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Re: Bug#879619: Autopkgtest for ncbi-tools6

Hi Aaron, Hi Andreas,

Please, have a look at my two last commits (https://salsa.debian.org/med-team/ncbi-tools6/commits/master). Actually, the first one was made a month ago.

On Tue, 17 Apr 2018 at 03:48 Aaron M. Ucko <ucko@debian.org> wrote:
Liubov Chuprikova <chuprikovalv@gmail.com> writes:

> At the moment, the following commands are still lacking tests:
>    - *asn2ff*, *gbseqget*, *findspl* (their output indicates they are
>    obsolete and/or unsupported)

- asn2ff plays the same general role as asn2flat, and should be possible to
  test similarly.

I tried to run it in a similar way to asn2asn. It throws an error which starts with "The asn2ff flatfile generator is obsolete and unsupported.  Please switch to using asn2gb/SeqEntryToGnbk in the future."

- gbseqget is like insdseqget, but formally uses GenBank-specific
  notation; as such, it requires network access.

I added a test for gbseqget within if statement which checks for internet connection.
- findspl also requires network access, and will need to be patched in the
  same fashion as taxblast; I'll take care of it when I get a chance.

>    - *asndhuff*, *nps2gps* (I can't figure out what kind of inputs they
>    require)

- I'm not sure where you'd find input for asndhuff.
- nps2gps takes a text Bioseq-set or Seq-entry of class nuc-prot, as
  obtained by (for instance) idfetch -g1234.

A test for nps2gps also presents now.
>    - *fa2htgs*, *spidey* (they look too complicated for me and require much
>    time to understand how they work)

That's fair.  You can always come back to them later if you feel inspired.

I have also finished with spidey and fa2htgs today.
>    - *taxblast* doesn't generate an output file and only generates an
>    *incomplete* html

I'm not sure what's up with that, but as previously noted, it requires
network access anyway.

>    - *errhdr*, *sortbyquote* (I can't figure out even what they are
>    supposed to do)

- errhdr is a developer tool, working with files of the format found in
- sortbyquote is also a developer tool, essentially a variant of sort
  that ignores everything outside quotation marks (and generally has far
  fewer options).
I'm not sure any of these is critical to test, but some
should be relatively straightforward to work in at this point, and as
noted I'm not quite ready to upload a new version anyway.

Aaron, thank you for the explanations! They helped me a lot!

Aaron, Andreas: what is your opinion about the whole test? Could we consider it as completed?

With regards,

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