XChem Business Knowledge Unit. Service, Client, API, persistent store.
Project description
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
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 it is ignored.
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 something like 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
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