Initial commit

.Rbuildignore

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+^bljars\.Rproj$
+^\.Rproj\.user$

.gitignore

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+# These are some examples of commonly ignored file patterns.
+# You should customize this list as applicable to your project.
+# Learn more about .gitignore:
+#     https://www.atlassian.com/git/tutorials/saving-changes/gitignore
+
+# Node artifact files
+node_modules/
+dist/
+
+# Compiled Java class files
+*.class
+
+# Compiled Python bytecode
+*.py[cod]
+
+# Log files
+*.log
+
+
+# Maven
+target/
+dist/
+
+# JetBrains IDE
+.idea/
+
+# Unit test reports
+TEST*.xml
+
+# Generated by MacOS
+.DS_Store
+
+# Generated by Windows
+Thumbs.db
+
+# Applications
+*.app
+*.exe
+*.war
+
+# Large media files
+*.mp4
+*.tiff
+*.avi
+*.flv
+*.mov
+*.wmv
+
+.Rproj.user
+
+
+inst

DESCRIPTION

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+Package: BLJars
+Version: 0.0.2
+Date: 2021-07-14
+Title: Data package for distributing rTASSEL and rPHG jar files
+Authors@R: 
+    person(given = "Brandon",
+           family = "Monier",
+           role = c("aut", "cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-6797-1221"))
+Description: 
+    The role of this R package is to generate a JVM and distribute
+    necessary jar files for interacting with the TASSEL and PHG APIs. This is
+    used in two packages generated by the Buckler Lab: rTASSEL and rPHG.
+License: `use_gpl3_license()`
+URL:
+    https://bitbucket.org/bucklerlab/bljars/src/master/
+Depends:
+    rJava
+Imports:
+    cli,
+    jsonlite
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(initializeJars)

R/initializer.R

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+## ----
+#' @title Get TASSEL standalone JAR metadata
+#'
+#' @description Get commit history and download links
+#'
+#' @param apiPath Path to TASSEL Bitbucket API.
+#' @param pageLen Number of pages to return. Defaults to \code{100}.
+#'
+#' @return A data.frame
+getCommitMetaData <- function(
+    apiPath = "https://api.bitbucket.org/2.0/repositories/tasseladmin/tassel-5-standalone/src/master/",
+    pageLen = 100
+) {
+    urlLib <- paste0(apiPath, "/lib?pagelen=", pageLen)
+
+    cli::cli_progress_step("Downloading JSON info", spinner = TRUE)
+    jsonTop <- jsonlite::fromJSON(apiPath)
+    jsonLib <- jsonlite::fromJSON(urlLib)
+
+    jsonTop$values$attributes[sapply(jsonTop$values$attributes, is.null)] <- NA
+    jsonLib$values$attributes[sapply(jsonLib$values$attributes, is.null)] <- NA
+
+
+    cli::cli_progress_step("Collecting metdata", spinner = TRUE)
+    urlLibDF <- data.frame(
+        jar        = jsonLib$values$path,
+        attribute  = unlist(jsonLib$values$attributes),
+        commitMeta = jsonLib$values$commit$links$self$href,
+        downLink   = jsonLib$values$links$self$href
+    )
+    urlTopDF <- data.frame(
+        jar        = jsonTop$values$path,
+        attribute  = unlist(jsonTop$values$attributes),
+        commitMeta = jsonTop$values$commit$links$self$href,
+        downLink   = jsonTop$values$links$self$href
+    )
+
+    cli::cli_progress_step("Cleaning up data", spinner = TRUE)
+    urlLibDF <- urlLibDF[!grepl(".ini$|.dylib$", urlLibDF$jar), ]
+    urlTopDF <- urlTopDF[urlTopDF$jar == "sTASSEL.jar", ]
+    urlMasterDf <- rbind(urlTopDF, urlLibDF)
+    urlMasterDf$commitDate <- as.Date("")
+
+    cli::cli_progress_step("Collecting commit history", spinner = TRUE)
+    j <- 1
+    for (i in urlMasterDf$commitMeta) {
+        tmpJson <- jsonlite::fromJSON(i)
+        urlMasterDf$commitDate[j] <- as.Date(tmpJson$date)
+        j <- j + 1
+    }
+
+    rownames(urlMasterDf) <- NULL
+    urlMasterDf$jar <- gsub("lib/", "", urlMasterDf$jar)
+
+    return(urlMasterDf)
+}
+
+
+
+## ----
+#' @title Initialize \code{BLJars}.
+#'
+#' @description Download jar files to designated directory
+#'
+#' @return void
+#' @export
+initializeJars <- function() {
+
+    fields <- getDirFields()
+
+    if (!dir.exists(fields$fullJava)) {
+        dir.create(fields$fullJava, recursive = TRUE)
+    }
+
+    md <- getCommitMetaData()
+
+    if (!dir.exists(fields$fullMeta)) {
+        dir.create(fields$fullMeta, recursive = TRUE)
+    }
+
+    write.csv(
+        x = md,
+        file = fields$metaPath,
+        row.names = FALSE,
+        quote = FALSE
+    )
+
+    j <- 1
+    cli::cli_progress_bar("Downloading jar files", total = nrow(md))
+    for (i in md$downLink) {
+        dest <- paste0(fields$fullJava, md$jar[j])
+        utils::download.file(i, dest, quiet = TRUE)
+        cli::cli_progress_update()
+        j <- j + 1
+    }
+    cli::cli_alert_success("Downloaded {nrow(md)} jar files.")
+}
+
+
+

