nlp-cli
This is the NLP sandbox command line client.
nlp-cli community
Commands for NLP Sandbox users.
nlp-cli community [OPTIONS] COMMAND [ARGS]...
Options
-
-c<synapse_config> Synapse configuration file
- Default
/github/home/.synapseConfig
nlp-cli datanode
Commands to interact with NLP Data Node.
nlp-cli datanode [OPTIONS] COMMAND [ARGS]...
delete-dataset
Delete a dataset in the data node
nlp-cli datanode delete-dataset [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Required Dataset id
get-annotation
Get annotation for a NLP data node dataset.
nlp-cli datanode get-annotation [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Required Dataset Id
-
--annotation_store_id<annotation_store_id> Required Dataset Id
-
--annotation_id<annotation_id> Required Annotation Id
-
--output<output> Output json filepath
get-annotation-store
Create annotation store for a NLP data node dataset.
nlp-cli datanode get-annotation-store [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Required Dataset id
-
--annotation_store_id<annotation_store_id> Required Dataset id
-
--create_if_missing Create resource if missing
list-annotations
List annotations of a NLP data node annotation store.
nlp-cli datanode list-annotations [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Required Dataset id
-
--annotation_store_id<annotation_store_id> Required Dataset id
-
--output<output> Output json filepath
list-datasets
List annotations of a NLP data node annotation store.
nlp-cli datanode list-datasets [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--output<output> Output json filepath
list-notes
Gets clinical notes of a NLP data node FHIR store.
nlp-cli datanode list-notes [OPTIONS]
Options
-
--output<output> Output json filepath
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Required Dataset id
-
--fhir_store_id<fhir_store_id> Required Dataset id
store-annotations
Store annotations in an NLP data node annotation store. The annotation store is deleted if it already exists. Sets the annotation_id as the note id.
nlp-cli datanode store-annotations [OPTIONS]
Options
-
--data_node_host<data_node_host> Data node host
- Default
-
--dataset_id<dataset_id> Dataset id
-
--annotation_store_id<annotation_store_id> Required Annotation store id
-
--annotation_json<annotation_json> Required Json file with annotations to store
nlp-cli tool
Commands to interact with NLP Tools.
nlp-cli tool [OPTIONS] COMMAND [ARGS]...
annotate-note
Annotate a note with specified annotator
nlp-cli tool annotate-note [OPTIONS]
Options
-
--annotator_host<annotator_host> Required Annotator host.
-
--note_json<note_json> Required Clinical notes json
-
--output<output> Specify output json path
-
--tool_type<tool_type> Required The type of tool.
- Options
nlpsandbox:date-annotator | nlpsandbox:person-name-annotator | nlpsandbox:location-annotator | nlpsandbox:contact-annotator | nlpsandbox:id-annotator | nlpsandbox:covid-symptom-annotator