diff --git a/medcat-service/README.md b/medcat-service/README.md index 791d58ae3..149ee34c4 100644 --- a/medcat-service/README.md +++ b/medcat-service/README.md @@ -1,18 +1,10 @@ # MedCAT Service -A REST API wrapper for [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/), allowing you to send text for processing and receive structured annotations in response. +Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/) models, allowing you to send text for processing and receive structured annotations in response. -Feel free to ask questions on the github issue tracker or on our [discourse website](https://discourse.cogstack.org) which is frequently used by our development team! +See the documentation on https://docs.cogstack.org/ for the docs on medcat service. -## API specification - -The API definition follows the one defined in [CogStack GATE NLP Service](https://github.com/CogStack/gate-nlp-service/). Currently, there are 3 endpoints defined, that consume and return data in JSON format: - -- *GET* `/api/info` - displays general information about the MedCAT application, -- *POST* `/api/process` - processes the provided documents and returns back the annotations, -- *POST* `/api/process_bulk` - processes the provided list of documents and returns back the annotations. - -The full specification is available is [OpenAPI](https://github.com/CogStack/gate-nlp-service/tree/devel/api-specs) specification. +This README file contains information for local usage and devloper guides. ## Running the application @@ -77,222 +69,8 @@ Or, if you wish to use the above mentioned script ( the sample model is download DONE! ``` -## API Example use - -Assuming that the application is running on the `localhost` with the API exposed on port `5000`, one can run: - -```bash -curl -XPOST http://localhost:5000/api/process \ - -H 'Content-Type: application/json' \ - -d '{"content":{"text":"The patient was diagnosed with leukemia."}}' -``` - -and the received result: - -```json -{ - "result": {"text": "The patient was diagnosed with leukemia.", - - "annotations": {"entities": {"0": {"pretty_name": "Patients", "cui": "C0030705", "type_ids": ["T101"], "types": ["Patient or Disabled Group"], "source_value": "patient", "detected_name": "patient", "acc": 0.99, "context_similarity": 0.99, "start": 4, "end": 11, "icd10": [], "ontologies": [], "snomed": [], "id": 0, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999303817749023, "name": "Status"}}}, "1": {"pretty_name": "Diagnosis", "cui": "C0011900", "type_ids": ["T060"], "types": ["Diagnostic Procedure"], "source_value": "diagnosed", "detected_name": "diagnosed", "acc": 0.6657139492748229, "context_similarity": 0.6657139492748229, "start": 16, "end": 25, "icd10": [], "ontologies": [], "snomed": [], "id": 1, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999918341636658, "name": "Status"}}}, "2": {"pretty_name": "leukemia", "cui": "C0023418", "type_ids": ["T191"], "types": ["Neoplastic Process"], "source_value": "leukemia", "detected_name": "leukemia", "acc": 0.2572544372951888, "context_similarity": 0.2572544372951888, "start": 31, "end": 39, "icd10": [], "ontologies": [], "snomed": [], "id": 2, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999804496765137, "name": "Status"}}}}, "tokens": []}, - - "success": true, - "timestamp": "2021-11-11T11:54:28.856+00:00" - }, - "medcat_info": {"service_app_name": "MedCAT", "service_language": "en", "service_version": "1.2.5", "service_model": "MedMen"} -} -``` - -Additional DE-ID query sample (make sure you have a de-id model loaded): - -```bash -curl -XPOST \ - -H 'Content-Type: application/json' \ - -d '{"content":{"text":"Patient Information: Full Name: John Michael Doe \n Gender: Male \n Date of Birth: January 15, 1975 (Age: 49) \n Patient ID: 567890123 \n Address: 1234 Elm Street, Springfield, IL 62701 \n Phone Number: (555) 123-4567 \n Email: \n Emergency Contact: Jane Doe (Wife) \n Phone: (555) 987-6543 \n Relationship: Spouse"}}' -``` - -Make sure you have the following option enabled in `envs/(medcat|medcat_deid).env` , `DEID_MODE=True`. - -process_bulk example : - -```bash -curl -XPOST http://localhost:5000/api/process_bulk \ - -H 'Content-Type: application/json' \ - -d '{"content": [{"text":"The patient was diagnosed with leukemia."}, {"text": "The patient was diagnosed with cancer."