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14 changed files with 377 additions and 65 deletions

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@ -186,7 +186,7 @@
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright 2021-2023 Athena Research and Innovation Center (ARC)
Copyright 2021-2024 OpenAIRE AMKE
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.

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@ -1,4 +1,5 @@
# UrlsWorker
### [![Jenkins build status](https://jenkins-dnet.d4science.org/buildStatus/icon?job=UrlsWorker)](https://jenkins-dnet.d4science.org/job/UrlsWorker/)
The Worker's Application, requests assignments from the [**Controller**](https://code-repo.d4science.org/lsmyrnaios/UrlsController) and processes them with the help of the [__PublicationsRetriever__](https://github.com/LSmyrnaios/PublicationsRetriever) software and downloads the available full-texts.<br>
Then, it posts the results to the Controller, which in turn, requests from the Worker, the full-texts which are not already found by other workers, in batches.<br>
@ -16,9 +17,5 @@ We use Facebook's [**Zstandard**](https://facebook.github.io/zstd/) compression
<br>
**Notes**:
- The above script, installs the [PublicationsRetriever](https://github.com/LSmyrnaios/PublicationsRetriever) software, as a library and then compiles and runs the whole Application.<br>
- If you want to just run the app, then run the script with the argument "1": ```./installAndRun.sh 1```. In this scenario, apart from the SpringBoot-app not re-building,
the [PublicationsRetriever](https://github.com/LSmyrnaios/PublicationsRetriever) software, will not be re-installed as well.<br>
- If you want to avoid re-installing the [PublicationsRetriever](https://github.com/LSmyrnaios/PublicationsRetriever) software, but still building the Worker's application, run the script with the argument "0", followed by the argument "1": ```./installAndRun.sh 0 1```, i.e. when using a development (non-published) version
or when nothing has changed and wanting to avoid the time-overhead.<br>
- If you want to just run the app, then run the script with the argument "1": ```./installAndRun.sh 1```. In this scenario, the SpringBoot-app will not be re-built.<br>
<br>

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@ -6,15 +6,20 @@ plugins {
java {
group = 'eu.openaire.urls_worker'
version = '2.1.8-SNAPSHOT'
version = '2.1.9-SNAPSHOT'
sourceCompatibility = JavaVersion.VERSION_1_8
}
repositories {
mavenCentral()
flatDir {
dirs 'libs'
maven {
name "d4science"
url "https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots/"
}
// Enable the following, in case you want to test temporal-jars.
/*flatDir {
dirs 'libs'
}*/
}
dependencies {
@ -32,22 +37,22 @@ dependencies {
// Enable the validation annotations.
//implementation group: 'jakarta.validation', name: 'jakarta.validation-api', version: '3.0.2'
implementation ("eu.openaire:publications_retriever:1.1-SNAPSHOT") {
implementation ("eu.openaire:publications_retriever:1.2-SNAPSHOT") {
exclude group: 'ch.qos.logback', module: 'logback-core'
exclude group: 'ch.qos.logback', module: 'logback-classic'
exclude group: 'org.slf4j', module: 'slf4j-api'
exclude group: 'io.minio' // This is not used in the Worker, since it's the Controller which uploads the full-texts to S3. It also includes an older "commons-compress" version which causes problems.
}
implementation group: 'com.google.guava', name: 'guava', version: '33.0.0-jre'
implementation group: 'com.google.guava', name: 'guava', version: '33.1.0-jre'
// https://mvnrepository.com/artifact/com.google.code.gson/gson
implementation 'com.google.code.gson:gson:2.10.1'
implementation("org.apache.commons:commons-compress:1.25.0") {
implementation("org.apache.commons:commons-compress:1.26.1") {
exclude group: 'com.github.luben', module: 'zstd-jni'
}
implementation 'com.github.luben:zstd-jni:1.5.5-11' // Even though this is part of the above dependency, the Apache commons rarely updates it, while the zstd team makes improvements very often.
implementation 'com.github.luben:zstd-jni:1.5.6-3' // Even though this is part of the above dependency, the Apache commons rarely updates it, while the zstd team makes improvements very often.
// Also, for compressing, we strangely need it to be explicitly declared independently, otherwise it does not work.
testImplementation 'org.springframework.security:spring-security-test'

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@ -21,5 +21,5 @@ echo '/swapfile none swap sw 0 0' | sudo tee -a /etc/fstab
# Adjusting the Swappiness Property
cat /proc/sys/vm/swappiness
sudo sysctl vm.swappiness=10 # Setting it closer to 0, makes the swaps more rare. (10 %)
sudo sysctl vm.swappiness=10 # Setting it closer to 0, makes the swaps more rare: 10%. The default is 60%.
echo "vm.swappiness=10" | sudo tee -a /etc/sysctl.conf # Append it to that file in order for the custom "swappiness" to be available on restart.

