birm / uploadheatmaps

uploadHeatmaps.sh

File Preparation

Start the import process by storing the data in an import folder. The directory should be: quip folder/data/heatmaps/input folder/ on the quip host server. You only need to copy the "heatmap_XXXXXXXXXXXXXXXXXX.json" files for import. The metadata file is unnecessary because the manifest contains the required data.

Under the input directory "import folder", with the heatmap files, you need to also add a manifest file that contains data about the heatmaps you are loading. The heatmap files and be distributed under multiple directories in the "import folder" as long as the path is defined in manifest with a relative path (i.e. "./study1/heatmap01.json").

Usage

To load the current input files with a manifest named "manifest.csv":

[ root@dockhost:~ ]$ docker exec -it quip-hmloader uploadHeatmaps.sh -c <PathDB Collection>  -i <input folder> -o <output folder> [options]

For the full usage info type:

bash-3.2$ ~/uploadHeatmaps/uploadHeatmaps.sh --help
Usage: $ uploadHeatmaps.sh [options] -c <pathDB_collection> -i <input folder> -o <output folder>
  Options:
    -c, --collection <pathDB_collection>: PathDB Collection for heatmaps (*this parameter required)
    -i, --input <input_folder>: Folder where heatmaps are loaded from (*this parameter required)
    -o, --output <output_folder>: Folder where converted heatmaps are imported from (*this parameter required)
    -q, --quip-host <host>: ip or hostname of PathDB Server (default: quip-pathdb)
    -h, --data-host <host>: ip or hostname of database (default: ca-mongo)
    -m, --manifest <manifest name> (default: manifest.csv)
    -d, --database <database name> (default: camic)
    -p, --port <database port> (default: 27017)

    --help Display full help usage.
  Notes: requires mongoDB client tools installed on running server

Depending on the number of images and their resolution it may take some time to complete. Do not stop the process until it completes. If an error occurs then no data will be uploaded.