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’