=False),
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Column("runtime_value", Boolean, default=False),
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Index('ix_workflow_step_input_workflow_step_id_name_unique', "workflow_step_id", "name", unique=True, mysql_length={'name': 200}),
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@@ -1056,7 +1056,7 @@ model.WorkflowRequestStepState.table = Table(
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Column("workflow_invocation_id", Integer,
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ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")),
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Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
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Column("value", JSONType))
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Column("value", MutableJSONType))
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model.WorkflowRequestInputParameter.table = Table(
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"workflow_request_input_parameters", metadata,
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@@ -1072,7 +1072,7 @@ model.WorkflowRequestInputStepParameter.table = Table(
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Column("id", Integer, primary_key=True),
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Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
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Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
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Column("parameter_value", JSONType),
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Column("parameter_value", MutableJSONType),
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)
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model.WorkflowRequestToInputDatasetAssociation.table = Table(
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@@ -1131,7 +1131,7 @@ model.WorkflowInvocationStep.table = Table(
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Column("state", TrimmedString(64), index=True),
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Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
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Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
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Column("action", JSONType, nullable=True))
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Column("action", MutableJSONType, nullable=True))
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model.WorkflowInvocationOutputDatasetAssociation.table = Table(
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"workflow_invocation_output_dataset_association", metadata,
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@@ -1157,7 +1157,7 @@ model.WorkflowInvocationOutputValue.table = Table(
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Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
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Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
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Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
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Column("value", JSONType),
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Column("value", MutableJSONType),
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)
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model.WorkflowInvocationStepOutputDatasetAssociation.table = Table(
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@@ -1227,9 +1227,9 @@ model.FormDefinition.table = Table(
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Column("name", TrimmedString(255), nullable=False),
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Column("desc", TEXT),
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Column("form_definition_current_id", Integer, ForeignKey("form_definition_current.id", use_alter=True), index=True, nullable=False),
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Column("fields", JSONType),
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Column("fields", MutableJSONType),
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Column("type", TrimmedString(255), index=True),
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Column("layout", JSONType))
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Column("layout", MutableJSONType))
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model.FormValues.table = Table(
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"form_values", metadata,
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@@ -1237,7 +1237,7 @@ model.FormValues.table = Table(
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Column("create_time", DateTime, default=now),
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Column("update_time", DateTime, default=now, onupdate=now),
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Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
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Column("content", JSONType))
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Column("content", MutableJSONType))
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model.Page.table = Table(
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"page", metadata,
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@@ -1298,7 +1298,7 @@ model.VisualizationRevision.table = Table(
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Column("visualization_id", Integer, ForeignKey("visualization.id"), index=True, nullable=False),
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Column("title", TEXT),
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Column("dbkey", TEXT),
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Column("config", JSONType),
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Column("config", MutableJSONType),
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Index('ix_visualization_revision_dbkey', 'dbkey', mysql_length=200),
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)
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@@ -15,6 +15,7 @@ from collections.abc import Mapping
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from os.path import abspath
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from sqlalchemy.orm import object_session
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from sqlalchemy.orm.attributes import flag_modified
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import galaxy.model
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from galaxy.util import (
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@@ -133,6 +134,7 @@ class MetadataCollection(Mapping):
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self.parent._metadata[name] = self.spec[name].unwrap(value)
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else:
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self.parent._metadata[name] = value
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flag_modified(self.parent, '_metadata')
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def remove_key(self, name):
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if name in self.parent._metadata:
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@@ -226,6 +228,7 @@ class MetadataCollection(Mapping):
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dataset.validated_state = JSONified_dict['__validated_state__']
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if '__validated_state_message__' in JSONified_dict:
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dataset.validated_state_message = JSONified_dict['__validated_state_message__']
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flag_modified(dataset, '_metadata')
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def to_JSON_dict(self, filename=None):
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meta_dict = {}
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@@ -17,7 +17,7 @@ from sqlalchemy.orm import (
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from galaxy.model import tool_shed_install as install_model
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from galaxy.model.base import ModelMapping
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from galaxy.model.custom_types import (
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JSONType,
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MutableJSONType,
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TrimmedString
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)
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from galaxy.model.orm.engine_factory import build_engine
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@@ -36,9 +36,9 @@ install_model.ToolShedRepository.table = Table("tool_shed_repository", metadata,
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Column("installed_changeset_revision", TrimmedString(255)),
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Column("changeset_revision", TrimmedString(255), index=True),
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Column("ctx_rev", TrimmedString(10)),
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Column("metadata", JSONType, nullable=True),
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Column("metadata", MutableJSONType, nullable=True),
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Column("includes_datatypes", Boolean, index=True, default=False),
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Column("tool_shed_status", JSONType, nullable=True),
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Column("tool_shed_status", MutableJSONType, nullable=True),
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Column("deleted", Boolean, index=True, default=False),
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Column("uninstalled", Boolean, default=False),
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Column("dist_to_shed", Boolean, default=False),
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@@ -10,7 +10,7 @@ from sqlalchemy.orm import backref, mapper, relation
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import tool_shed.webapp.model
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import tool_shed.webapp.util.shed_statistics as shed_statistics
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from galaxy.model.base import SharedModelMapping
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from galaxy.model.custom_types import JSONType, TrimmedString
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from galaxy.model.custom_types import MutableJSONType, TrimmedString
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from galaxy.model.orm.engine_factory import build_engine
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from galaxy.model.orm.now import now
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from tool_shed.webapp.model import APIKeys, Category, Component, ComponentReview
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@@ -118,7 +118,7 @@ Repository.table = Table("repository", metadata,
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Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
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Column("private", Boolean, default=False),
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Column("deleted", Boolean, index=True, default=False),
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Column("email_alerts", JSONType, nullable=True),
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Column("email_alerts", MutableJSONType, nullable=True),
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Column("times_downloaded", Integer),
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Column("deprecated", Boolean, default=False))
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@@ -129,8 +129,8 @@ RepositoryMetadata.table = Table("repository_metadata", metadata,
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Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
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Column("changeset_revision", TrimmedString(255), index=True),
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Column("numeric_revision", Integer, index=True),
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Column("metadata", JSONType, nullable=True),
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Column("tool_versions", JSONType, nullable=True),
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Column("metadata", MutableJSONType, nullable=True),
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Column("tool_versions", MutableJSONType, nullable=True),
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Column("malicious", Boolean, default=False),
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Column("downloadable", Boolean, default=True),
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Column("missing_test_components", Boolean, default=False, index=True),
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