Add genomes

EBI-Metagenomics · Feb 5, 2024 · 91082bb · 91082bb
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commit 91082bb
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diff --git a/R/doQuery.R b/R/doQuery.R
@@ -1,10 +1,10 @@
-#' Search MGnify database for studies, samples, runs, analyses, biomes, and
-#' assemblies.
+#' Search MGnify database for studies, samples, runs, analyses, biomes,
+#' assemblies, and genomes.
 #'
 #' @details
 #' \code{doQuery} is a flexible query function, harnessing the "full"
 #' power of the JSONAPI MGnify search filters. Search results may be filtered
-#' by metadata value, associated study/sample/analyese etc. Details of the
+#' by metadata value, associated study/sample/analyse etc. Details of the
 #' capabilities may be found
 #' \href{https://emg-docs.readthedocs.io/en/latest/api.html#customising-queries}{here}.
 #' Currently, the following filters are available (based on examination of the
@@ -103,7 +103,8 @@ NULL
 #' @export
 setMethod("doQuery", signature = c(x = "MgnifyClient"), function(
         x, type = c(
-            "studies", "samples", "runs", "analyses", "biomes", "assemblies"),
+            "studies", "samples", "runs", "analyses", "biomes", "assemblies",
+            "genomes"),
         accession = NULL, as.df = TRUE, max.hits = 200, ...){
     ############################### INPUT CHECK ################################
     if( !(.is_non_empty_string(type)) ){

diff --git a/R/getMetadata.R b/R/getMetadata.R
@@ -94,7 +94,8 @@ setMethod("getMetadata", signature = c(x = "MgnifyClient"), function(
         max.hits = max.hits, ...)
     # If metadata was not found, return the NULL value
     if(is.null(dat)){
-        warning("Failed to find study metadata for ", accession, call. = FALSE)
+        warning(
+            "\nFailed to find study metadata for ", accession, call. = FALSE)
         return(dat)
     }
 
@@ -116,15 +117,17 @@ setMethod("getMetadata", signature = c(x = "MgnifyClient"), function(
         sample_df <- .mgnify_attr_list_to_df_row(
             sample_met[[1]], metadata_key = "sample-metadata")
     } else{
-        warning("Failed to find sample metadata for ", accession, call. = FALSE)
+        warning(
+            "\nFailed to find sample metadata for ", accession, call. = FALSE)
         sample_df <- data.frame(accession=NA)
     }
     # It turns out that a sample might not be part of a study - if it's been
     # harvested...
     if(!is.null(study_met)){
         study_df <- .mgnify_attr_list_to_df_row(study_met[[1]])
     } else{
-        warning("Failed to find study metadata for ", accession, call. = FALSE)
+        warning(
+            "\nFailed to find study metadata for ", accession, call. = FALSE)
         study_df <- data.frame(accession=NA)
     }
     # Add colnames to sample, study and analysis tables
@@ -150,7 +153,7 @@ setMethod("getMetadata", signature = c(x = "MgnifyClient"), function(
     if( !is.null(sample_met[[1]]$relationships$biome$data$id) ){
         full_df$biome_string <- sample_met[[1]]$relationships$biome$data$id
     } else {
-        warning("Failed to find biome entry for ", accession, call = FALSE)
+        warning("\nFailed to find biome entry for ", accession, call = FALSE)
     }
     return(full_df)
 }
diff --git a/R/getResult.R b/R/getResult.R
@@ -207,7 +207,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
             }
         } else{
             warning(
-                "No taxonomy data was found for the dataset.",
+                "\nNo taxonomy data was found for the dataset.",
                 call. = FALSE)
         }
     }
@@ -260,7 +260,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
                 }
             }
         } else{
-            warning("No functional data found for the dataset.", call. = FALSE)
+            warning("\nNo functional data found for the dataset.", call. = FALSE)
         }
     }
     return(result)
@@ -421,7 +421,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     # Check if any biom files was found
     if( is.null(available_biom_files) || length(available_biom_files) == 0 ){
         warning(
-            "No BIOM data found for accession '", accession, "'.",
+            "\nNo BIOM data found for accession '", accession, "'.",
             call. = FALSE)
         return(NULL)
     }
@@ -432,7 +432,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     if( sum(biom_position) == 0 ){
         if( show.warnings ){
             warning(
-                "Unable to locate requested taxonomy type ", taxa.su, ". ",
+                "\nUnable to locate requested taxonomy type ", taxa.su, ". ",
                 "This is likely due to the current analysis having been ",
                 "performed on an older version of the MGnify pipeline. ",
                 "The available BIOM file will be used instead.",
@@ -470,7 +470,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
         # If the file was not successfully downloaded
         if( res$status_code != 200 ){
             warning(
-                biom_url, ": ", content(res, ...)$errors[[1]]$detail,
+                "\n", biom_url, ": ", content(res, ...)$errors[[1]]$detail,
                 " A biom listed in 'accession' is missing from the ",
                 "output.", call. = FALSE)
             # Remove the downloaded file, it includes only info on errors
@@ -528,7 +528,8 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
                 # If the file was not successfully downloaded
                 if( res$status_code != 200 ){
                     warning(
-                        tree_url, ": ", content(res, ...)$errors[[1]]$detail,
+                        "\n", tree_url, ": ",
+                        content(res, ...)$errors[[1]]$detail,
                         " A phylogenetic tree listed in 'accession' is ",
                         "missing from the output.", call. = FALSE)
                 }
@@ -802,7 +803,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
             # If the file was not successfully downloaded
             if( res$status_code != 200 ){
                 warning(
-                    data_url, ": ", content(res, ...)$errors[[1]]$detail,
+                    "\n", data_url, ": ", content(res, ...)$errors[[1]]$detail,
                     " Could not load the file from database. The data ",
                     "from the file is not included in the output.",
                     call. = FALSE)
@@ -833,7 +834,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     # with missing downloads, we have to check if we
     # actually got a valid file:
     if( ncol(tmp_df) < 3 ){
-        warning("Invalid download for ", accession, call. = FALSE)
+        warning("\nInvalid download for ", accession, call. = FALSE)
         return(NULL)
     }
 
@@ -856,15 +857,15 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     }else if( "run_accession" %in% colnames(metadata_df) ){
         accession <- metadata_df$run_accession[[1]]
     } else{
-        warning("Failed to data on ", accession, call. = FALSE)
+        warning("\nFailed to data on ", accession, call. = FALSE)
         return(NULL)
     }
 
     # Get the correct sample and subset the data so that it includes only
     # the sample and info columns
     column_position <- match(accession, colnames(tmp_df))
     if( (is.na(column_position) || length(column_position) != 1) ){
-        warning("Failed to find column ", accession, call. = FALSE)
+        warning("\nFailed to find column ", accession, call. = FALSE)
         return(NULL)
     }
     # Ensure that the counts are numeric

diff --git a/R/searchAnalysis.R b/R/searchAnalysis.R
@@ -98,7 +98,7 @@ setMethod("searchAnalysis", signature = c(x = "MgnifyClient"), function(
             res <- lapply(jsondat, function(x) x$id)
         } else {
             res <- accurl
-            warning("Analyses not found for studies ", x, call. = FALSE)
+            warning("\nAnalyses not found for studies ", x, call. = FALSE)
         }
         return(res)
     }, .progress=show.messages)
@@ -159,7 +159,7 @@ setMethod("searchAnalysis", signature = c(x = "MgnifyClient"), function(
     runurl <- .mgnify_get_x_for_y(
         client, x, "samples","runs", use.cache = use.cache, ...)
     if(is.null(runurl)){
-        warning("Analyses not found for samples ", x, call. = FALSE)
+        warning("\nAnalyses not found for samples ", x, call. = FALSE)
         return(runurl)
     }
     # If found, get data for runs
@@ -207,7 +207,8 @@ setMethod("searchAnalysis", signature = c(x = "MgnifyClient"), function(
                 # If we've got to this point, I give up - just return an empty
                 # list...
                 warning(
-                    "Failed to find an analysis for sample ", x, call. = FALSE)
+                    "\nFailed to find an analysis for sample ", x,
+                    call. = FALSE)
             }
         }
         # Get analyses IDs

diff --git a/R/utils.R b/R/utils.R
@@ -280,7 +280,7 @@
     }
     # Give warning if data is not found.
     if( is.null(final_data) ){
-        warning(warning_msg, call. = FALSE)
+        warning("\n", warning_msg, call. = FALSE)
     }
     return(final_data)
 }

diff --git a/inst/extdata/vignette_MGnifyR_long b/inst/extdata/vignette_MGnifyR_long