Organism not found

[alessio colantoni]

Hello, I am working with the R package WebGestaltR_0.4.4. I have been using

for two years without problems. Today I got the "Organism is missing error" when I use the

WebGestaltR function on the same dataset I used without problems in the past. I tried both the ORA and GSEA analyses, and other hsapiens and mmusculus datasets, but I get always the same error. I suspect that the APIs are not working, as is suggested from the traceback I am posting here. Would it be possible to fix this? 

8.

stop(webApiError(mapR))

7.

idMappingGene(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, sourceIdType = sourceIdType, targetIdType = targetIdType, collapseMethod = collapseMethod, mappingOutput = mappingOutput, outputFileName = outputFileName, hostName = hostName)

6.

idMapping(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, sourceIdType = geneType, targetIdType = NULL, collapseMethod = collapseMethod, mappingOutput = FALSE, cache = cache, hostName = hostName)

5.

.uploadGeneExistingOrganism(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, geneType = geneType, collapseMethod = collapseMethod, geneSet = geneSet, cache = cache, hostName = hostName)

4.

loadInterestGene(organism = organism, dataType = "rnk", inputGeneFile = interestGeneFile, inputGene = interestGene, geneType = interestGeneType, collapseMethod = collapseMethod, cache = cache, hostName = hostName, geneSet = geneSet)

3.

WebGestaltRGsea(organism = organism, enrichDatabase = enrichDatabase, enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType, enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile, interestGeneFile = interestGeneFile, interestGene = interestGene, ...

2.

WebGestaltR(organism = "hsapiens", enrichDatabase = cateGory, outputDirectory = OUT.DIR.GSEA[[1]], enrichMethod = "GSEA", interestGene = rankList[0:1000, ], interestGeneType = "ensembl_gene_id", nThreads = 20, projectName = projName, ...)

1.

gseaEnrich_single(resLFC_D7.anno, "Day7_G203G_G203R", "geneontology_Biological_Process", sigMethod = "top", topThr = 40)

[John Elizarraras]

This was due to an update to the API from http to https. The original http version was restored, so you should be able to run your scripts without any changes on your end. The new version will use https by default.

If you are still having problems with this in the future, you can manually set hostName to https://www.webgestalt.org/

For example

WebGestaltR(organism = "hsapiens", enrichDatabase = cateGory, outputDirectory = OUT.DIR.GSEA[[1]], enrichMethod = "GSEA", interestGene = rankList[0:1000, ], interestGeneType = "ensembl_gene_id", nThreads = 20, projectName = projName, hostName="https://www.webgestalt.org/")

Best,

John

[alessio colantoni]

Dear John,

now it is working. Thank you so much.

Best regards,

Alessio

[Alejandro Valenzuela]

Hello,

I found the same problem some weeks ago, and it was solved when using the parameter hostname="https:/www.webgestalt.org/" in the WebgestaltR function as you suggested,

But today the problem appeared again, even using this webgestalt hostname link, any clues how to solve this?

This is the function I run-->

 WebGestaltR(enrichMethod = "ORA",
              organism = "hsapiens",
              enrichDatabase = "pathway_KEGG",
              hostName = "https:/www.webgestalt.org/",
              interestGene = as.character(Val_genes),
              interestGeneType = "genesymbol",
              referenceGene = as.character(Back_genes),
              fdrThr = 0.05,
              referenceGeneType = "genesymbol",
              outputDirectory = "Webgestalt_ENRICH_JUL23/",
              projectName = "trait1")

Thank you and look forward to your answer,

Alejandro

[Yuxing Liao]

Hi, could you try again? There was a problem with the server earlier today.

Yuxing

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