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ramiromagno / gwasrapidd

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
https://rmagno.eu/gwasrapidd/
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Response code 500 when using get_studies() #25

Closed mightyphil2000 closed 2 years ago

mightyphil2000 commented 2 years ago

When I run:

gwasrapidd::get_studies(reported_trait = "Glioma")

I get this error message: Warning message: In gc_request_all(resource_url = resource_url, base_url = base_url, : The request for https://www.ebi.ac.uk/gwas/rest/api/studies/search/findByDiseaseTrait?diseaseTrait=Glioma failed: response code was 500.

Do you know why I am getting this error?

ramiromagno commented 2 years ago

I will look into it!

ramiromagno commented 2 years ago

It seems it might have been a GWAS Catalog server fluke. Just tried it now and it seems to be working. Could you try it yourself again?

library(gwasrapidd)
get_studies(reported_trait = "Glioma")
#> An object of class "studies"
#> Slot "studies":
#> # A tibble: 9 × 13
#>   study_id     reported_trait initial_sample_size replication_sampl… gxe   gxg  
#>   <chr>        <chr>          <chr>               <chr>              <lgl> <lgl>
#> 1 GCST000439   Glioma         1,878 European anc… 2,545 European an… FALSE FALSE
#> 2 GCST001633   Glioma         1,856 European anc… 5,015 European an… FALSE FALSE
#> 3 GCST001058   Glioma         4,147 European anc… <NA>               FALSE FALSE
#> 4 GCST001194   Glioma         781 European ances… <NA>               FALSE FALSE
#> 5 GCST003228   Glioma         1,783 Northern Eur… 1,490 European an… FALSE FALSE
#> 6 GCST004347   Glioma         12,469 European an… <NA>               FALSE FALSE
#> 7 GCST005931   Glioma         4,831 European anc… <NA>               FALSE FALSE
#> 8 GCST007842   Glioma         992 Han Chinese an… 2,105 Han Chinese… FALSE FALSE
#> 9 GCST90020047 Glioma         485 Han Chinese an… <NA>               FALSE FALSE
#> # … with 7 more variables: snp_count <int>, qualifier <chr>, imputed <lgl>,
#> #   pooled <lgl>, study_design_comment <chr>, full_pvalue_set <lgl>,
#> #   user_requested <lgl>
#> 
#> Slot "genotyping_techs":
#> # A tibble: 9 × 2
#>   study_id     genotyping_technology       
#>   <chr>        <chr>                       
#> 1 GCST000439   Genome-wide genotyping array
#> 2 GCST001633   Genome-wide genotyping array
#> 3 GCST001058   Genome-wide genotyping array
#> 4 GCST001194   Genome-wide genotyping array
#> 5 GCST003228   Genome-wide genotyping array
#> 6 GCST004347   Genome-wide genotyping array
#> 7 GCST005931   Genome-wide genotyping array
#> 8 GCST007842   Genome-wide genotyping array
#> 9 GCST90020047 Genome-wide genotyping array
#> 
#> Slot "platforms":
#> # A tibble: 10 × 2
#>    study_id     manufacturer
#>    <chr>        <chr>       
#>  1 GCST000439   Illumina    
#>  2 GCST001633   Illumina    
#>  3 GCST001058   Illumina    
#>  4 GCST001194   Illumina    
#>  5 GCST003228   Illumina    
#>  6 GCST004347   Illumina    
#>  7 GCST005931   Affymetrix  
#>  8 GCST005931   Illumina    
#>  9 GCST007842   Illumina    
#> 10 GCST90020047 Affymetrix  
#> 
#> Slot "ancestries":
#> # A tibble: 13 × 4
#>    study_id     ancestry_id type        number_of_individuals
#>    <chr>              <int> <chr>                       <int>
#>  1 GCST000439             1 initial                      5548
#>  2 GCST000439             2 replication                  5498
#>  3 GCST001633             1 initial                      6811
#>  4 GCST001633             2 replication                 16616
#>  5 GCST001058             1 initial                     11582
#>  6 GCST001194             1 initial                      4773
#>  7 GCST003228             1 initial                     11582
#>  8 GCST003228             2 replication                  3213
