Complete package of changes - descriptions in commit notes

.dockerignore

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+logs
+.git
+.github
+.idea

.github/workflows/maven.yml

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+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches: [ "main", "refactoring" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      name: Checkout
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: maven
+
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml

.gitignore

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 *.class
 *.project
 *.classpath
+.fastRequest
 *.iml
 .idea/
 # Package Files #
 *.jar
 *.war
 *.ear
 *.log
-/bin/
+/docker/
 /.settings/
 .DS_Store
+.flattened-pom.xml
+dependency-reduced-pom.xml
+target
+logs
 
+
+HELP.md
+target/
+!../.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+/.jpb/jpb-settings.xml
+config/**/*

.mvn/jvm.config

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+-Xmx2048m -Djava.awt.headless=true -XX:ParallelGCThreads=4 -XX:ConcGCThreads=4 -Djava.util.concurrent.ForkJoinPool.common.parallelism=4 -XX:CICompilerCount=4 -XX:+UseParallelGC -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -XX:MinHeapFreeRatio=20 -XX:MaxHeapFreeRatio=40 -XX:+ExitOnOutOfMemoryError

.mvn/maven.config

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+-Drevision=2.0.0-SNAPSHOT

.mvn/wrapper/maven-wrapper.properties

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+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.5/apache-maven-3.9.5-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar

.sdkmanrc

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+# Enable auto-env through the sdkman_auto_env config
+# Add key=value pairs of SDKs to use below
+java=17.0.9-tem
+maven=3.9.6

README.md

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-core [![Build Status](https://travis-ci.org/TheTransitClock/transitime.svg?branch=develop)](https://travis-ci.org/TheTransitClock/transitime)
-====
+# :fire::fire: TransitTime :fire::fire:
 
 The complete core Java software for the Transitime real-time transit information project. The goal is to use any type of real-time GPS data to generate useful public transportation information. The system is for both letting passengers know the status of their vehicles and helping agencies more effectively manage their systems. By providing a complete open-source system, agencies can have a cost effective system and have full ownership of it. 
 
 The software is currently being used in a production environment for MBTA Commuter Rail and for several smaller agencies.
 
-<b>Build</b>
+## :hammer: Setup
+In order to build & run the application make sure you have the following requirements fulfilled:
+- [ ] you have maven installed
+- [ ] you have java 17 or later installed
+- [ ] you have docker installed
 
-The software is made up of three modules which can each be built with maven. See BUILD.md
+### :wrench: Building
+The software is made up of multiple modules which can each be built with maven.
+The core functionality is in the [core](core) project. The REST api & webapp is in [app](app) folder.
 
-The core functionality is in the transitime project. The REST api is in transitimeApi and the user Web applicaton is in transitimeWebapp.
+```shell
+# this will build all the modules of the application
+mvn clean install
+```
 
-<b>Setup</b>
+### :runner: Running
+In order to run the application you need a postgres database available, or you could use docker to start an instance
+```shell
+docker run --rm -e POSTGRES_PASSWORD=transitclock -e POSTGRES_DB=transitclock -p 5432:5432 postgres:15-alpine
+```
 
-The main module is transitTime. This has several standalone programs in the org.transitime.applications package.
+#### :blue_book: Configuration
+- **Properties file**
 
-SchemaGenerator.java will generate the SQL to create the database structures you need to run on.<br/>
-DBTest.java can be used to test that the database can be connected to.<br/>
-GTFSFileProcessor.java will read a GTFS file into this database structure.<br/>
-Core.java is as the name implies is the workhorse of the system. <br/>
-RmiQuery.java allows you make queries to the server run in core from the command line.<br/>
-CreateAPIKey.java a test app to allow you create test/demo key to access REST api webapp.<br/>
-CreateWebAgency.java is used to create and agency that will work in transitimeWebapp.<br/>
+After docker has started, and you have postgress running you need to fine tune the application properties
+Please adjust the fields were you see comments starting with ```##!!!```.
 
