Merge pull request #1 from KPMP/KPMP-1127_InitialStateManager

Kpmp 1127 initial state manager

.gitignore

@@ -20,3 +20,7 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+.classpath
+build/
+.settings
+.project

.gradle/buildOutputCleanup/cache.properties

@@ -0,0 +1,2 @@
+#Tue Sep 03 12:03:55 EDT 2019
+gradle.version=4.6

.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version

@@ -0,0 +1 @@
+

.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version

@@ -0,0 +1 @@
+

.metadata/.plugins/org.eclipse.jdt.ui/OpenTypeHistory.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<typeInfoHistroy/>

.metadata/.plugins/org.eclipse.jdt.ui/QualifiedTypeNameHistory.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<qualifiedTypeNameHistroy/>

.metadata/.plugins/org.eclipse.jdt.ui/dialog_settings.xml

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+	<section name="org.eclipse.jdt.internal.ui.packageview.PackageExplorerPart">
+		<item value="2" key="layout"/>
+		<item value="true" key="group_libraries"/>
+		<item value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;&#x0A;&lt;packageExplorer group_libraries=&quot;1&quot; layout=&quot;2&quot; linkWithEditor=&quot;0&quot; rootMode=&quot;1&quot; workingSetName=&quot;Aggregate for window 1567525588140&quot;&gt;&#x0A;&lt;customFilters userDefinedPatternsEnabled=&quot;false&quot;&gt;&#x0A;&lt;xmlDefinedFilters&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.StaticsFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.buildship.ui.packageexplorer.filter.gradle.buildfolder&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.NonSharedProjectsFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.internal.ui.PackageExplorer.EmptyInnerPackageFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.m2e.MavenModuleFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.buildship.ui.packageexplorer.filter.gradle.subProject&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.ClosedProjectsFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.EmptyLibraryContainerFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.PackageDeclarationFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.pde.ui.BinaryProjectFilter1&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.LocalTypesFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.pde.ui.ExternalPluginLibrariesFilter1&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.FieldsFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.NonJavaProjectsFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer_patternFilterId_.*&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.SyntheticMembersFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.ContainedLibraryFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.internal.ui.PackageExplorer.HideInnerClassFilesFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.DeprecatedMembersFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.ImportDeclarationFilter&quot; isEnabled=&quot;true&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.NonJavaElementFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.LibraryFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.CuAndClassFileFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.internal.ui.PackageExplorer.EmptyPackageFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;child filterId=&quot;org.eclipse.jdt.ui.PackageExplorer.NonPublicFilter&quot; isEnabled=&quot;false&quot;/&gt;&#x0A;&lt;/xmlDefinedFilters&gt;&#x0A;&lt;/customFilters&gt;&#x0A;&lt;/packageExplorer&gt;" key="memento"/>
+		<item value="1" key="rootMode"/>
+		<item value="false" key="linkWithEditor"/>
+	</section>
+</section>

.metadata/.plugins/org.eclipse.m2e.logback.configuration/logback.1.9.1.20180912-1601.xml

@@ -0,0 +1,43 @@
+<configuration scan="true">
+  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+    <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
+      <pattern>%date [%thread] %-5level %logger{35} - %msg%n</pattern>
+    </encoder>
+    <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+      <level>OFF</level> <!-- change to DEBUG to mimic '-consolelog' behaviour -->
+    </filter>
+  </appender>
+
+  <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
+    <File>${org.eclipse.m2e.log.dir}/0.log</File>
+    <rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
+      <FileNamePattern>${org.eclipse.m2e.log.dir}/%i.log</FileNamePattern>
+      <MinIndex>1</MinIndex>
+      <MaxIndex>10</MaxIndex>
+    </rollingPolicy>
+    <triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
+      <MaxFileSize>100MB</MaxFileSize>
+    </triggeringPolicy>
+    <encoder class="ch.qos.logback.classic.encoder.PatternLayoutEncoder">
+      <pattern>%date [%thread] %-5level %logger{35} - %msg%n</pattern>
+    </encoder>
+  </appender>
+
+  <appender name="EclipseLog" class="org.eclipse.m2e.logback.appender.EclipseLogAppender">
+    <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+      <level>WARN</level>
+    </filter>
+  </appender>
+
+  <appender name="MavenConsoleLog" class="org.eclipse.m2e.logback.appender.MavenConsoleAppender">
+  </appender>
+
+  <root level="INFO">
+    <appender-ref ref="FILE" />
+    <appender-ref ref="STDOUT" />
+    <appender-ref ref="EclipseLog" />
+    <appender-ref ref="MavenConsoleLog" />
+  </root>
+
+  <logger name="com.ning.http.client" level="INFO" />
+</configuration>

