Add SystemUtil for querying common system properties

src/main/scala/com/fulcrumgenomics/commons/util/SystemUtil.scala

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+/*
+ * The MIT License
+ *
+ * Copyright (c) 2020 Fulcrum Genomics
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ */
+
+package com.fulcrumgenomics.commons.util
+
+import scala.util.Properties.{isLinux, isMac, propOrNone}
+import scala.util.matching.Regex
+
+/** System utility defaults and methods. Many methods mock functions in `org.apache.commons:commons-lang3`. */
+object SystemUtil {
+
+  /** The current operating system architecture */
+  lazy val OsArch: Option[String] = safePropOrNone(property = "os.arch")
+
+  /** The current operating system version */
+  lazy val OsVersion: Option[String] = safePropOrNone(property = "os.version")
+
+  /** Gets a system property. Returns None if not found, or if a security manager does not allow us to retrieve the property. */
+  def safePropOrNone(property: String): Option[String] = {
+    try { propOrNone(property) }
+    catch { case _: SecurityException => None } // not allowed to look at this property
+  }
+
+  /** Returns true if the architecture is the given name, false otherwise. */
+  def isOsArch(name: String): Boolean = OsArch.contains(name)
+
+  /** Returns true if the architecture matches the given regular expression, false otherwise. */
+  def isOsArch(regex: Regex): Boolean = OsArch.exists(a => regex.pattern.matcher(a).matches)
+
+  /** Returns true if the operating system version is the given name, false otherwise. */
+  def isOsVersion(name: String): Boolean = OsVersion.contains(name)
+
+  /** Returns true if the operating system version matches the given regular expression, false otherwise. */
+  def isOsVersion(regex: Regex): Boolean = OsVersion.exists(v => regex.pattern.matcher(v).matches)
+
+  /** True if the current system might support the Intel Inflater and Deflater, false otherwise. */
+  lazy val IntelCompressionLibrarySupported: Boolean = {
+    if (!isLinux && !isMac) false
+    else if (isOsArch(name = "ppc64le")) false
+    else if (isMac && isOsVersion("10\\.14\\..+".r)) false // FIXME: https://github.com/Intel-HLS/GKL/issues/101
+    else true
+  }
+}

src/test/scala/com/fulcrumgenomics/commons/util/SystemUtilTest.scala

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+/*
+ * The MIT License
+ *
+ * Copyright (c) 2020 Fulcrum Genomics
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ */
+
+package com.fulcrumgenomics.commons.util
+
+import org.scalatest.OptionValues
+
+import scala.util.matching.Regex
+
+class SystemUtilTest extends UnitSpec with OptionValues {
+
+  private def matches(original: String, exact: String => Boolean, regex: Regex => Boolean): Unit = {
+    original.length should be > 1
+
+    val prefix = original.dropRight(1)
+    val suffix = original.drop(1)
+
+    exact(original) shouldBe true
+    exact(prefix) shouldBe false
+    exact(suffix) shouldBe false
+
+    regex(s"$original*".r) shouldBe true
+    regex(s"$original.*".r) shouldBe true
+    regex(s"$original.+".r) shouldBe false
+
+    regex(s"$prefix.*".r) shouldBe true
+    regex(s"$prefix.".r) shouldBe true
+    regex(prefix.r) shouldBe false
+
+    regex(s".*$suffix".r) shouldBe true
+    regex(s".$suffix".r) shouldBe true
+    regex(suffix.r) shouldBe false
+  }
+
+  "SystemUtil" should "match the OS version exactly and with a regex" in {
+    matches(SystemUtil.OsVersion.value, s => SystemUtil.isOsVersion(s), r => SystemUtil.isOsVersion(r))
+  }
+
+  it should "match the OS architecture exactly and with a regex" in {
+    matches(SystemUtil.OsArch.value, s => SystemUtil.isOsArch(s), r => SystemUtil.isOsArch(r))
+  }
+}