galaxy.objectstore package¶
Submodules¶
galaxy.objectstore.azure_blob module¶
Object Store plugin for the Microsoft Azure Block Blob Storage system
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class
galaxy.objectstore.azure_blob.
AzureBlobObjectStore
(config, config_xml)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Object store that stores objects as blobs in an Azure Blob Container. A local cache exists that is used as an intermediate location for files between Galaxy and Azure.
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create
(obj, **kwargs)[source]¶ Mark the object (obj) as existing in the store, but with no content.
This method will create a proper directory structure for the file if the directory does not already exist.
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delete
(obj, entire_dir=False, **kwargs)[source]¶ Delete the object identified by obj.
Parameters: entire_dir (boolean) – If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies only for and in conjunction with the extra_dir or obj_dir options.
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empty
(obj, **kwargs)[source]¶ Test if the object identified by obj has content.
If the object does not exist raises ObjectNotFound.
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file_ready
(obj, **kwargs)[source]¶ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return
True
if so,False
otherwise.
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get_data
(obj, start=0, count=-1, **kwargs)[source]¶ Fetch count bytes of data offset by start bytes using obj.id.
If the object does not exist raises ObjectNotFound.
Parameters: - start (int) – Set the position to start reading the dataset file
- count (int) – Read at most count bytes from the dataset
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get_filename
(obj, **kwargs)[source]¶ Get the expected filename with absolute path for object with id obj.id.
This can be used to access the contents of the object.
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get_object_url
(obj, **kwargs)[source]¶ Return the URL for direct acces if supported, otherwise return None.
Note: need to be careful to not bypass dataset security with this.
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size
(obj, **kwargs)[source]¶ Return size of the object identified by obj.
If the object does not exist, return 0.
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update_from_file
(obj, file_name=None, create=False, **kwargs)[source]¶ Inform the store that the file associated with obj.id has been updated.
If file_name is provided, update from that file instead of the default. If the object does not exist raises ObjectNotFound.
Parameters: - file_name (string) – Use file pointed to by file_name as the source for updating the dataset identified by obj
- create (boolean) – If True and the default dataset does not exist, create it first.
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galaxy.objectstore.pithos module¶
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class
galaxy.objectstore.pithos.
PithosObjectStore
(config, config_xml)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Object store that stores objects as items in a Pithos+ container. Cache is ignored for the time being.
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empty
(obj, **kwargs)[source]¶ Returns: weather the object has content Raises: ObjectNotFound –
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exists
(obj, **kwargs)[source]¶ Check if file exists, fix if file in cache and not on Pithos+ :returns: weather the file exists remotely or in cache
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get_data
(obj, start=0, count=-1, **kwargs)[source]¶ Fetch (e.g., download) data :param start: Chunk of data starts here :param count: Fetch at most as many data, fetch all if negative
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galaxy.objectstore.pulsar module¶
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class
galaxy.objectstore.pulsar.
PulsarObjectStore
(config, config_xml)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Object store implementation that delegates to a remote Pulsar server.
This may be more aspirational than practical for now, it would be good to Galaxy to a point that a handler thread could be setup that doesn’t attempt to access the disk files returned by a (this) object store - just passing them along to the Pulsar unmodified. That modification - along with this implementation and Pulsar job destinations would then allow Galaxy to fully manage jobs on remote servers with completely different mount points.
This implementation should be considered beta and may be dropped from Galaxy at some future point or significantly modified.
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create
(obj, **kwds)[source]¶ Mark the object (obj) as existing in the store, but with no content.
This method will create a proper directory structure for the file if the directory does not already exist.
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delete
(obj, **kwds)[source]¶ Delete the object identified by obj.
Parameters: entire_dir (boolean) – If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies only for and in conjunction with the extra_dir or obj_dir options.
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empty
(obj, **kwds)[source]¶ Test if the object identified by obj has content.
If the object does not exist raises ObjectNotFound.
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file_ready
(obj, **kwds)[source]¶ Check if a file corresponding to a dataset is ready to be used.
Return True if so, False otherwise
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get_data
(obj, **kwds)[source]¶ Fetch count bytes of data offset by start bytes using obj.id.
If the object does not exist raises ObjectNotFound.
Parameters: - start (int) – Set the position to start reading the dataset file
- count (int) – Read at most count bytes from the dataset
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get_filename
(obj, **kwds)[source]¶ Get the expected filename with absolute path for object with id obj.id.
This can be used to access the contents of the object.
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get_object_url
(obj, extra_dir=None, extra_dir_at_root=False, alt_name=None)[source]¶ Return the URL for direct acces if supported, otherwise return None.
Note: need to be careful to not bypass dataset security with this.
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size
(obj, **kwds)[source]¶ Return size of the object identified by obj.
If the object does not exist, return 0.
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update_from_file
(obj, **kwds)[source]¶ Inform the store that the file associated with obj.id has been updated.
