igicerovsky/elisa-report

ELISA report generation

ELISA Report Generation

Python project for automatic report generation from Hamilton measurements.

Prerequisities

To install python libraries use

pip install -r requirements.txt

Install pandoc frpm pandoc website.

Install latex from any of the distributions.

Buld distribution of elisarep

For experts only.
To build a hemrep library execute following command:

python -m build --sdist --wheel

Running the script

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

Config file config.json

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 3σ 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
    ]
}

Running with exported photometer txt data

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

HAMILTON

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

Profiling

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