Ipad 508 enable model designation for multimodel plots

DESCRIPTION

@@ -11,7 +11,7 @@ Description:
   deployed online to be explored by collaborators. The dashboard includes
   'sortable' tables, interactive plots including network visualization, and
   fine-grained filtering based on statistical significance.
-Version: 1.13.16
+Version: 1.13.20
 Authors@R: c(
   person("Terrence", "Ernst", role = c("aut"),
          comment = "Web application"),

NEWS.md

@@ -1,3 +1,21 @@
+# 1.13.20
+
+* The release tarball includes version 1.9.3 of the web app
+
+* Fix bug in `importStudy()` that resulted in mapping table not being imported.
+
+# 1.13.19
+
+* The release tarball includes version 1.9.2 of the web app
+
+# 1.13.18
+
+* The release tarball includes version 1.9.1 of the web app
+
+# 1.13.17
+
+* The release tarball includes version 1.9.0 of the web app
+
 * Update `getBarcodeData()` to pass lowest statistic value. Change enables barcode plot to accommodate negative numbers.
 
 # 1.13.16

R/check.R

@@ -410,6 +410,17 @@ checkPlots <- function(plots) {
       if (is.null(plotEntry[["displayName"]])) {
         stop(sprintf("Must define displayName for plot \"%s\"", plotID))
       }
+      # For multiModel plots, check if field 'models' is available and, if so,
+      # check if models != 'all' is associated with plotType multiModel
+      if (!is.null(plotEntry[["models"]])) {
+        models <- plotEntry[["models"]]
+        if ((length(models) > 1 || models != 'all') && !any(plotEntry[["plotType"]] %in% "multiModel")) {
+          stop(
+            sprintf("For field models != 'all' plotType field requires 'multiModel'.\n"),
+            sprintf("The custom plot \"%s\" has models \"%s\" and plotType \"%s\".", plotID, paste(c(models), collapse=', '), paste(c(plotEntry[["plotType"]]), collapse=', '))
+          )
+        }
+      }
     }
   }
 

R/import.R

@@ -72,6 +72,7 @@ importStudy <- function(study, libraries = NULL) {
     plots = getPlots(study, quiet = TRUE, libraries = libraries),
     barcodes = getBarcodes(study, quiet = TRUE, libraries = libraries),
     reports = reports,
+    mapping = getMapping(study, quiet = TRUE, libraries = libraries),
     resultsLinkouts = getResultsLinkouts(study, quiet = TRUE, libraries = libraries),
     enrichmentsLinkouts = getEnrichmentsLinkouts(study, quiet = TRUE, libraries = libraries),
     metaFeaturesLinkouts = getMetaFeaturesLinkouts(study, quiet = TRUE, libraries = libraries),

R/validate.R

@@ -262,6 +262,35 @@ validatePlots <- function(study) {
     modelID <- models[i]
     modelPlots <- getPlots(study, modelID, quiet = TRUE)
     if (isEmpty(modelPlots)) next
+    # Validate concordance between plots field models (when models != 'all') and
+    # model names from mapping object
+    for (q in seq_along(modelPlots)) {
+      plotEntry <- names(modelPlots[[q]])
+      if (any(plotEntry %in% 'models')) {
+        plotModelNames <- modelPlots[[q]][['models']]
+
+        if (plotModelNames == 'all') next
+
+        mappingNames <- names(study[["mapping"]])
+        if (modelID %in% mappingNames) {
+          mapName <- modelID
+        } else {
+          mapName <- 'default'
+        }
+        map <- study[["mapping"]][[mapName]]
+        mapModelNames <- colnames(map)
+        if (any(!plotModelNames %in% mapModelNames)) {
+          stop(
+            sprintf("The custom plot \"%s\" has invalid model(s).\n", names(modelPlots)[q]),
+            sprintf("At least one element from field models (\"%s\") is not found in the mapping object \"%s\" column names (\"%s\").",
+                    paste(c(plotModelNames), collapse=', '),
+                    mapName,
+                    paste(mapModelNames, collapse=', '))
+          )
+        }
+      }
+    }
+
     # Custom plots no longer require assays, since they can plot columns from
     # the results table. If assays are unavailable, send a message and then
     # skip the rest of the validation between assays with
@@ -308,9 +337,7 @@ validatePlots <- function(study) {
       stop("Some of the column names of the assays table are missing from the sampleID column in the samples table\n",
            sprintf("modelID: %s", modelID))
     }
-
   } # outer loop of modelIDs
-
   return(invisible(TRUE))
 }
 

R/zzz.R

@@ -10,7 +10,7 @@ OmicNavigatorPrefix <- "ONstudy"
 
 # The R package is meant to be used with a specific version of the app. If a
 # user has an older or newer version installed, send a warning.
-versionAppPinned <- "1.8.9"
+versionAppPinned <- "1.9.3"
 
 # The extra packages required to run the app
 appPackages <- c(