Python project for automatic report generation from Hamilton measurements.
To install python libraries use
pip install -r requirements.txt
Install pandoc
frpm pandoc website.
Install latex
from any of the distributions.
For experts only.
To build a hemrep library execute following command:
python -m build --sdist --wheel
python .\report_gen.py --help
usage: report_gen.py [-h] [--analysis ANALYSIS] [--cfg CFG]
[--ifld IFLD]
options:
-h, --help show this help message and exit
--analysis ANALYSIS analysis directory
--cfg CFG config and params directory
--ifld IFLD initial analysis folder
--cgf
is path to the configuration directory.
--ifld
set an initial folder where GUI analysis folder shall open at start.
--analysis
is path to a folder with finished Hamilton analysis, e.g. C:/work/hamilton/230801_AAV9-ELISA_sey_GN004240-053
If analysis directory is not given, GUI window opens to select the diectory.
Analysis folder name is parsed to retrieve certain analysis information!
The structume shall be [DATE]_[METHOD]_[USER]_[GN]
, where the fields are separated by underscore character _
where
[DATE]
is a date in format %y%m%d
(230801)
[GN]
is analysis identifier (GN004240-033)
[PROTOCOL]
is a protocol name (AAV9-ELISA)
[USER]
is user name/code (sey)
The working directory must contain following files in given format:
[DATE]_[GN]_-_worklist-ELISA.xls
[DATE]_[GN]_-_[PROTOCOL]_Parameters.csv
Examples:
230426_GN004240-033_-_worklist-ELISA.xls
230426_GN004240-033_-_AAV9-ELISA_Parameters.csv
Command line argument is used to define a folder containing configuration file, and other files necessary to execute report_gen.py
programm.
python report_gen.py --cfg ./data
Important: if relative path is used for --cfg
argument, the path is relative to the current execution/working directory!
To make sure intended folder path is used, provide absolute path.
python report_gen.py --cfg C:/work/elisa-report/data
Configuration file config.json
is a json format file containing configurable parameters. It could be located in either default folder ./data
or in local analysis folder. If the file is located in the analysis folder it has precedence (is meant to be modified by a user). Though, if the config file is not found in analysis folder it is read from the default location in the ./data
folder.
referenceValue
is identified automatically from the analysis folder name (see above). If the analysis folder name contains a string AAV8
or AAV9
reference value for given AAV*
is used, otherwise an exception is thrown.
Validity limits are defined for AAV9 or AAV8. Test validity is checked according to 3ฯ limits. Control result shall lie within interval <limits[0]
, limits[1]
>. Default limits should not be used, and are defined so that the report_gen
doesn't thow exception (fail).
The file shall contain entries listed below.
{
"pandoc_bin": "c:/work/pandoc/pandoc",
"pdflatex_bin": "c:/Users/hwn6193/AppData/Local/Programs/MiKTeX/miktex/bin/x64/pdflatex",
"reference_docx": "custom-reference.docx",
"plate_layout_id": "plate_layout_ident.csv",
"plate_layout_num": "plate_layout_num.csv",
"plate_layout_dil_id": "plate_layout_dil_id.csv",
"numeric_warning_disable": true,
"AAV9": {
"SOP": "SOP-234702",
"MHF": "DMD-211328",
"referenceValue": 1.7954e+10,
"limits": [
1.888E+12,
2.703E+12
]
},
"AAV8": {
"SOP": "SOP-236462",
"MHF": "DMD-211877",
"referenceValue": 2.1167E+10,
"limits": [
1.119E+11,
1.648E+11
]
},
"default": {
"referenceValue": 1.0E+10,
"limits": [
1.0E+10,
1.0E+12
]
},
"dilutions": [
1.0,
2.0,
4.0,
8.0,
16.0,
32.0,
64.0
]
}
This is a prefered way to run the preocessing of the results and following report generation.
--cfg
argument is a path of config directory, containing params.json
, layout *.csv
files, custom-reference.docx
and params.json
python report_gen.py DIR_NAME --cfg ./data
To export data in TXT format run the SoftMax Pro softare, and open given analysis. From the main menu choose 'Export' and select the Export to XML XLS TXT
option.
Export measurements for all plates.
Make sure the exported file name matches the folder name structure!
folder name example 230922_AAV9-ELISA_fff_GN004360-086
corresponding file name example 230922_AAV9-ELISA_1_20230922_103137.txt
Folder with Hamilton related stuff.
Hamilton
Define profiling in launch.json
in VS Code:
{
"name": "profiler",
"type": "python",
"request": "launch",
"module": "cProfile",
"args": [
"-o",
"./.tmp/tmp.prof",
"report_gen.py",
"--analysis",
"c:/work/hamilton/analysis/231213_AAV9-ELISA_sey_GN004240-068",
"--cfg",
"C:/work/elisa-report/data"
]
}
Run the profing server... (make su snakeviz is installed pip install snakeviz
)
python -m snakeviz .tmp/tmp.prof --server