Merge pull request #173 from ropensci/patch_T171

Patch t171

.Rbuildignore

@@ -21,3 +21,4 @@ revdep
 ^pkgdown$
 ^codecov\.yml$
 ^revdep$
+^CRAN-SUBMISSION$

R/allgensnp.R

@@ -18,7 +18,25 @@ allgensnp <- function(snp = NA, usersubset = FALSE, ...) {
   }else{
     url2 <- paste(osnp_base(), "snps/", snp, ".json", sep = "")
   }
-  out <- os_GET(url2, list(), ...)
+
+  tryCatch(
+    {
+      out <- os_GET(url2, list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
+
   tt <- jsonlite::fromJSON(out, FALSE)
   rbl(lapply(tt, function(z) {
     snp <- data.frame(z$snp, stringsAsFactors = FALSE)

R/allphenotypes.R

@@ -24,7 +24,24 @@
 #' datalist[c("mouth size", "SAT Writing")] # get data.frame for 'ADHD'
 #' }
 allphenotypes <- function(df = FALSE, ...) {
-  out <- os_GET(paste0(osnp_base(), "phenotypes.json"), list(), ...)
+  tryCatch(
+    {
+      out <- os_GET(paste0(osnp_base(), "phenotypes.json"), list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
+
   out <- jsonlite::fromJSON(out, simplifyVector = FALSE)
   if (df) {
     ldply(out, function(x) {

R/annotations.R

@@ -30,7 +30,25 @@
 annotations <- function(snp = NA,
                         output = c("all", "plos", "mendeley", "snpedia", "metadata"), ...) {
   url <- paste0(osnp_base(), "snps/json/annotation/", snp, ".json")
-  out <- os_GET(url, list(), ...)
+
+  tryCatch(
+    {
+      out <- os_GET(url, list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
+
   out <- jsonlite::fromJSON(out, FALSE)
   source_ <- match.arg(
     output, c("all", "plos", "mendeley", "snpedia", "metadata"),

R/fetch_genotypes.R

@@ -45,10 +45,25 @@
 #' }
 fetch_genotypes <- function(url, rows = 100, filepath = NULL, quiet = TRUE, ...) {
   if (is.null(filepath)) filepath <- tempfile(fileext = ".txt")
-  utils::download.file(url, destfile = filepath, quiet = quiet, ...)
+
+  tryCatch(
+    {
+      utils::download.file(url, destfile = filepath, quiet = quiet, ...)
+    },
+    error = function(e) {
+      message("Failed to retrieve data. Please check the URL or try again later.")
+      stop("No URL available")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      return(NULL)
+    }
+  )
   df <- utils::read.table(filepath,
-    sep = "\t", nrows = rows, header = FALSE,
-    comment.char = "#", stringsAsFactors = FALSE
+                          sep = "\t", nrows = rows, header = FALSE,
+                          comment.char = "#", stringsAsFactors = FALSE
   )
   stats::setNames(df, c("rsid", "chromosome", "position", "genotype"))
 }

R/genotypes.R

@@ -15,7 +15,24 @@
 #' }
 genotypes <- function(snp = NA, userid = NA, df = FALSE, ...) {
   url2 <- paste0(paste0(osnp_base(), "snps/json/"), snp, "/", userid, ".json")
-  res <- os_GET(url2, list(), ...)
+
+ tryCatch(
+    {
+      res <- os_GET(url2, list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
   genotypes_ <- jsonlite::fromJSON(res, FALSE)
 
   if (df) {

R/phenotypes.R

@@ -23,7 +23,24 @@
 #' }
 phenotypes <- function(userid = NA, df = FALSE, ...) {
   url2 <- paste0(paste0(osnp_base(), "phenotypes/json/"), userid, ".json")
-  res <- os_GET(url2, list(), ...)
+
+  tryCatch(
+    {
+      res <- os_GET(url2, list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
   out <- jsonlite::fromJSON(res, FALSE)
 
   userid <- gsub("-", ",", userid)

R/phenotypes_byid.R

@@ -23,7 +23,25 @@ phenotypes_byid <- function(phenotypeid = NA,
     paste0(osnp_base(), "phenotypes/json/variations/"),
     phenotypeid, ".json"
   )
-  res <- os_GET(url2, list(), ...)
+
+  tryCatch(
+    {
+      res <- os_GET(url2, list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
+
   out <- jsonlite::fromJSON(res, FALSE)
 
   return_2 <- match.arg(return_, c("description", "knownvars", "users"), FALSE)

R/users.R

@@ -16,7 +16,26 @@
 #' data[[2]] # users without links to genome data
 #' }
 users <- function(df = FALSE, ...) {
-  res <- os_GET(paste0(osnp_base(), "users.json"), list(), ...)
+
+
+  tryCatch(
+    {
+      res <- os_GET(paste0(osnp_base(), "users.json"), list(), ...)
+      ## need to check what it returns
+      # Process the data or perform any desired operations
+    },
+    error = function(e) {
+      message("Failed to retrieve data from OpenSNP. Please check the URL or try again later.")
+      stop("Error - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+    ,
+    warning = function(w) {
+      message("Warning: Data retrieval resulted in a warning.")
+      # Handle warnings if necessary
+      stop("Warning - Failed to retrieve data from OpenSNP or connection is interrupted")
+    }
+  )
+
   users_ <- jsonlite::fromJSON(res, FALSE)
   if (!df) {
     users_

cran-comments.md

@@ -46,9 +46,20 @@ We checked 1 reverse dependencies (0 from CRAN + 1 from Bioconductor), comparing
  * We saw 0 new problems
  * We failed to check 0 packages
 
