queueGenerator (qg)

Motivation:

anno 2010

• fgcz naming convention,
• injecting bfabric sample IDs and order IDs, ...
• automatic linking to meta data in bfabric ...
• on some point we want to have it in bfabric

Challenges

• ((autoQC_user|QC)) - autoQC01, autoQC03, autoQC4; soon: ((autoQC05)), ((autoQC06)), ((autoQC07)), ((autoQC08))
• blanc/clean/wash runs
• plate, e.g., 96WP, / multiplate systems
• LC systems: .eksigent(), .water(), ..., nanoElute() , .vanquish()
• instrument control software, e.g., XCalibur, HyStar
• (block) randomization run order / across plates
• multi order
• acquisition of a sample set multiple times (with different methods, eg. pos and neg mode)
• DIL (metabolomics)
• ...
• Legacy code

Workflow/Pipeline

0. user -> enters samples in bfabric
1. qg queries bfabric sample of project
2. ...

Package Organization

• inst/extdata/instrument.csv - table instrument;area;system;lc
• R/config.R - general configuration, e.g., Hystar driver, insertSample FUN
• R/configProteomics.R - configuration for proteomics
• R/configMetabolomics.R - configuration for metabolomics
• R/lc-systems.R - LC systems mainly how to write the possitions

See also

• https://fgcz-intranet.uzh.ch/tiki-index.php?page=sw.queueGenerator
• runs as virtual machine: http://fgcz-c-072.uzh.ch:4001/extractPlateId/

Sample use cases

cont	instument	LC.	system	position	type	area	test
36104	ASTRAL_1	MCLASS	XC SII	1:A,1	vial	P
35270	EXPLORIS_3	VANQUISH		1:A1	vial	M	git
35117	TIMSTOF_1	EVOSEP	HyStar	1:A1	plate	P
36946	EXPLORIS_2	EVOSEP.		1:A1	vial	P
37142	EXPLORIS_2	EVOSEP		1:A1	plate 479[34]	P
37146	EXPLORIS_2	EVOSEP	Chronos	1:A1	vial	P
28073	ASTRAL	VANQUISH				P
xxx	EXPLORIS_2	MCLASS	XC LCdevs		vial	P

Usage

1. install python3 bfabricPy package

uv tool install bfabric-scripts   

2. run the SOAP REST Proxy

BFABRICPY_CONFIG_ENV=FGCZSTABLE  bfabric_flask.py

set HOME .Renviron

login="$USER"
webservicepassword="eXXXe3XXX55dc39eXXXaeb763ec2XXXX"
bfabricposturl="http://127.0.0.1:5000/"

install

devtools::install_github("fgcz/qg")

and use the queue generator

shiny::shinyApp(ui = qg::.buildQgUI , server = qg::.buildQgServer) -> qg
qg

## Have a lot of fun!

Read how to use it on the command line:

browserViewer("qg")