Correlation issues #718
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akumar289 ***@***.***> aliandika:
GeneNetwork tux01:gene:2.11-rc2-testing-85ad78373
run_sample_corr_cmd() got an unexpected keyword argument 'corr_method' (error)
Running literature correlation and running into the above error
@alex doesn't this mean that gn3 changes have not
been seen by tux01? If so, could you ping Arun to
update the server. Otherwise, could you collab
with Zach on a fix and track that on
gn-gemtext-threads?
@akumar289 thanks for this report. We are looking
into this. Sorry for the inconvenience.
…--
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I was wondering if there is any update regarding this? |
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I can't update to the latest code because it complains about not being able
to import rust-correlation. I assume this is because a new profile needs to
be built after updating guix-bioinformatics, but the same way I used to do
this no longer seems to work (it now complains about not being able to find
"genenetwork2").
…On Thu, Aug 11, 2022 at 4:01 AM BonfaceKilz ***@***.***> wrote:
akumar289 ***@***.***> aliandika:
> GeneNetwork tux01:gene:2.11-rc2-testing-85ad78373
> run_sample_corr_cmd() got an unexpected keyword argument 'corr_method'
(error)
>
> Running literature correlation and running into the above error
>
@alex doesn't this mean that gn3 changes have not
been seen by tux01? If so, could you ping Arun to
update the server. Otherwise, could you collab
with Zach on a fix and track that on
gn-gemtext-threads?
@akumar289 thanks for this report. We are looking
into this. Sorry for the inconvenience.
--
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(hkp://keys.openpgp.org))
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zsloan ***@***.***> aliandika:
I can't update to the latest code because it complains about not being able
to import rust-correlation. I assume this is because a new profile needs to
be built after updating guix-bioinformatics, but the same way I used to do
this no longer seems to work (it now complains about not being able to find
"genenetwork2").
Perhaps @Arun can help; he has access to
production. FWIW, I tested out a build of the
latest GN2 and created a profile for it locally,
and things work just fine.
… On Thu, Aug 11, 2022 at 4:01 AM BonfaceKilz ***@***.***>
wrote:
> akumar289 ***@***.***> aliandika:
>
> > GeneNetwork tux01:gene:2.11-rc2-testing-85ad78373
> > run_sample_corr_cmd() got an unexpected keyword argument 'corr_method'
> (error)
> >
> > Running literature correlation and running into the above error
> >
>
> @alex doesn't this mean that gn3 changes have not
> been seen by tux01? If so, could you ping Arun to
> update the server. Otherwise, could you collab
> with Zach on a fix and track that on
> gn-gemtext-threads?
>
> @akumar289 thanks for this report. We are looking
> into this. Sorry for the inconvenience.
--
(To agree without understanding is inane.
To disagree without understanding is impudent.)
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It looks like the profile needs to be rebuilt. I don't yet have access to production, though I am trying to get access. So, I can't help immediately. Maybe @pjotrp can. |
Did a literature correlation using the Full Retina database and produced this error again
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Dear Aman, GN team.
I confirm that this is an error for ALL symbols. I used SHH as a well known
mouse symbol. Here is the trait I used:
*https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
<https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P>*
Here is the set-up in GN2
[image: Screen Shot 2022-08-16 at 8.59.12 AM.png]
And here is the error.
GeneNetwork tux01:gene:2.11-rc2-HEAD-fcd2897fa
run_sample_corr_cmd() got an unexpected keyword argument
'corr_method' (error)
Zach, are you the right person to fix this error today?
It has been down now for about a week or more.
…On Tue, Aug 16, 2022 at 07:49 akumar289 ***@***.***> wrote:
FWIW
Did a literature correlation using the Full Retina database and produced
this error again
GeneNetwork tux01:gene:2.11-rc2-HEAD-fcd2897fa
run_sample_corr_cmd() got an unexpected keyword argument 'corr_method'
(error)
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@BonfaceKilz I don't doubt that there's some way to do this; it's just that the old command for it no longer seems to work. This is the command I was using (to create a profile in my branch): env GUIX_PACKAGE_PATH='/home/zas1024/guix-bioinformatics:/home/zas1024/guix-past/modules' /home/zas1024/.config/guix/current/bin/guix install genenetwork2 -p ~/opt/gn2__20220812 --substitute-urls="http://guix.genenetwork.org https://berlin.guixsd.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org" It complains about there being no "genenetwork2" package; I tried substituting in a couple alternatives in case the names changed at some point (since I remember it used to be "python3-genenetwork2" until it was changed to genenetwork2, IIRC, and I also tried "genenetwork"). Instead of asking like this, is there a way I can check myself? |
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I reverted to earlier commits that I think should get the literature
correlation working again (but may lose other changes from the past couple
weeks).
