code update

added trycatch for fetch and related helper functions
boldsystems-central · Sep 12, 2024 · 3d33a8e · 3d33a8e
1 parent 1a04458
commit 3d33a8e
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Showing 9 changed files with 94 additions and 87 deletions.
diff --git a/R/bold.fetch.R b/R/bold.fetch.R
@@ -342,21 +342,13 @@ bold.fetch<-function(param.data,
 
     {
 
-     stop("Input params can only be either processid, sampleid, datasets or bin_uri")
+     stop("Input params can only be either processid, sampleid, dataset or project_codes and bin_uri")
 
      return(FALSE)
 
       }
 
 
-  if(nrow(json.df)==0)
-
-  {
-
-    stop("Data could not be retrieved. Please re-check the parameters.")
-
-  }
-
 
     # a separate filter function is used to filter the retrieved data
 
@@ -396,19 +388,6 @@ bold.fetch<-function(param.data,
 
   }
 
-  # If the resulting data (after filtering) is empty
-
-  if(nrow(json.df)==0)
-
-  {
-
-    stop("The output has no data.It could either be due to wrong range of values or incorrect names. Please re-check the filter/s used")
-
-    return(FALSE)
-
-  }
-
-
 
   # If user wants to export the data
 

diff --git a/R/helper.connect.pvt.fetch.bins.R b/R/helper.connect.pvt.fetch.bins.R
@@ -142,11 +142,6 @@ fetch.bold.bins<-function(data.input,
     }
 
 
-    # # removing empty results
-    #
-    # result = Filter(function(df) nrow(df) > 0, result.pre.filter)
-
-
     # Generating the data frame
 
 
@@ -175,12 +170,18 @@ fetch.bold.bins<-function(data.input,
 
  # Convert the 'coord' character data into two numeric columns 'lat','lon'
 
-  json.df = json.df%>%
-    tidyr::separate(coord,
-                    c("lat","lon"),
-                    sep=",",
-                    remove = T)%>%
-    dplyr::mutate(across(c(lat,lon), ~ as.numeric(.x)))
+  json.df <- tryCatch({
+    json.df %>%
+      tidyr::separate(coord, c("lat", "lon"),
+                      sep = ",",
+                      remove = TRUE) %>%
+      dplyr::mutate(across(c(lat, lon),
+                           ~ as.numeric(.x)))
+  }, error = function(e) {
+    message("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+    return(NULL)
+  })
+
 
  return(json.df)
 

diff --git a/R/helper.connect.pvt.fetch.datasets.R b/R/helper.connect.pvt.fetch.datasets.R
@@ -177,12 +177,14 @@ fetch.bold.datasets<-function(data.input,
 
 # Convert the 'coord' character data into two numeric columns 'lat','lon'
 
-    json.df = json.df%>%
-      tidyr::separate(coord,
-                      c("lat","lon"),
-                      sep=",",
-                      remove = T)%>%
-      dplyr::mutate(across(c(lat,lon), ~ as.numeric(.x)))
+  json.df <- tryCatch({
+    json.df %>%
+      tidyr::separate(coord, c("lat", "lon"), sep = ",", remove = TRUE) %>%
+      dplyr::mutate(across(c(lat, lon), ~ as.numeric(.x)))
+  }, error = function(e) {
+    message("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+    return(NULL)
+  })
 
   return(json.df)
 

diff --git a/R/helper.connect.pvt.fetch.processids.R b/R/helper.connect.pvt.fetch.processids.R
@@ -109,7 +109,7 @@ fetch.bold.processid<-function(data.input,
 
     {
 
-      stop("Error occurred during data download. Please re-check param.data,param.query, param.index or the api_key")
+      stop("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
 
     }
 
@@ -127,34 +127,20 @@ fetch.bold.processid<-function(data.input,
       dplyr::bind_rows(.)
 
 
-    if(nrow(json.df)==0)
-
-    {
-
-      stop("Search resulted in an empty dataset. Please re-check the input data.")
-
-    }
-
-    else
-
-    {
-
-      json.df
-
-    }
-
-  }
+ }
 
 
 
     # Convert the 'coord' character data into two numeric columns 'lat','lon'
 
-    json.df = json.df%>%
-      tidyr::separate(coord,
-                      c("lat","lon"),
-                      sep=",",
-                      remove = T)%>%
-      dplyr::mutate(across(c(lat,lon), ~ as.numeric(.x)))
+  json.df <- tryCatch({
+    json.df %>%
+      tidyr::separate(coord, c("lat", "lon"), sep = ",", remove = TRUE) %>%
+      dplyr::mutate(across(c(lat, lon), ~ as.numeric(.x)))
+  }, error = function(e) {
+    message("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+    return(NULL)
+  })
 