}] }' -``` - -example bulk result : - -```json -{ - "result": [ - { - "text": "The patient was diagnosed with leukemia.", - "annotations": { - "0": { - "pretty_name": "Patients", - "cui": "C0030705", - "type_ids": [ - "T101" - ], - "types": [ - "Patient or Disabled Group" - ], - "source_value": "patient", - "detected_name": "patient", - "acc": 0.99, - "context_similarity": 0.99, - "start": 4, - "end": 11, - "id": 0, - "meta_anns": { - "Status": { - "value": "Affirmed", - "confidence": 0.9999303817749023, - "name": "Status" - } - } - }, - "1": { - "pretty_name": "Diagnosis", - "cui": "C0011900", - "type_ids": [ - "T060" - ], - "types": [ - "Diagnostic Procedure" - ], - "source_value": "diagnosed", - "detected_name": "diagnosed", - "acc": 0.6657139492748229, - "context_similarity": 0.6657139492748229, - "start": 16, - "end": 25, - "id": 1, - "meta_anns": { - "Status": { - "value": "Affirmed", - "confidence": 0.9999918341636658, - "name": "Status" - } - } - }, - "2": { - "pretty_name": "leukemia", - "cui": "C0023418", - "type_ids": [ - "T191" - ], - "types": [ - "Neoplastic Process" - ], - "source_value": "leukemia", - "detected_name": "leukemia", - "acc": 0.2572544372951888, - "context_similarity": 0.2572544372951888, - "start": 31, - "end": 39, - "id": 2, - "meta_anns": { - "Status": { - "value": "Affirmed", - "confidence": 0.9999804496765137, - "name": "Status" - } - } - } - }, - "success": true, - "timestamp": "2021-12-08T18:49:55.255+00:00" - }, - { - "text": "The patient was diagnosed with cancer.", - "annotations": { - "0": { - "pretty_name": "Patients", - "cui": "C0030705", - "type_ids": [ - "T101" - ], - "types": [ - "Patient or Disabled Group" - ], - "source_value": "patient", - "detected_name": "patient", - "acc": 0.99, - "context_similarity": 0.99, - "start": 4, - "end": 11, - "id": 0, - "meta_anns": { - "Status": { - "value": "Affirmed", - "confidence": 0.9999236464500427, - "name": "Status" - } - } - }, - "2": { - "pretty_name": "cancer diagnosis", - "cui": "C0920688", - "type_ids": [ - "T060" - ], - "types": [ - "Diagnostic Procedure" - ], - "source_value": "diagnosed with cancer", - "detected_name": "diagnosed~with~cancer", - "acc": 1, - "context_similarity": 1, - "start": 16, - "end": 37, - "id": 2, - "meta_anns": { - "Status": { - "value": "Affirmed", - "confidence": 0.9999957084655762, - "name": "Status" - } - } - } - }, - "success": true, - "timestamp": "2021-12-08T18:49:55.255+00:00" - } - ], - "medcat_info": { - "service_app_name": "MedCAT", - "service_language": "en", - "service_version": "1.2.6", - "service_model": "MedMen" - } -} - -``` - -IMPORTANT info regarding annotation output style -As the changes from MedCAT intoduced dictionary annotation/entity output. - -The mode in which annotation entities should be outputted in the JSON response, - by default this was outputted as a "list" of dicts in older versions, so the output would be : - - ```json - {"annotations": [{"id": "0", "cui" : "C1X..", ..}, {"id":"1", "cui": "...."}]} - ``` - - newer versions of MedCAT (1.2+) output entities as a dict, where the id of the entity is a key and the rest of the data is a value, so for "dict", - the output is - - ```json - {"annotations": [{"0": {"cui": "C0027361", "id": 0,.....}, "1": {"cui": "C001111", "id": 1......}}]} - ``` -This setting can be configured in the ```./env/medcat.env``` file, using the ```MEDCAT_ANNOTATIONS_ENTITY_OUTPUT_MODE``` variable. -By default, the output of these entities is set to respect the output of the MedCAT package, hence the latter will be used. Please change the above mentioned env variable and make sure your CogStack-Nifi annotation script is adapted accordingly. - -Please note that the returned NLP annotations will depend on the underlying model used. For evaluation, we can only provide a very basic model trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions). Models utilising [SNOMED CT](https://www.england.nhs.uk/digitaltechnology/digital-primary-care/snomed-ct/) or [UMLS](https://www.nlm.nih.gov/research/umls/index.html) may require applying for licenses from the copyright holders. - -## Configuration +## Local Env Configuration In the current implementation, configuration for both MedCAT Service application and MedCAT NLP library is based on environment variables. These will be provided usually in the files in the `env` directory: @@ -302,96 +80,6 @@ In the current implementation, configuration for both MedCAT Service application Both files allow tailoring MedCAT for specific use-cases. When running MedCAT Service, these variables need to be loaded into the current working environment. -## spaCy models - -When using MedCAT for a different language than English, it can be useful to use a different spaCy model. A spaCy model can be included in the MedCAT model pack, but when not using this functionality, it