CellSearch Tool Hub

A modular desktop and CLI toolbox for cell line lookup, enrichment, CSV utilities, folder generation, and SOP preparation.

The project bundles several local tools into a single tkinter application and keeps generated data in a central outputs/ directory.

Features

• Cellosaurus search workflow with list-first selection
• Pipeline execution for cello+, PubMed, descriptions/PDFs, price lookup, and optional AFS export
• Run archive with indexed output history
• Embedded CSV comparison tool
• AFS conversion utilities
• Folder generation from text input
• Embedded SOP builder with CSV import and PDF workflow
• CLI entry points for scripted usage

Project Structure

CellSearchHub/
|-- app.py
|-- cli.py
|-- hub/
|-- bundled_tools/
|-- outputs/
|-- scripts/
|-- .gitignore
|-- PUBLISHING_BLACKLIST.md
|-- README.md

Important folders:

• hub/ Core UI, pipeline, path handling, and adapters.

• bundled_tools/ Local copies of the underlying tools used by the hub.

• outputs/ Central storage for runs, logs, and generated master files.

• scripts/ PowerShell wrappers for launching the GUI or running the pipeline headlessly.

Requirements

Recommended environment:

• Windows
• Python 3.11+ or 3.12
• A working tkinter installation

Optional, depending on the tools you use:

• lualatex for SOP PDF generation
• internet access for Cellosaurus, PubMed, price lookup, and description downloads

Getting Started

1. Clone the repository

git clone
cd CellSearchHub

2. Start the desktop app

python .\app.py

Alternative PowerShell launcher:

.\scripts\start_tool_hub.ps1

3. Typical workflow

1. Search a cell line via Cellosaurus using the list workflow.
2. Select the correct match.
3. Run the pipeline.
4. Review outputs in the Workflow and Outputs tabs.
5. Optionally export AFS rows or continue with SOP preparation.

Main Tabs

Workflow

Primary search and pipeline execution tab.

Includes:

• Cellosaurus search
• pipeline options
• live log
• latest cello+, AFS, PubMed, and price outputs

Outputs

Run archive and output browser.

Includes:

• run index built from summary.json
• summary view
• per-run cello+, AFS, PubMed, and prices output views
• quick access to run folders and summary files

CSV

CSV utility area.

Includes:

• AFS conversion
• embedded universal CSV comparison tool

Generate Folders

Creates folder structures from text input and writes them into the configured output base directory.

SOP

Embedded SOP tool for CSV-driven document preparation and PDF generation.

CLI Usage

Search

python .\cli.py search "HeLa"

Run pipeline

python .\cli.py run --search-query "HeLa" --cvcl CVCL_0030 --name "HeLa"

PowerShell wrapper

.\scripts\run_pipeline.ps1 -SearchQuery "HeLa" -Cvcl CVCL_0030 -Name "HeLa"

Output Layout

Generated files are stored centrally under outputs/.

Typical run structure:

outputs/runs/<timestamp>_<cvcl>_<name>/
|-- 01_cello_plus/
|-- 02_pubmed/
|-- 03_descriptions/
|-- 04_prices/
|-- 05_afs/
|-- 06_summary/
`-- logs/

Important shared outputs:

• outputs/cello_plus/cello_plus_master_rows.csv
• outputs/cello_plus/cello_plus_master_columns.csv
• outputs/afs/afs_master_list.csv
• outputs/run_index.json

Notes on Data and Publishing

This repository is designed so local data stays centralized under outputs/. That makes cleanup easier and reduces the risk of committing generated files.

Before publishing or pushing to a public repository:

• review .gitignore
• review PUBLISHING_BLACKLIST.md
• confirm that no local CSV, logs, PDFs, images, or run archives are staged

Useful checks:

git status --ignored
git diff --cached
git ls-files

Development Notes

The hub prefers bundled local scripts over external scattered dependencies. If you update one of the original tools, copy the required changes into bundled_tools/ as well.

If you move the project folder, the run index and summary loading are designed to rebuild or normalize paths as needed.