Failed to download annotation resource PROGENy from OmniPath

[Urja25]

Hi,

I am unable to retrieve Progeny data through OmnipathR. Here is the error:

> remotes::install_github('saezlab/OmnipathR')
> library(OmnipathR)
> packageVersion(OmnipathR)
Error: object 'OmnipathR' not found
> net <- decoupleR::get_progeny(organism = 'human', top = 500)
[2024-12-06 10:34:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-06 10:34:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-06 10:34:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-06 10:34:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-12-06 10:34:48] [TRACE]   [OmnipathR] Cache file path: /home/u855h/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-06 10:34:49] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-06 10:34:49] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-12-06 10:34:49] [TRACE]   [OmnipathR] Cache file path: /home/u855h/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-06 10:34:49] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-12-06 10:34:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-12-06 10:34:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/u855h/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-12-06 10:34:49] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-12-06 10:34:49] [SUCCESS] [OmnipathR] Loaded 2 annotation records from cache.
[2024-12-06 10:34:49] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.
Error in value[[3L]](cond) : 
  [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.

I am using R 4.4.0.

[deeenes]

There is a download error happening, which is hidden, but it also not covered by the log trace above, I'm missing the lines where the first attempt happens:

[2024-12-06 11:09:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-06 11:09:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-06 11:09:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-12-06 11:09:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-06 11:09:46] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-06 11:09:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-06 11:09:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-06 11:09:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`

To test out what's the original error, you can call this directly:

library(readr)
p <- read_tsv('https://omnipathdb.org/annotations?resources=PROGENy&license=academic')

[Urja25]

Thanks for the quick response. I installed PROGENy and did the following:

## We load the required packages
library(Seurat)
library(decoupleR)
library(OmnipathR)
packageVersion("decoupleR")
packageVersion("OmnipathR")

# interactions <- omnipath(
#   resources = c('SignaLink3', 'PhosphoSite', 'SIGNOR')
# )

# BiocManager::install("progeny")
# library(progeny)

# Only needed for data handling and plotting
library(dplyr)
library(tibble)
library(tidyr)
library(patchwork)
library(ggplot2)
library(pheatmap)

p <- Seurat::DimPlot(seurat_obj, 
                     reduction = "umap", 
                     label = TRUE, 
                     pt.size = 0.5) + 
  Seurat::NoLegend()
p


# omnipath_cache_wipe()
# omnipath_set_console_loglevel('trace')
# options(OmnipathR.static = TRUE)
# options(OmnipathR.server = "https://omnipathdb.org")
# OmnipathR::clear_cache()

net <- data("model_human_full", package = "progeny")
net
library(dplyr)

net_prepared <- model_human_full %>%
  rename(
    source = pathway,
    target = gene,
    weight = weight
  )
net_prepared
colnames(net_prepared)
net_prepared <- subset(net_prepared, !is.na(source) & !is.na(target))

mat <- as.matrix(seurat_obj@assays$RNA$data)

acts <- decoupleR::run_mlm(mat = mat, 
                           net = net_prepared, 
                           .source = 'source', 
                           .target = 'target',
                           .mor = 'weight', 
                           minsize = 5)

I get the following error:

> acts <- decoupleR::run_mlm(mat = mat, 
+                            net = net_prepared, 
+                            .source = 'source', 
+                            .target = 'target',
+                            .mor = 'weight', 
+                            minsize = 5)
Error in mor_mat[[.target, .source]] <- .weight : 
  [[ ]] subscript out of bounds

packageVersion("decoupleR")
[1] ‘2.9.7’
packageVersion("OmnipathR")
[1] ‘3.15.1’
packageVersion("progeny")
[1] ‘1.26.0’

[PauBadiaM]

Any updates on this @deeenes ?

[deeenes]

Hi @Urja25, Apologies for getting back to you with so much delay. If it's still relevant, I add some details below. progeny is an old, deprecated package, which indeed carries the original pathway scores as static data. Our current solution is to retrieve the scores from a web service, by the OmnipathR package.

Unfortunately in the logs above we don't see enough information about the original error. At the same time, over the last few weeks the downloader infrastructure of OmnipathR went thorough a major overhaul, and I also adjusted the error handling here in decoupleR. I recommend to perform the downloads again with an empty cache, after reinstalling both packages. If it still fails, the log will show much more information since the updates.

library(remotes)
remotes::install_github('saezlab/OmnipathR@devel')
remotes::install_github('saezlab/decoupleR@devel')

In a new R session:

library(decoupleR)
library(OmnipathR)

options(omnipathr.curl_verbose = TRUE)
omnipath_set_cachedir(tempdir())

net <- decoupleR::get_progeny(organism = 'human', top = 500)

omnipath_logfile()