can be useful to install models in the Docker image. This can be done by setting a build-time variable. See the `SPACY_MODELS` variable in [Dockerfile](Dockerfile) for default value and usage. - -## Service Environment vars - -MedCAT Service application are defined in `envs/(app|app_deid).env` file. - -The following environment variables are available for tailoring the MedCAT Service `gunicorn` server: - -- `SERVER_HOST` - specifies the host address (default: `0.0.0.0`), -- `SERVER_PORT` - the port number used (default: `5000`), -- `SERVER_WORKERS` - the number of workers serving the Flask app working in parallel (default: `1` ; only used in production server). -- `SERVER_WORKER_TIMEOUT` - the max timeout (in sec) for receiving response from worker (default: `300` ; only used with production server). -- `SERVER_GUNICORN_MAX_REQUESTS` - maximum number of requests a worker will process before restarting (default: `1000`), -- `SERVER_GUNICORN_MAX_REQUESTS_JITTER` - adds randomness to `MAX_REQUESTS` to avoid all workers restarting simultaneously (default: `50`), -- `SERVER_GUNICORN_EXTRA_ARGS` - any additional Gunicorn CLI arguments you want to pass (default: none). (Example value: "SERVER_GUNICORN_EXTRA_ARGS=--backlog 20") - -The following environment variables are available for tailoring the MedCAT Service wrapper: - -- `APP_MODEL_NAME` - an informative name of the model used by MedCAT (optional), -- `APP_MODEL_CDB_PATH` - the path to the model's concept database, -- `APP_MODEL_VOCAB_PATH` - the path to the model's vocabulary, -- `APP_MODEL_META_PATH_LIST` - the list of paths to meta-annotation models, each separated by `:` character (optional), -- `APP_BULK_NPROC` - the number of threads used in bulk processing (default: `8`), -- `APP_MEDCAT_MODEL_PACK` - MedCAT Model Pack path, if this parameter has a value IT WILL BE LOADED FIRST OVER EVERYTHING ELSE (CDB, Vocab, MetaCATs, etc.) declared above. -- `APP_ENABLE_METRICS` - Enable prometheus metrics collection served on the path /metrics -- `APP_ENABLE_DEMO_UI` - Enable the demo user interface to try models. (Default: `False`) -- `APP_DEMO_UI_PATH` - Customise the path of the demo UI. (Default: `/`) - -### Shared Memory (`DOCKER_SHM_SIZE`) - -The MedCAT service uses PyTorch multiprocessing and memory-mapped models, which rely on Linux shared memory (`/dev/shm`). -By default, Docker limits this to **64 MB**, which is insufficient for NLP models. - -Use the environment variable `DOCKER_SHM_SIZE` to control the size of shared memory inside the container. -You can set this variable in the `env/general.env` file. - -- **Recommended**: `8g` for bulk inference (`APP_BULK_NPROC > 1`) -- **Minimum**: `1g` for single-process inference (`APP_BULK_NPROC=1`) - -Example: - -```env -DOCKER_SHM_SIZE=8g -``` - -### Telemetry -MedCAT Service supports exporting traces using Opentelemetry -To enable distributed tracing and telemetry in the MedCAT Service, several environment variables must be set. These can be configured in your environment files or exported in your startup scripts (see `start_service_debug.sh` and related files): - -| Environment Variable | Description | Example Value | -|--------------------------------------------|---------------------------------------------------------------------------------------------------|---------------------------------------| -| `APP_ENABLE_TRACING` | Enable OpenTelemetry tracing in the application. | `True` | -| `OTEL_TRACES_EXPORTER` | Exporter to use for traces (commonly `otlp`). | `otlp` | -| `OTEL_SERVICE_NAME` | Logical service name for your traces. | `medcat-service` | -| `OTEL_EXPORTER_OTLP_ENDPOINT` | URL for your OpenTelemetry collector. | `http://localhost:4317` | -| `OTEL_EXPORTER_OTLP_PROTOCOL` | Protocol to use for OTLP exporter. | `grpc` | -| `OTEL_METRICS_EXPORTER` | Set to `none` to disable metrics export, or another value if metrics are enabled. | `none` | -| `OTEL_PYTHON_FASTAPI_EXCLUDED_URLS` | Comma-separated list of URLs to exclude from tracing and metrics (e.g., health/metrics endpoints).