Merge develop into release to make a new Release Candidate (#1574)

* make conflicts network matcher opt test easier to follow
* couple more small tweaks to optimizer
* Fix error reporting in ConflateCaseTest.cpp (it was ambiguous before) (#1570)
Comment out a few trace statements that were causing a test failure (and appliedd appropriate warnings)
* remove warning
* Update to latest Oracle release of java (#1572)
* Update to latest Oracle jdk
* Fixing whitespace
* Fixing typo in comment
* Updates for JAVA_HOME
* Stop jdk from upgrading automatically during provisioning
* remove unused var
* update copyright headers

VagrantProvision.sh

@@ -13,6 +13,8 @@ fi
 
 echo "Updating OS..."
 sudo apt-get -qq update > Ubuntu_upgrade.txt 2>&1
+# Don't automatically update the oracle jdk, we need to control the version
+sudo apt-mark -qq hold oracle-java8-installer oracle-java8-set-default >> Ubuntu_upgrade.txt 2>&1
 sudo apt-get -q -y upgrade >> Ubuntu_upgrade.txt 2>&1
 sudo apt-get -q -y dist-upgrade >> Ubuntu_upgrade.txt 2>&1
 
@@ -22,21 +24,21 @@ sudo service ntp stop
 sudo ntpd -gq
 sudo service ntp start
 
-if ! java -version 2>&1 | grep --quiet 1.8.0_112; then
+if ! java -version 2>&1 | grep --quiet 1.8.0_131; then
     echo "### Installing Java 8..."
 
     # jdk-8u112-linux-x64.tar.gz's official checksums:
-    #    sha256: 777bd7d5268408a5a94f5e366c2e43e720c6ce4fe8c59d9a71e2961e50d774a5
-    #    md5: de9b7a90f0f5a13cfcaa3b01451d0337
-    echo "de9b7a90f0f5a13cfcaa3b01451d0337  /tmp/jdk-8u112-linux-x64.tar.gz" > /tmp/jdk.md5
-
-    if [ ! -f /tmp/jdk-8u112-linux-x64.tar.gz ] || ! md5sum -c /tmp/jdk.md5; then
-        echo "Downloading jdk-8u112-linux-x64.tar.gz ...."
-        sudo wget --quiet --no-check-certificate --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie" http://download.oracle.com/otn-pub/java/jdk/8u112-b15/jdk-8u112-linux-x64.tar.gz -P /tmp
-        echo "Finished download of jdk-8u112-linux-x64.tar.gz"
+    #    sha256:  62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236
+    #    md5: 75b2cb2249710d822a60f83e28860053
+    echo "75b2cb2249710d822a60f83e28860053  /tmp/jdk-8u131-linux-x64.tar.gz " > /tmp/jdk.md5
+
+    if [ ! -f /tmp/jdk-8u131-linux-x64.tar.gz ] || ! md5sum -c /tmp/jdk.md5; then
+        echo "Downloading jdk-8u131-linux-x64.tar.gz ...."
+        sudo wget --quiet --no-check-certificate --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie" http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz -P /tmp
+        echo "Finished download of jdk-8u131-linux-x64.tar.gz"
     fi
 
-    sudo tar -xvzf /tmp/jdk-8u112-linux-x64.tar.gz --directory=/tmp >/dev/null
+    sudo tar -xvzf /tmp/jdk-8u131-linux-x64.tar.gz --directory=/tmp >/dev/null
 
     if [[ ! -e /usr/lib/jvm ]]; then
         sudo mkdir /usr/lib/jvm
@@ -46,7 +48,7 @@ if ! java -version 2>&1 | grep --quiet 1.8.0_112; then
         fi
     fi
 
-    sudo mv -f /tmp/jdk1.8.0_112 /usr/lib/jvm/oracle_jdk8
+    sudo mv -f /tmp/jdk1.8.0_131 /usr/lib/jvm/oracle_jdk8
     sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/oracle_jdk8/jre/bin/java 9999
     sudo update-alternatives --install /usr/bin/javac javac /usr/lib/jvm/oracle_jdk8/bin/javac 9999
     echo "### Done with Java 8 install..."