-Details on how to run each of these and their respective parameters are in the README for the transitime module.
+```properties
+##!!! STATIC GTFS FEED
+transitclock.gtfs.url=
+transitclock.gtfs.dirName=/var/transitclock/cache
+transitclock.gtfs.intervalMsec=86400000
+transitclock.autoBlockAssigner.autoAssignerEnabled=true
+transitclock.autoBlockAssigner.ignoreAvlAssignments=false
+transitclock.autoBlockAssigner.allowableEarlySeconds=600
+transitclock.autoBlockAssigner.allowableLateSeconds=600
 
-Once this is set up the next step is to set up the transitimeApi which is a RESTful API. This API makes RMI calls to the RMI Server started by Core.java to provide results. This is a war file which can be deployed into Tomcat.  
+transitclock.avl.feedTimeoutInMSecs=30000
+##!!! RT FEED URI
+transitclock.avl.gtfsRealtimeFeedURI=
+transitclock.avl.maxSpeed=100
+transitclock.avl.numThreads=1
+transitclock.avl.queueSize=2400
+transitclock.avl.minLatitude=43
+transitclock.avl.maxLatitude=48
+transitclock.avl.maxLongitude=30
+transitclock.avl.minLongitude=20
+transitclock.avl.feedPollingRateSecs=15
 
-The transitimeWebapp in turn is a web application which uses the transitTimeAPI to provided a user interface. This is a war file which can be deployed into Tomcat. This connects to the database and the connection information is configured in hibernate.cfg.xml in the src/main/resources directory. Currently this needs to be deployed on the same server as the API.
+transitclock.blockLoading.agressive=false
 
-The transitimeQuickStart can be built with mvn install and ran using java -jar transitimeQuickStart it is currently a work in progress but the gui elements can be seen.
+transitclock.cache.core.daysPopulateHistoricalCache=0
 
-[![Build Status](https://zenodo.org/badge/DOI/10.5281/zenodo.3550975.svg)](https://zenodo.org/record/3550975#.XdgmVedKjOQ)
+transitclock.core.agencyId=stpt
+transitclock.core.allowableEarlyDepartureTimeForLoggingEvent=180
+transitclock.core.allowableEarlyForLayoverSeconds=1800
+transitclock.core.allowableEarlySecondsForInitialMatching=1200
+transitclock.core.allowableEarlyTimeForEarlyDepartureSecs=180
+transitclock.core.allowableLateAtTerminalForLoggingEvent=240
+transitclock.core.allowableLateDepartureTimeForLoggingEvent=360
+transitclock.core.allowableLateSeconds=2700
+transitclock.core.allowableNumberOfBadMatches=4
+transitclock.core.afterStopDistance=100
+transitclock.core.beforeStopDistance=100
+transitclock.core.cache.tripDataHistoryCache=org.transitclock.core.dataCache.ehcache.scheduled.TripDataHistoryCache
+transitclock.core.cache.errorCacheClass=org.transitclock.core.dataCache.ehcache.KalmanErrorCache
+transitclock.core.cache.stopArrivalDepartureCache=org.transitclock.core.dataCache.ehcache.StopArrivalDepartureCache
+transitclock.core.cache.stopPathPredictionCache=org.transitclock.core.dataCache.StopPathPredictionCache
+transitclock.core.cache.dwellTimeModelCache=org.transitclock.core.dataCache.ehcache.scheduled.DwellTimeModelCache
+transitclock.core.distanceFromLayoverForEarlyDeparture=250
+transitclock.core.dwelltime.model=org.transitclock.core.predictiongenerator.scheduled.dwell.DwellAverage
+transitclock.core.dwelltime.headwayGeneratorClass=org.transitclock.core.headwaygenerator.LastArrivalsHeadwayGenerator
+transitclock.core.exclusiveBlockAssignments=true
+transitclock.core.fillHistoricalCaches=0
+transitclock.core.layoverDistance=1000
+transitclock.core.longDistanceDeadheadingSpeed=20
+transitclock.core.matchHistoryMaxSize=40
+transitclock.core.maxHeadingOffsetFromSegment=200
+transitclock.core.maxPredictionTimeForDbSecs=1200
+transitclock.core.maxPredictionsTimeSecs=1800
+transitclock.core.minDistanceForDelayed=60
+transitclock.core.minDistanceForNoProgress=60
+transitclock.core.onlyNeedArrivalDepartures=false
+#transitclock.core.predictionGeneratorClass=org.transitclock.core.predictiongenerator.scheduled.traveltime.kalman.KalmanPredictionGeneratorImpl
+transitclock.core.shortDistanceDeadheadingSpeed=10
+transitclock.core.timeForDeterminingDelayedSecs=300
+transitclock.core.timeForDeterminingNoProgress=360000
+transitclock.core.trackHistoricalCaches=false
+transitclock.core.useArrivalPredictionsForNormalStops=false
 