| `/api/health,/metrics` | -| `OTEL_EXPERIMENTAL_RESOURCE_DETECTORS` | Additional resource detectors to use (comma-separated). | `containerid,os` | - -**Example:** - -Add these lines to your `env/app.env` or export them before starting the service: - -```env -APP_ENABLE_TRACING=True -OTEL_EXPORTER_OTLP_ENDPOINT="http://localhost:4317" -OTEL_TRACES_EXPORTER=otlp -OTEL_SERVICE_NAME=medcat-service -OTEL_EXPORTER_OTLP_PROTOCOL="grpc" -OTEL_METRICS_EXPORTER=none -OTEL_PYTHON_FASTAPI_EXCLUDED_URLS="/api/health,/metrics" -OTEL_EXPERIMENTAL_RESOURCE_DETECTORS="containerid,os" -``` - -See https://opentelemetry-python.readthedocs.io/en/latest/sdk/environment_variables.html for the full list of opentelemetry environment variables. - -## Performance Tuning - -Theres a range of factors that might impact the performance of this service, the most obvious being the size of the processed documents (amount of text per document) as well as the resources of the machine on which the service operates. -The main settings that can be used to improve the performance when querying large amounts of documents are : `SERVER_WORKERS` (number of flask web workers that chan handle parallel requests) and `APP_BULK_NPROC` (threads for annotation processing). - -## MedCAT library - -MedCAT parameters are defined in selected `envs/medcat*` file. - -For details on available MedCAT parameters please refer to [the official GitHub repository](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/). - ## Local development For local development, set up a Python virtual environment, install dependencies with pip, and make sure to also install the local MedCAT core library (the `medcat-v2` folder) in editable mode. diff --git a/medcat-service/docs/assets/demo-anoncat.png b/medcat-service/docs/assets/demo-anoncat.png new file mode 100644 index 000000000..568427679 Binary files /dev/null and b/medcat-service/docs/assets/demo-anoncat.png differ diff --git a/medcat-service/docs/assets/demo-api.webm b/medcat-service/docs/assets/demo-api.webm new file mode 100644 index 000000000..df02bacaa Binary files /dev/null and b/medcat-service/docs/assets/demo-api.webm differ diff --git a/medcat-service/docs/assets/demo-medcat.png b/medcat-service/docs/assets/demo-medcat.png new file mode 100644 index 000000000..b7fac7ecc Binary files /dev/null and b/medcat-service/docs/assets/demo-medcat.png differ diff --git a/medcat-service/docs/index.md b/medcat-service/docs/index.md new file mode 100644 index 000000000..3df08afb1 --- /dev/null +++ b/medcat-service/docs/index.md @@ -0,0 +1,40 @@ +# Medcat service documentation + +Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/) models, allowing you to perform named entity resolution and deidentification of medical text over an API. + +Feel free to ask questions on the github issue tracker or on our [discourse website](https://discourse.cogstack.org) which is frequently used by our development team! + +## Demo + + +## Features + +### Clinical NLP over HTTP + +- **Single-document processing** — `POST /api/process` accepts free-text clinical notes and returns entities with CUIs, types, spans, and meta-annotations (for example negation and subject). +- **Bulk processing** — `POST /api/process_bulk` processes many documents in one request, with parallel annotation via configurable worker threads (`APP_BULK_NPROC`). +- **Meta-annotation filtering** — Optional `meta_anns_filters` on `/api/process` let you return only entities that match selected meta-annotation values (for example affirmed presence or patient subject). +- **AnonCAT De-identification** - Detect and redact identifiable information in clinical text by loading an AnonCAT model. See [API examples](user-guide/api-example-use.md). + +### Demo UI + +- **Interactive model trial** — A user friendly UI to try out medcat models and see the results. See [Demo UI](user-guide/demo-ui.md). + +### Operations and observability + +- **Health endpoints** — Kubernetes-friendly liveness (`/api/health/live`) and readiness (`/api/health/ready`) checks that verify the model is loaded. +- **Service metadata** — `GET /api/info` returns application name, language, version, and loaded model details. +- **Metrics** — Optional prometheus metrics of the service on `/metrics` when `APP_ENABLE_METRICS=True`. +- **Tracing** — Distributed tracing export for production deployments. See [Configuration](setup/configuration.md#telemetry). + + +## Get started + +| Topic | Guide | +|-------|-------| +| Install with Helm or Docker Compose | [Installation](setup/installation.md) | +| Environment variables and tuning | [Configuration](setup/configuration.md) | +| `curl` examples for process and bulk APIs | [API example use](user-guide/api-example-use.md) | +| Try models in the browser | [Demo UI](user-guide/demo-ui.md) | diff --git a/medcat-service/docs/pyproject.toml b/medcat-service/docs/pyproject.toml new file mode 100644 index 000000000..3245ce467 --- /dev/null +++ b/medcat-service/docs/pyproject.toml @@ -0,0 +1,19 @@ +[project] +name = "medcat-trainer-documentation" +version = "0.1.0" +description = "MedCAT Service Documentation" +readme = "README.md" +requires-python = ">=3.10" +dependencies = [ + "mkdocs-material>=9.7.0", + "termynal>=0.13.1", +] + +[project.optional-dependencies] +dev = [ + "ruff>=0.12.11", +] + +[tool.ruff] +line-length = 120 + diff --git a/medcat-service/docs/reference/extensions.md b/medcat-service/docs/reference/extensions.md new file mode 100644 index 000000000..2fea1e8bb --- /dev/null +++ b/medcat-service/docs/reference/extensions.md @@ -0,0 +1,5 @@ +# Extending Medcat Service + +## spaCy models + +When using MedCAT for a different language than English, it can be useful to use a different spaCy model. A spaCy model can be included in the MedCAT model pack, but when not using this functionality, it can be useful to install models in the Docker image. This can be done by setting a build-time variable. See the `SPACY_MODELS` variable in [Dockerfile](https://github.com/CogStack/cogstack-nlp/blob/e5827a806c100abafb7c5a70f917d560fdfc374c/medcat-service/Dockerfile) for default value and usage. \ No newline at end of file diff --git a/medcat-service/docs/setup/configuration.md b/medcat-service/docs/setup/configuration.md new file mode 100644 index 000000000..6368c6ec5 --- /dev/null +++ b/medcat-service/docs/setup/configuration.md @@ -0,0 +1,75 @@ +# Configuration + +Medcat service can be configured with environment variables on startup. + +## Service Environment vars + + + +The following environment variables are available for tailoring the MedCAT Service `gunicorn` server: + +- `SERVER_HOST` - specifies the host address (default: `0.0.0.0`), +- `SERVER_PORT` - the port number used (default: `5000`), +- `SERVER_WORKERS` - the number of workers serving the Flask app working in parallel (default: `1` ; only used in production server). +- `SERVER_WORKER_TIMEOUT` - the max timeout (in sec) for receiving response from worker (default: `300` ; only used with production server). +- `SERVER_GUNICORN_MAX_REQUESTS` - maximum number of requests a worker will process before restarting (default: `1000`), +- `SERVER_GUNICORN_MAX_REQUESTS_JITTER` - adds randomness to `MAX_REQUESTS` to avoid all workers restarting simultaneously (default: `50`), +- `SERVER_GUNICORN_EXTRA_ARGS` - any additional Gunicorn CLI arguments you want to pass (default: none). (Example value: "SERVER_GUNICORN_EXTRA_ARGS=--backlog 20") + +The following environment variables are available for tailoring the MedCAT Service wrapper: + +- `APP_MODEL_NAME` - an informative name of the model used by MedCAT (optional), +- `APP_MODEL_CDB_PATH` - the path to the model's concept database, +- `APP_MODEL_VOCAB_PATH` - the path to the model's vocabulary, +- `APP_MODEL_META_PATH_LIST` - the list of paths to meta-annotation models, each separated by `:` character (optional), +- `APP_BULK_NPROC` - the number of threads used in bulk processing (default: `8`), +- `APP_MEDCAT_MODEL_PACK` - MedCAT Model Pack path, if this parameter has a value IT WILL BE LOADED FIRST OVER EVERYTHING ELSE (CDB, Vocab, MetaCATs, etc.) declared above. +- `APP_ENABLE_METRICS` - Enable prometheus metrics collection served on the path /metrics +- `APP_ENABLE_DEMO_UI` - Enable the demo user interface to try models. (Default: `False`) +- `APP_DEMO_UI_PATH` - Customise the path of the demo UI. (Default: `/`) + +### Shared Memory (`DOCKER_SHM_SIZE`) + +The MedCAT service uses PyTorch multiprocessing and memory-mapped models, which rely on Linux shared memory (`/dev/shm`). +By default, Docker limits this to **64 MB**, which is insufficient for NLP models. + +Use the environment variable `DOCKER_SHM_SIZE` to control the size of shared memory inside the container. +You can set this variable in the `env/general.env` file. + +- **Recommended**: `8g` for bulk inference (`APP_BULK_NPROC > 1`) +- **Minimum**: `1g` for single-process inference (`APP_BULK_NPROC=1`) + +Example: + +```env +DOCKER_SHM_SIZE=8g +``` + +### Telemetry +MedCAT Service supports exporting traces using Opentelemetry +To enable distributed tracing and telemetry in the MedCAT Service, several environment variables must be set. These can be configured in your environment files or exported in your startup scripts (see `start_service_debug.sh` and related files): + +| Environment Variable | Description | Example Value | +|--------------------------------------------|---------------------------------------------------------------------------------------------------|---------------------------------------| +| `APP_ENABLE_TRACING` | Enable OpenTelemetry tracing in the application. | `True` | +| `OTEL_TRACES_EXPORTER` | Exporter to use for traces (commonly `otlp`). | `otlp` | +| `OTEL_SERVICE_NAME` | Logical service name for your traces. | `medcat-service` | +| `OTEL_EXPORTER_OTLP_ENDPOINT` | URL for your OpenTelemetry collector. | `http://localhost:4317` | +| `OTEL_EXPORTER_OTLP_PROTOCOL` | Protocol to use for OTLP exporter. | `grpc` | +| `OTEL_METRICS_EXPORTER` | Set to `none` to disable metrics export, or another value if metrics are enabled. | `none` | +| `OTEL_PYTHON_FASTAPI_EXCLUDED_URLS` | Comma-separated list of URLs to exclude from tracing and metrics (e.g., health/metrics endpoints).