Workflow Setup Visualization Prototype

Initial setup: Clone the repository, create an environment, activate the environment, with venv:

Clone the repository:

git clone [email protected]:als-computing/workflow-viz.git
cd workflow-viz

Setup an environment, with venv:

python3 -m venv workflow-viz-env
source workflow-viz-env/bin/activate

or Anaconda:

conda create --name workflow-viz-env python=3.9 
conda activate workflow-viz-env

and install the requirements:

pip install -r requirements.txt

Initial + beamtime setup: Set correct paths

In a file .env, set the following variables and adapt the path

TILED_URI="http://127.0.0.1:8888"
TILED_API_KEY="<randomly generated key>"
TILED_WHITELIST="<comma seperated list of file or directory names to process>"
TILED_BLACKLIST="<comma seperated list of file or directory names to ignore>"
PREFECT_API_URL="http://127.0.0.1:4200/api"
PATH_TO_RAW_DATA="<path to folder>"
PATH_TO_PROCESSED_DATA="<path to folder>"
PATH_TO_RAW_DATA_CATALOG="./tiled/db/catalog.db"
PATH_TO_PROCESSED_DATA_CATALOG="./tiled/db/catalog_processed.db"
PREFECT_API_URL="http://127.0.0.1:4200/api"

Either PATH_TO_RAW_DATA and PATH_TO_PROCESSED_DATA may be contained in the same directory. They must match with the corresponding variables in the SAXSWAXS-workflows environment. Additionally, the TILED_API_KEY needs to be the same.

If TILED_WHITELIST is empty, no files/directories will be skipped, but if it is not one needs to specify all names to be whitelisted (including top-level directory names, e.g. "raw, processed, <beamtimeid>").

All entries in TILED_BLACKLIST cause any directory or file containing a substring of the listed entries to be skipped.

Beamtime setup: Start up a Tiled

Within two seperate processes, start the Tiled server

tiled/tiled_config_serve.sh

and register the already existing files to Tiled

tiled/tiled_catalog_register.sh

Beamtime setup: Start up the Dash application

python app.py

Alternative: Initial setup with Docker:

docker network create workflow_viz_default

Set up the environment file .env as above.

Copyright

MLExchange Copyright (c) 2023, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.