Wrapper API¶

The following are wrappers around common Orion data types that allow for simplified testing of workfloes.

Utilities¶

wrappers.using_orion() → bool¶: Method to check whether the tests are being run against Orion

WorkFloe Wrapper¶

class artemis.wrappers.WorkFloeWrapper(workfloe_path='', upload=False, run_timeout=600, queue_timeout=600, reuse: bool = False, package=None, workfloe_spec=None, orion_job=None, using_orion=NOTHING, last_refresh=None, start_time=None, local_job=NOTHING)¶

cancel() → None¶: Cancels a running workfloe, only useful when running a job as non-blocking in Orion.

classmethod get_workfloe(workfloe_path: str, run_timeout: int = 600, queue_timeout: int = 600, upload: bool = False, package=None) → artemis.wrappers.WorkFloeWrapper¶

Create a WorkFloeWrapper that will be cleaned up at the end of the tests

Parameters

workfloe_path (string) – Path to the local workfloe
run_timeout (int) – How long to run floe before canceling
queue_timeout (int) – How long to wait for the floe to start Only used when testing against Orion
upload (bool) – Tries to upload floe to Orion and expects cubes to already be on orion. WARNING: Preliminary API that is fragile

Returns

WorkFloeWrapper

Return type

WorkFloeWrapper

property identifier: Union[int, str]¶

Returns either the path of the WorkFloe or the Orion WorkFloe Job Id that specifies the Job

Returns: Workfloe Path or Orion Job Id

property logs: Generator[None, None, Any]¶

Returns an iterator of bytes that makes up the Job Logs

Locally raises an ArtemisError :rtype: iter

property reason: str¶

The reason for why the state is the way it is. If the reason isn’t empty then something went wrong

Locally always returns “” :rtype: string

start(parameters: Dict, name: str = '', block: bool = True) → None¶

Triggers the Workfloe to be run.

Parameters

parameters (dict) – Parameters to run the Floe with, see below
name (string) – Optional name to give floe, otherwise it will default to the path name
block (bool) – Whether the call to start should block or not, only supported if testing against orion

Raises

WorkFloeException: Something went wrong while running the floe

Returns

None

The parameter dictionary is expected to be structured as follows

{
  "promoted": {
    "promoted_name": "value"
  },
  "cube": {
    "cube_name": {
      "param_name": "value"
    }
  }
}

property state: str¶

The state of the Workfloe as it is right now

Locally always returns complete :rtype: string

property status: Dict¶

Retrieves the status of the Workfloe job. The status is the summary of the current job.

Locally raises an ArtemisError :rtype: dict

wait(max_wait: int = 600) → None¶

Waits on Workfloe until it is complete

Should only be used if you are running workfloes in a non-blocking manner

Input Wrappers¶

DatasetWrapper¶

class artemis.wrappers.DatasetWrapper(dataset_path='', dataset_obj=None)¶

classmethod from_file(dataset_path: str, reuse: bool = False) → artemis.wrappers.DatasetWrapper¶

Create a DatasetWrapper that will be cleaned up at the end of the tests

Parameters

dataset_path (string) – Path to the local dataset (.oedb)
reuse (bool) – Whether to cache the dataset for testing

Returns

DatasetWrapper

Return type

DatasetWrapper

classmethod get_dataset(dataset_path: str, reuse: bool = False) → artemis.wrappers.DatasetWrapper¶

Create a DatasetWrapper that will be cleaned up at the end of the tests

Parameters

dataset_path (string) – Path to the local dataset (.oedb)
reuse (bool) – Whether to cache the dataset for testing

Returns

DatasetWrapper

Return type

DatasetWrapper

property identifier: Union[int, str]¶

Provides the File Path or the Orion Dataset Id to the resource that is being used.

Returns: Dataset path or Orion Dataset Id

FileWrapper¶

class artemis.wrappers.FileWrapper(file_path='', file_obj=None, reuse=True)¶

classmethod from_file(file_path: str, reuse: bool = False) → artemis.wrappers.FileWrapper¶

Create a FileWrapper that will be cleaned up at the end of the tests

Parameters

file_path (string) – Path to the local file
reuse (bool) – Whether to cache the file for testing

Returns

FileWrapper

Return type

FileWrapper

classmethod get_file(file_path: str, reuse: bool = False) → artemis.wrappers.FileWrapper¶

Create a FileWrapper that will be cleaned up at the end of the tests

Parameters

file_path (string) – Path to the local file
reuse (bool) – Whether to cache the file for testing

Returns

FileWrapper

Return type

FileWrapper

property identifier: Union[int, str]¶

Provides the File Path or the Orion File Id to the resource that is being used.

Returns: File path or Orion File Id

CollectionWrapper¶

class artemis.wrappers.CollectionWrapper(resource=None, num_shards: int = 0, v2=False)¶

Utility for testing floes that require Collections.

Requires an authenticated Orion Client to perform creation of ShardCollection objects, even if not running tests against orion.

classmethod from_collection(collection: orionclient.types.shards.ShardCollection) → artemis.wrappers.CollectionWrapper¶: Provide a preconstructed collection as input. Allows for automatic clean up collections as a part of Artemis cleanup.

classmethod from_file(file_path: str, as_records: bool = True, num_shards: int = 10, v2: bool = False) → artemis.wrappers.CollectionWrapper¶

Convert a file into a collection automatically.

Parameters

file_path (string) – Path to file, must be readable by OEChem
as_records (bool) – Convert molecular file to records, otherwise writes as oeb.gz
num_shards (int item per shard if unable to pack in the requested number of shards.) – Number of shards to create from file, defaults to 1

property identifier: int¶

Returns the id of the collection

Returns: Collection id
Return type: int

property metadata: Dict¶

Returns the metadata of the collection

Returns: Collection metadata
Return type: dict

Output Wrappers¶

OutputDatasetWrapper¶

class artemis.wrappers.OutputDatasetWrapper(dataset_name='', extension='.oedb', temp=None, orion_resource=None)¶

A Utility class to be able to retrieve the output values of a dataset

property count: int¶

Return the number of records in a dataset

Returns: Number of records in dataset
Return type: int

property identifier: str¶

Provides the output name of the Dataset, this is a random file name

Returns: Name of the output dataset
Return type: string

property path: str¶

Path to the output Dataset.

This will download the Dataset from Orion when it is requested

Returns: Path to the Dataset
Return type: string

records() → Generator[openeye.oechem.OEMolRecord, None, None]¶

Return the records contained with the output dataset as an iterator of OEMolRecords

Returns: Iterator of OEMolRecords

OutputFileWrapper¶

class artemis.wrappers.OutputFileWrapper(file_name='', extension='.txt', temp=None)¶

property identifier: str¶

Provides the output name of the file, this is a random file name

Returns: Name of the output file
Return type: string

property path: str¶

Path to the output file.

This will download the file from Orion when it is requested

Returns: Path to the Dataset
Return type: string

property size: int¶

Size of the output file.

Returns: Size of the output file
Return type: int

OutputCollectionWrapper¶

class artemis.wrappers.OutputCollectionWrapper(name=None, resource=None, v2=False)¶

get() → orionclient.types.shards.ShardCollection¶

Returns the collection that was output

Returns: Output shard collection
Return type: ShardCollection

property identifier: str¶: Returns the randomly generated name of the output collection