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gradle/wrapper/gradle-wrapper.jar vendored Normal file

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@ -1,6 +1,6 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
networkTimeout=10000
validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME

249
gradlew vendored Executable file
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@ -0,0 +1,249 @@
#!/bin/sh
#
# Copyright © 2015-2021 the original authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
##############################################################################
#
# Gradle start up script for POSIX generated by Gradle.
#
# Important for running:
#
# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
# noncompliant, but you have some other compliant shell such as ksh or
# bash, then to run this script, type that shell name before the whole
# command line, like:
#
# ksh Gradle
#
# Busybox and similar reduced shells will NOT work, because this script
# requires all of these POSIX shell features:
# * functions;
# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
# * compound commands having a testable exit status, especially «case»;
# * various built-in commands including «command», «set», and «ulimit».
#
# Important for patching:
#
# (2) This script targets any POSIX shell, so it avoids extensions provided
# by Bash, Ksh, etc; in particular arrays are avoided.
#
# The "traditional" practice of packing multiple parameters into a
# space-separated string is a well documented source of bugs and security
# problems, so this is (mostly) avoided, by progressively accumulating
# options in "$@", and eventually passing that to Java.
#
# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
# see the in-line comments for details.
#
# There are tweaks for specific operating systems such as AIX, CygWin,
# Darwin, MinGW, and NonStop.
#
# (3) This script is generated from the Groovy template
# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
# within the Gradle project.
#
# You can find Gradle at https://github.com/gradle/gradle/.
#
##############################################################################
# Attempt to set APP_HOME
# Resolve links: $0 may be a link
app_path=$0
# Need this for daisy-chained symlinks.
while
APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
[ -h "$app_path" ]
do
ls=$( ls -ld "$app_path" )
link=${ls#*' -> '}
case $link in #(
/*) app_path=$link ;; #(
*) app_path=$APP_HOME$link ;;
esac
done
# This is normally unused
# shellcheck disable=SC2034
APP_BASE_NAME=${0##*/}
# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD=maximum
warn () {
echo "$*"
} >&2
die () {
echo
echo "$*"
echo
exit 1
} >&2
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
case "$( uname )" in #(
CYGWIN* ) cygwin=true ;; #(
Darwin* ) darwin=true ;; #(
MSYS* | 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: $JAVA_HOME
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD=java
if ! command -v java >/dev/null 2>&1
then
die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
fi
# Increase the maximum file descriptors if we can.
if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
case $MAX_FD in #(
max*)
# In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
# shellcheck disable=SC2039,SC3045
MAX_FD=$( ulimit -H -n ) ||
warn "Could not query maximum file descriptor limit"
esac
case $MAX_FD in #(
'' | soft) :;; #(
*)
# In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
# shellcheck disable=SC2039,SC3045
ulimit -n "$MAX_FD" ||
warn "Could not set maximum file descriptor limit to $MAX_FD"
esac
fi
# Collect all arguments for the java command, stacking in reverse order:
# * args from the command line
# * the main class name
# * -classpath
# * -D...appname settings
# * --module-path (only if needed)
# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
# For Cygwin or MSYS, switch paths to Windows format before running java
if "$cygwin" || "$msys" ; then
APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
JAVACMD=$( cygpath --unix "$JAVACMD" )
# Now convert the arguments - kludge to limit ourselves to /bin/sh
for arg do
if
case $arg in #(
-*) false ;; # don't mess with options #(
/?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
[ -e "$t" ] ;; #(
*) false ;;
esac
then
arg=$( cygpath --path --ignore --mixed "$arg" )
fi
# Roll the args list around exactly as many times as the number of
# args, so each arg winds up back in the position where it started, but
# possibly modified.
#
# NB: a `for` loop captures its iteration list before it begins, so
# changing the positional parameters here affects neither the number of
# iterations, nor the values presented in `arg`.
shift # remove old arg
set -- "$@" "$arg" # push replacement arg
done
fi
# 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" "-Xms64m"'
# Collect all arguments for the java command:
# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
# and any embedded shellness will be escaped.
# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
# treated as '${Hostname}' itself on the command line.
set -- \
"-Dorg.gradle.appname=$APP_BASE_NAME" \
-classpath "$CLASSPATH" \
org.gradle.wrapper.GradleWrapperMain \
"$@"
# Stop when "xargs" is not available.
if ! command -v xargs >/dev/null 2>&1
then
die "xargs is not available"
fi
# Use "xargs" to parse quoted args.
#
# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
#
# In Bash we could simply go:
#
# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
# set -- "${ARGS[@]}" "$@"
#
# but POSIX shell has neither arrays nor command substitution, so instead we
# post-process each arg (as a line of input to sed) to backslash-escape any
# character that might be a shell metacharacter, then use eval to reverse
# that process (while maintaining the separation between arguments), and wrap
# the whole thing up as a single "set" statement.
#
# This will of course break if any of these variables contains a newline or
# an unmatched quote.
#
eval "set -- $(
printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
xargs -n1 |
sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
tr '\n' ' '
)" '"$@"'
exec "$JAVACMD" "$@"

