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throw error and quit if input dir is obviously wrong #36

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dizak opened this issue May 9, 2018 · 3 comments
Open

throw error and quit if input dir is obviously wrong #36

dizak opened this issue May 9, 2018 · 3 comments
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@Setnea
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enhancement new feature update generic change, too small to call it a feature

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@dizak
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dizak commented May 9, 2018

4f5823a

Proposed change

If there no fastq files or for other reason the input directory is obviously wrong, everything tries and fails. It should be detected before mothur is called.
@dizak dizak added the update generic change, too small to call it a feature label May 9, 2018
@Setnea
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Setnea commented May 11, 2018

I can fix it when I will be working on issue #22 .

@Setnea Setnea self-assigned this May 11, 2018
@Setnea Setnea added the enhancement new feature label Jul 3, 2018
Setnea added a commit that referenced this issue Jul 9, 2018
@Setnea
Validate input dir function #36
7ed3c7c 
Function validates if the defined directory contains files required for analysis (illumina PE mode: at least one pair of forward & reverse)
@Setnea
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Setnea commented Jul 13, 2018 •
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Current travis build does not support new input directory validation.
Software exits if the input directory does not contain proper fastq fails, and because of that some files cannot be created and compared (see branch args_fix)

Edit: Travis build was ok, the new functions didn't support analysis-only mode. Fixed.

Setnea referenced this issue Jul 17, 2018
@Setnea
Move verify_input_directory function to different section to exlude i…
90474e6 
…ts execution from analysis-only runs
Setnea added a commit that referenced this issue Jul 17, 2018
@Setnea
Verify_input_dir function update #36
77f90f4 
Make function more flexible and editable by parsing some previously hard coded variables as function arguments.
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dizak added a commit that referenced this issue Jul 18, 2018
@dizak
UPD:CI for #36
014fc58
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dizak commented Jul 18, 2018

Added CI tests for the input validation. After mothulity.py is called with the nonsense input directory, its warning is redirected to a file which is then compared with the reference logs from test_data/logs/. @Setnea it means that you need to make it identical.

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