Install & Configuration

Install

NexusLIMS-Logger is distributed as portable binary executable compiled in corresponding OS. There is no installation (or pre-requisites) required to run the executable, except proper configuration (see below).

NexusLIMS-Logger can also be excuted as normal Python program as well with the source code. Developers can take following steps:

$ git clone https://github.com/Euclid-Techlabs-LLC/NexusLIMS-Logger.git -b devgcp
$ cd NexusLIMS-Logger && pip install -e ".[dev]"

Configuration

NexusLIMS-Logger requires several configuration settings to run, which must be properly set. The settings are read from:

  1. environment variables. (priority)

  2. $HOME/nexuslims/gui/config.json

The settings includes the following item:

Setting Name

Explaination

NEXUSLIMSGUI_DBAPI_URL

root URL of database API

NEXUSLIMSGUI_DBAPI_USERNAME

user name to validate database API request

NEXUSLIMSGUI_DBAPI_PASSWORD

password to validate database API request

NEXUSLIMSGUI_FILESTORE_PATH

system directory path of instrument raw data output folder, file changes therein will be watched and sync-ed to the cloud storage

NEXUSLIMSGUI_FILETYPES_SYNC

list of file types allowed to be watched and sync-ed

NEXUSLIMSGUI_SYNC_INTERVAL_SECONDS

file transfer interval in seconds

NEXUSLIMSGUI_DATA_BUCKET

bucket name of cloud storage which raw data is sync-ed to

NEXUSLIMSGUI_GCP_PROJECT

project ID of GCP

An example can be seen ($ROOT/src/nexuslims_logger/config.json)

 1{
 2    "NEXUSLIMSGUI_DBAPI_URL": "https://<API_URL>",
 3    "NEXUSLIMSGUI_DBAPI_USERNAME": "DBAPI_USERNAME",
 4    "NEXUSLIMSGUI_DBAPI_PASSWORD": "DBAPI_PASSWORD",
 5    "NEXUSLIMSGUI_FILESTORE_PATH": "/path/to/raw/data/dir",
 6    "NEXUSLIMSGUI_FILETYPES_SYNC": [
 7        ".dm3"
 8    ],
 9    "NEXUSLIMSGUI_SYNC_INTERVAL_SECONDS": 600,
10    "NEXUSLIMSGUI_DATA_BUCKET": "GCP_BUCKET_NAME",
11    "NEXUSLIMSGUI_GCP_PROJECT": "nexuslims-computing"
12}

Start

NexusLIMS-Logger can be started by double-clicking on the icon, like normal desktop GUI.

To start with source code, run python -m nexuslims_logger.run or nexuslimslogger in the terminal.

Help

Please contact developers in Euclid Techlabs Contributors.