Orthology translation does not work: oma_pairwise fails with HTTP 503

[ZZQ-1117]

net <- get_progeny(organism = 'mouse', top = 500)

[2024-04-23 21:14:14] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
Error in usemethod( mutate ) no applicable method for 'mutate' applied to an object of class list

[deeenes]

Hello, Could you please share a full trace (by traceback, or by rlang::last_trace), and also the output of sessionInfo()?

[ZZQ-1117]

您的邮件已收到，正忙，稍后给您回复......

[ZZQ-1117]

> library(decoupleR)
> library(dplyr)
> library(tibble)
> library(tidyr)
> library(ggplot2)
> library(pheatmap)
> library(ggrepel)
> net <- get_progeny(organism = 'human', top = 500)
[2024-04-24 01:26:29] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
> net <- get_progeny(organism = 'mouse', top = 500)
[2024-04-24 01:26:46] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
Error in UseMethod("mutate") : "mutate"没有适用于"list"目标对象的方法
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggrepel_0.9.5   pheatmap_1.0.12 ggplot2_3.5.0   tidyr_1.3.1     tibble_3.2.1   
[6] dplyr_1.1.4     decoupleR_2.9.7

loaded via a namespace (and not attached):
  [1] logger_0.3.0            readxl_1.4.3            rlang_1.1.3            
  [4] magrittr_2.0.3          compiler_4.3.1          systemfonts_1.0.5      
  [7] vctrs_0.6.5             devEMF_4.4-2            rvest_1.0.4            
 [10] stringr_1.5.1           httpcode_0.3.0          pkgconfig_2.0.3        
 [13] crayon_1.5.2            fastmap_1.1.1           backports_1.4.1        
 [16] ellipsis_0.3.2          utf8_1.2.4              promises_1.2.1         
 [19] rmarkdown_2.26          tzdb_0.4.0              ragg_1.2.7             
 [22] bit_4.0.5               purrr_1.0.2             xfun_0.43              
 [25] jsonlite_1.8.8          progress_1.2.3          later_1.3.2            
 [28] uuid_1.2-0              BiocParallel_1.34.2     tweenr_2.0.2           
 [31] broom_1.0.5             parallel_4.3.1          prettyunits_1.2.0      
 [34] R6_2.5.1                stringi_1.8.3           RColorBrewer_1.1-3     
 [37] parallelly_1.37.0       lubridate_1.9.3         cellranger_1.1.0       
 [40] Rcpp_1.0.12             knitr_1.46              base64enc_0.1-3        
 [43] readr_2.1.5             httpuv_1.6.14           Matrix_1.6-5           
 [46] igraph_2.0.3            timechange_0.3.0        tidyselect_1.2.1       
 [49] rstudioapi_0.15.0       yaml_2.3.8              codetools_0.2-19       
 [52] curl_5.2.0              lattice_0.22-5          shiny_1.8.0            
 [55] withr_3.0.0             flextable_0.9.4         askpass_1.2.0          
 [58] evaluate_0.23           polyclip_1.10-6         zip_2.3.1              
 [61] stargazer_5.2.3         xml2_1.3.6              pillar_1.9.0           
 [64] checkmate_2.3.1         generics_0.1.3          vroom_1.6.5            
 [67] hms_1.1.3               munsell_0.5.1           scales_1.3.0           
 [70] xtable_1.8-4            OmnipathR_3.10.1        glue_1.7.0             
 [73] gdtools_0.3.6           tools_4.3.1             gfonts_0.2.0           
 [76] data.table_1.15.0       openxlsx_4.2.5.2        rgl_1.2.8              
 [79] cowplot_1.1.3           grid_4.3.1              colorspace_2.1-0       
 [82] export_0.3.0            ggforce_0.4.2           cli_3.6.2              
 [85] rappdirs_0.3.3          rvg_0.3.3               textshaping_0.3.7      
 [88] officer_0.6.5           fontBitstreamVera_0.1.1 fansi_1.0.6            
 [91] gtable_0.3.4            selectr_0.4-2           digest_0.6.34          
 [94] fontquiver_0.2.1        crul_1.4.0              htmlwidgets_1.6.4      
 [97] farver_2.1.1            htmltools_0.5.7         lifecycle_1.0.4        
[100] httr_1.4.7              mime_0.12               bit64_4.0.5            
[103] fontLiberation_0.1.0    openssl_2.1.1           MASS_7.3-60.0.1   



> traceback
function (x = NULL, max.lines = getOption("traceback.max.lines", 
    getOption("deparse.max.lines", -1L))) 
{
    n <- length(x <- .traceback(x, max.lines = max.lines))
    if (n == 0L) 
        cat(gettext("No traceback available"), "\n")
    else {
        for (i in 1L:n) {
            xi <- x[[i]]
            label <- paste0(n - i + 1L, ": ")
            m <- length(xi)
            srcloc <- if (!is.null(srcref <- attr(xi, "srcref"))) {
                srcfile <- attr(srcref, "srcfile")
                paste0(" at ", basename(srcfile$filename), "#", 
                  srcref[1L])
            }
            if (isTRUE(attr(xi, "truncated"))) {
                xi <- c(xi, " ...")
                m <- length(xi)
            }
            if (!is.null(srcloc)) {
                xi[m] <- paste0(xi[m], srcloc)
            }
            if (m > 1) 
                label <- c(label, rep(substr("          ", 1L, 
                  nchar(label, type = "w")), m - 1L))
            cat(paste0(label, xi), sep = "\n")
        }
    }
    invisible(x)
}
<bytecode: 0x0000024a8f63f2a8>
<environment: namespace:base> 

[ZZQ-1117]

"human" can run successfully, but "mouse" will error

Thank you

[deeenes]

Thanks! Above you pasted the code of the traceback function, you have to call it: traceback(). Also, before checking again, I'd recommend to update OmnipathR from git:

remotes::install_github('saezlab/OmnipathR')

[ZZQ-1117]

I am so sorry, I have updated "OmnipathR" according to your suggestion. Unfortunately, it shows the same error.