hoot-core-test/src/test/cpp/hoot/core/test/ConflateCaseTest.cpp

@@ -72,14 +72,13 @@ ConflateCaseTest::ConflateCaseTest(QDir d, QStringList confs) :
 
 void ConflateCaseTest::runTest()
 {
+  TestUtils::resetEnvironment();
   LOG_DEBUG("Running conflate case test...");
 
   // configures and cleans up the conf() environment
   LOG_VART(_confs);
   SetupTest st(_confs);
 
-  bool failed = false;
-
   ConflateCmd cmd;
 
   if (QFileInfo(_d, "README.txt").exists() == false)
@@ -124,15 +123,10 @@ void ConflateCaseTest::runTest()
 
   if (result != 0)
   {
-    failed = true;
+    CPPUNIT_ASSERT_MESSAGE(QString("Conflate command had nonzero exit status").toStdString(), false);
   }
 
   if (!TestUtils::compareMaps(expected.absoluteFilePath(), testOutput))
-  {
-    failed = true;
-  }
-
-  if (failed)
   {
     CPPUNIT_ASSERT_MESSAGE(QString("Maps do not match").toStdString(), false);
   }

hoot-rnd/src/main/cpp/hoot/rnd/conflate/network/EdgeMatchSetFinder.cpp

@@ -177,7 +177,10 @@ bool EdgeMatchSetFinder::_addEdgeNeighborsToEnd(ConstEdgeMatchPtr em,
   {
     LOG_VART(neighbor1);
     LOG_VART(em->contains(neighbor1));
-    LOG_VART(_details->getPartialEdgeMatchScore(neighbor1, em->getString2()->getLastEdge()));
+
+    // Calling this non-const function can alter the state of the map, and lead to different
+    // behaviors at different log levels! Beware!
+    //LOG_VART(_details->getPartialEdgeMatchScore(neighbor1, em->getString2()->getLastEdge()));
 
     // if the neighbor pair score is non-zero
     if (em->contains(neighbor1) == false &&
@@ -198,7 +201,10 @@ bool EdgeMatchSetFinder::_addEdgeNeighborsToEnd(ConstEdgeMatchPtr em,
     LOG_VART(neighbor2);
     LOG_VART(em->contains(neighbor2));
     LOG_VART(_details->isStringCandidate(em->getString2()->getLastEdge(), neighbor2));
-    LOG_VART(_details->getPartialEdgeMatchScore(neighbor2, em->getString1()->getLastEdge()));
+
+    // Calling this non-const function can alter the state of the map, and lead to different
+    // behaviors at different log levels! Beware!
+    //LOG_VART(_details->getPartialEdgeMatchScore(neighbor2, em->getString1()->getLastEdge()));
 
     // if the neighbor pair score is non-zero
     if (em->contains(neighbor2) == false &&
@@ -230,7 +236,10 @@ bool EdgeMatchSetFinder::_addEdgeNeighborsToStart(ConstEdgeMatchPtr em,
   {
     LOG_VART(neighbor1);
     LOG_VART(em->getString2()->getFirstEdge());
-    LOG_VART(_details->getPartialEdgeMatchScore(neighbor1, em->getString2()->getFirstEdge()));
+
+    // Calling this non-const function can alter the state of the map, and lead to different
+    // behaviors at different log levels! Beware!
+    //LOG_VART(_details->getPartialEdgeMatchScore(neighbor1, em->getString2()->getFirstEdge()));
 
     // if the neighbor pair score is non-zero
     if (em->contains(neighbor1) == false &&
@@ -250,7 +259,10 @@ bool EdgeMatchSetFinder::_addEdgeNeighborsToStart(ConstEdgeMatchPtr em,
   {
     LOG_VART(neighbor2);
     LOG_VART(em->getString1()->getFirstEdge());
-    LOG_VART(_details->getPartialEdgeMatchScore(neighbor2, em->getString1()->getFirstEdge()));
+
+    // Calling this non-const function can alter the state of the map, and lead to different
+    // behaviors at different log levels! Beware!
+    //LOG_VART(_details->getPartialEdgeMatchScore(neighbor2, em->getString1()->getFirstEdge()));
 
     // if the neighbor pair score is non-zero
     if (em->contains(neighbor2) == false &&