Copyright (C) 2020 RIKEN

Synopsis

• This repository contains the source codes for bd5lint, a tool that analyzes BD5 file format and flag syntactic errors and suspicious constructs.

Usage

usage: bd5lint.py [-h] [-v] FILE

Validation of BD5 formatted files.

positional arguments: FILE BD5 formatted filename

optional arguments: -h, --help show this help message and exit -v, --verbose verbose mode (default: False)

For example: python3 bd5lint.py -v test/testbd5_dim_3D_t1.h

Detailed description

Detailed description can be found on the link below. https://docs.google.com/document/d/1x6oTgNifqhn9RXEuFVs2J4ByT_mDJ-Pzp0RLT3cwibw/edit?usp=sharing

Reference

BD5: an open HDF5-based data format to represent quantitative biological dynamics data Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami bioRxiv 2020.04.26.062976; doi: https://doi.org/10.1101/2020.04.26.062976

Test

• Functional Test

  python3 functional_test.py

1. • invalid BD5 file with no data group. "test/testbd5_data1.h5",
2. • invalid BD5 file with missing element "test/testbd5_data_01.h5",
3. • invalid BD5 file with object t1 which is not in objectDef. "test/testbd5_data_0_object_t1.h5",
4. • invalid BD5 file with dim 2D but it has z dimension. "test/testbd5_dim_2t_bd5.h5",
5. • valid BD5 file with dim 3D "test/testbd5_dim_3D.h5",
6. • invalid BD5 file - object entity is a line but it has radius "test/testbd5_line_radius.h5",
7. • invalid BD5 file - it has object1 instead of the correct syntax object "test/testbd5_object1.h5",
8. • invalid BD5 file with no objectDef "test/testbd5_objectDef1.h5",
9. • invalid BD5 file with dim as 3D, but with inconsistent entity 'line' at ID 1_47. "test/testbd5_object_0_1_47_points.h5",
10. • invalid BD5 file with no scaleUnit "test/testbd5_scaleUnit1.h5",
11. • invalid BD5 file with entity sphere but no radius "test/testbd5_sphere_no_radius.h5",
12. • invalid BD5 file with dim as 3D, but with inconsistent entity 'line' at ID 1_41. "test/testbd5_dim_3D_I_41_line.h5",
13. • valid BD5 file "test/testbd5_dim_3D_t1.h5"
14. • valid BD5 file with 0D+T dimension "test/testbd5_0seed_0D_bd5.h5"