model Package¶
model
Package¶
Galaxy data model classes
Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
-
class
galaxy.model.
DataManagerHistoryAssociation
(id=None, history=None, user=None)[source]¶ Bases:
object
-
class
galaxy.model.
DataManagerJobAssociation
(id=None, job=None, data_manager_id=None)[source]¶ Bases:
object
-
class
galaxy.model.
Dataset
(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)[source]¶ Bases:
object
-
conversion_messages
= <galaxy.util.bunch.Bunch object>¶
-
engine
= None¶
-
extra_files_path
¶
-
file_name
¶
-
file_path
= '/tmp/'¶
-
non_ready_states
= ('upload', 'queued', 'running', 'setting_metadata')¶
-
object_store
= None¶
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
ready_states
= ('discarded', 'ok', 'failed_metadata', 'paused', 'error', 'new', 'empty')¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
user_can_purge
¶
-
-
class
galaxy.model.
DatasetCollection
(id=None, collection_type=None, populated=True)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
-
dataset_elements
¶
-
dataset_instances
¶
-
dict_collection_visible_keys
= ('id', 'collection_type')¶
-
dict_element_visible_keys
= ('id', 'collection_type')¶
-
populated
¶
-
populated_states
= <galaxy.util.bunch.Bunch object>¶
-
state
¶
-
waiting_for_elements
¶
-
-
class
galaxy.model.
DatasetCollectionElement
(id=None, collection=None, element=None, element_index=None, element_identifier=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
Associates a DatasetInstance (hda or ldda) with a DatasetCollection.
-
dataset
¶
-
dataset_instance
¶
-
dict_collection_visible_keys
= ('id', 'element_type', 'element_index', 'element_identifier')¶
-
dict_element_visible_keys
= ('id', 'element_type', 'element_index', 'element_identifier')¶
-
element_object
¶
-
element_type
¶
-
is_collection
¶
-
-
class
galaxy.model.
DatasetCollectionInstance
(collection=None, deleted=False)[source]¶ Bases:
object
,galaxy.model.HasName
-
set_from_dict
(new_data)[source]¶ Set object attributes to the values in dictionary new_data limiting to only those keys in dict_element_visible_keys.
Returns a dictionary of the keys, values that have been changed.
-
state
¶
-
-
class
galaxy.model.
DatasetInstance
(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None)[source]¶ Bases:
object
A base class for all ‘dataset instances’, HDAs, LDAs, etc
-
conversion_messages
= <galaxy.util.bunch.Bunch object>¶
-
convert_dataset
(trans, target_type)[source]¶ Converts a dataset to the target_type and returns a message indicating status of the conversion. None is returned to indicate that dataset was converted successfully.
-
creating_job
¶
-
datatype
¶
-
dbkey
¶
-
ext
¶
-
extra_files_path
¶
-
file_name
¶
-
find_conversion_destination
(accepted_formats, **kwd)[source]¶ Returns ( target_ext, existing converted dataset )
-
get_converted_dataset
(trans, target_ext)[source]¶ Return converted dataset(s) if they exist, along with a dict of dependencies. If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
-
get_datasources
(trans)[source]¶ Returns datasources for dataset; if datasources are not available due to indexing, indexing is started. Return value is a dictionary with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}).
-
get_metadata_dataset
(dataset_ext)[source]¶ Returns an HDA that points to a metadata file which contains a converted data with the requested extension.
-
get_raw_data
()[source]¶ Returns the full data. To stream it open the file_name and read/write as needed
-
is_pending
¶ Return true if the dataset is neither ready nor in error
-
metadata
¶
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
source_dataset_chain
¶
-
source_library_dataset
¶
-
state
¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
DatasetTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
DatasetToValidationErrorAssociation
(dataset, validation_error)[source]¶ Bases:
object
-
class
galaxy.model.
DefaultQuotaAssociation
(type, quota)[source]¶ Bases:
galaxy.model.Quota
,galaxy.model.item_attrs.Dictifiable
-
dict_element_visible_keys
= ('type',)¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
DeferredJob
(state=None, plugin=None, params=None)[source]¶ Bases:
object
-
check_interval
¶
-
is_check_time
¶
-
last_check
¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
Event
(message=None, history=None, user=None, galaxy_session=None)[source]¶ Bases:
object
-
class
galaxy.model.
