initial base implementation

Dockerfile

+FROM gradle:6.3-jdk8
+ADD . /
+WORKDIR /
+RUN gradle --no-daemon --no-scan --no-build-cache distTar
+RUN cd /build/distributions && tar xf app.tar
+
+FROM openjdk:8-jre-alpine
+COPY --from=0 /build/distributions/app /app
+CMD /app/bin/fedora-metadata-extractor

LICENSE

@@ -629,8 +629,8 @@ to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    Fedora Metadata Extractor
-    Copyright (C) 2020  memoriav / Memobase 2020 / services / postprocessing
+    record-parser
+    Copyright (C) 2020  memoriav / Memobase 2020 / services
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as published

README.md

-# Fedora Metadata Extractor
+### Fedora Metadata Extractor
 
 extracts, parses and propagates metadata from Fedora
\ No newline at end of file

build.gradle

+plugins {
+    id 'application'
+    id 'distribution'
+    id 'org.jetbrains.kotlin.jvm' version '1.3.71'
+    id 'com.palantir.git-version' version '0.11.0'
+    id 'org.jlleitschuh.gradle.ktlint' version '9.2.1'
+}
+
+group 'org.memobase'
+version = gitVersion()
+mainClassName = 'org.memobase.App'
+
+jar {
+    manifest {
+        attributes 'Main-Class': 'org.memobase.App'
+    }
+}
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+repositories {
+    jcenter()
+    maven {
+        url  "https://dl.bintray.com/memoriav/memobase"
+    }
+}
+
+ext {
+    kafkaV = '2.3.1'
+    log4jV = '2.11.2'
+}
+
+dependencies {
+    implementation 'org.memobase:memobase-service-utilities:1.4.0'
+    implementation 'org.memobase:fedora-client:0.1.2'
+
+    // Logging Framework
+    implementation "org.apache.logging.log4j:log4j-api:${log4jV}"
+    implementation "org.apache.logging.log4j:log4j-core:${log4jV}"
+
+    // Kafka Imports
+    implementation "org.apache.kafka:kafka-streams:${kafkaV}"
+
+    // RDF Library
+    implementation 'org.apache.jena:apache-jena:3.14.0'
+
+    // JSON Library
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.11.+'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.11.+'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.11.+'
+    implementation "com.fasterxml.jackson.module:jackson-module-kotlin:2.11.+"
+
+    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8'
+    implementation "org.jetbrains.kotlin:kotlin-script-runtime:1.3.71"
+    implementation "org.jetbrains.kotlin:kotlin-reflect:1.3.71"
+
+    testCompile("org.junit.jupiter:junit-jupiter:5.4.2")
+    testImplementation 'org.assertj:assertj-core:3.15.0'
+
+    // https://mvnrepository.com/artifact/org.apache.kafka/kafka-streams-test-utils
+    testCompile group: 'org.apache.kafka', name: 'kafka-streams-test-utils', version: kafkaV
+}
+
+compileKotlin {
+    kotlinOptions.jvmTarget = "1.8"
+}
+compileTestKotlin {
+    kotlinOptions.jvmTarget = "1.8"
+}
+
+
+test {
+    useJUnitPlatform()
+    testLogging {
+        events "passed", "skipped", "failed"
+    }
+}
+
+sourceSets {
+    main.kotlin.srcDirs += 'src/main/kotlin'
+    main.resources.srcDirs = [ "src/main/resources" ]
+    main.resources.includes = [ "**/*.yml", "**/*.xml"]
+    test.kotlin.srcDirs += 'src/test/kotlin'
+    test.resources.srcDirs = [ "src/test/resources" ]
+    test.resources.includes = [ "**/*.yml", "**/*.xml"]
+}
+
+plugins.withType(DistributionPlugin) {
+    distTar {
+        archiveFileName = 'app.tar'
+    }
+}
\ No newline at end of file

chart/Chart.yaml

+apiVersion: v2
+name: fedora-metadata-extractor
+description: A micro service deployment to extract metadata from fedora based on the event stream.
+type: application
+version: 0.0.0
+appVersion: 0.0.0
+
+maintainers:
+  - name: Jonas Waeber
+    email: jonas.waeber@unibas.ch

chart/templates/app-config.yml

+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: "{{ .Values.deploymentName }}-app-config"
+  namespace: memobase
+data:
+  APPLICATION_ID: "{{ .Values.deploymentName }}-deployment"
+  TOPIC_IN: "{{ .Values.inputTopic }}"
+  TOPIC_OUT: "{{ .Values.outputTopic }}"
+  TOPIC_PROCESS: "{{ .Values.deploymentName }}-reporting"
\ No newline at end of file

chart/templates/deployment.yml

+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: "{{ .Values.deploymentName }}-deployment"
+  namespace: memobase
+  labels:
+    app: "{{ .Values.deploymentName }}-deployment"
+spec:
+  selector:
+    matchLabels:
+      app: "{{ .Values.deploymentName }}-deployment"
+  replicas: 1
+  template:
+    metadata:
+      labels:
+        app: "{{ .Values.deploymentName }}-deployment"
+        tier: post-processing
+    spec:
+      containers:
+        - name: "{{ .Values.deploymentName }}-container"
+          image: "{{.Values.registry}}/{{ .Values.image }}:{{ .Values.tag }}"
+          imagePullPolicy: Always
+          envFrom:
+          - configMapRef:
+              name: "{{ .Values.kafkaConfigs }}"
+          - configMapRef:
+              name: "{{ .Values.deploymentName}}-app-config"
+          - secretRef:
+              name: "{{ .Values.fedoraConfigs }}"
+      restartPolicy: Always

