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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Error in PlatypusDB_find_CDR3s function #53

Open beginner984 opened 1 year ago

beginner984 commented 1 year ago

Hi

Sorry, I get error in PlatypusDB_find_CDR3s function

I tried to change the names in project metadata but did not work

Any suggestion please?

> names(projects_metadata)
[1] "agrafiotis2021a"     "horns2020a"          "khatun2021a"         "kreiner2021a"        "kreiner2021b"       
[6] "kuhn2021a"           "mathew2021a"         "merkenschlager2021a" "neumeier2021a"       "neumeier2021b"      
[11] "sandu2021a"          "shlesinger2022a"     "shlesinger2022b"     "shlesinger2022c"     "yermanos2021a"      
[16] "yermanos2021b"       "yermanos2022a"       "yermanos2022b"       "yermanos2022c"       "yewdell2021a"       
[21] "yost2019"           
> names(projects_metadata)=paste(names(projects_metadata), "__CDR3s", sep="")
> names(projects_metadata)
[1] "agrafiotis2021a__CDR3s"     "horns2020a__CDR3s"          "khatun2021a__CDR3s"        
[4] "kreiner2021a__CDR3s"        "kreiner2021b__CDR3s"        "kuhn2021a__CDR3s"          
[7] "mathew2021a__CDR3s"         "merkenschlager2021a__CDR3s" "neumeier2021a__CDR3s"      
[10] "neumeier2021b__CDR3s"       "sandu2021a__CDR3s"          "shlesinger2022a__CDR3s"    
[13] "shlesinger2022b__CDR3s"     "shlesinger2022c__CDR3s"     "yermanos2021a__CDR3s"      
[16] "yermanos2021b__CDR3s"       "yermanos2022a__CDR3s"       "yermanos2022b__CDR3s"      
[19] "yermanos2022c__CDR3s"       "yewdell2021a__CDR3s"        "yost2019__CDR3s"           
>                     public_clones <- PlatypusDB_find_CDR3s(VDJ.cdr3s.aa = c("CMRYGNYWYFDVW") , VJ.cdr3s.aa = c("CLQHGESPFTF"), projects.to.search = "ALL")
Failed to load agrafiotis2021a__CDR3s. Skipping this dataset 

Failed to load horns2020a__CDR3s. Skipping this dataset 

Failed to load khatun2021a__CDR3s. Skipping this dataset 

Failed to load kreiner2021a__CDR3s. Skipping this dataset 

Failed to load kreiner2021b__CDR3s. Skipping this dataset 

Failed to load kuhn2021a__CDR3s. Skipping this dataset 

Failed to load mathew2021a__CDR3s. Skipping this dataset 

Failed to load merkenschlager2021a__CDR3s. Skipping this dataset 

Failed to load neumeier2021a__CDR3s. Skipping this dataset 

Failed to load neumeier2021b__CDR3s. Skipping this dataset 

Error in load(url(url_), envir = .GlobalEnv) : 
  cannot open the connection to 'https://storage.googleapis.com/platypusdb_cdr3s/sandu2021a__CDR3s.RData'
In addition: Warning message:
  In load(url(url_), envir = .GlobalEnv) :
  cannot open URL 'https://storage.googleapis.com/platypusdb_cdr3s/sandu2021a__CDR3s.RData': HTTP status was '404 Not Found'
Error in get(to_download[i]) : object 'sandu2021a__CDR3s' not found
>
vickreiner commented 1 year ago

Hi,

this must be an issue with the database on our side. We will check that and update!