If file_name is provided, update from that file instead of the default. If the object does not exist raises ObjectNotFound.
Parameters: - file_name (string) – Use file pointed to by file_name as the source for updating the dataset identified by obj
- create (boolean) – If True and the default dataset does not exist, create it first.
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galaxy.objectstore.rods module¶
Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
The module is named rods to avoid conflicting with the PyRods module, irods
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class
galaxy.objectstore.rods.
IRODSObjectStore
(config, file_path=None, extra_dirs=None)[source]¶ Bases:
galaxy.objectstore.DiskObjectStore
Galaxy object store based on iRODS
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create
(*args, **kwargs)¶
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delete
(*args, **kwargs)¶
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empty
(*args, **kwargs)¶
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exists
(*args, **kwargs)¶
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get_data
(*args, **kwargs)¶
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get_filename
(*args, **kwargs)¶
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size
(obj, **kwargs)[source]¶ Override ObjectStore’s stub by return file size on disk.
Returns 0 if the object doesn’t exist yet or other error.
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update_from_file
(*args, **kwargs)¶
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galaxy.objectstore.s3 module¶
Object Store plugin for the Amazon Simple Storage Service (S3)
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class
galaxy.objectstore.s3.
S3ObjectStore
(config, config_xml)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Object store that stores objects as items in an AWS S3 bucket. A local cache exists that is used as an intermediate location for files between Galaxy and S3.
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create
(obj, **kwargs)[source]¶ Mark the object (obj) as existing in the store, but with no content.
This method will create a proper directory structure for the file if the directory does not already exist.
-
delete
(obj, entire_dir=False, **kwargs)[source]¶ Delete the object identified by obj.
Parameters: entire_dir (boolean) – If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies only for and in conjunction with the extra_dir or obj_dir options.
-
empty
(obj, **kwargs)[source]¶ Test if the object identified by obj has content.
If the object does not exist raises ObjectNotFound.
-
file_ready
(obj, **kwargs)[source]¶ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return
True
if so,False
otherwise.
-
get_data
(obj, start=0, count=-1, **kwargs)[source]¶ Fetch count bytes of data offset by start bytes using obj.id.
If the object does not exist raises ObjectNotFound.
Parameters: - start (int) – Set the position to start reading the dataset file
- count (int) – Read at most count bytes from the dataset
-
get_filename
(obj, **kwargs)[source]¶ Get the expected filename with absolute path for object with id obj.id.
This can be used to access the contents of the object.
-
get_object_url
(obj, **kwargs)[source]¶ Return the URL for direct acces if supported, otherwise return None.
Note: need to be careful to not bypass dataset security with this.
-
size
(obj, **kwargs)[source]¶ Return size of the object identified by obj.
If the object does not exist, return 0.
-
update_from_file
(obj, file_name=None, create=False, **kwargs)[source]¶ Inform the store that the file associated with obj.id has been updated.
If file_name is provided, update from that file instead of the default. If the object does not exist raises ObjectNotFound.
Parameters: - file_name (string) – Use file pointed to by file_name as the source for updating the dataset identified by obj
- create (boolean) – If True and the default dataset does not exist, create it first.
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class
galaxy.objectstore.s3.
SwiftObjectStore
(config, config_xml)[source]¶ Bases:
galaxy.objectstore.s3.S3ObjectStore
Object store that stores objects as items in a Swift bucket. A local cache exists that is used as an intermediate location for files between Galaxy and Swift.
galaxy.objectstore.s3_multipart_upload module¶
Split large file into multiple pieces for upload to S3. This parallelizes the task over available cores using multiprocessing. Code mostly taken form CloudBioLinux.
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galaxy.objectstore.s3_multipart_upload.
mp_from_ids
(s3server, mp_id, mp_keyname, mp_bucketname)[source]¶ Get the multipart upload from the bucket and multipart IDs.
This allows us to reconstitute a connection to the upload from within multiprocessing functions.
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galaxy.objectstore.s3_multipart_upload.
multimap
(*args, **kwds)[source]¶ Provide multiprocessing imap like function.
The context manager handles setting up the pool, worked around interrupt issues and terminating the pool on completion.
Module contents¶
objectstore package, abstraction for storing blobs of data for use in Galaxy.
all providers ensure that data can be accessed on the filesystem for running tools
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class
galaxy.objectstore.
DiskObjectStore
(config, config_xml=None, file_path=None, extra_dirs=None)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Standard Galaxy object store.
Stores objects in files under a specific directory on disk.
>>> from galaxy.util.bunch import Bunch >>> import tempfile >>> file_path=tempfile.mkdtemp() >>> obj = Bunch(id=1) >>> s = DiskObjectStore(Bunch(umask=0o077, jobs_directory=file_path, new_file_path=file_path, object_store_check_old_style=False), file_path=file_path) >>> s.create(obj) >>> s.exists(obj) True >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat'
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create
(obj, **kwargs)[source]¶ Override ObjectStore’s stub by creating any files and folders on disk.
