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WSI Worker

This script converts one SVS to a DZI pyramid, links the converted assets into the DPR's file structure, and updates the DPR database.

Building the Docker Image

  1. Build the base image in docker/wsi-worker-base
  2. Tag with kingstonduo/wsi-worker-base (plus version) and push
  3. Build the worker image in docker/wsi-worker
  4. Tag with kingstonduo/wsi-worker (plus version) and push

First Time Set-Up

To get started quickly, create a .env file in wsi-worker/scripts and then call ./run-wsi-worker.sh. To initialize the .env file, copy wsi-worker/scripts/.env.example and modify it to suit your environment (see ".env File" below).

Example Run

  1. Put an SVS file into the host's "SVS file drop zone" directory indicated by ENV_JOB_IN_DIR
  2. cd wsi-worker/scripts to make that your working directory with your .env file
  3. Start up your environment's docker-compose under heavens-docker/delphinus, otherwise the DB update will fail
  4. Run the below command to convert the SVS to DZI and link it in the file system and to the DPR database

./run-wsi-worker.sh KPMP-Ex1 KPMP-Ex1_PAS_1of1 abc123 pas

Arguments

  1. KPMP ID
  2. SVS filename without the .svs extension
  3. Package File ID from the Data Lake
  4. Slide type. Values are 'LM', 'EM', 'IF'.
  5. [Optional] stain type. Values are 'he', 'pas', 'silver', 'tri', 'frz', 'tol' and 'cr'. Defaults to 'pas'

.env File

  1. ENV_IMAGE: defaults to kingstonduo/wsi-worker
  2. ENV_LINK_SRC_DIR: container KE data directory, defaults to /data/knowledgeEnvironment/deepZoom
  3. ENV_LINK_DST_DIR: container DPR data directory, defaults to /data/deepZoomImages
  4. ENV_LINK_SRC_DIR_HOST: Host KE data directory, maps to ENV_LINK_SRC_DIR
  5. ENV_LINK_DST_DIR_HOST: Host DPR data directory, maps to ENV_LINK_DST_DIR
  6. ENV_JOB_IN_DIR: the host directory holding the source files (.jpg/.jpeg, .svs, .tif) to be handled by the job
  7. ENV_JOB_OUT_DIR: the host directory to hold link.sh and error.txt if errors are logged

Outputs

  1. ENV_JOB_OUT_DIR receives byproduct files used in the job
  2. ENV_LINK_SRC_DIR receives the DZI assets from the SVS conversion
  3. ENV_LINK_DST_DIR gets symlinks to DZI assets stored in the ENV_LINK_SRC_DIR
  4. delphinus-mongodb container gets updated participant and slide records in the "patients" collection