> traceback()
29: mutate(., across(starts_with("id_organism"), ~str_extract(.x, 
        "([^_]*)")))
28: filter(., !str_detect(id_organism_a, sprintf("%s\\d+", organism_a)) & 
        !str_detect(id_organism_b, sprintf("%s\\d+", organism_b)) & 
        mapping %in% mappings)
27: "oma_pairwise" %>% generic_downloader(reader_param = list(col_names = c("id_organism_a", 
        "id_organism_b", "mapping", "oma_group"), col_types = cols(), 
        comment = "#"), url_param = list(organism_a, organism_b, 
        id_type)) %>% mutate(across(starts_with("id_organism"), ~str_extract(.x, 
        "([^_]*)"))) %>% filter(!str_detect(id_organism_a, sprintf("%s\\d+", 
        organism_a)) & !str_detect(id_organism_b, sprintf("%s\\d+", 
        organism_b)) & mapping %in% mappings) %>% {
        if (only_ids) 
            select(., id_organism_a, id_organism_b)
        else .
    }
26: (function (organism_a = "human", organism_b = "mouse", id_type = "uniprot", 
        mappings = c("1:1", "1:m", "n:1", "n:m"), only_ids = TRUE) 
    {
        .slow_doctest()
        if (id_type == "genesymbol") {
            id_type <- "uniprot"
            return(environment() %>% as.list %>% exec(oma_pairwise_genesymbols, 
                !!!.))
        }
        id_organism_a <- id_organism_b <- mapping <- NULL
        organism_a %<>% oma_code
        organism_b %<>% oma_code
        id_type %<>% oma_id_type
        args <- match.call() %>% as.list %>% tail(-1L)
        for (arg in names(args)) {
            if (is.null(get(arg)) || any(is.na(get(arg)))) {
                msg <- sprintf("Could not recognize %s: `%s`.", if (arg == 
                    "id_type") 
                    "ID type"
                else "organism", args[[arg]])
     ...
25: exec(loader, !!!param)
24: load_db(key, param = param)
23: get_db(db_name, param = orthology_param)
22: select(., -any_of("hgroup"))
21: set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
20: get_db(db_name, param = orthology_param) %>% select(-any_of("hgroup")) %>% 
        set_names(c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL)) %>% {
        if (translate_complexes) 
            bind_rows(., complex_orthology(orthology = ., identifiers = data %>% 
                pull(!!sym(column)), one_to_many = translate_complexes))
        else .
    }
19: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
        replace = TRUE)
18: OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
17: OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
        replace = TRUE) %>% OmnipathR::translate_ids(., uniprot, 
        genesymbol, organism = organism)
16: tryCatch(OmnipathR::import_omnipath_annotations(resources = name, 
        ..., wide = TRUE), error = function(e) {
        tryCatch(OmnipathR::static_table(query = "annotations", resource = name, 
            organism = organism), error = function(e) {
            msg <- sprintf(paste0("[decoupleR] Failed to download annotation resource `%s` ", 
                "from OmniPath. For more information, see the OmnipathR log."), 
                name)
            OmnipathR::omnipath_msg("error", msg)
            stop(msg)
        })
    }) %>% {
        if (organism != 9606L) 
            OmnipathR::orthology_translate_column(., "uniprot", target_organism = organism, 
                replace = TRUE) %>% OmnipathR::translate_ids(., uniprot, 
                genesymbol, organism = organism)
        else .
    }
15: get_resource("PROGENy", organism = organism)
14: dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
13: dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
12: dplyr::select(., genesymbol, p_value, pathway, weight)
11: dplyr::group_by(., pathway)
10: dplyr::group_split(.)
9: vctrs_vec_compat(.x, .purrr_user_env)
8: map_("list", .x, .f, ..., .progress = .progress)
7: purrr::map(., function(df) {
       df %>% dplyr::arrange(p_value) %>% head(top)
   })
6: list2(...)
5: dplyr::bind_rows(.)
4: dplyr::select(., pathway, genesymbol, weight, p_value)
3: rlang::set_names(., c("source", "target", "weight", "p_value"))
2: get_resource("PROGENy", organism = organism) %>% dplyr::distinct(pathway, 
       genesymbol, .keep_all = TRUE) %>% dplyr::mutate(weight = as.double(weight), 
       p_value = as.double(p_value)) %>% dplyr::select(genesymbol, 
       p_value, pathway, weight) %>% dplyr::group_by(pathway) %>% 
       dplyr::group_split() %>% purrr::map(function(df) {
       df %>% dplyr::arrange(p_value) %>% head(top)
   }) %>% dplyr::bind_rows() %>% dplyr::select(pathway, genesymbol, 
       weight, p_value) %>% rlang::set_names(c("source", "target", 
       "weight", "p_value"))
1: get_progeny(organism = "mouse", top = 500)

[deeenes]

Thanks for the traceback, I found that OMA, the resource that we use for gene orthology data, has updated its HTTP API very recently. Hence I have to do some updates in OmnipathR, adjusting it to the new API. I'll do this most likely tomorrow, and let you know here once ready. Thank you for reporting this issue!

[deeenes]

Hello, I've done the updates required by the new OMA API. If you update OmnipathR from github, I expect it should work:

remotes::install_github('saezlab/OmnipathR')