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galaxy.model.store package¶
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class
galaxy.model.store.
ImportOptions
(allow_edit=False, allow_library_creation=False, allow_dataset_object_edit=None)[source]¶ Bases:
object
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class
galaxy.model.store.
ModelImportStore
(import_options=None, app=None, user=None, object_store=None)[source]¶ Bases:
object
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object_key
¶ Key used to connect objects in metadata.
Legacy exports used ‘hid’ but associated objects may not be from the same history and a history may contain multiple objects with the same ‘hid’.
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trust_hid
¶ Trust HID when importing objects into a new History.
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class
galaxy.model.store.
ObjectImportTracker
[source]¶ Bases:
object
Keep track of new and existing imported objects.
Needed to re-establish connections and such in multiple passes.
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class
galaxy.model.store.
BaseDirectoryImportModelStore
(import_options=None, app=None, user=None, object_store=None)[source]¶
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class
galaxy.model.store.
DirectoryImportModelStore1901
(archive_dir, **kwd)[source]¶ Bases:
galaxy.model.store.BaseDirectoryImportModelStore
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object_key
= 'hid'¶
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class
galaxy.model.store.
DirectoryImportModelStoreLatest
(archive_dir, **kwd)[source]¶ Bases:
galaxy.model.store.BaseDirectoryImportModelStore
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object_key
= 'encoded_id'¶
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class
galaxy.model.store.
ModelExportStore
[source]¶ Bases:
object
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class
galaxy.model.store.
DirectoryModelExportStore
(export_directory, app=None, for_edit=False, serialize_dataset_objects=None, export_files=None, strip_metadata_files=True)[source]¶ Bases:
galaxy.model.store.ModelExportStore
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__init__
(export_directory, app=None, for_edit=False, serialize_dataset_objects=None, export_files=None, strip_metadata_files=True)[source]¶ Parameters: - export_directory – path to export directory. Will be created if it does not exist.
- app – Galaxy App or app-like object. Must be provided if for_edit and/or serialize_dataset_objects are True
- for_edit – Allow modifying existing HDA and dataset metadata during import.
- serialize_dataset_objects – If True will encode IDs using the host secret. Defaults for_edit.
- export_files – How files should be exported, can be ‘symlink’, ‘copy’ or None, in which case files will not be serialized.
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galaxy.model.store.
get_export_dataset_filename
(name, ext, hid)[source]¶ Builds a filename for a dataset using its name an extension.
Submodules¶
galaxy.model.store.discover module¶
Utilities for discovering files to add to a model store.
Working with input “JSON” format used for Fetch API, galaxy.json imports, etc… High-level utilities in this file can be used during job output discovery or for persisting Galaxy model objects corresponding to files in other contexts.
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class
galaxy.model.store.discover.
ModelPersistenceContext
[source]¶ Bases:
object
Class for creating datasets while finding files.
This class implement the create_dataset method that takes care of populating metadata required for datasets and other potential model objects.
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create_dataset
(ext, designation, visible, dbkey, name, filename=None, extra_files=None, metadata_source_name=None, info=None, library_folder=None, link_data=False, primary_data=None, init_from=None, dataset_attributes=None, tag_list=None, sources=None, hashes=None, created_from_basename=None, final_job_state='ok')[source]¶
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populate_collection_elements
(collection, root_collection_builder, filenames, name=None, metadata_source_name=None, final_job_state='ok')[source]¶
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tag_handler
¶ Return a galaxy.model.tags.TagHandler-like object for persisting tags.
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user
¶ If bound to a database, return the user the datasets should be created for.
Return None otherwise.
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add_library_dataset_to_folder
(library_folder, ld)[source]¶ Add library dataset to persisted library folder.
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create_library_folder
(parent_folder, name, description)[source]¶ Create a library folder ready from supplied attributes for supplied parent.
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add_output_dataset_association
(name, dataset)[source]¶ If discovering outputs for a job, persist output dataset association.
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class
galaxy.model.store.discover.
PermissionProvider
[source]¶ Bases:
object
Interface for working with permissions while importing datasets with ModelPersistenceContext.
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permissions
¶
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class
galaxy.model.store.discover.
MetadataSourceProvider
[source]¶ Bases:
object
Interface for working with fetching input dataset metadata with ModelPersistenceContext.
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class
galaxy.model.store.discover.
SessionlessModelPersistenceContext
(object_store, export_store, working_directory)[source]¶ Bases:
galaxy.model.store.discover.ModelPersistenceContext
A variant of ModelPersistenceContext that persists to an export store instead of database directly.
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tag_handler
¶
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user
¶
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galaxy.model.store.discover.
persist_extra_files
(object_store, src_extra_files_path, primary_data)[source]¶
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galaxy.model.store.discover.
persist_target_to_export_store
(target_dict, export_store, object_store, work_directory)[source]¶
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galaxy.model.store.discover.
persist_elements_to_hdca
(model_persistence_context, elements, hdca, collector=None)[source]¶
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galaxy.model.store.discover.
persist_elements_to_folder
(model_persistence_context, elements, library_folder)[source]¶
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galaxy.model.store.discover.
persist_hdas
(elements, model_persistence_context, final_job_state='ok')[source]¶
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class
galaxy.model.store.discover.
DiscoveredFile
(path, collector, match)¶ Bases:
tuple
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collector
¶ Alias for field number 1
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match
¶ Alias for field number 2
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path
¶ Alias for field number 0
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class
galaxy.model.store.discover.
DiscoveredFileError
(error_message, collector, match)¶ Bases:
tuple
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collector
¶ Alias for field number 1
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error_message
¶ Alias for field number 0
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match
¶ Alias for field number 2
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path
= None¶
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galaxy.model.store.discover.
discovered_file_for_element
(dataset, job_working_directory, parent_identifiers=[], collector=None)[source]¶
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class
galaxy.model.store.discover.
JsonCollectedDatasetMatch
(as_dict, collector, filename, path=None, parent_identifiers=[])[source]¶ Bases:
object
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designation
¶
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element_identifiers
¶
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raw_element_identifiers
¶
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name
¶ Return name or None if not defined by the discovery pattern.
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dbkey
¶
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ext
¶
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visible
¶
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link_data
¶
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tag_list
¶
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object_id
¶
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sources
¶
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hashes
¶
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created_from_basename
¶
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extra_files
¶
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class
galaxy.model.store.discover.
RegexCollectedDatasetMatch
(re_match, collector, filename, path=None)[source]¶ Bases:
galaxy.model.store.discover.JsonCollectedDatasetMatch