| `/api/health,/metrics` | +| `OTEL_EXPERIMENTAL_RESOURCE_DETECTORS` | Additional resource detectors to use (comma-separated). | `containerid,os` | + + +See https://opentelemetry-python.readthedocs.io/en/latest/sdk/environment_variables.html for the full list of opentelemetry environment variables. + +## Performance Tuning + +Theres a range of factors that might impact the performance of this service, the most obvious being the size of the processed documents (amount of text per document) as well as the resources of the machine on which the service operates. +The main settings that can be used to improve the performance when querying large amounts of documents are : `SERVER_WORKERS` (number of flask web workers that chan handle parallel requests) and `APP_BULK_NPROC` (threads for annotation processing). + +## MedCAT library + +MedCAT parameters are defined in selected `envs/medcat*` file. + +For details on available MedCAT parameters please refer to [the official GitHub repository](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/). \ No newline at end of file diff --git a/medcat-service/docs/setup/installation.md b/medcat-service/docs/setup/installation.md new file mode 100644 index 000000000..4ea80722c --- /dev/null +++ b/medcat-service/docs/setup/installation.md @@ -0,0 +1,40 @@ +# Installation + +Medcat Service can be run using helm or docker compose + +The recommended approach is using helm + +## Helm installation + +Bring up medcat service with one line using helm + +``` +helm install medcat-service-helm oci://registry-1.docker.io/cogstacksystems/medcat-service-helm +``` + +See [medcat-service-helm](https://docs.cogstack.org/en/latest/platform/deployment/helm/charts/medcat-service-helm/) for the full documentation of how to use this chart. + +## Docker compose + +You also can bring up medcat service using docker compose with an example like this: + + +```yaml +name: cogstack-medcat-service +services: + medcat-service: + image: cogstacksystems/medcat-service:${IMAGE_TAG-latest} + restart: unless-stopped + environment: + # Uses a preloaded model pack example inside the image + - APP_MEDCAT_MODEL_PACK=/cat/models/examples/example-medcat-v2-model-pack.zip + - APP_ENABLE_METRICS=True + - APP_ENABLE_DEMO_UI=True + ports: + - "5555:5000" +``` + +You can now access medcat service on `localhost:5555` + +See the other examples and scenarios for running medcat service on [cogstack-nlp github](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-service/docker) + diff --git a/medcat-service/docs/user-guide/api-example-use.md b/medcat-service/docs/user-guide/api-example-use.md new file mode 100644 index 000000000..bef50bdc7 --- /dev/null +++ b/medcat-service/docs/user-guide/api-example-use.md @@ -0,0 +1,217 @@ +## API Example use + +This page gives examples for how to call the service and what will be returned. + + +Assuming that the application is running on the `localhost` with the API exposed on port `5000`, one can run: + +```bash +curl -XPOST http://localhost:5000/api/process \ + -H 'Content-Type: application/json' \ + -d '{"content":{"text":"The patient was diagnosed with leukemia."}}' +``` + +and the received result: + +```json +{ + "result": {"text": "The patient was diagnosed with leukemia.", + + "annotations": {"entities": {"0": {"pretty_name": "Patients", "cui": "C0030705", "type_ids": ["T101"], "types": ["Patient or Disabled Group"], "source_value": "patient", "detected_name": "patient", "acc": 0.99, "context_similarity": 0.99, "start": 4, "end": 11, "icd10": [], "ontologies": [], "snomed": [], "id": 0, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999303817749023, "name": "Status"}}}, "1": {"pretty_name": "Diagnosis", "cui": "C0011900", "type_ids": ["T060"], "types": ["Diagnostic Procedure"], "source_value": "diagnosed", "detected_name": "diagnosed", "acc": 0.6657139492748229, "context_similarity": 0.6657139492748229, "start": 16, "end": 25, "icd10": [], "ontologies": [], "snomed": [], "id": 1, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999918341636658, "name": "Status"}}}, "2": {"pretty_name": "leukemia", "cui": "C0023418", "type_ids": ["T191"], "types": ["Neoplastic Process"], "source_value": "leukemia", "detected_name": "leukemia", "acc": 0.2572544372951888, "context_similarity": 0.2572544372951888, "start": 31, "end": 39, "icd10": [], "ontologies": [], "snomed": [], "id": 2, "meta_anns": {"Status": {"value": "Affirmed", "confidence": 0.9999804496765137, "name": "Status"}}}}, "tokens": []}, + + "success": true, + "timestamp": "2021-11-11T11:54:28.856+00:00" + }, + "medcat_info": {"service_app_name": "MedCAT", "service_language": "en", "service_version": "1.2.5", "service_model": "MedMen"} +} +``` + +Additional DE-ID query sample (make sure you have a de-id model loaded): + +```bash +curl -XPOST \ + -H 'Content-Type: application/json' \ + -d '{"content":{"text":"Patient Information: Full Name: John Michael Doe \n Gender: Male \n Date of Birth: January 15, 1975 (Age: 49) \n Patient ID: 567890123 \n Address: 1234 Elm Street, Springfield, IL 62701 \n Phone Number: (555) 123-4567 \n Email: \n Emergency Contact: Jane Doe (Wife) \n Phone: (555) 987-6543 \n Relationship: Spouse"}}' +``` + +Make sure you have the following option enabled in `envs/(medcat|medcat_deid).env` , `DEID_MODE=True`. + +process_bulk example : + +```bash +curl -XPOST http://localhost:5000/api/process_bulk \ + -H 'Content-Type: application/json' \ + -d '{"content": [{"text":"The patient was diagnosed with leukemia."}, {"text": "The patient was diagnosed with cancer."}] }' +``` + +example bulk result : + +```json +{ + "result": [ + { + "text": "The patient was diagnosed with leukemia.", + "annotations": { + "0": { + "pretty_name": "Patients", + "cui": "C0030705", + "type_ids": [ + "T101" + ], + "types": [ + "Patient or Disabled Group" + ], + "source_value": "patient", + "detected_name": "patient", + "acc": 0.99, + "context_similarity": 0.99, + "start": 4, + "end": 11, + "id": 0, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999303817749023, + "name": "Status" + } + } + }, + "1": { + "pretty_name": "Diagnosis", + "cui": "C0011900", + "type_ids": [ + "T060" + ], + "types": [ + "Diagnostic Procedure" + ], + "source_value": "diagnosed", + "detected_name": "diagnosed", + "acc": 0.6657139492748229, + "context_similarity": 0.6657139492748229, + "start": 16, + "end": 25, + "id": 1, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999918341636658, + "name": "Status" + } + } + }, + "2": { + "pretty_name": "leukemia", + "cui": "C0023418", + "type_ids": [ + "T191" + ], + "types": [ + "Neoplastic Process" + ], + "source_value": "leukemia", + "detected_name": "leukemia", + "acc": 0.2572544372951888, + "context_similarity": 0.2572544372951888, + "start": 31, + "end": 39, + "id": 2, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999804496765137, + "name": "Status" + } + } + } + }, + "success": true, + "timestamp": "2021-12-08T18:49:55.255+00:00" + }, + { + "text": "The patient was diagnosed with cancer.", + "annotations": { + "0": { + "pretty_name": "Patients", + "cui": "C0030705", + "type_ids": [ + "T101" + ], + "types": [ + "Patient or Disabled Group" + ], + "source_value": "patient", + "detected_name": "patient", + "acc": 0.99, + "context_similarity": 0.99, + "start": 4, + "end": 11, + "id": 0, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999236464500427, + "name": "Status" + } + } + }, + "2": { + "pretty_name": "cancer diagnosis", + "cui": "C0920688", + "type_ids": [ + "T060" + ], + "types": [ + "Diagnostic Procedure" + ], + "source_value": "diagnosed with cancer", + "detected_name": "diagnosed~with~cancer", + "acc": 1, + "context_similarity": 1, + "start": 16, + "end": 37, + "id": 2, + "meta_anns": { + "Status": { + "value": "Affirmed", + "confidence": 0.9999957084655762, + "name": "Status" + } + } + } + }, + "success": true, + "timestamp": "2021-12-08T18:49:55.255+00:00" + } + ], + "medcat_info": { + "service_app_name": "MedCAT", + "service_language": "en", + "service_version": "1.2.6", + "service_model": "MedMen" + } +} + +``` + +IMPORTANT info regarding annotation output style +As the changes from MedCAT intoduced dictionary annotation/entity output. + +The mode in which annotation entities should be outputted in the JSON response, + by default this was outputted as a "list" of dicts in older versions, so the output would be : + + ```json + {"annotations": [{"id": "0", "cui" : "C1X..", ..}, {"id":"1", "cui": "...."}]} + ``` + + newer versions of MedCAT (1.2+) output entities as a dict, where the id of the entity is a key and the rest of the data is a value, so for "dict", + the output is + + ```json + {"annotations": [{"0": {"cui": "C0027361", "id": 0,.....