Add checks

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.7
+Version: 0.7.1
 Authors@R:
     person(
         given = "Brandon",

NEWS.md

@@ -1,3 +1,12 @@
+## rPHG2 0.8
+* Fixed missing IDs returned in `readHapIds()` method calls.
+  + missing values (i.e., `"null"`) now return as `NA`s in the matrix object
+* Removed `rlang::abort()` condition in `initPhg()`
+  + Now returns "warning" message instead of low-level `stop()` procedure
+* Modified the `PHGLocalCon()` constructor to now take in either files or a
+  directory path
+
+
 ## rPHG2 0.7
 * Added new parameter to `plotHaploCounts()`:
   + `geom`

R/class_phg_con_local.R

@@ -54,18 +54,47 @@ setValidity("PHGLocalCon", function(object) {
 #' DB data for a given set of PHG-related methods.
 #'
 #' @param hVcfFiles
-#' A list of \href{https://github.com/maize-genetics/phg_v2/blob/main/docs/hvcf_specifications.md}{hVCF}
-#' files as a \code{character} vector
+#' A path to a directory or file containing valid \href{https://github.com/maize-genetics/phg_v2/blob/main/docs/hvcf_specifications.md}{hVCF}
+#' files (ending in either \code{.h.vcf} or \code{.h.vcf.gz}) as a
+#' \code{character} vector
 #'
 #' @export
 PHGLocalCon <- function(hVcfFiles) {
-    # This is probably overkill right now, but will revisit once the TileDB
-    # C API is better integrated in PHGv2...
+    # TODO - This is probably overkill right now, but will revisit once the TileDB
+    #        C API is better integrated in PHGv2...
+
+    # Initial type checking
+    if (!is.vector(hVcfFiles) || !is.character(hVcfFiles)) {
+        rlang::abort("Input is not a valid 'character' vector")
+    }
+
+    # Check if directory or files exist
+    procFiles <- NULL
+    hvcfExtPattern <- "\\.h\\.vcf(\\.gz)?$"
+    if (any(dir.exists(hVcfFiles))) {
+        # Get all files ending with .h.vcf or .h.vcf.gz in the directory
+        procFiles <- list.files(
+            path       = hVcfFiles,
+            pattern    = hvcfExtPattern,
+            full.names = TRUE
+        )
+
+        if (length(procFiles) == 0) {
+            rlang::abort("No files ending with .h.vcf or .h.vcf.gz found in provided directory")
+        }
+    } else if (any(file.exists(hVcfFiles))) {
+        if (any(grepl(hvcfExtPattern, hVcfFiles))) {
+            procFiles <- hVcfFiles[grepl(hvcfExtPattern, hVcfFiles)]
+        }
+    } else {
+        rlang::abort("The input path is neither a valid directory nor a valid file")
+    }
+
     methods::new(
         Class     = "PHGLocalCon",
         phgType   = "local",
         host      = NA_character_, # making this NA for now
-        hVcfFiles = normalizePath(hVcfFiles)
+        hVcfFiles = normalizePath(procFiles)
     )
 }
 
@@ -93,6 +122,7 @@ setMethod(
         present <- cli::col_green(cli::symbol$square_small_filled)
         absent  <- cli::col_grey(cli::symbol$square_small)
 
+        #' TODO - implement with direct calls to TileDB
         dbUriStatus <- ifelse(is.na(object@host), absent, present)
 
         if (any(is.na(object@hVcfFiles))) {

R/class_phg_dataset.R

@@ -183,7 +183,7 @@ setMethod(
 
             uniqHaps <- data.frame(
                 rr_id   = colnames(hapIds),
-                n_haplo = apply(hapIds, 2, function(it) length(unique(it[it != "null"])))
+                n_haplo = apply(hapIds, 2, function(it) length(unique(it[!is.na(it)])))
             )
 
             return(tibble::as_tibble(

R/init_phg.R

@@ -14,6 +14,15 @@
 #'
 #' @export
 initPhg <- function(phgPath, check = TRUE, verbose = TRUE) {
+    # Set up CLI message components
+    #   Note: I **know** there are easier ways of accomplishing this but I
+    #         need to do this 'ad-hoc' for JupyterHub notebooks!
+    cliSuccess <- cli::col_green(cli::symbol$tick)
+    cliInform  <- cli::col_blue(cli::symbol$info)
+    cliNote    <- cli::col_red(cli::symbol$warning)
+    cliWarn    <- cli::col_red(cli::symbol$cross)
+    cliBullet  <- cli::symbol$bullet
+
     if (!is.character(phgPath) || !dir.exists(phgPath)) {
         rlang::abort("PHG library path ('phgPath') provided does not exist")
     }
@@ -22,33 +31,27 @@ initPhg <- function(phgPath, check = TRUE, verbose = TRUE) {
         rlang::abort("Cannot find 'phg_v2.jar' in library path")
     }
 
+    # Check if JVM is already initialized - if it is, show warning message and
+    # move on
+    loadMsg <- paste0(cliSuccess, " PHG JARs added to class path")
     if (isJvmInitialized() && "phg_v2.jar" %in% basename(rJava::.jclassPath())) {
-        rlang::abort("PHGv2 JARs already added to class path")
+        loadMsg <- paste0(cliWarn, " PHGv2 JARs already added to class path - skipping...")
+    } else {
+        tryCatch(
+            {
+                rJava::.jinit()
+                rJava::.jaddClassPath(dir(phgPath, full.names = TRUE))
+            },
+            error = function(e) {
+                rlang::abort("Java initialization or class path addition failed", parent = e)
+            }
+        )
     }
 
