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cms

CLI for various CogStack ModelServe operations

Usage:

$ cms [OPTIONS] COMMAND [ARGS]...

Options:

  • --model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]
  • --host TEXT
  • --port TEXT
  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

Commands:

  • serve: This serves various CogStack NLP models
  • train: This pretrains or fine-tunes various...
  • register: This pushes a pretrained NLP model to the...
  • export-model-apis: This generates a model-specific API...
  • build: This builds an OCI-compliant image to...
  • export-openapi-spec: This generates an API document for all...
  • stream: This groups various stream operations
  • package: This groups various package operations
  • mcp: Run the MCP server for accessing CMS...

cms serve

This serves various CogStack NLP models

Usage:

$ cms serve [OPTIONS]

Options:

  • --model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]: The type of the model to serve [required]
  • --model-path TEXT: Either the file path to the local model package or the URL to the remote one
  • --mlflow-model-uri models:/MODEL_NAME/ENV: The URI of the MLflow model to serve
  • --host TEXT: The hostname of the server [default: 127.0.0.1]
  • --port TEXT: The port of the server [default: 8000]
  • --model-name TEXT: The string representation of the model name
  • --streamable / --no-streamable: Serve the streamable endpoints only [default: no-streamable]
  • --device [default|cpu|cuda|mps]: The device to serve the model on [default: default]
  • --llm-engine [CMS|vLLM]: The engine to use for text generation [default: CMS]
  • --load-in-4bit / --no-load-in-4bit: Load the model in 4-bit precision, used by 'huggingface_llm' models [default: no-load-in-4bit]
  • --load-in-8bit / --no-load-in-8bit: Load the model in 8-bit precision, used by 'huggingface_llm' models [default: no-load-in-8bit]
  • --debug / --no-debug: Run in the debug mode
  • --help: Show this message and exit.

cms train

This pretrains or fine-tunes various CogStack NLP models

Usage:

$ cms train [OPTIONS]

Options:

  • --model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]: The type of the model to train [required]
  • --base-model-path TEXT: The file path to the base model package to be trained on
  • --mlflow-model-uri models:/MODEL_NAME/ENV: The URI of the MLflow model to train
  • --training-type [supervised|unsupervised|meta_supervised]: The type of training [required]
  • --data-file-path TEXT: The path to the training asset file [required]
  • --epochs INTEGER: The number of training epochs [default: 1]
  • --log-frequency INTEGER: The number of processed documents or epochs after which training metrics will be logged [default: 1]
  • --hyperparameters TEXT: The overriding hyperparameters serialised as JSON string [default: {}]
  • --description TEXT: The description of the training or change logs
  • --model-name TEXT: The string representation of the model name
  • --device [default|cpu|cuda|mps]: The device to train the model on [default: default]
  • --load-in-4bit / --no-load-in-4bit: Load the model in 4-bit precision, used by 'huggingface_llm' models [default: no-load-in-4bit]
  • --load-in-8bit / --no-load-in-8bit: Load the model in 8-bit precision, used by 'huggingface_llm' models [default: no-load-in-8bit]
  • --debug / --no-debug: Run in the debug mode
  • --help: Show this message and exit.

cms register

This pushes a pretrained NLP model to the CogStack ModelServe registry

Usage:

$ cms register [OPTIONS]

Options:

  • --model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]: The type of the model to register [required]
  • --model-path TEXT: The file path to the model package [required]
  • --model-name TEXT: The string representation of the registered model [required]
  • --training-type [supervised|unsupervised|meta_supervised]: The type of training the model went through
  • --model-config TEXT: The string representation of a JSON object
  • --model-metrics TEXT: The string representation of a JSON array
  • --model-tags TEXT: The string representation of a JSON object
  • --debug / --no-debug: Run in the debug mode
  • --help: Show this message and exit.

cms export-model-apis

This generates a model-specific API document for enabled endpoints

Usage:

$ cms export-model-apis [OPTIONS]

Options:

  • --model-type [medcat_snomed|medcat_umls|medcat_icd10|medcat_opcs4|medcat_deid|anoncat|transformers_deid|huggingface_ner|huggingface_llm]: The type of the model to serve [required]
  • --add-training-apis / --no-add-training-apis: Add training APIs to the doc [default: no-add-training-apis]
  • --add-evaluation-apis / --no-add-evaluation-apis: Add evaluation APIs to the doc [default: no-add-evaluation-apis]
  • --add-previews-apis / --no-add-previews-apis: Add preview APIs to the doc [default: no-add-previews-apis]
  • --add-user-authentication / --no-add-user-authentication: Add user authentication APIs to the doc [default: no-add-user-authentication]
  • --exclude-unsupervised-training / --no-exclude-unsupervised-training: Exclude the unsupervised training API [default: no-exclude-unsupervised-training]
  • --exclude-metacat-training / --no-exclude-metacat-training: Exclude the metacat training API [default: no-exclude-metacat-training]
  • --model-name TEXT: The string representation of the model name
  • --help: Show this message and exit.

cms build

This builds an OCI-compliant image to containerise CMS

Usage:

$ cms build [OPTIONS]

Options:

