/tabby-explore

Primary LanguagePython

Tabby file explorations

My scripts

Convert tabby file listing to catalog metadata: tabby2filemeta.py

Usage: python tabby2filemeta.py ds_file_path target_file

Input is a dataset tabby file (so we can get dataset id), we assume the following convention to get matching files file:

  • dataset: PROJECT_dataset-name.tsv
  • file: PROJECT_dataset-name_files.tsv

Make a file listing from an ftp server: list_pride.py

I used this script to create a tabby file listing contents of several ProteomeXchange datasets (input & output hardcoded).

Convert ProteomeXchange dataset to catalog metadata

I did a very basic and incomplete conversion of ProteomeXchange XML file to catalog dataset metadata. Input & output hardcoded.

My Workflow:

  • create tabby files
    • hand-edit a dataset tabby file
    • create files tabby file with list_pride.py
  • translate tabby files
    • tubby2catalog from catalog-utilities
    • tabby2filemeta.py from this repo
  • create catalog with datalad catalog create
    • edit catalog config to accept any source
    • add translated tabby files