}, "1": {"cui": "C001111", "id": 1......}}]} + ``` + +This setting can be configured in the ```./env/medcat.env``` file, using the ```MEDCAT_ANNOTATIONS_ENTITY_OUTPUT_MODE``` variable. +By default, the output of these entities is set to respect the output of the MedCAT package, hence the latter will be used. Please change the above mentioned env variable and make sure your CogStack-Nifi annotation script is adapted accordingly. + +Please note that the returned NLP annotations will depend on the underlying model used. For evaluation, we can only provide a very basic model trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions). Models utilising [SNOMED CT](https://www.england.nhs.uk/digitaltechnology/digital-primary-care/snomed-ct/) or [UMLS](https://www.nlm.nih.gov/research/umls/index.html) may require applying for licenses from the copyright holders. \ No newline at end of file diff --git a/medcat-service/docs/user-guide/demo-ui.md b/medcat-service/docs/user-guide/demo-ui.md new file mode 100644 index 000000000..589f510ad --- /dev/null +++ b/medcat-service/docs/user-guide/demo-ui.md @@ -0,0 +1,62 @@ +# Demo UI + +MedCAT Service includes a browser-based demo UI built with [Gradio](https://www.gradio.app/). It lets you try the loaded model on sample or custom text without writing API clients. + +## Enable the demo UI + +!!! tip + The demo UI is **disabled by default**. Set these environment variables before starting the service: + + | Variable | Description | Default | + |----------|-------------|---------| + | `APP_ENABLE_DEMO_UI` | Mount the Gradio UI on the FastAPI app | `False` | + | `APP_DEMO_UI_PATH` | URL path for the UI (empty string mounts at `/`) | `/` | + + See [Configuration](../setup/configuration.md) for more details + +The interface adapts to the model you load: + +| Mode | When | What you see | +|------|------|----------------| +| **MedCAT** | Default (`DEID_MODE=False`) | Named entity recognition with highlighted concepts and entity details | +| **AnonCAT** | De-identification (`DEID_MODE=True`) | PHI detection, optional redaction, and a de-identified text output | + + + +## MedCAT (named entity recognition) + +When the service runs with a standard MedCAT model pack, the demo UI shows the **MedCAT** interface. + +![Demo UI: MedCAT named entity recognition](../assets/demo-medcat.png) + +### Using the UI + +1. Enter clinical text in **Input Text**, or pick an example from the dropdown (short note, discharge summary, or a note containing PII for comparison). +2. Click **Annotate** to run the loaded model. +3. Review results in the right-hand panel: + - **Processed Text** — input with recognized spans highlighted in color. + - **Annotation Details** — click a highlighted span to see the concept name, CUI, confidence, and character offsets. + - **All Annotations** — expandable table of every entity returned by the model. + +Click **Clear** to reset the input and results. + +Recognized concepts depend entirely on the model pack you configured via `APP_MEDCAT_MODEL_PACK` or the individual CDB/vocabulary paths. Meta-annotation values from the model (for example negation or subject) are reflected in the underlying API responses; the demo table focuses on core entity fields. + +## AnonCAT (de-identification) + +When `DEID_MODE=True` (or `MEDCAT_DEID_MODE=True`) and an AnonCAT / de-ID model pack is loaded, the demo UI switches to the **AnonCAT** interface. + +![Demo UI: AnonCAT de-identification](../assets/demo-anoncat.png) + +### Using the UI + +1. Enter text in **Input Text**, or use an example (short note or a note with personally identifiable information). +2. Optionally enable **Redact** to replace detected PHI with `[***]` in the de-identified output. When unchecked, identifiable spans are still highlighted in **Details**, but the de-identified text keeps the original surface forms. +3. Click **Deidentify** to process the note. +4. Review results across tabs: + - **Deidentification** — the processed note with redaction applied when **Redact** is enabled. + - **Details** — same highlighted view and per-entity details as the MedCAT UI. + +Default service redaction for API calls is controlled separately by `DEID_REDACT` (default `True`). 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Reference: + - Extending Medcat Service: reference/extensions.md + + +plugins: + - search + - termynal + +markdown_extensions: + - admonition + - attr_list + - pymdownx.details + - pymdownx.superfences + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg