Merge pull request #4 from maize-genetics/fix-demo-params

Fix `DEMO` endpoint from returning incorrect data

Author: btmonier

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rPHG
-Version: 0.2.1
+Version: 0.2.2
 Date: 2019-06-03
 Title: R front-end for the practical haplotype graph
 Authors@R: c(
@@ -72,6 +72,6 @@ Encoding: UTF-8
 LazyData: true
 VignetteBuilder:
     knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 biocViews:
     GenomeWideAssociation

NEWS

@@ -1,3 +1,8 @@
+## CHANGES IN VERSION 0.2.2
+* Fixed issue with `DEMO` method endpoint returning incorrect dimensional data
+  for specific Maize PHGv1 methods
+
+
 ## CHANGES IN VERSION 0.2.1
 * Added new function, `plotDot()`
   + Creates dot plots from `.anchorspro` files

NEWS.md

@@ -1,3 +1,8 @@
+## rPHG 0.2.2
+* Fixed issue with `DEMO` method endpoint returning incorrect dimensional data
+  for specific Maize PHGv1 methods
+
+
 ## rPHG 0.2.1
 * Added new function, `plotDot()`
   + Creates dot plots from `.anchorspro` files

R/class_phg_method.R

@@ -251,7 +251,7 @@ setMethod(
         if (conType == "local") {
             phgDataSetFromLocal(conObj, conMethod, verbose)
         } else if (conType == "server") {
-            phgDataSetFromServer(conObj, conMethod, verbose, conDemo)
+            phgDataSetFromServer(conObj, conMethod, conDemo, verbose)
         }
     }
 )

R/constants.R

@@ -25,7 +25,7 @@ BRAPI_PARAMS <- list(
     "METHOD_RR_SIZE"     = "dimensionCallSetPageSize=%i",
     "METHOD_RR_PAGE"     = "dimensionCallSetPage=%i",
     "METHOD_SAMPLE_SIZE" = "dimensionVariantPageSize=%i",
-    "METHOD_SAMPLE_PAGE" = "dimensionVariantPagePage=%i"
+    "METHOD_SAMPLE_PAGE" = "dimensionVariantPage=%i"
 )
 
 

R/read_hap_ids.R

@@ -73,6 +73,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
         )
     )
 
+
     message(verbInfo[2])
     pb <- utils::txtProgressBar(
         min     = 0,
@@ -92,7 +93,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
 
     message(verbInfo[3])
     fullResp <- do.call(
-        what = "cbind",
+        what = "rbind",
         args = lapply(
             X   = respVector,
             FUN = function(x) {
@@ -101,10 +102,10 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
         )
     )
 
-    colnames(fullResp) <- paste0("R", seq_len(ncol(fullResp)))
-    rownames(fullResp) <- samplesFromServer(conObj, conMethod, conDemo)
+    rownames(fullResp) <- paste0("R", seq_len(nrow(fullResp)))
+    colnames(fullResp) <- samplesFromServer(conObj, conMethod, conDemo)
 
-    return(fullResp)
+    return(t(fullResp))
 }
 
 

R/read_ref_ranges.R

@@ -29,7 +29,7 @@ refRangesFromServer <- function(conObj, conMethod, conDemo) {
                 if (conDemo) {
                     BRAPI_PARAMS$DEMO_N_RR_TOTAL
                 } else {
-                    BRAPI_PARAMS$MAX_N_RR_SIZE
+                    BRAPI_PARAMS$MAX_N_RR_TOTAL
                 }
             )
         )

R/utilities_api_brapi.R

@@ -36,7 +36,7 @@ amUrlContextStringBuilder <- function(
             BRAPI_PARAMS$REST_KV_SEP,
             BRAPI_PARAMS$METHOD_SAMPLE_PAGE
         ),
-        methodId, rrPageSize, samplePageSize, rrPage, samplePage
+        methodId, rrPageSize, samplePageSize, samplePage, rrPage
     )
 
     return(amContextString)

vignettes/rphg_walkthrough.Rmd

@@ -85,7 +85,7 @@ If you would like to use a PHG web service, we can use the following
 similar method:
 
 ```{r, echo=TRUE, eval=TRUE}
-"demo.hub.maizegenetics.net" |> PHGServerCon()
+"phg.maizegdb.org" |> PHGServerCon()
 ```
 
 Here, a URL pointing to a PHG web service is supplied to the