+transitclock.db.batchSize=4000
+transitclock.db.dbName=STPT
+transitclock.db.dbPassword=transitclock
+transitclock.db.dbUserName=transitclock
+transitclock.db.dbHost=localhost:5432
+transitclock.db.storeDataInDatabase=true
+transitclock.db.dbType=postgresql
+
+
+transitclock.predAccuracy.stopsPerTrip=1000
+transitclock.predAccuracy.maxPredTimeMinutes=30
+
+transitclock.prediction.data.kalman.mindays=3
+transitclock.prediction.data.kalman.maxdays=5
+transitclock.prediction.data.kalman.maxdaystosearch=21
+transitclock.prediction.data.kalman.percentagePredictionMethodDifferencene=50
+transitclock.prediction.data.kalman.tresholdForDifferenceEventLog=60000
+transitclock.prediction.rls.lambda=0.9
+
+transitclock.timeout.pollingRateSecs=60
+
+transitclock.modules.optionalModulesList=org.transitclock.core.avl.GtfsRealtimeModule;org.transitclock.core.predAccuracy.PredictionAccuracyModule;org.transitclock.gtfs.GtfsUpdatedModule
+##!!! absolute location to the hibernate.cfg.xml file
+transitclock.hibernate.configFile=
+transitclock.logging.dir=/var/transitclock/logs
+transitclock.web.mapTileUrl=http://tile.openstreetmap.org/{z}/{x}/{y}.png
+```
+
+- **hibernate config file sample**
+```xml
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE hibernate-configuration SYSTEM
+        "http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
+
+<hibernate-configuration>
+    <session-factory>
+        <property name="hibernate.connection.driver_class">
+            org.postgresql.Driver
+        </property>
+        <property name="hibernate.hikari.autoCommit">false</property>
+
+        <!-- Enable full SQL logging that also shows the
+             parameters being used. show_sql is not really
+             useful since it duplicates the output of the SQL.
+             format_sql makes sql more readable but takes up
+             more space. OK for now but should disable in the
+             future. use_sql_comments adds comments that might
+             be nice, but again, should probably be disabled
+             in the future. -->
+<!--        <property name="hibernate.show_sql">true</property>-->
+<!--        <property name="hibernate.format_sql">true</property>-->
+<!--        <property name="hibernate.use_sql_comments">true</property>-->
+        <property name="hibernate.hbm2ddl.auto">create-drop</property>
+        <property name="hibernate.hikari.minimumIdle">5</property>
+        <property name="hibernate.hikari.maximumPoolSize">20</property>
+        <property name="hibernate.hikari.idleTimeout">30000</property>
+        <property name="hibernate.jdbc.batch_size">25</property>
+ </session-factory>
+</hibernate-configuration>
+```
+
+#### :bomb: Starting the application
+```shell
+JAVA_OPTS="-Dtransitclock.configFiles=/location-to-properties-file/transitclock.properties -Dtransitclock.apikey=f78a2e9a"
+GTFS_TO_IMPORT="url to gtfs you want to import"
+
+java $JAVA_OPTS -jar app/target/transitclock.jar --gtfs-url $GTFS_TO_IMPORT
+```
+
+### :whale: Running using Docker
+Simplest way to run the transitclock would be using ```docker```, actually ```docker compose```. For it to happen you would be to map your config into the transitclock container using a configuration as follows:
+```yaml
+version: "3.18"
+services:
+  db:
+    image: postgres:15-alpine
+    restart: always
+    environment:
+      POSTGRES_PASSWORD: transitclock
+      POSTGRES_DB: transitclock
+    ports:
+      - "5432:5432"
+  gtfsrt-validator:
+    image: ghcr.io/mobilitydata/gtfs-realtime-validator:latest
+    ports:
+      - "9090:8080"
+  transitclock:
+    image: otrro/transitclock-server:latest
+    depends_on:
+      - db
+    environment:
+      AGENCYID: transitclock # not that relevant anymore since will be coming from your file
+      AGENCYNAME: transitclock # has to match what is configured in the file for transitclock.db.dbName and should match POSTGRES_DB specified for postgress
+      GTFS_URL: https://your feed location
+      GTFSRTVEHICLEPOSITIONS: https://rt feed location # can be configured in the file directly
+      PGPASSWORD: transitclock
+      POSTGRES_PORT_5432_TCP_ADDR: db
+      POSTGRES_PORT_5432_TCP_PORT: 5432
+    volumes:
+      # this mapps the transitclock.properties file that is near to docker-compose file to the one in container that is used by the app
+      ### IMPORTANT NOTE: make sure you have this config transitclock.hibernate.configFile=/app/config/hibernate.cfg.xml
+      - ./transitclock.properties:/app/config/transitclock.properties
+    ports:
+      - "8080:8080"
+    command:
+      - --gtfs-url
+      - https://your feed location
+```
+
+After doing this you just simply need to:
+```shell
+# if you have compose plugin for docker installed
+docker compose up # in the folder where you have save the previous content as docker-compose.yaml
+
+# if you have the actual docker-compose application
+docker-compose up
+```