92
gradlew.bat vendored Normal file
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@ -0,0 +1,92 @@
@rem
@rem Copyright 2015 the original author or authors.
@rem
@rem Licensed under the Apache License, Version 2.0 (the "License");
@rem you may not use this file except in compliance with the License.
@rem You may obtain a copy of the License at
@rem
@rem https://www.apache.org/licenses/LICENSE-2.0
@rem
@rem Unless required by applicable law or agreed to in writing, software
@rem distributed under the License is distributed on an "AS IS" BASIS,
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@rem See the License for the specific language governing permissions and
@rem limitations under the License.
@rem
@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=.
@rem This is normally unused
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
@rem Resolve any "." and ".." in APP_HOME to make it shorter.
for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
@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" "-Xms64m"
@rem Find java.exe
if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
if %ERRORLEVEL% equ 0 goto execute
echo. 1>&2
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
echo. 1>&2
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
echo location of your Java installation. 1>&2
goto fail
:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
if exist "%JAVA_EXE%" goto execute
echo. 1>&2
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
echo. 1>&2
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
echo location of your Java installation. 1>&2
goto fail
: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 %*
:end
@rem End local scope for the variables with windows NT shell
if %ERRORLEVEL% equ 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!
set EXIT_CODE=%ERRORLEVEL%
if %EXIT_CODE% equ 0 set EXIT_CODE=1
if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
exit /b %EXIT_CODE%
:mainEnd
if "%OS%"=="Windows_NT" endlocal
:omega

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@ -11,55 +11,19 @@ handle_error () {
cd "${0%/*}" || handle_error "Could not change-dir to this script's dir!" 1
justRun=0
avoidReInstallingPublicationsRetriever=0
if [[ $# -eq 1 ]]; then
justRun=$1
elif [[ $# -eq 2 ]]; then
justRun=$1
avoidReInstallingPublicationsRetriever=$2
elif [[ $# -gt 2 ]]; then
echo -e "Wrong number of arguments given: ${#} (more than 2)\nPlease execute it like: script.sh <justRun: 0 | 1> <avoidReInstallingPublicationsRetriever: 0 | 1>"; exit 2
elif [[ $# -gt 1 ]]; then
echo -e "Wrong number of arguments given: ${#} (more than 1)\nPlease execute it like: script.sh <justRun: 0 | 1>"; exit 2
fi
gradleVersion="8.5"
gradleVersion="8.7"
shouldBeCarefulWithMaxHeap=0 # This is NOT a cmd-arg.
if [[ justRun -eq 0 ]]; then
if [[ avoidReInstallingPublicationsRetriever -eq 1 ]]; then
if [[ ! -f ./libs/publications_retriever-1.1-SNAPSHOT.jar ]]; then
echo -e "\n\nThe required \"PublicationsRetriever\" software has not been installed yet, thus the script will override the user-defined value of \"avoidReInstallingPublicationsRetriever\" to FALSE..\n\n"
avoidReInstallingPublicationsRetriever=0; # In case the jar-file does not exists, then make sure we follow the normal procedure, independently from what the user requested.
fi
fi
if [[ avoidReInstallingPublicationsRetriever -eq 0 ]]; then
if [ ! -d libs ]; then
mkdir libs || handle_error "The directory \"libs\" could not be created! Exiting.." 3
fi
cd libs || exit 4
git clone https://github.com/LSmyrnaios/PublicationsRetriever.git # We assume there is no previously source-code here, if so, it will be overwritten.
# Keep a backup of the previous JAR file, if it exists.
if [ -f ./publications_retriever-1.1-SNAPSHOT.jar ]; then
mv ./publications_retriever-1.1-SNAPSHOT.jar ./publications_retriever-1.1-SNAPSHOT_BACKUP.jar
fi
cd PublicationsRetriever && sudo apt install -y maven && mvn clean install
# Copy the created JAR file to the top libs directory.
cp target/publications_retriever-1.1-SNAPSHOT.jar ../publications_retriever-1.1-SNAPSHOT.jar
# Delete the directory with the source-code.
cd ../ && rm -rf PublicationsRetriever
# Clean, (re)build and run the project.
cd ../
fi
# Install the specified Gradle-build-tool version, if it does not exist.
if [[ ! -d /opt/gradle/gradle-${gradleVersion} ]]; then
wget https://services.gradle.org/distributions/gradle-${gradleVersion}-bin.zip
@ -86,7 +50,7 @@ if [[ justRun -eq 0 ]]; then
#gradle tasks # For debugging installation
#gradle -v # For debugging installation
gradle clean build
gradle clean build # --refresh-dependencies # --info
else
export PATH=/opt/gradle/gradle-${gradleVersion}/bin:$PATH # Make sure the gradle is still accessible (it usually isn't without the "export").
fi