 
 

diff --git a/R/helper.connect.pvt.fetch.projects.R b/R/helper.connect.pvt.fetch.projects.R
@@ -177,12 +177,15 @@ fetch.bold.project<-function(data.input,
 
   # Convert the 'coord' character data into two numeric columns 'lat','lon'
 
-  json.df = json.df%>%
-    tidyr::separate(coord,
-                    c("lat","lon"),
-                    sep=",",
-                    remove = T)%>%
-    dplyr::mutate(across(c(lat,lon), ~ as.numeric(.x)))
+  json.df <- tryCatch({
+    json.df %>%
+      tidyr::separate(coord, c("lat", "lon"), sep = ",", remove = TRUE) %>%
+      dplyr::mutate(across(c(lat, lon), ~ as.numeric(.x)))
+  }, error = function(e) {
+    message("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+    return(NULL)
+  })
+
 
   return(json.df)
 

diff --git a/R/helper.connect.pvt.fetch.sampleids.R b/R/helper.connect.pvt.fetch.sampleids.R
@@ -148,12 +148,15 @@ fetch.bold.sampleid<-function(data.input,
 
   # Convert the 'coord' character data into two numeric columns 'lat','lon'
 
-    json.df = json.df%>%
-      tidyr::separate(coord,
-                      c("lat","lon"),
-                      sep=",",
-                      remove = T)%>%
-      dplyr::mutate(across(c(lat,lon), ~ as.numeric(.x)))
+  json.df <- tryCatch({
+    json.df %>%
+      tidyr::separate(coord, c("lat", "lon"), sep = ",", remove = TRUE) %>%
+      dplyr::mutate(across(c(lat, lon), ~ as.numeric(.x)))
+  }, error = function(e) {
+    message("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+    return(NULL)
+  })
+
 
 
   return(json.df)

diff --git a/R/helper.get_data4connect.pvt.fetch.bins.R b/R/helper.get_data4connect.pvt.fetch.bins.R
@@ -38,9 +38,7 @@ get_data_bins<-function (data_for_bins,
     {
 
       # Handle the error for the POST request
-      message("An error occurred during data download: ", e$message)
-
-      return(NULL)
+      stop("An error occurred during data download: ", e$message)
 
 
     }
@@ -80,10 +78,22 @@ get_data_bins<-function (data_for_bins,
                                    "\n")[[1]], # split the content (here each process or sample id)
                           function(x) fromJSON(x)) # convert to JSON string and lapply converts that into a list
 
-  # COnvert the list to a data frame
+  # Convert the list to a data frame
+
+  input_data2 <- tryCatch({
+    df <- json_data_bins %>%
+      data.frame(.)
+
+    if (nrow(df) == 0) {
+      stop("The resulting data frame is empty.")
+    }
+
+    df
+  }, error = function(e) {
+    # Handle the error for the data frame conversion
+    stop("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
 
-  input_data2 = json_data_bins%>%
-    data.frame(.)
+  })
 
 
   return(input_data2)

diff --git a/R/helper.get_data4connect.pvt.fetch.dataset.R b/R/helper.get_data4connect.pvt.fetch.dataset.R
@@ -80,11 +80,22 @@ get_data_datasets<-function (data_for_datasets,
                                    "\n")[[1]], # split the content (here each process or sample id)
                           function(x) fromJSON(x)) # convert to JSON string and lapply converts that into a list
 
-  # COnvert the list to a data frame
+  # Convert the list to a data frame
 
-  input_data2 = json_data_datasets%>%
-    data.frame(.)
+  input_data2 <- tryCatch({
+    df <- json_data_datasets %>%
+      data.frame(.)
 
+    if (nrow(df) == 0) {
+      stop("The resulting data frame is empty.")
+    }
+
+    df
+  }, error = function(e) {
+    # Handle the error for the data frame conversion
+    stop("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+
+  })
 
   return(input_data2)
 

diff --git a/R/helper.get_data4connect.pvt.fetch.project.R b/R/helper.get_data4connect.pvt.fetch.project.R
@@ -79,10 +79,22 @@ get_data_projects<-function (data_for_projects,
                                        "\n")[[1]], # split the content (here each process or sample id)
                               function(x) fromJSON(x)) # convert to JSON string and lapply converts that into a list
 
-  # COnvert the list to a data frame
+  # Convert the list to a data frame
 
-  input_data2 = json_data_project%>%
-    data.frame(.)
+  input_data2 <- tryCatch({
+    df <- json_data_project %>%
+      data.frame(.)
+
+    if (nrow(df) == 0) {
+      stop("The resulting data frame is empty.")
+    }
+
+    df
+  }, error = function(e) {
+    # Handle the error for the data frame conversion
+    stop("Error occurred during data download. Please re-check the param.data, query.param, param.index or the api_key.")
+
+  })
 
 
   return(input_data2)