ExternalService
(name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None)[source]¶ Bases:
object
-
data_transfer_protocol
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
FormDefinition
(name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name')¶
-
dict_element_visible_keys
= ('id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout')¶
-
get_widgets
(user, contents={}, **kwd)[source]¶ Return the list of widgets that comprise a form definition, including field contents if any.
-
supported_field_types
= [<class 'galaxy.web.form_builder.AddressField'>, <class 'galaxy.web.form_builder.CheckboxField'>, <class 'galaxy.web.form_builder.PasswordField'>, <class 'galaxy.web.form_builder.SelectField'>, <class 'galaxy.web.form_builder.TextArea'>, <class 'galaxy.web.form_builder.TextField'>, <class 'galaxy.web.form_builder.WorkflowField'>, <class 'galaxy.web.form_builder.WorkflowMappingField'>, <class 'galaxy.web.form_builder.HistoryField'>]¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
GalaxySession
(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)[source]¶ Bases:
object
-
total_disk_usage
¶
-
-
class
galaxy.model.
GalaxySessionToHistoryAssociation
(galaxy_session, history)[source]¶ Bases:
object
-
class
galaxy.model.
GenomeIndexToolData
(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)[source]¶ Bases:
object
-
class
galaxy.model.
Group
(name=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name')¶
-
dict_element_visible_keys
= ('id', 'name')¶
-
-
class
galaxy.model.
GroupQuotaAssociation
(group, quota)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_element_visible_keys
= ('group',)¶
-
-
class
galaxy.model.
History
(id=None, name=None, user=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.HasName
-
activatable_datasets
¶
-
active_contents
¶ Return all active contents ordered by hid.
-
active_datasets_children_and_roles
¶
-
copy
(name=None, target_user=None, activatable=False, all_datasets=False)[source]¶ Return a copy of this history using the given name and target_user. If activatable, copy only non-deleted datasets. If all_datasets, copy non-deleted, deleted, and purged datasets.
-
default_name
= 'Unnamed history'¶
-
dict_collection_visible_keys
= ('id', 'name', 'published', 'deleted')¶
-
dict_element_visible_keys
= ('id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', 'published', 'importable', 'slug', 'empty')¶
-
empty
¶
-
get_disk_size_bytes
¶
-
latest_export
¶
-
-
class
galaxy.model.
HistoryDatasetAssociation
(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)[source]¶ Bases:
galaxy.model.DatasetInstance
,galaxy.model.item_attrs.Dictifiable
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.HasName
Resource class that creates a relation between a dataset and a user history.
-
history_content_type
¶
-
quota_amount
(user)[source]¶ Return the disk space used for this HDA relevant to user quotas.
If the user has multiple instances of this dataset, it will not affect their disk usage statistic.
-
-
class
galaxy.model.
HistoryDatasetAssociationDisplayAtAuthorization
(hda=None, user=None, site=None)[source]¶ Bases:
object
-
class
galaxy.model.
HistoryDatasetAssociationRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶
-
class
galaxy.model.
HistoryDatasetAssociationTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
HistoryDatasetCollectionAssociation
(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=[])[source]¶ Bases:
galaxy.model.DatasetCollectionInstance
,galaxy.model.item_attrs.Dictifiable
Associates a DatasetCollection with a History.
-
copy
(element_destination=None)[source]¶ Create a copy of this history dataset collection association. Copy underlying collection.
-
editable_keys
= ('name', 'deleted', 'visible')¶
-
history_content_type
¶
-
-
class
galaxy.model.
HistoryDatasetCollectionRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶
-
class
galaxy.model.
HistoryDatasetCollectionTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
HistoryTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
Bases:
object
-
class
galaxy.model.
ImplicitlyConvertedDatasetAssociation
(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)[source]¶ Bases:
object
-
class
galaxy.model.
ImplicitlyCreatedDatasetCollectionInput
(name, input_dataset_collection)[source]¶ Bases:
object
-
class
galaxy.model.
ItemRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶ Bases:
object
-
class
galaxy.model.
ItemTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'user_tname', 'user_value')¶
-
dict_element_visible_keys
= ('id', 'user_tname', 'user_value')¶
-
-
class
galaxy.model.