R/utils.R

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+getDirFields <- function(pkg = "BLJars", sep = "/") {
+    pkgDir   <- find.package(pkg)
+    javaDir  <- "java/"
+    metaDir  <- "extdata/"
+    metaFile <- "bljars_metadata.csv"
+
+    return(
+        list(
+            pkgDir   = pkgDir,
+            javaDir  = javaDir,
+            metaDir  = metaDir,
+            fullJava = paste0(pkgDir, sep, javaDir),
+            fullMeta = paste0(pkgDir, sep, metaDir),
+            metaPath = paste0(pkgDir, sep, metaDir, metaFile)
+        )
+    )
+}
+
+

R/zzz.R

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+.onLoad <- function(libname, pkgname) {
+    ## naive check for JAR detection
+    fields <- getDirFields()
+    if (any(grepl("jar", list.files(fields$fullJava)))) {
+        rJava::.jpackage(pkgname, lib.loc = libname)
+        rJava::.jaddClassPath(dir(file.path(getwd(), "inst/java"), full.names = TRUE))
+    }
+}
+
+
+.onAttach <- function(libname, pkgname) {
+    fields <- getDirFields()
+    if (!any(grepl("jar", list.files(fields$fullJava)))) {
+        msg <- paste0(
+            "This looks like your first time running BLJars:", "\n",
+            "  * Please run 'initializeJars()'", "\n",
+            "    - This will download JAR files to the package.", "\n",
+            "  * Once finished, please reload the BLJars package."
+        )
+    } else {
+        tasselMain <- rJava::J("net/maizegenetics/tassel/TASSELMainFrame")
+
+        msg <- paste0(
+            "BLJars package successfully loaded:", "\n",
+            "  * BLJars version....... ", utils::packageVersion("BLJars"), "\n",
+            "  * PHG version.......... ", NULL, "\n",
+            "  * TASSEL version....... ", tasselMain$version, "\n",
+            "  * Build date........... ", tasselMain$versionDate, "\n"
+        )
+
+    }
+
+    packageStartupMessage(msg)
+}
+
+

README.md

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-# bljars
-R package for distributing jar files for rTASSEL and rPHG methods.
+# BLJars
+
+## Overview
+The role of this R package is to inialize a JVM and distribute
+necessary jar files for interacting with the TASSEL and PHG APIs. This is
+used in two packages generated by the Buckler Lab: `rTASSEL` and `rPHG`.
+
+This is currently in a semi-workable stage with the `*/feature/no-jars` 
+experimental branches of `rTASSEL` and `rPHG`. In order to use this, the
+user will need to manually initialize:
+
+```
+library(BLJars)
+```
+
+...and then load `rTASSEL` and/or `rPHG`:
+
+```
+library(rTASSEL)
+library(rPHG)
+```
+
+
+## Contacts
+
+* Brandon Monier ([email protected]) - _Author, Maintainer_

bljars.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace