Closed emollier closed 10 months ago
Hi @emollier a recent pull request from @MrCurtis addressed this (see history above). This has been pushed out to CPAN in release 1.7.7. Thanks for reporting!
The error is still here in 1.7.7 on 10 May 2022
The error is still here in 1.7.7 on 10 May 2022
NCBI changed the database again, including:
Also, I changed the test for 'Trimorus ovatus' to 'Zaphod Beeblebrox', because you shouldn't test the functionality of reporting "No hit" for an actual species name, as it's likely to be added to the database eventually (as happened with P. ovatus).
I'll commit my fix here when I figure out how.
We may want to consider how to future-proof these tests to not fail from remote database changes, though to be honest they don’t happen often.
On Jan 25, 2023, at 1:31 PM, Phil Goetz @.***> wrote:
The error is still here in 1.7.7 on 10 May 2022
NCBI changed the database again, including:
Also, I changed the test for 'Trimorus ovatus' to 'Zaphod Beeblebrox', because you shouldn't test the functionality of reporting "No hit" for an actual species name, as it's likely to be added to the database eventually (as happened with P. ovatus).
I'll commit my fix here when I figure out how.
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I'm still seeing this bug a year and a half since it was closed. Is there a workaround? Or has this package just been impossible to install?
t/Taxonomy.t ........... 7/?
# Failed test at t/Taxonomy.t line 48.
t/Taxonomy.t ........... 43/?
# Failed test at t/Taxonomy.t line 102.
# got: 'Actinomycetes'
# expected: 'Actinomycetia'
t/Taxonomy.t ........... 68/?
# Failed test 'Correct: No hit'
# at t/Taxonomy.t line 181.
# got: '2890685'
# expected: 'No hit'
t/Taxonomy.t ........... 69/? # Looks like you failed 3 tests of 69.
Hi @esiefker sorry, I haven't been seeing notifications for this repo so I'm glad you replied back. To be honest I'm happy it still works, even though the tests have been failing. Let me see what I can do to address this.
I committed my fixes, and got this message:
You’re making changes in a project you don’t have write access to. Submitting a change will write it to a new branch in your fork philgoetz/Bio-DB-NCBIHelper, so you can send a pull request.
Is that sufficient for someone with write privs to move my changes into the main branch?
Is that sufficient for someone with write privs to move my changes into the main branch?
I think I found the patch on your github clone. I'll take care of merging it, give me a few minutes.
@philgoetz I've split your fix into separate commits and pushed them.
I'm closing this issue (but someone else should test it and make a new release).
@carandraug I'll set up tests and make a new release, thanks for the merge!
@philgoetz @esiefker v1.7.8 has been pushed to CPAN. It will take a little while to show up, but should be ready pretty soon
Greetings,
While investigating Debian Bug#983239, I tried running the test suite straight from origin/master and obtained the following output:
Is it possible the source NCBI database had some kind of shift recently?
Kind Regards, Étienne.