On Tue, Aug 16, 2022 at 9:03 AM Rob Williams ***@***.***>
wrote:
… Dear Aman, GN team.
I confirm that this is an error for ALL symbols. I used SHH as a well known
mouse symbol. Here is the trait I used:
*
https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
<
https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
>*
Here is the set-up in GN2
[image: Screen Shot 2022-08-16 at 8.59.12 AM.png]
And here is the error.
GeneNetwork tux01:gene:2.11-rc2-HEAD-fcd2897fa
run_sample_corr_cmd() got an unexpected keyword argument
'corr_method' (error)
Zach, are you the right person to fix this error today?
It has been down now for about a week or more.
On Tue, Aug 16, 2022 at 07:49 akumar289 ***@***.***> wrote:
> FWIW
>
> Did a literature correlation using the Full Retina database and produced
> this error again
>
> GeneNetwork tux01:gene:2.11-rc2-HEAD-fcd2897fa
> run_sample_corr_cmd() got an unexpected keyword argument 'corr_method'
> (error)
>
> —
> Reply to this email directly, view it on GitHub
> <
#718 (comment)
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zsloan ***@***.***> aliandika:
> Perhaps @Arun can help; he has access to production. FWIW, I tested out a build of the latest GN2 and created a profile for it locally, and things work just fine.
@BonfaceKilz I don't doubt that there's some way to do this; it's just that the old command for it no longer seems to work. This is the command I was using (to create a profile in my branch):
env GUIX_PACKAGE_PATH='/home/zas1024/guix-bioinformatics:/home/zas1024/guix-past/modules' /home/zas1024/.config/guix/current/bin/guix install genenetwork2 -p ~/opt/gn2__20220812 --substitute-urls="http://guix.genenetwork.org https://berlin.guixsd.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org"
Ah I see. Arun is getting access to production so
he may be able to help.
It complains about there being no "genenetwork2" package; I tried substituting in a couple alternatives in case the names changed at some point (since I remember it used to be "python3-genenetwork2" until it was changed to genenetwork2, IIRC, and I also tried "genenetwork"). Instead of asking like this, is there a way I can check myself?
Yeah. One quick way, adapting you command above
would be to run:
/home/zas1024/.config/guix/current/bin/guix \
search -L /home/zas1024/guix-bioinformatics \
-L /home/zas1024/guix-past/modules genenetwork2
The above will tell you what version of GN2 we are
running. Alternatively, a more manual way to
check where GN2 is located and what version it's
at would be by looking directly in the upstream
repository here:
<https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/branch/master/gn/packages/genenetwork.scm#L158>
FWIW, you could jump to where genenetwork2 -
assuming the package is called "genenetwork2"
which it is atm - is defined by running:
/home/zas1024/.config/guix/current/bin/guix \
edit -L /home/zas1024/guix-bioinformatics \
-L /home/zas1024/guix-past/modules genenetwork2
and you can quickly see what commit GN2 is on.
I HTH'ed.
PS:
env GUIX_PACKAGE_PATH='/home/zas1024/guix-bioinformatics:/home/zas1024/guix-past/modules' /home/zas1024/.config/guix/current/bin/guix search
is equivalent to:
/home/zas1024/.config/guix/current/bin/guix -L /home/zas1024/guix-bioinformatics -L /home/zas1024/guix-past/modulessearch
Whereby the "-L" typically refers to [from the man
page]:
-L, --load-path=DIR prepend DIR to the package module search path
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(To agree without understanding is inane.
To disagree without understanding is impudent.)