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@ -47,7 +47,7 @@ public class AssignmentsHandler {
private final String workerId;
private final String controllerBaseUrl;
private final int maxAssignmentsLimitPerBatch;
private final int maxAssignmentsBatchesToHandleBeforeShutdown;
public final int maxAssignmentsBatchesToHandleBeforeShutdown;
public static List<UrlReport> urlReports = null;
private static final int expectedDatasourcesPerRequest = 1400; // Per 10_000 assignments.

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@ -65,12 +65,6 @@ public class ScheduledTasks {
return;
}
// The user might have just requested the Worker to shut-down.
if ( GeneralController.shouldShutdownWorker ) { // Make sure the worker shuts-down, in case the user sends the relevant request, while the worker is stuck in a data-request error-loop.
AssignmentsHandler.shouldNotRequestMore = true;
return;
}
if ( rootPath.getFreeSpace() < requiredFreeSpace ) {
// It's not safe to proceed with downloading more files and risk of "noSpaceLeft" error.
// Wait for the Controller to take the full-texts and any remaining files to be deleted, so that more free-space becomes available.

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@ -5,6 +5,7 @@ import eu.openaire.urls_worker.components.plugins.PublicationsRetrieverPlugin;
import eu.openaire.urls_worker.util.UriBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@ -22,6 +23,9 @@ public class GeneralController {
private static final Logger logger = LoggerFactory.getLogger(GeneralController.class);
@Autowired
AssignmentsHandler assignmentsHandler;
private final String controllerIp;
private final String workerReportsDirPath;
private final String workerId;
@ -67,8 +71,10 @@ public class GeneralController {
String finalMsg = "";
if ( shouldShutdownWorker )
finalMsg = "The worker has already received a \"shutdownWorker\" request (which was not canceled afterwards). ";
else
else {
shouldShutdownWorker = true;
AssignmentsHandler.shouldNotRequestMore = true;
}
finalMsg += "The worker will shutdown, after finishing current work.";
logger.info(initMsg + finalMsg);
@ -85,6 +91,9 @@ public class GeneralController {
return responseEntity;
shouldShutdownWorker = false;
if ( AssignmentsHandler.numHandledAssignmentsBatches < assignmentsHandler.maxAssignmentsBatchesToHandleBeforeShutdown )
AssignmentsHandler.shouldNotRequestMore = false; // Make sure the worker shuts-down, in case the user sends the relevant request, while the worker is stuck in a data-request error-loop.
String finalMsg = "Any previous \"shutdownWorker\"-request is canceled. The \"maxAssignmentsBatchesToHandleBeforeShutdown\" will still be honored (if it's set).";
logger.info(initMsg + finalMsg);
return ResponseEntity.ok().body(finalMsg + "\n");

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@ -34,6 +34,7 @@ workerReportsDirPath: ${HOME}/workerReports/
# LOGGING LEVELS
logging.config=classpath:logback-spring.xml
logging.file.path=logs
logging.level.root=INFO
logging.level.org.springframework.web=INFO
logging.level.org.springframework.security=WARN

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@ -2,10 +2,10 @@
<configuration debug="false">
<appender name="RollingFile" class="ch.qos.logback.core.rolling.RollingFileAppender">
<file>logs/UrlsWorker.log</file>
<file>${LOG_PATH}/UrlsWorker.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
<fileNamePattern>logs/UrlsWorker.%i.log.zip</fileNamePattern>
<fileNamePattern>${LOG_PATH}/UrlsWorker.%i.log.zip</fileNamePattern>
<minIndex>1</minIndex>
<maxIndex>10</maxIndex>
</rollingPolicy>
@ -27,6 +27,7 @@
</appender>
<root level="debug">
<!-- <appender-ref ref="Console" /> -->
<appender-ref ref="RollingFile" />
</root>