-    tryCatch(
-        {
-            rJava::.jinit()
-            rJava::.jaddClassPath(dir(phgPath, full.names = TRUE))
-        },
-        error = function(e) {
-            rlang::abort("Java initialization or class path addition failed", parent = e)
-        }
-    )
-
-    # Set up CLI message components
-    #   Note: I **know** there are easier ways of accomplishing this but I
-    #         need to do this 'ad-hoc' for JupyterHub notebooks!
-    cliSuccess <- cli::col_green(cli::symbol$tick)
-    cliInform  <- cli::col_blue(cli::symbol$info)
-    cliWarn    <- cli::col_red(cli::symbol$warning)
-    cliBullet  <- cli::symbol$bullet
-
     # Get version stats
     jvmStats   <- jvmStats()
 
     # Get PHG version messages / set up load message
-    loadMsg           <- paste0(cliSuccess, " PHG JARs added to class path")
     currentPhgVersion <- phgVersion(jvmStats)
     cliCurrent        <- cli::style_bold(currentPhgVersion)
     phgMsg            <- paste0("  ", cliBullet, " PHG version....: ", cliCurrent)
@@ -75,7 +78,7 @@ initPhg <- function(phgPath, check = TRUE, verbose = TRUE) {
             phgWarnMsg <- sprintf(
                 "  %s\n  %s %sCurrent version of PHGv2 (%s) is out of date (%s)\n    %s consider updating (%s)",
                 cli::symbol$line,
-                cliWarn,
+                cliNote,
                 cli::style_bold(cli::symbol$sup_1),
                 cliCurrent,
                 cliLatest,

R/read_hap_ids.R

@@ -13,6 +13,10 @@ hapIdsFromJvmGraph <- function(jvmGraph, nThreads) {
     jm <- interface$getHapIdMatrixFromGraph(jvmGraph, nThreads)
     rm <- jm |> kotlin2DArrayToRMatrix()
 
+    # Convert missing IDs to R NAs
+    missingValues <- c("", "null")
+    rm[rm %in% missingValues] <- NA
+
     return(rm)
 }
 

README.md

@@ -7,9 +7,9 @@
 <!-- badges: end -->
 
 `rPHG2` is a system to interact with and retrieve information from **version 2** 
-of the Practical Haplotype Graph (PHGv2) - a general, graph-based, computational 
-framework for genotype inference. This is accomplished by leveraging the 
-[Breeding](https://brapi.org/) and 
+of the [Practical Haplotype Graph (PHGv2)](https://phg.maizegenetics.net/) - a 
+general, graph-based, computational framework for genotype inference. This is 
+accomplished by leveraging the [Breeding](https://brapi.org/) and 
 [PHG](https://github.com/maize-genetics/phg_v2) APIs.
 
 ## Installation
@@ -30,8 +30,7 @@ initPhg("my/phg/jar/path")
 
 
 # Create a connection
-locCon <- list.files("my/hvcf/dir") |>
-    PHGLocalCon()
+locCon <- PHGLocalCon("my/hvcf/dir")
 
 
 # Build a graph

tests/testthat/setup.R

@@ -112,7 +112,9 @@ initPhg(phgLibPath)
 
 ## Test post-initialization ----
 testthat::test_that("JVM init checker works", {
-    testthat::expect_error(rPHG2::initPhg(phgLibPath))
+    msg <- utils::capture.output(rPHG2::initPhg(phgLibPath))
+
+    testthat::expect_match(msg[1], "PHGv2 JARs already added to class path" )
 })
 
 

tests/testthat/test_class_phg_con_local.R

@@ -1,11 +1,22 @@
-test_that("Local connection tests", {
+test_that("General local connection tests", {
     hVcfFileDir <- system.file("extdata", package = "rPHG2")
     hVcfFiles   <- list.files(hVcfFileDir, pattern = ".h.vcf$", full.names = TRUE)
     locCon      <- PHGLocalCon(hVcfFiles)
 
-    locConOutput <- utils::capture.output(locCon)
+    expect_error(PHGLocalCon(mtcars))
+    expect_error(PHGLocalCon(tempdir()))
+    expect_error(PHGLocalCon(tempfile()))
 
+    locConOutput <- utils::capture.output(locCon)
     expect_equal(length(locConOutput), 3)
 
 })
 
+
+test_that("Local connection from directory", {
+    hVcfFileDir <- system.file("extdata", package = "rPHG2")
+    locCon      <- PHGLocalCon(hVcfFileDir)
+    locConOutput <- utils::capture.output(locCon)
+    expect_equal(length(locConOutput), 3)
+
+})

vignettes/rPHG2.Rmd

@@ -94,6 +94,15 @@ localCon <- hVcfFiles |> PHGLocalCon()
 localCon
 ```
 
+Additionally, if you have a **directory** of valid hVCF files, you can simply
+pass the directory path to the constructor. In the following example, I will
+point to the `extdata` data directory _without_ pointing to singular hVCF files
+that is found within the package:
+
+```{r, eval=TRUE, echo=TRUE}
+system.file("extdata", package = "rPHG2") |> PHGLocalCon()
+```
+
 From here, we can move to the [next section](#creating-jvm-objects) to create a `HaplotypeGraph`
 object interface with the JVM.