Job
[source]¶ Bases:
object
,galaxy.model.HasJobMetrics
,galaxy.model.item_attrs.Dictifiable
-
check_if_output_datasets_deleted
()[source]¶ Return true if all of the output datasets associated with this job are in the deleted state
-
dict_collection_visible_keys
= ['id', 'state', 'exit_code', 'update_time', 'create_time']¶
-
dict_element_visible_keys
= ['id', 'state', 'exit_code', 'update_time', 'create_time']¶ A job represents a request to run a tool given input datasets, tool parameters, and output datasets.
-
finished
¶
-
get_external_output_metadata
()[source]¶ The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task.
-
get_id_tag
()[source]¶ Return a tag that can be useful in identifying a Job. This returns the Job’s get_id
-
get_param_values
(app, ignore_errors=False)[source]¶ Read encoded parameter values from the database and turn back into a dict of tool parameter values.
-
mark_deleted
(track_jobs_in_database=False)[source]¶ Mark this job as deleted, and mark any output datasets as discarded.
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
JobExportHistoryArchive
(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None, datasets_attrs_filename=None, jobs_attrs_filename=None)[source]¶ Bases:
object
-
export_name
¶
-
preparing
¶
-
ready
¶
-
up_to_date
¶ Return False, if a new export should be generated for corresponding history.
-
-
class
galaxy.model.
JobExternalOutputMetadata
(job=None, dataset=None)[source]¶ Bases:
object
-
dataset
¶
-
-
class
galaxy.model.
JobImportHistoryArchive
(job=None, history=None, archive_dir=None)[source]¶ Bases:
object
-
class
galaxy.model.
JobMetricNumeric
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
-
class
galaxy.model.
JobMetricText
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
-
class
galaxy.model.
JobToImplicitOutputDatasetCollectionAssociation
(name, dataset_collection)[source]¶ Bases:
object
-
class
galaxy.model.
JobToOutputDatasetCollectionAssociation
(name, dataset_collection_instance)[source]¶ Bases:
object
-
class
galaxy.model.
Library
(name=None, description=None, synopsis=None, root_folder=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
,galaxy.model.HasName
-
dict_collection_visible_keys
= ('id', 'name')¶
-
dict_element_visible_keys
= ('id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id')¶
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
LibraryDataset
(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)[source]¶ Bases:
object
-
info
¶
-
name
¶
-
upload_options
= [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]¶
-
-
class
galaxy.model.
LibraryDatasetCollectionAssociation
(id=None, collection=None, name=None, deleted=False, folder=None)[source]¶ Bases:
galaxy.model.DatasetCollectionInstance
,galaxy.model.item_attrs.Dictifiable
Associates a DatasetCollection with a library folder.
-
editable_keys
= ('name', 'deleted')¶
-
-
class
galaxy.model.
LibraryDatasetCollectionRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶
-
class
galaxy.model.
LibraryDatasetCollectionTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
LibraryDatasetDatasetAssociation
(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)[source]¶
-
class
galaxy.model.
LibraryDatasetDatasetAssociationPermissions
(action, library_item, role)[source]¶ Bases:
object
-
class
galaxy.model.
LibraryDatasetDatasetInfoAssociation
(library_dataset_dataset_association, form_definition, info)[source]¶ Bases:
object
-
inheritable
¶
-
-
class
galaxy.model.
LibraryFolder
(name=None, description=None, item_count=0, order_id=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
,galaxy.model.HasName
-
activatable_library_datasets
¶
-
dict_element_visible_keys
= ('id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted')¶
-
library_path
¶
-
parent_library
¶
-
-
class
galaxy.model.
LibraryFolderInfoAssociation
(folder, form_definition, info, inheritable=False)[source]¶ Bases:
object
-
class
galaxy.model.
LibraryInfoAssociation
(library, form_definition, info, inheritable=False)[source]¶ Bases:
object
-
class
galaxy.model.
Page
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_element_visible_keys
= ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted']¶
-
-
class
galaxy.model.
PageRevision
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_element_visible_keys
= ['id', 'page_id', 'title', 'content']¶
-
-
class
galaxy.model.
PageTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
Bases:
object
-
class
galaxy.model.
PostJobAction
(action_type, workflow_step, output_name=None, action_arguments=None)[source]¶ Bases:
object
-
class
galaxy.model.