#>  9 GCST004347             1 initial                     30659
#> 10 GCST005931             1 initial                     18723
#> 11 GCST007842             1 initial                      2000
#> 12 GCST007842             2 replication                  5479
#> 13 GCST90020047           1 initial                       970
#> 
#> Slot "ancestral_groups":
#> # A tibble: 13 × 3
#>    study_id     ancestry_id ancestral_group
#>    <chr>              <int> <chr>          
#>  1 GCST000439             1 European       
#>  2 GCST000439             2 European       
#>  3 GCST001633             1 European       
#>  4 GCST001633             2 European       
#>  5 GCST001058             1 European       
#>  6 GCST001194             1 European       
#>  7 GCST003228             1 European       
#>  8 GCST003228             2 European       
#>  9 GCST004347             1 European       
#> 10 GCST005931             1 European       
#> 11 GCST007842             1 East Asian     
#> 12 GCST007842             2 East Asian     
#> 13 GCST90020047           1 East Asian     
#> 
#> Slot "countries_of_origin":
#> # A tibble: 6 × 5
#>   study_id     ancestry_id country_name major_area region
#>   <chr>              <int> <chr>        <chr>      <chr> 
#> 1 GCST003228             1 <NA>         <NA>       <NA>  
#> 2 GCST003228             2 <NA>         <NA>       <NA>  
#> 3 GCST005931             1 <NA>         <NA>       <NA>  
#> 4 GCST007842             1 <NA>         <NA>       <NA>  
#> 5 GCST007842             2 <NA>         <NA>       <NA>  
#> 6 GCST90020047           1 <NA>         <NA>       <NA>  
#> 
#> Slot "countries_of_recruitment":
#> # A tibble: 38 × 5
#>    study_id   ancestry_id country_name major_area       region               
#>    <chr>            <int> <chr>        <chr>            <chr>                
#>  1 GCST000439           1 U.S.         Northern America <NA>                 
#>  2 GCST000439           1 U.K.         Europe           Northern Europe      
#>  3 GCST000439           2 Sweden       Europe           Northern Europe      
#>  4 GCST000439           2 Germany      Europe           Western Europe       
#>  5 GCST000439           2 France       Europe           Western Europe       
#>  6 GCST001633           1 Finland      Europe           Northern Europe      
#>  7 GCST001633           1 Sweden       Europe           Northern Europe      
#>  8 GCST001633           1 U.S.         Northern America <NA>                 
#>  9 GCST001633           1 Israel       Asia             Western Asia         
#> 10 GCST001633           1 Australia    Oceania          Australia/New Zealand
#> # … with 28 more rows
#> 
#> Slot "publications":
#> # A tibble: 9 × 7
#>   study_id     pubmed_id publication_date publication      title author_fullname
#>   <chr>            <int> <date>           <chr>            <chr> <chr>          
#> 1 GCST000439    19578367 2009-07-05       Nat Genet        Geno… Shete S        
#> 2 GCST001633    22886559 2012-08-11       Hum Genet        Geno… Rajaraman P    
#> 3 GCST001058    21531791 2011-04-29       Hum Mol Genet    Chro… Sanson M       
#> 4 GCST001194    21827660 2011-08-09       BMC Med Genomics Comb… Yang TH        
#> 5 GCST003228    26424050 2015-10-01       Nat Commun       Geno… Kinnersley B   
#> 6 GCST004347    28346443 2017-03-27       Nat Genet        Geno… Melin BS       
#> 7 GCST005931    29743610 2018-05-09       Sci Rep          Sex-… Ostrom QT      
#> 8 GCST007842    30714141 2019-02-04       Int J Cancer     Two … Chen H         
#> 9 GCST90020047  34319593 2021-07-28       Int J Cancer     Gene… Li N           
#> # … with 1 more variable: author_orcid <chr>

Created on 2021-11-23 by the reprex package (v2.0.1)

mightyphil2000 commented 2 years ago

Thanks Ramiro

Yes it's working now!

