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setup script should elegantly handle incorrect database dir

Open yannickwurm opened this issue 4 years ago • 2 comments

Currently it dies - it should just ask again

[2020-03-14 11:11:41] INFO  Configuration file not found: /Users/Yannick/.sequenceserver.conf

Database dir not set.

SequenceServer needs to know where your FASTA files or BLAST+ databases are.
Please enter the path to the relevant directory (default: current directory).

Press Ctrl+C to quit.

>> ~/db
[2020-03-14 11:21:27] INFO  Configuration file not found: /Users/Yannick/.sequenceserver.conf
Could not find database dir: /Users/Yannick/db
➜  Developer ls ~/db
ls: /Users/Yannick/db: No such file or directory
➜  Developer ls ~/db

yannickwurm avatar Mar 14 '20 18:03 yannickwurm

I think the setup script should do the same for 'path to blast binaries' as well and can be done by defining a little helper method that prompts and re-prompts the user for input till valid (i.e., file exists and is a directory).

yeban avatar Mar 25 '20 12:03 yeban

I have submitted a PR for this (though I still need to get the tests passing): #499

Iain-S avatar Nov 09 '20 16:11 Iain-S