(D4F09EB110177E03C28E2FE1F5BBAE1E0392253F
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Re-ran Lit correlation and ran into a new error (I think): Settings were lit correlation, top 1000, HEI Full Retina Illumina V6.2 (Apr10) RankInv, trait ID: ILMN_2547762
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Ah, I think that is new. Thanks for giving the dataset/options. I'll take a
look.
…On Wed, Aug 17, 2022, 5:32 PM akumar289 ***@***.***> wrote:
I reverted to earlier commits that I think should get the literature
correlation working again (but may lose other changes from the past couple
weeks). On Tue, Aug 16, 2022 at 9:03 AM Rob Williams *@*.
*> wrote: … <#m_58585285515054626_> Dear Aman, GN team. I confirm that
this is an error for ALL symbols. I used SHH as a well known mouse symbol.
Here is the trait I used: *
https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
<https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P>
<
https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P
<https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P>
> Here is the set-up in GN2 [image: Screen Shot 2022-08-16 at 8.59.12
AM.png] And here is the error. GeneNetwork
tux01:gene:2.11-rc2-HEAD-fcd2897fa run_sample_corr_cmd() got an unexpected
keyword argument 'corr_method' (error) Zach, are you the right person to
fix this error today? It has been down now for about a week or more. On
Tue, Aug 16, 2022 at 07:49 akumar289 @.**> wrote: > FWIW > > Did a
literature correlation using the Full Retina database and produced > this
error again > > GeneNetwork tux01:gene:2.11-rc2-HEAD-fcd2897fa >
run_sample_corr_cmd() got an unexpected keyword argument 'corr_method' >
(error) > > — > Reply to this email directly, view it on GitHub > < #718
(comment)
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re-ran Literature correlation and ran into I think a new error:
settings were lit correlation, top 1000, HEI Full Retina Illumina V6.2
(Apr10) RankInv
GeneNetwork tux01:gene:2.11-rc2-HEAD-e8bd857c6
Command '['python3', '-m', 'scripts.sample_correlations', 'pearson',
'/home/gn2/production/tmp/gn2/tmp8443bcr5/traitfile_3xYdm0U3Mt',
'/home/gn2/production/tmp/gn2/tmp8443bcr5/targetdb_2ITMn1AKO2',
'/home/gn2/production/tmp/gn2/tmp8443bcr5/corrs_sdDUH2Amcb']' returned
non-zero exit status 1. (error)HEI Full Retina Illumina V6.2 (Apr10)
RankInv
<http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Illum_Retina_BXD_RankInv0410>
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Was wondering if there was any update on this? Appreciate your help. I tried the same inputs as before and the same error appears as above
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I think I know what's happening with the literature correlation issue (I
believe it applies to any situation where you try to do literature
correlation against a dataset different from the dataset of the trait in
question), but probably won't be able to merge the fix for it until after
this week, since we're trying to avoid touching the production server
during that time.
…On Tue, Aug 23, 2022 at 2:33 PM akumar289 ***@***.***> wrote:
Was wondering if there was any update on this? Appreciate your help. I
tried the same inputs as before and the same error appears as above
GeneNetwork tux01:gene:2.11-rc2-HEAD-3e1f9f2b6
Command '['python3', '-m', 'scripts.sample_correlations', 'pearson',
'/home/gn2/production/tmp/gn2/tmp0_rp41hc/traitfile_dWcRNY6DsK',
'/home/gn2/production/tmp/gn2/tmp0_rp41hc/targetdb_qRZDu4Mmez',
'/home/gn2/production/tmp/gn2/tmp0_rp41hc/corrs_nQBccOkS5A']' returned
non-zero exit status 1. (error)
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Understood. However, I ran the literature correlation against the same dataset of the trait in question. |
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Was this the Hippocampus trait 1427571_at correlated against the same
Hippocampus dataset? The trait link above is for that trait, but in a later
comment you mentioned the Retina dataset.
Literature correlations works for me if I do the above trait against its
own dataset, but returned an error if I changed the target dataset to the
Retina one.
…On Tue, Aug 23, 2022 at 3:55 PM akumar289 ***@***.***> wrote:
Understood. However, I ran the literature correlation against the same
dataset of the trait in question.
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Running literature correlation and running into the above error
Running a sample r correlation and run into the above error
Running a partial correlation produces this above error
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