rockingester 1.1.1

XChem Business Knowledge Unit. Service, Client, API, persistent store.

XChem Business Knowledge Unit. Service, Client, API, persistent store.

Installation

pip install rockingester

rockingester --version

Legacy information

The formulatrix pipeline code is here:

/dls/science/groups/i04-1/software/luigi_pipeline/imager_pipe

This is a working directory of

https://github.com/xchem/formulatrix_pipe

The formulatrix pipeline puts images here:

/dls/science/groups/i04-1/software/luigi_pipeline/imager_pipe/SubwellImages/9b5j_2023-03-23_RI1000-0276-3drop

Does this have anything useful?

https://gitlab.diamond.ac.uk/cnp64921/dlsformulatrix.uploader/-/blob/master/formulatrix_uploader.py

As for the luigi stuff, one of the scripts in the /dls/science/groups/i04-1/software/luigi_pipeline/imager_pipe/ creates the filename after extracting info from the SQL server on the Formulatrix. I think the 9b5j part is the barcode, yes, but you might have to dig into the scripts there to find out the logic behind it all.

By the way if you want to access the FOrmulatrix /Rockmaker from Windows you can brose to access the RockMaker Imager \cs04r-nas01-02rockimager

You see like: \cs04r-nas01-02rockimagerrockimagerRockMakerStorageWellImages539plateID_14539batchID_72673

The batch ID proably relates to the inspection… a plate is inspected multiple times and each inspection has a batch ID. There may be some clues in the get_barcodes.py script in the imager_pipe directory.

Algorithm

Looks in SubwellImages directory.

Uses first 4 letters of each subdirectory as “barcode”.

If barcode is NOT in the plates mined from the formulatrix, then moves subdirectory to SubwellImages_nobarcode.

Otherrwise, if name of plate is a valid visit name, and the visit directory exists, then copies the images to the visit directory and inserts them into the database.

Otherwise ignores the subdirectory.

We have to leave all plate directories in SubwellImages since this is where Texrank expects them.

After we don’t need Texrank, then we can move the non-visit directories into SubwellImages_novisit, and move (instead of copy) them for good visits. This will keep SubwellImages clean and more efficient to poll.

Documentation

See https://www.cs.diamond.ac.uk/rockingester for more detailed documentation.

Building and viewing the documents locally:

git clone git+https://gitlab.diamond.ac.uk/scisoft/bxflow/rockingester.git
cd rockingester
virtualenv /scratch/$USER/venv/rockingester
source /scratch/$USER/venv/rockingester/bin/activate
pip install -e .[dev]
make -f .rockingester/Makefile validate_docs
browse to file:///scratch/$USER/venvs/rockingester/build/html/index.html

Topics for further documentation:

• TODO list of improvements

• change log