tcp-lab / biotea Goto Github PK

Describe the bug
All commands crash due to LegacyVersion being removed in the packaging package. Biotea version 1.0.3.

To Reproduce
Steps to reproduce the behavior:

1. Install biotea
2. Run any command

This is due to how incompatible containers are detected. We just check a static list in bioTEA. A system for dynamically detecting the versions (by comparing major versions) should be implemented instead.

Some checks in the docker_wrapper are missing, namely:

https://github.com/CMA-Lab/bioTEA/blob/df38557ae0f0b33a0e5fda8c8938cefbbec5020d/bioTea/docker_wrapper.py#L188-L195

Error below:

2022-05-16 15:10:22,175 [ERROR] bioTea.docker_wrapper: Invalid arguments passed to interface. Please open an issue with the bioTEA logs.
Traceback (most recent call last):
  File "/home/hedmad/Files/Repos/Edmund/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 258, in parse_arguments
    self.possible_args[key](value)
  File "/home/hedmad/Files/Repos/Edmund/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 197, in __call__
    raise ValueError(f"Argument check failed. Invalid argument {argument}")
ValueError: Argument check failed. Invalid argument 10000000000.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/hedmad/Files/Repos/Edmund/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 416, in run_biotea_box
    parsed_args = interface.parse_arguments(**arguments)
  File "/home/hedmad/Files/Repos/Edmund/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 261, in parse_arguments
    raise ValueError(f"Argument check failed for key {key}: {value}")
ValueError: Argument check failed for key n_plots: 10000000000.0

The type checker is probably faulty. This is an old bug I thought was fixed, regarding the difference between float and int in the interface.

Describe the bug
Many Agilent arrays fail to be processed by BioTEA prepare. Some examples include:

• GSE102238
• GSE91035
• GSE71729
• GSE40098

To Reproduce
Steps to reproduce the behavior:

1. Download the data of the above GEO datasets;
2. Try and run BioTEA prepare against the data;
3. BioTEA fails just after "reading input files..."

Desktop:

• OS: Arch Linux
• BioTEA Version (Run biotea info biotea): 1.1.0
• Docker engine version (Run docker --version): N/A
• BioTEA container version (if applicable): 1.0.4

Describe the bug
Sometimes, the download of packages from Bioconductor (e.g. in the prep modules) fails, and the container crashes.

To Reproduce
Steps to reproduce the behavior:

1. Install biotea
2. Run the analysis presented in the paper
3. When downloading pd.hugene.1.0.st.v1, sometimes the download cannot be run, an the resulting timeout causes a crash.

Expected behavior
Expected to download the package as normal.

Desktop:

• OS: Arch Linux
• BioTEA Version (Run biotea info biotea): 1.0.0
• Docker engine version (Run docker --version): 20.10.17, build 100c70180f
• BioTEA container version (if applicable): latest (1.0.1)

Describe the bug
On a new analysis, setting the experimental_design > batches variable to anything other than None causes a ValueError:

Traceback (most recent call last):
  File "/home/hedmad/Files/panc_dec22/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 292, in parse_arguments
    self.possible_args[key](value)
  File "/home/hedmad/Files/panc_dec22/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 231, in __call__
    raise ValueError(f"Argument check failed. Invalid argument {argument}")
ValueError: Argument check failed. Invalid argument one, two, one, two

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/hedmad/Files/panc_dec22/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 450, in run_biotea_box
    parsed_args = interface.parse_arguments(**arguments)
  File "/home/hedmad/Files/panc_dec22/env/lib/python3.10/site-packages/bioTea/docker_wrapper.py", line 295, in parse_arguments
    raise ValueError(f"Argument check failed for key {key}: {value}")
ValueError: Argument check failed for key batches: one, two, one, two

To Reproduce
Steps to reproduce the behavior:

1. Create a new folder, with a virtual environment.
2. Install bioTea
3. Create a mock dataset with 4 random columns of data + a probe_id column.
4. Create a new option file with biotea initialize
5. Set the batches variable
6. Run the analysis with biotea analyze

Expected behavior
The batches should be parsed as normal.

Desktop:

• OS: Windows Subsystems for Linux running Arch
• BioTEA Version: 1.0.2
• Docker engine version: 20.10.21
• BioTEA container version: 1.0.2

This is part of a larger issue of R error messages, but a good start would be to look at the code and catch errors, giving better error messages.

The problem: The internal database file is just a .csv file generated manually through scripting. Database packages were downloaded on-the-fly, their annotations dumped, merged and cleaned. However, generating more or updated files is for now undefined. Additionally, the internal database file is only useful for Human chips.

Proposed Solution: A biotea annotations generate command that is used to generate these files. Additionally, biotea annotations apply should be updated to allow local files to act as annotation sources.
The new command should be executed by the box, as the annotation sources need to be manipulated in R (they are bioconductor packages).

Note: The way I did it was with R to dump the information, and Python to clean it up (as it is just much, much faster). Just to say that we might need further processing with Python after R. We therefore have to decide whether to do it all in the box, or R in the box and Python outside.

The default value for the plot-number option in various modules is something like 10000000.

This was a bad patch to deal with the fact that the default value has to be the same as the input value (there is no or check in the biotea CLI parsers). This should be addressed by adding something like an Inf string, or even false.