Prerelease issues

Question

Prerelease issues

Closed this issue 2 years ago · 5 comments

jfy133 commented 2 years ago

When testing just now I've noticed the following things:

Viewer

The Dir library table for metagenome-hostassociated seems to hjave sample_host column right at the end when you download it?
Why is the nf-core/mag csv saved as a ZIP file?
Would it make sense to have run_accesion as the ERR code in the nf-core/taxprofiler output?
~~Why is aMeta only containing the R1/forward read (one for @NikolayOskolkov )~~ Edit: aMeta only accepts single-end or already merged reads. I will document
The nf-core/fetchngs accession sheet seems to have additional columns (possibly of fAstq size? I'm not sure...)

Convert

All convert commands get a TypeError: run_convert() got an unexpected keyword argument 'library_output' error

(amdirt) james@bionb103:/tmp$ AMDirT convert ancientmetagenome-hostassociated_samples.tsv ancientmetagenome-hostassociated_sample -o .
2023-04-18 13:11:50.843 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.845 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.846 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.846 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.846 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.847 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.848 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-18 13:11:50.848 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
Traceback (most recent call last):
File "/home/james/bin/miniconda3/envs/amdirt/bin/AMDirT", line 33, in <module>
  sys.exit(load_entry_point('AMDirT', 'console_scripts', 'AMDirT')())
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
  return self.main(*args, **kwargs)
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/core.py", line 1055, in main
  rv = self.invoke(ctx)
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
  return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
  return ctx.invoke(self.callback, **ctx.params)
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/core.py", line 760, in invoke
  return __callback(*args, **kwargs)
File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
  return f(get_current_context(), *args, **kwargs)
File "/home/james/git/spaam-community/AMDirT/AMDirT/cli.py", line 154, in convert
  run_convert(**kwargs, **ctx.obj)
TypeError: run_convert() got an unexpected keyword argument 'library_output'

Convert is missing the AncientMEtagenomeDir Liobraries, citations and download script options

convert prints streamlit info even though streamlit isn't involved (presumably)

2023-04-19 08:59:01.113 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.115 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.115 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.116 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.116 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.117 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.117 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.118 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
AMDirT [INFO]: Preparing nf-core/eager table
2023-04-19 08:59:01.612 
  Warning: to view this Streamlit app on a browser, run it with the following
  command:

    streamlit run /home/james/bin/miniconda3/envs/amdirt/bin/AMDirT [ARGUMENTS]
2023-04-19 08:59:01.612 No runtime found, using MemoryCacheStorageManager
2023-04-19 08:59:01.622 No runtime found, using MemoryCacheStorageManager
AMDirT [INFO]: Preparing Bibtex citation file
2023-04-19 08:59:01.639 No runtime found, using MemoryCacheStorageManager
AMDirT [INFO]: Writing filtered libraries table
Traceback (most recent call last):
  File "/home/james/bin/miniconda3/envs/amdirt/bin/AMDirT", line 33, in <module>
    sys.exit(load_entry_point('AMDirT', 'console_scripts', 'AMDirT')())
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/james/bin/miniconda3/envs/amdirt/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/james/git/spaam-community/AMDirT/AMDirT/cli.py", line 154, in convert
    run_convert(**kwargs, **ctx.obj)
  File "/home/james/git/spaam-community/AMDirT/AMDirT/convert/__init__.py", line 132, in run_convert
    fw.write(accession_table["curl_script"])
UnboundLocalError: local variable 'accession_table' referenced before assignment

Answer 1 · 2023-04-18T13:19:09.000Z

All convert commands get a TypeError: run_convert() got an unexpected keyword argument 'library_output' error
Fixed with b45211f

Answer 2 · 2023-04-18T13:23:46.000Z

Convert is missing the AncientMEtagenomeDir Liobraries, citations and download script options

It already has them, they're just generated by default, hence not in the CLI options

libraries table: https://github.com/SPAAM-community/AMDirT/blob/ddb3fd31dd945cdd49170f7ac2b9c56a7448ad03/AMDirT/convert/__init__.py#L122

bibtex: https://github.com/SPAAM-community/AMDirT/blob/ddb3fd31dd945cdd49170f7ac2b9c56a7448ad03/AMDirT/convert/__init__.py#L118

Answer 3 · 2023-04-18T13:26:00.000Z

Why is the nf-core/mag csv saved as a ZIP file?

Because it has two files, once for PE libraries, and one for SE libraries

Answer 4 · 2023-04-18T15:17:49.000Z

Convert is missing the AncientMEtagenomeDir Liobraries, citations and download script options

It already has them, they're just generated by default, hence not in the CLI options

libraries table: https://github.com/SPAAM-community/AMDirT/blob/ddb3fd31dd945cdd49170f7ac2b9c56a7448ad03/AMDirT/convert/__init__.py#L122

bibtex: https://github.com/SPAAM-community/AMDirT/blob/ddb3fd31dd945cdd49170f7ac2b9c56a7448ad03/AMDirT/convert/__init__.py#L118

Hmm okay, i'll check again tomorrow - however I sort of feel that this inconsistent behaviour might be confusing (given this is for powerusers).

Mag zip

Ah ok I will also check this but definitely will need to be documented as I said in slack or bigger emphasis maybe...

Answer 5 · 2023-04-19T08:44:59.000Z

INote I've fixed the UnboundLocalError: local variable 'accession_table' referenced before assignment error in convert #113 , but streamlit stuff still applies