Quota
(name='', description='', amount=0, operation='=')[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
amount
¶
-
dict_collection_visible_keys
= ('id', 'name')¶
-
dict_element_visible_keys
= ('id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups')¶
-
display_amount
¶
-
valid_operations
= ('+', '-', '=')¶
-
-
class
galaxy.model.
Request
(name=None, desc=None, request_type=None, user=None, form_values=None, notification=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name', 'state')¶
-
is_complete
¶
-
is_new
¶
-
is_rejected
¶
-
is_submitted
¶
-
is_unsubmitted
¶
-
last_comment
¶
-
latest_event
¶
-
samples_have_common_state
¶ Returns the state of this request’s samples when they are all in one common state. Otherwise returns False.
-
samples_with_bar_code
¶
-
samples_without_library_destinations
¶
-
state
¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
RequestEvent
(request=None, request_state=None, comment='')[source]¶ Bases:
object
-
class
galaxy.model.
RequestType
(name=None, desc=None, request_form=None, sample_form=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name', 'desc')¶
-
dict_element_visible_keys
= ('id', 'name', 'desc', 'request_form_id', 'sample_form_id')¶
-
external_services
¶
-
final_sample_state
¶
-
get_external_services_for_manual_data_transfer
(trans)[source]¶ Returns all external services that use manual data transfer
-
permitted_actions
= <galaxy.util.bunch.Bunch object>¶
-
rename_dataset_options
= <galaxy.util.bunch.Bunch object>¶
-
run_details
¶
-
-
class
galaxy.model.
RequestTypeExternalServiceAssociation
(request_type, external_service)[source]¶ Bases:
object
-
class
galaxy.model.
Role
(name='', description='', type='system', deleted=False)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name')¶
-
dict_element_visible_keys
= ('id', 'name', 'description', 'type')¶
-
private_id
= None¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
Sample
(name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
adding_to_library_dataset_files
¶
-
bulk_operations
= <galaxy.util.bunch.Bunch object>¶
-
dict_collection_visible_keys
= ('id', 'name')¶
-
inprogress_dataset_files
¶
-
latest_event
¶
-
queued_dataset_files
¶
-
run_details
¶
-
state
¶
-
supported_field_types
= [<class 'galaxy.web.form_builder.CheckboxField'>, <class 'galaxy.web.form_builder.SelectField'>, <class 'galaxy.web.form_builder.TextField'>, <class 'galaxy.web.form_builder.WorkflowField'>, <class 'galaxy.web.form_builder.WorkflowMappingField'>, <class 'galaxy.web.form_builder.HistoryField'>]¶
-
transfer_error_dataset_files
¶
-
transferred_dataset_files
¶
-
transferring_dataset_files
¶
-
untransferred_dataset_files
¶
-
-
class
galaxy.model.
SampleDataset
(sample=None, name=None, file_path=None, status=None, error_msg=None, size=None, external_service=None)[source]¶ Bases:
object
-
transfer_status
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
StoredWorkflow
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'name', 'published', 'deleted')¶
-
dict_element_visible_keys
= ('id', 'name', 'published', 'deleted')¶
-
-
class
galaxy.model.
StoredWorkflowRatingAssociation
(id=None, user=None, item=None, rating=0)[source]¶
-
class
galaxy.model.
StoredWorkflowTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
Bases:
object
-
class
galaxy.model.
Task
(job, working_directory, prepare_files_cmd)[source]¶ Bases:
object
,galaxy.model.HasJobMetrics
A task represents a single component of a job.
-
get_external_output_metadata
()[source]¶ The external_output_metadata is currently a backref to JobExternalOutputMetadata. It exists for a job but not a task, and when a task is cancelled its corresponding parent Job will be cancelled. So None is returned now, but that could be changed to self.get_job().get_external_output_metadata().
-
get_id_tag
()[source]¶ Return an id tag suitable for identifying the task. This combines the task’s job id and the task’s own id.
-
get_job_runner_external_id
()[source]¶ Runners will use the same methods to get information about the Task class as they will about the Job class, so this method just returns the task’s external id.
-
get_job_runner_name
()[source]¶ Since runners currently access Tasks the same way they access Jobs, this method just refers to this instance’s runner.
-
get_param_values
(app)[source]¶ Read encoded parameter values from the database and turn back into a dict of tool parameter values.
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
TaskMetricNumeric
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
-
class
galaxy.model.
TaskMetricText
(plugin, metric_name, metric_value)[source]¶ Bases:
galaxy.model.BaseJobMetric
-
class
galaxy.model.
ToolTagAssociation
(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
TransferJob
(state=None, path=None, info=None, pid=None, socket=None, params=None)[source]¶ Bases:
object
-
states
= <galaxy.util.bunch.Bunch object>¶
-
terminal_states
= ['error', 'done']¶
-
-
class
galaxy.model.
User
(email=None, password=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
all_roles
()[source]¶ Return a unique list of Roles associated with this user or any of their groups.
-
calculate_disk_usage
()[source]¶ Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories.
-
dict_collection_visible_keys
= ('id', 'email', 'username')¶
-
dict_element_visible_keys
= ('id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage')¶
-
get_disk_usage
(nice_size=False)[source]¶ Return byte count of disk space used by user or a human-readable string if nice_size is True.
-
nice_total_disk_usage
¶ Return byte count of disk space used in a human-readable string.
-
total_disk_usage
¶ Return byte count of disk space used by user or a human-readable string if nice_size is True.
-
use_pbkdf2
= True¶ Data for a Galaxy user or admin and relations to their histories, credentials, and roles.
-
static
user_template_environment
(user)[source]¶ >>> env = User.user_template_environment(None) >>> env['__user_email__'] 'Anonymous' >>> env['__user_id__'] 'Anonymous' >>> user = User('foo@example.com') >>> user.id = 6 >>> user.username = 'foo2' >>> env = User.user_template_environment(user) >>> env['__user_id__'] '6' >>> env['__user_name__'] 'foo2'
-
-
class
galaxy.model.
UserAction
(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)[source]¶ Bases:
object
-
class
galaxy.model.
UserAddress
(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)[source]¶ Bases:
object
-
class
galaxy.model.
UserQuotaAssociation
(user, quota)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_element_visible_keys
= ('user',)¶
-
-
class
galaxy.model.
ValidationError
(message=None, err_type=None, attributes=None)[source]¶ Bases:
object
-
class
galaxy.model.
Visualization
(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)[source]¶ Bases:
object
-
class
galaxy.model.
VisualizationRevision
(visualization=None, title=None, dbkey=None, config=None)[source]¶ Bases:
object
-
class
galaxy.model.
VisualizationTagAssociation
(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]¶
Bases:
object
-
class
galaxy.model.
WorkRequestTagAssociation
(id=None, user=None, workflow_request_id=None, tag_id=None, user_tname=None, value=None)[source]¶
-
class
galaxy.model.
Workflow
(uuid=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('name', 'has_cycles', 'has_errors')¶
-
dict_element_visible_keys
= ('name', 'has_cycles', 'has_errors')¶
-
-
class
galaxy.model.
WorkflowInvocation
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
active
¶ Indicates the workflow invocation is somehow active - and in particular valid actions may be performed on its ``WorkflowInvocationStep``s.
-
dict_collection_visible_keys
= ('id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state')¶
-
dict_element_visible_keys
= ('id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state')¶
-
states
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
WorkflowInvocationStep
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ('id', 'update_time', 'job_id', 'workflow_step_id', 'action')¶
-
dict_element_visible_keys
= ('id', 'update_time', 'job_id', 'workflow_step_id', 'action')¶
-
-
class
galaxy.model.
WorkflowRequest
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
-
dict_collection_visible_keys
= ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']¶
-
dict_element_visible_keys
= ['id', 'name', 'type', 'state', 'history_id', 'workflow_id']¶
-
-
class
galaxy.model.
WorkflowRequestInputParameter
(name=None, value=None, type=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
Workflow-related parameters not tied to steps or inputs.
-
dict_collection_visible_keys
= ['id', 'name', 'value', 'type']¶
-
types
= <galaxy.util.bunch.Bunch object>¶
-
-
class
galaxy.model.
WorkflowRequestStepState
(workflow_step=None, name=None, value=None)[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
Workflow step value parameters.
-
dict_collection_visible_keys
= ['id', 'name', 'value', 'workflow_step_id']¶
-
-
class
galaxy.model.