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delete
(obj, entire_dir=False, **kwargs)[source]¶ Override ObjectStore’s stub; delete the file or folder on disk.
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get_data
(obj, start=0, count=-1, **kwargs)[source]¶ Override ObjectStore’s stub; retrieve data directly from disk.
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get_filename
(obj, **kwargs)[source]¶ Override ObjectStore’s stub.
If object_store_check_old_style is set to True in config then the root path is checked first.
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class
galaxy.objectstore.
DistributedObjectStore
(config, config_xml=None, fsmon=False)[source]¶ Bases:
galaxy.objectstore.NestedObjectStore
ObjectStore that defers to a list of backends.
When getting objects the first store where the object exists is used. When creating objects they are created in a store selected randomly, but with weighting.
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class
galaxy.objectstore.
HierarchicalObjectStore
(config, config_xml=None, fsmon=False)[source]¶ Bases:
galaxy.objectstore.NestedObjectStore
ObjectStore that defers to a list of backends.
When getting objects the first store where the object exists is used. When creating objects only the first store is used.
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class
galaxy.objectstore.
NestedObjectStore
(config, config_xml=None)[source]¶ Bases:
galaxy.objectstore.ObjectStore
Base for ObjectStores that use other ObjectStores.
Example: DistributedObjectStore, HierarchicalObjectStore
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class
galaxy.objectstore.
ObjectStore
(config, **kwargs)[source]¶ Bases:
object
ObjectStore abstract interface.
FIELD DESCRIPTIONS (these apply to all the methods in this class):
Parameters: - obj (StorableObject) – A Galaxy object with an assigned database ID accessible via the .id attribute.
- base_dir (string) – A key in self.extra_dirs corresponding to the base directory in which this object should be created, or None to specify the default directory.
- dir_only (boolean) – If True, check only the path where the file identified by obj should be located, not the dataset itself. This option applies to extra_dir argument as well.
- extra_dir (string) – Append extra_dir to the directory structure where the dataset identified by obj should be located. (e.g., 000/extra_dir/obj.id). Valid values include ‘job_work’ (defaulting to config.jobs_directory = ‘$GALAXY_ROOT/database/jobs_directory’); ‘temp’ (defaulting to config.new_file_path = ‘$GALAXY_ROOT/database/tmp’).
- extra_dir_at_root (boolean) – Applicable only if extra_dir is set. If True, the extra_dir argument is placed at root of the created directory structure rather than at the end (e.g., extra_dir/000/obj.id vs. 000/extra_dir/obj.id)
- alt_name (string) – Use this name as the alternative name for the created dataset rather than the default.
- obj_dir (boolean) – Append a subdirectory named with the object’s ID (e.g. 000/obj.id)
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create
(obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Mark the object (obj) as existing in the store, but with no content.
This method will create a proper directory structure for the file if the directory does not already exist.
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delete
(obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Delete the object identified by obj.
Parameters: entire_dir (boolean) – If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies only for and in conjunction with the extra_dir or obj_dir options.
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empty
(obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Test if the object identified by obj has content.
If the object does not exist raises ObjectNotFound.
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exists
(obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None)[source]¶ Return True if the object identified by obj exists, False otherwise.
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file_ready
(obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Check if a file corresponding to a dataset is ready to be used.
Return True if so, False otherwise
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get_data
(obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Fetch count bytes of data offset by start bytes using obj.id.
If the object does not exist raises ObjectNotFound.
Parameters: - start (int) – Set the position to start reading the dataset file
- count (int) – Read at most count bytes from the dataset
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get_filename
(obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Get the expected filename with absolute path for object with id obj.id.
This can be used to access the contents of the object.
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get_object_url
(obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Return the URL for direct acces if supported, otherwise return None.
Note: need to be careful to not bypass dataset security with this.
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size
(obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False)[source]¶ Return size of the object identified by obj.
If the object does not exist, return 0.
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update_from_file
(obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False)[source]¶ Inform the store that the file associated with obj.id has been updated.
If file_name is provided, update from that file instead of the default. If the object does not exist raises ObjectNotFound.
Parameters: - file_name (string) – Use file pointed to by file_name as the source for updating the dataset identified by obj
- create (boolean) – If True and the default dataset does not exist, create it first.
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class
galaxy.objectstore.
ObjectStorePopulator
(app)[source]¶ Bases:
object
Small helper for interacting with the object store and making sure all datasets from a job end up with the same object_store_id.
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galaxy.objectstore.
build_object_store_from_config
(config, fsmon=False, config_xml=None)[source]¶ Invoke the appropriate object store.
Will use the object_store_config_file attribute of the config object to configure a new object store from the specified XML file.
Or you can specify the object store type in the object_store attribute of the config object. Currently ‘disk’, ‘s3’, ‘swift’, ‘distributed’, ‘hierarchical’, ‘irods’, and ‘pulsar’ are supported values.