Collect lyDATA Tables Interactively

Collect lyDATA Tables Interactively#

Submodule to collect data interactively using a simple web interface.

With the simple command

lyscripts data collect

One can start a very basic web server that serves an interactive UI at http://localhost:8000/. There, one can enter patient, tumor, and lymphatic involvement data one by one. When completed, the “submit” button will parse, validate, and convert the data to serve a downloadable CSV file.

The resulting CSV file is in the correct format to be used in LyProX and for inference using our lymph-model library.

lyscripts.data.collect.serve_index_html() → HTMLResponse[source]#

Serve the index.html file at the URL’s root.

lyscripts.data.collect.serve_schema() → dict[str, Any][source]#

Serve the JSON schema for the patient and tumor records.

lyscripts.data.collect.serve_collector_js() → FileResponse[source]#

Serve the collector.js file under "http://{host}:{port}/collector.js".

This frontend JavaScript file loads the JSON-Editor library and initializes it using the schema returned by the serve_schema() function.

async lyscripts.data.collect.process(data: RootModel) → StreamingResponse[source]#

Process the submitted data to a DataFrame.

FastAPI will automatically parse the received JSON data into the list of instances of he pydantic type defined by the lydata.schema.create_full_record_model() function.

From this list, we create a pandas DataFrame and return it as a downloadable CSV file.

pydantic settings lyscripts.data.collect.CollectorCLI[source]#

Bases: BaseCLI

Serve a FastAPI web app for collecting involvement patterns as CSV files.

Show JSON schema
{
   "title": "CollectorCLI",
   "description": "Serve a FastAPI web app for collecting involvement patterns as CSV files.",
   "type": "object",
   "properties": {
      "configs": {
         "default": [
            "config.yaml"
         ],
         "description": "Path to the YAML file(s) that contain the configuration(s). Configs from YAML files may be overwritten by command line arguments. When multiple files are specified, the configs are merged in the order they are given. Note that every config file must have a `version: 1` key in it.",
         "items": {
            "format": "path",
            "type": "string"
         },
         "title": "Configs",
         "type": "array"
      },
      "hostname": {
         "default": "localhost",
         "description": "Hostname to run the FastAPI app on.",
         "title": "Hostname",
         "type": "string"
      },
      "port": {
         "default": 8000,
         "description": "Port to run the FastAPI app on.",
         "title": "Port",
         "type": "integer"
      }
   }
}

field hostname: str = 'localhost'#

Hostname to run the FastAPI app on.

field port: int = 8000#

Port to run the FastAPI app on.

cli_cmd() → None[source]#

Run the FastAPI app.

Command Help#

Usage: lyscripts data collect [-h] [--configs list[Path]] [--hostname str]
                              [--port int]

Serve a FastAPI web app for collecting involvement patterns as CSV files.

Options:
  -h, --help            show this help message and exit
  --configs list[Path]  Path to the YAML file(s) that contain the
                        configuration(s). Configs from YAML files may be
                        overwritten by command line arguments. When multiple
                        files are specified, the configs are merged in the
                        order they are given. Note that every config file must
                        have a `version: 1` key in it. (default:
                        ['config.yaml'])
  --hostname str        Hostname to run the FastAPI app on. (default:
                        localhost)
  --port int            Port to run the FastAPI app on. (default: 8000)
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