+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The CellEngine APIClient object is the low-level interface between the
+CellEngine API and entities in the Python SDK. After authenticating, you may
+either use the APIClient directly or interact with the higher-level SDK
+entities.
Assuming you have instantiated the APIClient object:
+
import cellengine
+client = cellengine.APIClient("username")
+# Password: <enter your password here>
+# Alternatively, set CELLENGINE_PASSWORD in your environment
+then the following sequences of commands are equivalent:
+exp = client.get_experiment(name="my experiment")
+fcsfile = client.get_fcs_file(experiment_id=exp._id, name="my fcs file")
+exp = cellengine.Experiment.get(name="my experiment")
+fcsfile = cellengine.FcsFile.get(experiment_id=exp._id, name="my fcs file")
+exp = cellengine.Experiment.get(name="my experiment")
+fcsfile = exp.get_fcs_file(name="my fcs file")
+The APIClient provides higher-level methods for interacting with
+CellEngine. It also provides _get, _post, _patch, and _delete methods
+for low-level interaction with the CellEngine
+API. If there is a higher-level feature
+that's missing, please feel free to open an Issue in
+GitHub.
base_url (to override the cellengine.com URL, generally for internal use)usernamepasswordtokenuser_idadminflagsauthenticatedcache_infocache_clearcellengine.APIClient
+
+
+
+ Bases: BaseAPIClient
authenticated = self._authenticate(self.username, self.password, self.token)
+
+
+ instance-attribute
+
+
+base_url = os.environ.get('CELLENGINE_BASE_URL', 'https://cellengine.com')
+
+
+ instance-attribute
+
+
+cache_clear = self._get_id_by_name.cache_clear
+
+
+ instance-attribute
+
+
+cache_info = self._get_id_by_name.cache_info
+
+
+ instance-attribute
+
+
+password = password or os.environ.get('CELLENGINE_PASSWORD')
+
+
+ instance-attribute
+
+
+token = token or os.environ.get('CELLENGINE_AUTH_TOKEN')
+
+
+ instance-attribute
+
+
+user_id = None
+
+
+ instance-attribute
+
+
+username = username or os.environ.get('CELLENGINE_USERNAME')
+
+
+ instance-attribute
+
+
+apply_tailoring(experiment_id, gate, fcs_file_ids)
+
+Tailor a gate to a file or files.
+ + +clone_experiment(_id, props={})
+
+create_fcs_file(experiment_id, body)
+
+Creates an FCS file by copying, concatenating and/or +subsampling existing file(s) from this or other experiments. Can be +used to import files from other experiments.
+ + +delete_all_gates_and_populations(experiment_id)
+
+delete_attachment(experiment_id, _id=None, name=None)
+
+Delete an attachment
+ + +delete_entity(experiment_id, entity_type, _id)
+
+delete_experiment(_id)
+
+Marks the experiment as deleted.
+Deleted experiments are permanently deleted after approximately +7 days. Until then, deleted experiments can be recovered.
+ + +delete_folder(_id)
+
+Marks the folder as deleted.
+Deleted folders are permanently deleted after approximately +7 days. Until then, deleted folders can be recovered.
+ + +delete_gate(experiment_id, _id=None, gid=None, exclude=None)
+
+Deletes a gate or a tailored gate family.
+Specify the top-level gid when working with compound gates (specifying
+the gid of a sector (i.e. one listed in model.gids) will result in no
+gates being deleted). If _id is specified, only that gate will be
+deleted, regardless of the other parameters specified. May be called as
+a static method from cellengine.Gate or from an Experiment instance.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ experiment_id
+ |
+
+ str
+ |
+
+
+
+ ID of experiment. + |
+ + required + | +
+ _id
+ |
+
+ Optional[str]
+ |
+
+
+
+ ID of the gate to delete. + |
+
+ None
+ |
+
+ gid
+ |
+
+ Optional[str]
+ |
+
+
+
+ ID of gate family to delete. + |
+
+ None
+ |
+
+ exclude
+ |
+
+ Optional[str]
+ |
+
+
+
+ Gate ID to exclude from deletion. Deprecated. Use the + untailoring API instead. + |
+
+ None
+ |
+
cellengine.Gate.delete_gate(experiment_id, gid = [gate family ID])
+# or
+experiment.delete_gate(_id = [gate ID])
+Returns:
+| Type | +Description | +
|---|---|
+ None
+ |
+
+
+
+ None + |
+
delete_gates(experiment_id, ids)
+
+download_attachment(experiment_id, _id=None, name=None)
+
+Download an attachment
+ + +download_fcs_file(experiment_id, fcs_file_id, **kwargs)
+
+Download events for a specific FcsFile
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ experiment_id
+ |
+
+ str
+ |
+
+
+
+ ID of the experiment + |
+ + required + | +
+ fcs_file_id
+ |
+
+ str
+ |
+
+
+
+ ID of the FcsFile + |
+ + required + | +
+ **kwargs
+ |
+
+ Any
+ |
+
+
+
+
|
+
+ {}
+ |
+
get_attachment(experiment_id, _id=None, name=None)
+
+get_attachments(experiment_id)
+
+get_compensation(experiment_id, _id=None, name=None)
+
+get_compensations(experiment_id, as_dict=False)
+
+get_experiment(_id=None, name=None)
+
+get_experiments()
+
+get_fcs_file(experiment_id, _id=None, name=None)
+
+get_fcs_files(experiment_id, as_dict=False)
+
+get_folder(_id=None, name=None)
+
+get_folders()
+
+get_gate(experiment_id, _id, as_dict=False)
+
+Gates cannot be retrieved by name because all gates in a group of
+tailored gates have the same name, and because compound gates have a
+names property instead of a name property.
get_gates(experiment_id, as_dict=False)
+
+get_plot(experiment_id, fcs_file_id, plot_type, x_channel, y_channel, z_channel=None, population_id=None, compensation=0, properties=None, raw=False)
+
+get_population(experiment_id, _id=None, name=None)
+
+get_populations(experiment_id)
+
+get_scaleset(experiment_id)
+
+Get the scaleset for an experiment.
