[Debian-med-packaging] Bug#879619: Autopkgtest for ncbi-tools6

[Liubov Chuprikova]

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 at debian.org> wrote:

> Liubov Chuprikova <chuprikovalv at 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starts with "The asn2ff flatfile generator is obsolete and unsupported.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
>   errmsg/.
> - 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,
Liubov
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