bw philip

From: Ramiro Magno @.> Sent: 23 November 2021 15:18 To: ramiromagno/gwasrapidd @.> Cc: Philip Haycock @.>; Author @.> Subject: Re: [ramiromagno/gwasrapidd] Response code 500 when using get_studies() (Issue #25)

It seems it might have been a GWAS Catalog server fluke. Just tried it now and it seems to be working. Could you try it yourself again?

library(gwasrapidd)

get_studies(reported_trait = "Glioma")

> An object of class "studies"

> Slot "studies":

> # A tibble: 9 × 13

> study_id reported_trait initial_sample_size replication_sampl… gxe gxg

>

> 1 GCST000439 Glioma 1,878 European anc… 2,545 European an… FALSE FALSE

> 2 GCST001633 Glioma 1,856 European anc… 5,015 European an… FALSE FALSE

> 3 GCST001058 Glioma 4,147 European anc… FALSE FALSE

> 4 GCST001194 Glioma 781 European ances… FALSE FALSE

> 5 GCST003228 Glioma 1,783 Northern Eur… 1,490 European an… FALSE FALSE

> 6 GCST004347 Glioma 12,469 European an… FALSE FALSE

> 7 GCST005931 Glioma 4,831 European anc… FALSE FALSE

> 8 GCST007842 Glioma 992 Han Chinese an… 2,105 Han Chinese… FALSE FALSE

> 9 GCST90020047 Glioma 485 Han Chinese an… FALSE FALSE

> # … with 7 more variables: snp_count , qualifier , imputed ,

> # pooled , study_design_comment , full_pvalue_set ,

> # user_requested

>

> Slot "genotyping_techs":

> # A tibble: 9 × 2

> study_id genotyping_technology

>

> 1 GCST000439 Genome-wide genotyping array

> 2 GCST001633 Genome-wide genotyping array

> 3 GCST001058 Genome-wide genotyping array

> 4 GCST001194 Genome-wide genotyping array

> 5 GCST003228 Genome-wide genotyping array

> 6 GCST004347 Genome-wide genotyping array

> 7 GCST005931 Genome-wide genotyping array

> 8 GCST007842 Genome-wide genotyping array

> 9 GCST90020047 Genome-wide genotyping array

>

> Slot "platforms":

> # A tibble: 10 × 2

> study_id manufacturer

>

> 1 GCST000439 Illumina

> 2 GCST001633 Illumina

> 3 GCST001058 Illumina

> 4 GCST001194 Illumina

> 5 GCST003228 Illumina

> 6 GCST004347 Illumina

> 7 GCST005931 Affymetrix

> 8 GCST005931 Illumina

> 9 GCST007842 Illumina

> 10 GCST90020047 Affymetrix

>

> Slot "ancestries":

> # A tibble: 13 × 4

> study_id ancestry_id type number_of_individuals

>

> 1 GCST000439 1 initial 5548

> 2 GCST000439 2 replication 5498

> 3 GCST001633 1 initial 6811

> 4 GCST001633 2 replication 16616

> 5 GCST001058 1 initial 11582

> 6 GCST001194 1 initial 4773

> 7 GCST003228 1 initial 11582

> 8 GCST003228 2 replication 3213

> 9 GCST004347 1 initial 30659

> 10 GCST005931 1 initial 18723

> 11 GCST007842 1 initial 2000

> 12 GCST007842 2 replication 5479

> 13 GCST90020047 1 initial 970

>

> Slot "ancestral_groups":

> # A tibble: 13 × 3

> study_id ancestry_id ancestral_group

>

> 1 GCST000439 1 European

> 2 GCST000439 2 European

> 3 GCST001633 1 European

> 4 GCST001633 2 European

> 5 GCST001058 1 European

> 6 GCST001194 1 European

> 7 GCST003228 1 European

> 8 GCST003228 2 European

> 9 GCST004347 1 European

> 10 GCST005931 1 European

> 11 GCST007842 1 East Asian

> 12 GCST007842 2 East Asian

> 13 GCST90020047 1 East Asian

>

> Slot "countries_of_origin":