+ + +get_statistics(experiment_id, statistics, channels, q=None, annotations=False, compensation_id=UNCOMPENSATED, fcs_file_ids=None, format='json', layout=None, percent_of='PARENT', population_ids=None)
+
+Request Statistics from CellEngine.
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ experiment_id
+ |
+
+ str
+ |
+
+
+
+ ID of the experiment. + |
+ + required + | +
+ statistics
+ |
+
+ List[str]
+ |
+
+
+
+ Statistics to calculate. Any of "mean", "median", +"quantile", "mad" (median absolute deviation), "geometricmean", +"eventcount", "cv", "stddev" or "percent" (case-insensitive). + |
+ + required + | +
+ q
+ |
+
+ int
+ |
+
+
+
+ quantile (required for "quantile" statistic) + |
+
+ None
+ |
+
+ channels
+ |
+
+ List[str]
+ |
+
+
+
+ for "mean", "median", "geometricMean", +"cv", "stddev", "mad" or "quantile" statistics. Names of channels +to calculate statistics for. + |
+ + required + | +
+ annotations
+ |
+
+ bool
+ |
+
+
+
+ Include file annotations in output +(defaults to False). + |
+
+ False
+ |
+
+ compensation_id
+ |
+
+ Union[Compensations, str]
+ |
+
+
+
+ Compensation to use for gating and statistics
+calculation. Defaults to uncompensated. In addition to a
+compensation ID, three special constants may be used:
+ |
+
+ UNCOMPENSATED
+ |
+
+ fcs_file_ids
+ |
+
+ Optional[List[str]]
+ |
+
+
+
+ FCS files to get statistics for. If +omitted, statistics for all non-control FCS files will be returned. + |
+
+ None
+ |
+
+ format
+ |
+
+ str
+ |
+
+
+
+ str: One of "TSV (with[out] header)", +"CSV (with[out] header)" or "json" (default), "pandas", +case-insensitive. + |
+
+ 'json'
+ |
+
+ layout
+ |
+
+ Optional[str]
+ |
+
+
+
+ str: The file (TSV/CSV) or object (JSON) layout. +One of "tall-skinny", "medium", or "short-wide". + |
+
+ None
+ |
+
+ percent_of
+ |
+
+ Optional[Union[str, List[str]]]
+ |
+
+
+
+ str or List[str]: Population ID or array of +population IDs. If omitted or the string "PARENT", will calculate +percent of parent for each population. If a single ID, will calculate +percent of that population for all populations specified by +population_ids. If a list, will calculate percent of each of +those populations. + |
+
+ 'PARENT'
+ |
+
+ population_ids
+ |
+
+ Optional[List[str]]
+ |
+
+
+
+ List[str]: List of population IDs. +Defaults to ungated. + |
+
+ None
+ |
+
Returns:
+| Name | Type | +Description | +
|---|---|---|
statistics |
+ Union[Dict, str, DataFrame]
+ |
+
+
+
+ Dict, String, or pandas.Dataframe + |
+
import_experiment_resources(experiment_id, src_experiment_id, what, channel_map, dst_population_id)
+
+post_compensation(experiment_id, body)
+
+post_experiment(experiment)
+
+Create a new experiment on CellEngine.
+ + +post_folder(folder)
+
+Create a new folder on CellEngine.
+ + +post_gate(experiment_id, body, params={})
+
+post_gates(experiment_id, body, params={})
+
+post_population(experiment_id, population)
+
+save_experiment_revision(_id, description)
+
+update_entity(experiment_id, _id, entity_type, body)
+
+update_experiment(_id, body)
+
+update_folder(_id, body)
+
+update_gate_family(experiment_id, gid, body={})
+
+upload_attachment(experiment_id, filepath, filename=None)
+
+Upload an attachment
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ filepath
+ |
+
+ str
+ |
+
+
+
+ Local path to file to upload. + |
+ + required + | +
+ filename
+ |
+
+ str
+ |
+
+
+
+ Optionally, specify a new name for the file. + |
+
+ None
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Attachment
+ |
+
+
+
+ The newly uploaded Attachment. + |
+
upload_fcs_file(experiment_id, filepath_or_data, filename=None)
+
+Upload an FCS file to CellEngine
+ + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
+ filepath_or_data
+ |
+
+ Union[str, BytesIO]
+ |
+
+
+
+ Local path to FCS file. + |
+ + required + | +
+ filename
+ |
+
+ Optional[str]
+ |
+
+
+
+ Optionally, specify a new name for the file. + |
+
+ None
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ FcsFile
+ |
+
+
+
+ The newly-uploaded FcsFile + |
+
\n {translation(\"search.result.term.missing\")}: {...missing}\n
\n }\n \n