chart/values.yaml

+############################################
+## Values in this section are the same for #
+## all jobs                                #
+############################################
+#image values
+registry: "cr.gitlab.switch.ch"
+image: "memoriav/memobase-2020/services/postprocessing/fedora-metadata-extractor"
+tag: "latest"
+
+deploymentName: fedora-metadata-extractor
+kafkaConfigs: prod-kafka-bootstrap-servers
+fedoraConfigs: prod-fedora-configs
+outputTopic: fedora-metadata-extractor-json-output
+inputTopic: fedora-events
\ No newline at end of file

gradle.properties

+kotlin.code.style=official
\ No newline at end of file

gradlew

+#!/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" "$@"

gradlew.bat

+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

insert_chart_versions.sh

+#!/usr/bin/env bash
+
+echo Creating release: $1
+sed -i "s/version: 0.0.0/version: $CI_COMMIT_TAG/g" ./chart/Chart.yaml
+sed -i "s/appVersion: 0.0.0/appVersion: $CI_COMMIT_TAG/g" ./chart/Chart.yaml
+sed -i "s/tag: \"latest\"/tag: $CI_COMMIT_TAG/g" ./chart/values.yaml
\ No newline at end of file

settings.gradle

+rootProject.name = 'fedora-metadata-extractor'
+

src/main/kotlin/App.kt

+/*
+ * fedora-metadata-extractor
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase
+
+import kotlin.system.exitProcess
+import org.apache.logging.log4j.LogManager
+
+class App {
+    companion object {
+        private val log = LogManager.getLogger("FedoraMetadataExtractionApp")
+        @JvmStatic fun main(args: Array<String>) {
+            try {
+                Service().run()
+            } catch (ex: Exception) {
+                ex.printStackTrace()
+                log.error("Stopping application due to error: " + ex.message)
+                exitProcess(1)
+            }
+        }
+    }
+}

src/main/kotlin/KafkaTopology.kt

+/*
+ * fedora-metadata-extractor
+ * Copyright (C) 2020 Memoriav
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package org.memobase
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import com.fasterxml.jackson.module.kotlin.registerKotlinModule
+import org.apache.jena.rdf.model.Model
+import org.apache.jena.rdf.model.ModelFactory
+import org.apache.jena.rdf.model.Property
+import org.apache.jena.rdf.model.Resource
+import org.apache.jena.riot.Lang
+import org.apache.jena.riot.RDFDataMgr
+import org.apache.kafka.streams.StreamsBuilder
+import org.apache.kafka.streams.Topology
+import org.apache.kafka.streams.kstream.Predicate
+import org.apache.logging.log4j.LogManager
+import org.memobase.fedora.FedoraClientImpl
+import org.memobase.model.EventMessage
+import org.memobase.rdf.NS
+import org.memobase.rdf.RDF
+import org.memobase.rdf.RICO
+import org.memobase.settings.SettingsLoader
+import java.io.StringWriter
+import java.net.URI
+import java.nio.charset.StandardCharsets
+
+class KafkaTopology(
+    private val settings: SettingsLoader
+) {
+    private val log = LogManager.getLogger("FedoraMetadataExtractor")
+
+    private val objectMapper = ObjectMapper().registerKotlinModule()
+    private val fedora = FedoraClientImpl.builder()
+        .urls(
+            settings.appSettings.getProperty("fedora.internalDomain"),
+            settings.appSettings.getProperty("fedora.externalDomain")
+        )
+        .credentials(
+            settings.appSettings.getProperty("fedora.user"),
+            settings.appSettings.getProperty("fedora.password")
+        )
+        .build()
+
+
+    fun build(): Topology {
+        val builder = StreamsBuilder()
+
+        val stream = builder.stream<String, String>(settings.inputTopic)
+
+
+        val objectBranches = stream
+            .mapValues { value -> parseMessage(value) }
+            .branch(
+                // TODO: Add actual values.
+                Predicate { _, value -> value.objectTypes == "rico:Record" },
+                Predicate { _, value ->
+                    value.objectTypes == "rico:CorporateBody" || value.objectTypes == "rico:RecordSet" }
+            )
+
+        objectBranches[0]
+            .mapValues { value -> requestPrimaryResource(value) }
+            .mapValues { value -> parseModel(value) }
+            .mapValues { value -> addStatus(value) }
+            .mapValues { value -> requestAdditionalRecordResources(value) }
+            .mapValues { value -> writeModel(value) }
+            .to(settings.outputTopic)
+
+        objectBranches[1]
+            .mapValues { value -> requestPrimaryResource(value) }
+            .mapValues { value -> parseModel(value) }
+            .mapValues { value -> addStatus(value) }
+            .mapValues { value -> writeModel(value) }
+            .to(settings.outputTopic)
+
+        return builder.build()
+    }
+
+
+    private fun parseMessage(data: String): EventMessage {
+        // can we assume that this is always correct? or should we handle parse errors?
+        return objectMapper.readValue(data, EventMessage::class.java)
+    }
+
+    private fun requestPrimaryResource(message: EventMessage): Pair<EventMessage, String> {
+        return Pair(message, fedora.fetchRdfResourceIntoString(URI.create(message.objectPath), "plain/text"))
+    }
+
+    private fun parseModel(input: Pair<EventMessage, String>): Pair<EventMessage, Model> {
+        val model = ModelFactory.createDefaultModel()
+        // TODO: Add exception handling
+        RDFDataMgr.read(model, input.second.byteInputStream(StandardCharsets.UTF_8), Lang.NT)
+        return Pair(input.first, model)
+    }
+
+    /**
+     *  Adds the status of the event message to the core resources.
+     *  Core resources are rico:Record, rico:CorporateBody (for institutions) and rico:RecordSet.