> # A tibble: 6 × 5

> study_id ancestry_id country_name major_area region

>

> 1 GCST003228 1

> 2 GCST003228 2

> 3 GCST005931 1

> 4 GCST007842 1

> 5 GCST007842 2

> 6 GCST90020047 1

>

> Slot "countries_of_recruitment":

> # A tibble: 38 × 5

> study_id ancestry_id country_name major_area region

>

> 1 GCST000439 1 U.S. Northern America

> 2 GCST000439 1 U.K. Europe Northern Europe

> 3 GCST000439 2 Sweden Europe Northern Europe

> 4 GCST000439 2 Germany Europe Western Europe

> 5 GCST000439 2 France Europe Western Europe

> 6 GCST001633 1 Finland Europe Northern Europe

> 7 GCST001633 1 Sweden Europe Northern Europe

> 8 GCST001633 1 U.S. Northern America

> 9 GCST001633 1 Israel Asia Western Asia

> 10 GCST001633 1 Australia Oceania Australia/New Zealand

> # … with 28 more rows

>

> Slot "publications":

> # A tibble: 9 × 7

> study_id pubmed_id publication_date publication title author_fullname

>

> 1 GCST000439 19578367 2009-07-05 Nat Genet Geno… Shete S

> 2 GCST001633 22886559 2012-08-11 Hum Genet Geno… Rajaraman P

> 3 GCST001058 21531791 2011-04-29 Hum Mol Genet Chro… Sanson M

> 4 GCST001194 21827660 2011-08-09 BMC Med Genomics Comb… Yang TH

> 5 GCST003228 26424050 2015-10-01 Nat Commun Geno… Kinnersley B

> 6 GCST004347 28346443 2017-03-27 Nat Genet Geno… Melin BS

> 7 GCST005931 29743610 2018-05-09 Sci Rep Sex-… Ostrom QT

> 8 GCST007842 30714141 2019-02-04 Int J Cancer Two … Chen H

> 9 GCST90020047 34319593 2021-07-28 Int J Cancer Gene… Li N

> # … with 1 more variable: author_orcid

Created on 2021-11-23 by the reprex packagehttps://reprex.tidyverse.org (v2.0.1)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ramiromagno/gwasrapidd/issues/25#issuecomment-976700255, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACSDAPQH2N44HJ5B34XVBZ3UNOWFZANCNFSM5ITWETYQ.

ramiromagno commented 2 years ago

Great, thanks!

mightyphil2000 commented 2 years ago

Hi Ramiro

I'm getting the same error again.

gwasrapidd::get_studies(reported_trait = "Glioma") Warning message: In gc_request_all(resource_url = resource_url, base_url = base_url, : The request for https://www.ebi.ac.uk/gwas/rest/api/studies/search/findByDiseaseTrait?diseaseTrait=Glioma failed: response code was 500.

ramiromagno commented 2 years ago

Hi Philip,

When I try it from my machine, it seems to be working okay; so I am guessing that the problem is with the GWAS Catalog server. It might be unstable for some reason at this time... Perhaps they are doing some sort of maintenance on the REST API. I don't know... My advice is to send an email to them asking about this issue: gwas-dev@ebi.ac.uk. Feel free to put in me in Cc for me to accompany this problem (My email is in the DESCRIPTION file of the gwasrapidd repo).

ramiromagno commented 2 years ago

Hi GWAS Devs,

I am getting 500 response errors all over again...

https://www.ebi.ac.uk/gwas/rest/api/studies https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0005537 etc...

On Wed, 24 Nov 2021 at 12:11, mightyphil2000 @.***> wrote:

Hi Ramiro

I'm getting the same error again.

Warning message: In gc_request_all(resource_url = resource_url, base_url = base_url, : The request for https://www.ebi.ac.uk/gwas/rest/api/studies/search/findByDiseaseTrait?diseaseTrait=Glioma failed: response code was 500.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/ramiromagno/gwasrapidd/issues/25#issuecomment-977818669, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEXRG4E4SQAHKYQKVUA4BETUNTI75ANCNFSM5ITWETYQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

ramiromagno commented 2 years ago

Hi Philip,

I got an update from the GWAS team. It seems that these downtime issues are now resolved. Please let me know if it is working for you.