  • --dockerfile-path TEXT: The path to the Dockerfile [required]
  • --context-dir TEXT: The directory containing the set of files accessible to the build [required]
  • --model-name TEXT: The string representation of the model name [default: CMS model]
  • --user-id INTEGER: The ID for the non-root user [default: 1000]
  • --group-id INTEGER: The group ID for the non-root user [default: 1000]
  • --http-proxy TEXT: The string representation of the HTTP proxy
  • --https-proxy TEXT: The string representation of the HTTPS proxy
  • --no-proxy TEXT: The string representation of addresses by-passing proxies [default: localhost,127.0.0.1]
  • --version-tag TEXT: The version tag of the built image [default: latest]
  • --backend [docker build|docker buildx build]: The backend used for building the image [default: docker build]
  • --help: Show this message and exit.

cms export-openapi-spec

This generates an API document for all endpoints defined in CMS

Usage:

$ cms export-openapi-spec [OPTIONS]

Options:

  • --api-title TEXT: The string representation of the API title [default: CogStack Model Serve APIs]
  • --help: Show this message and exit.

cms stream

This groups various stream operations

Usage:

$ cms stream [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • json-lines: This gets NER entities as a JSON Lines stream
  • chat: This gets NER entities by chatting with...

cms stream json-lines

This gets NER entities as a JSON Lines stream

Usage:

$ cms stream json-lines [OPTIONS]

Options:

  • --jsonl-file-path TEXT: The path to the JSON Lines file [required]
  • --base-url TEXT: The CMS base url [default: http://127.0.0.1:8000]
  • --timeout-in-secs INTEGER: The max time to wait before disconnection [default: 0]
  • --debug / --no-debug: Run in the debug mode
  • --help: Show this message and exit.

cms stream chat

This gets NER entities by chatting with the model

Usage:

$ cms stream chat [OPTIONS]

Options:

  • --base-url TEXT: The CMS base url [default: ws://127.0.0.1:8000]
  • --debug / --no-debug: Run in the debug mode
  • --help: Show this message and exit.

cms package

This groups various package operations

Usage:

$ cms package [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • hf-model: This packages a remotely hosted or locally...
  • hf-dataset: This packages a remotely hosted or locally...

cms package hf-model

This packages a remotely hosted or locally cached Hugging Face model into a model package

Usage:

$ cms package hf-model [OPTIONS]

Options:

  • --hf-repo-id TEXT: The repository ID of the model to download from Hugging Face Hub, e.g., 'google-bert/bert-base-cased'
  • --hf-repo-revision TEXT: The revision of the model to download from Hugging Face Hub
  • --cached-model-dir TEXT: The path to the cached model directory, will only be used if --hf-repo-id is not provided
  • --output-model-package TEXT: The path where the model package will be saved, minus any format-specific extension, e.g., './model_packages/bert-base-cased'
  • --archive-format [zip|gztar]: The archive format of the model package, e.g., 'zip' or 'gztar' [default: zip]
  • --remove-cached / --no-remove-cached: Whether to remove the downloaded cache after the model package is saved [default: no-remove-cached]
  • --help: Show this message and exit.

cms package hf-dataset

This packages a remotely hosted or locally cached Hugging Face dataset into a dataset package

Usage:

$ cms package hf-dataset [OPTIONS]

Options:

  • --hf-dataset-id TEXT: The repository ID of the dataset to download from Hugging Face Hub, e.g., 'stanfordnlp/imdb'
  • --hf-dataset-revision TEXT: The revision of the dataset to download from Hugging Face Hub
  • --cached-dataset-dir TEXT: The path to the cached dataset directory, will only be used if --hf-dataset-id is not provided
  • --output-dataset-package TEXT: The path where the dataset package will be saved, minus any format-specific extension, e.g., './dataset_packages/imdb'
  • --archive-format [zip|gztar]: The archive format of the dataset package, e.g., 'zip' or 'gztar' [default: zip]
  • --remove-cached / --no-remove-cached: Whether to remove the downloaded cache after the dataset package is saved [default: no-remove-cached]
  • --trust-remote-code / --no-trust-remote-code: Whether to trust and use the remote script of the dataset [default: no-trust-remote-code]
  • --help: Show this message and exit.

cms mcp

Run the MCP server for accessing CMS capabilities

Usage:

$ cms mcp [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • run: Run the MCP server for accessing CMS...

cms mcp run

Run the MCP server for accessing CMS capabilities

Usage:

$ cms mcp run [OPTIONS]

Options:

  • --host TEXT: The hostname of the MCP server [default: 127.0.0.1]
  • --port INTEGER: The port of the MCP server [default: 8080]
  • --transport TEXT: The transport type (either 'stdio', 'sse' or 'http') [default: http]
  • --cms-base-url TEXT: The base URL of the CMS API [default: http://localhost:8000]
  • --cms-api-key TEXT: The API key for authenticating with the CMS API
  • --mcp-api-keys TEXT: Comma-separated API keys for authenticating MCP clients
  • --cms-mcp-oauth-enabled / --no-cms-mcp-oauth-enabled: Whether to enable OAuth2 authentication for MCP clients
  • --github-client-id TEXT: The GitHub OAuth2 client ID
  • --github-client-secret TEXT: The GitHub OAuth2 client secret
  • --google-client-id TEXT: The Google OAuth2 client ID
  • --google-client-secret TEXT: The Google OAuth2 client secret
  • --debug / --no-debug: Run in debug mode
  • --help: Show this message and exit.