WorkflowRequestToInputDatasetAssociation
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
Workflow step input dataset parameters.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']¶
-
-
class
galaxy.model.
WorkflowRequestToInputDatasetCollectionAssociation
[source]¶ Bases:
object
,galaxy.model.item_attrs.Dictifiable
Workflow step input dataset collection parameters.
-
dict_collection_visible_keys
= ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']¶
-
-
class
galaxy.model.
WorkflowStepConnection
[source]¶ Bases:
object
-
NON_DATA_CONNECTION
= '__NO_INPUT_OUTPUT_NAME__'¶
-
non_data_connection
¶
-
custom_types
Module¶
-
class
galaxy.model.custom_types.
JSONType
(*args, **kwargs)[source]¶ Bases:
sqlalchemy.sql.type_api.TypeDecorator
Represents an immutable structure as a json-encoded string.
If default is, for example, a dict, then a NULL value in the database will be exposed as an empty dict.
-
impl
¶ alias of
LargeBinary
-
-
class
galaxy.model.custom_types.
MetadataType
(*args, **kwargs)[source]¶ Bases:
galaxy.model.custom_types.JSONType
Backward compatible metadata type. Can read pickles or JSON, but always writes in JSON.
-
class
galaxy.model.custom_types.
MutationDict
[source]¶ Bases:
galaxy.model.custom_types.MutationObj
,dict
-
class
galaxy.model.custom_types.
MutationList
[source]¶ Bases:
galaxy.model.custom_types.MutationObj
,list
-
class
galaxy.model.custom_types.
MutationObj
[source]¶ Bases:
sqlalchemy.ext.mutable.Mutable
Mutable JSONType for SQLAlchemy from original gist: https://gist.github.com/dbarnett/1730610
Using minor changes from this fork of the gist: https://gist.github.com/miracle2k/52a031cced285ba9b8cd
And other minor changes to make it work for us.
-
class
galaxy.model.custom_types.
TrimmedString
(*args, **kwargs)[source]¶ Bases:
sqlalchemy.sql.type_api.TypeDecorator
-
impl
¶ alias of
String
-
-
class
galaxy.model.custom_types.
UUIDType
(*args, **kwargs)[source]¶ Bases:
sqlalchemy.sql.type_api.TypeDecorator
Platform-independent UUID type.
Based on http://docs.sqlalchemy.org/en/rel_0_8/core/types.html#backend-agnostic-guid-type Changed to remove sqlalchemy 0.8 specific code
CHAR(32), storing as stringified hex values.
-
impl
¶ alias of
CHAR
-
item_attrs
Module¶
-
class
galaxy.model.item_attrs.
Dictifiable
[source]¶ Mixin that enables objects to be converted to dictionaries. This is useful when for sharing objects across boundaries, such as the API, tool scripts, and JavaScript code.
-
class
galaxy.model.item_attrs.
UsesAnnotations
[source]¶ Mixin for getting and setting item annotations.
-
add_item_annotation
(db_session, user, item, annotation)[source]¶ Add or update an item’s annotation; a user can only have a single annotation for an item.
-
copy_item_annotation
(db_session, source_user, source_item, target_user, target_item)[source]¶ Copy an annotation from a user/item source to a user/item target.
-
-
class
galaxy.model.item_attrs.
UsesItemRatings
[source]¶ Mixin for getting and setting item ratings.
Class makes two assumptions: (1) item-rating association table is named <item_class>RatingAssocation (2) item-rating association table has a column with a foreign key referencing item table that contains the item’s id.
-
get_ave_item_rating_data
(db_session, item, webapp_model=None)[source]¶ Returns the average rating for an item.
-
mapping
Module¶
Details of how the data model objects are mapped onto the relational database are encapsulated here.
-
galaxy.model.mapping.
db_next_hid
(self)[source]¶ Override __next_hid to generate from the database in a concurrency safe way. Loads the next history ID from the DB and returns it. It also saves the future next_id into the DB.
Return type: int Returns: the next history id
-
galaxy.model.mapping.
init
(file_path, url, engine_options={}, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True)[source]¶ Connect mappings to the database
-
galaxy.model.mapping.
now
()¶ Return a new datetime representing UTC day and time.