.metadata/.plugins/org.eclipse.oomph.setup/workspace.setup

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<setup:Workspace
+    xmi:version="2.0"
+    xmlns:xmi="http://www.omg.org/XMI"
+    xmlns:setup="http://www.eclipse.org/oomph/setup/1.0"
+    name="workspace"/>

.metadata/.plugins/org.eclipse.pde.core/.cache/clean-cache.properties

@@ -0,0 +1,2 @@
+#Cached timestamps
+#Tue Sep 03 11:46:41 EDT 2019

.metadata/.plugins/org.eclipse.ui.intro/introstate

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<state reopen="true"/>

.metadata/.plugins/org.eclipse.ui.workbench/dialog_settings.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+	<section name="org.eclipse.ui.internal.QuickAccess">
+		<item value="-1" key="dialogHeight"/>
+		<item value="-1" key="dialogWidth"/>
+		<list key="textEntries">
+		</list>
+		<list key="orderedElements">
+		</list>
+		<list key="orderedProviders">
+		</list>
+		<list key="textArray">
+		</list>
+	</section>
+</section>

.metadata/.plugins/org.eclipse.ui.workbench/workingsets.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<workingSetManager>
+<workingSet editPageId="org.eclipse.jdt.internal.ui.DynamicSourcesWorkingSet" factoryID="org.eclipse.ui.internal.WorkingSetFactory" id="1567525584013_0" label="Java Main Sources" name="Java Main Sources"/>
+<workingSet editPageId="org.eclipse.jdt.internal.ui.DynamicSourcesWorkingSet" factoryID="org.eclipse.ui.internal.WorkingSetFactory" id="1567525584023_1" label="Java Test Sources" name="Java Test Sources"/>
+<workingSet aggregate="true" factoryID="org.eclipse.ui.internal.WorkingSetFactory" id="1567525588140_2" label="Window Working Set" name="Aggregate for window 1567525588140"/>
+</workingSetManager>

.metadata/version.ini

@@ -0,0 +1,3 @@
+#Tue Sep 03 11:46:22 EDT 2019
+org.eclipse.core.runtime=2
+org.eclipse.platform=4.9.0.v20180906-0745

.travis.yml

@@ -0,0 +1,17 @@
+dist: trusty
+language: java
+
+jdk:
+  - oraclejdk8
+
+install: true
+
+script:
+  - ./gradlew build 
+
+notifications:
+  email:
+    - rlreamy@umich.edu
+    - zwright@umich.edu
+    - cgates@umich.edu
+    - rossmith@umich.edu

README.md

@@ -1,2 +1,3 @@
 # stateManagerService
+
 The state manager service will do the work to keep track of the state of packages as they travel from the data lake to the knowledge environment.

build.gradle

@@ -0,0 +1,58 @@
+buildscript {
+    repositories {
+        mavenCentral()
+    }
+    dependencies {
+        classpath("org.springframework.boot:spring-boot-gradle-plugin:2.1.7.RELEASE")
+    }
+
+}
+
+plugins {
+    id 'com.palantir.docker' version '0.22.1'
+}
+
+group = 'kingstonduo'
+
+
+apply plugin: 'java'
+apply plugin: 'eclipse'
+apply plugin: 'idea'
+apply plugin: 'org.springframework.boot'
+apply plugin: 'io.spring.dependency-management'
+apply plugin: 'com.palantir.docker'
+
+jar {
+    baseName='stateManagerService'
+    version= '0.1'
+}
+
+repositories {
+    mavenCentral()
+}
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+dependencies {
+	compile 'org.springframework.boot:spring-boot-starter-web' 
+	compile 'org.apache.commons:commons-compress:1.17'
+	compile 'org.springframework.boot:spring-boot-starter-test'
+	compile 'org.springframework.data:spring-data-mongodb:2.0.8.RELEASE'
+	compile 'org.springframework.boot:spring-boot-starter-data-mongodb'
+	testCompile 'org.springframework.boot:spring-boot-starter-test'
+	testCompile 'org.mockito:mockito-core'
+}
+
+
+task unpack(type: Copy) {
+    dependsOn bootJar
+    from(zipTree(tasks.bootJar.outputs.files.singleFile))
+    into("build/dependency")
+}
+
+docker {
+    name "${project.group}/${jar.baseName}"
+    copySpec.from(tasks.unpack.outputs).into("dependency")
+    buildArgs(['DEPENDENCY': "dependency"])
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.6-all.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

gradlew

@@ -0,0 +1,172 @@
+#!/usr/bin/env sh
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+    echo "$*"
+}
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"