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Use the CLI for OCR

In addition to the app, you can use the LifeOmic Platform command line interface (CLI) to operate OCR. The CLI gives you the option of using a terminal environment and commands to perform OCR API functions. This option is especially useful for the bulk ingestion of files, scripting operations, and loading JSON files that contain an OCR configuration. OCR configuration files allow you to compose complex search lists and distribute standard OCR settings to multiple projects.

To use the CLI for OCR, you must first install and authenticate the CLI with your LifeOmic Platform account. Follow the Getting Started instructions to set up the CLI. If you want to use an API key for authentication, follow the Setting Up API Keys instructions.

Note: The OCR API rate-limiter allows a maximum of 10 create-doc operations per minute.

Note: Use the CLI command lo ocr help to reveal the CLI OCR commands.

Configure Project Settings and Create Search Lists​

  1. Enter lo projects list to obtain a list of projects and projects IDs and copy the project ID.

  2. Enter lo ocr get-config <projectId>.

    The command returns OCR configuration details for the project. These details include the OCR settings.

  3. Enter lo ocr create-config <projectId> <setting> '[ON | OFF]' to change an OCR setting. lo ocr create-config --help lists the available settings.

    Example: lo ocr create-config ee64951b-b593-4ba4-a97d-f6a2c0d8cc25 --spell-check-switch 'ON'

  4. Enter lo ocr create-config <projectId> --config-file 'path/to/config.json' to load a JSON configuration file containing search lists and OCR settings.

    Example: lo ocr create-config ee64951b-b593-4ba4-a97d-f6a2c0d8cc25 --config-file '/Users/jeffbeard/desktop/config.json'

    Use the following JSON template to create the config.json file.

{
    "denoiserSwitch": "ON | OFF | SMART",
    "pathPrefix": "ocr",
    "documentClassifier": "document-classifier-name",
    "classifierSwitch": "OFF | SEARCH | ML",
    "analyzeSwitch": "OFF | ON",
    "spellCheckerSwitch": "OFF | ON",
    "searchLists": {
        "lists": [
            {
                "title": "title-for-list-1",
                "searchTerms": [
                    {
                        "term": "search-text-1",
                        "coding": {
                            "code": "1",
                            "display": "display",
                            "system": "lifeomic.com"
                        },
                        "resourceType": ["MedicationAdministration"]
                    },
                    {
                        "term": "search-text-2"
                    }
                ]
            },
            {
                "title": "title-for-list-22",
                "searchTerms": [
                    {
                        "term": "search-text-3"
                    },
                    {
                        "term": "search-text-4"
                    }
                ]
            }
        ]
    }
}

Upload Files and Create an OCR Document​

  1. Enter lo files upload {<file>|<directory>} <projectId> to upload a file or a folder of files.

    Example: lo files upload consult_note.pdf ee64951b-b593-4ba4-a97d-f6a2c0d8cc25

    A successful upload displays the generated fileId string after ID:

    consult_note.pdf [==============================] 100% | ETA: 0s |
    138829/138829Upload complete: consult_note.pdf to consult_note.pdf,
    ID: 7119a2ee-f3fb-4e15-b864-3dafae812373

  2. Copy the fileId string after ID:

  3. Enter lo ocr create-document <projectId> <fileId> and use the copied data string for the fileId.

    The command initiates the OCR operations on the file and displays the documentReferenceId.

    documentReferenceId: 0d130601-d26f-4050-b9c0-406b32040016

  4. Copy the string after documentReferenceId:.

  5. Enter lo fhir get DocumentReference <documentReferenceId> and use the copied data string for the documentReferenceId to confirm OCR operations.

    The command displays information on the document including PrecisionOCR Service and SUCCESS.

    resourceType: DocumentReference
    meta:
    tag:
    -
      system: http://lifeomic.com/fhir/dataset
      code:   ee64951b-b593-4ba4-a97d-f6a2c0d8cc25
    -
      system: http://lifeomic.com/fhir/source
      code:   PrecisionOCR Service
    -
      system: http://lifeomic.com/ocr/document/status
      code:   SUCCESS

      ...............

  6. To confirm the document is also in the web application, open the LifeOmic Platform app and click OCR on the left side menu. The file name appears in the list of documents. OCR Confirm CLI