+
+4. A fourth note is related to the resubmission of the update following some failing tests on CRAN
+
+```
+* checking CRAN incoming feasibility ... [10s] NOTE
+Maintainer: 'Julia Gustavsen <[email protected]>'
+
+Days since last update: 4
+
+```
+
 ---
 
-This version includes more tests, some spelling corrections and some formatting corrections.
+This version includes more tests, fixes and catches for failing tests,some spelling corrections and some formatting corrections.
 
 
 Thanks!

tests/fixtures/allgensnp.yml

@@ -0,0 +1,49 @@
+http_interactions:
+- request:
+    method: get
+    uri: https://opensnp.org/snps/json/rs486907/1-8.json
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      User-Agent: libcurl/7.64.1 r-curl/5.0.1 crul/1.4.0
+      Accept-Encoding: gzip, deflate
+      Accept: application/json, text/xml, application/xml, */*
+  response:
+    status:
+      status_code: '200'
+      message: OK
+      explanation: Request fulfilled, document follows
+    headers:
+      cache-control: max-age=0, private, must-revalidate
+      connection: keep-alive
+      content-encoding: gzip
+      content-type: application/json; charset=utf-8
+      date: Fri, 30 Jun 2023 09:53:59 GMT
+      etag: W/"171b5a10145cfdc824a295229d993078"
+      server: nginx/1.18.0 + Phusion Passenger(R) 6.0.17
+      status:
+      - HTTP/1.1 200 OK
+      - 200 OK
+      strict-transport-security: max-age=31536000; includeSubDomains
+      transfer-encoding: chunked
+      vary: Accept-Encoding
+      x-content-type-options: nosniff
+      x-frame-options: SAMEORIGIN
+      x-powered-by: Phusion Passenger(R) 6.0.17
+      x-request-id: a2956f8d-9ec9-48ba-80bc-0426929b90b0
+      x-runtime: '0.446335'
+      x-xss-protection: 1; mode=block
+    body:
+      encoding: ''
+      file: no
+      string: '[{"snp":{"name":"rs486907","chromosome":"1","position":"182585422"},"user":{"name":"Bastian
+        Greshake Tzovaras","id":1,"genotypes":[{"genotype_id":9,"local_genotype":"TT"}]}},{"snp":{"name":"rs486907","chromosome":"1","position":"182585422"},"user":{"name":"Senficon","id":2,"genotypes":[]}},{"error":"Sorry,
+        we couldn''t find any information for SNP rs486907 and user 3"},{"error":"Sorry,
+        we couldn''t find any information for SNP rs486907 and user 4"},{"error":"Sorry,
+        we couldn''t find any information for SNP rs486907 and user 5"},{"snp":{"name":"rs486907","chromosome":"1","position":"182585422"},"user":{"name":"Nash
+        Parovoz","id":6,"genotypes":[{"genotype_id":5,"local_genotype":"CC"}]}},{"error":"Sorry,
+        we couldn''t find any information for SNP rs486907 and user 7"},{"snp":{"name":"rs486907","chromosome":"1","position":"182585422"},"user":{"name":"Samantha
+        B. Clark","id":8,"genotypes":[{"genotype_id":2,"local_genotype":"TT"}]}}]'
+  recorded_at: 2023-06-30 09:53:59 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.9.0

tests/fixtures/allgensnp_error.yml

@@ -0,0 +1,47 @@
+http_interactions:
+- request:
+    method: get
+    uri: https://opensnp.org/snps/json/rs486907/1-8.json
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      User-Agent: libcurl/7.64.1 r-curl/5.0.1 crul/1.4.0
+      Accept-Encoding: gzip, deflate
+      Accept: application/json, text/xml, application/xml, */*
+  response:
+    status:
+      status_code: '503'
+      message: Service Unavailable
+      explanation: The server cannot process the request due to a high load
+    headers:
+      status: HTTP/1.1 503 Service Temporarily Unavailable
+      server: nginx/1.18.0 (Ubuntu)
+      date: Fri, 30 Jun 2023 09:40:20 GMT
+      content-type: text/html
+      content-length: '307'
+      connection: keep-alive
+      etag: '"6467496a-133"'
+    body:
+      encoding: ''
+      file: no
+      string: |
+        <!DOCTYPE html>
+        <html>
+          <head>
+            <title>OpenSNP is down for maintenance</title>
+          </head>
+          <body>
+            <style>
+              h1 {
+                color:#0069d6;
+              }
+            </style>
+            <center>
+              <h1>openSNP</h1>
+              <h3>We are working on something. Please check again later.</h3>
+            </center>
+          </body>
+        </html>
+  recorded_at: 2023-06-30 09:40:20 GMT
+  recorded_with: vcr/1.2.0, webmockr/0.9.0