diff --git a/build/settings.gradle b/build/settings.gradle index d790bf35e109db3f87a4755aed2bffbcc3734e9f..13eb3369f542cda5ef296e82128a52694f9cd530 100644 --- a/build/settings.gradle +++ b/build/settings.gradle @@ -1,4 +1,6 @@ -includeFlat 'lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'lib-authentication', 'lib-dbmigration', 'server-application-server', - 'server-original-data-store', 'server-screening', 'core-plugin-openbis', 'app-openbis-installer', - 'lib-image-readers', 'test-ui-core', 'test-api-openbis-javascript', 'server-external-data-store', 'ui-admin', - 'lib-microservice-server', 'lib-transactional-file-system', 'server-data-store', 'ui-eln-lims', 'api-openbis-javascript' \ No newline at end of file +includeFlat 'lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'lib-authentication', + 'lib-dbmigration', 'server-application-server', 'server-original-data-store', 'server-screening', + 'core-plugin-openbis', 'app-openbis-installer', 'lib-image-readers', 'test-ui-core', + 'test-api-openbis-javascript', 'server-external-data-store', 'ui-admin', 'lib-microservice-server', + 'lib-transactional-file-system', 'server-data-store', 'ui-eln-lims', 'api-openbis-javascript', + 'lib-json' \ No newline at end of file diff --git a/lib-json/.gitignore b/lib-json/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..fe63103f29daac95f5989e4cfc75a0fb0cff693b --- /dev/null +++ b/lib-json/.gitignore @@ -0,0 +1,7 @@ +/build/ +/bin/ +/out/ +/.idea/ +/target/ +*.iml +*.eml \ No newline at end of file diff --git a/lib-json/build.gradle b/lib-json/build.gradle new file mode 100644 index 0000000000000000000000000000000000000000..c266252cfbbd36b5549cdd5f1752b2f89cdcfbf9 --- /dev/null +++ b/lib-json/build.gradle @@ -0,0 +1,30 @@ +apply plugin: 'java' +apply plugin: 'application' + +compileJava { + options.compilerArgs << '-parameters' +} + +compileTestJava { + options.compilerArgs << '-parameters' +} + +repositories { + ivy { + ivyPattern "https://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/[organisation]/[module]/[revision]/ivy.xml" + artifactPattern "https://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]" + } +} + +dependencies { + implementation 'fasterxml:jackson-annotations:2.9.10', + 'fasterxml:jackson-core:2.9.10', + 'fasterxml:jackson-databind:2.9.10.8', + 'fasterxml:jackson-datatype-jsr310:2.9.10' + testImplementation 'junit:junit:4.13.2' + testRuntimeOnly 'hamcrest:hamcrest-core:1.3' +} + +test { + useJUnitPlatform() +} \ No newline at end of file diff --git a/lib-json/gradle/wrapper/gradle-wrapper.jar b/lib-json/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000000000000000000000000000000000000..5c2d1cf016b3885f6930543d57b744ea8c220a1a Binary files /dev/null and b/lib-json/gradle/wrapper/gradle-wrapper.jar differ diff --git a/lib-json/gradle/wrapper/gradle-wrapper.properties b/lib-json/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000000000000000000000000000000000000..7745c4ec463c7bb1c4ff6a5e58db239890345152 --- /dev/null +++ b/lib-json/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/gradle/distribution/7.4/gradle-7.4-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/lib-json/gradlew b/lib-json/gradlew new file mode 100755 index 0000000000000000000000000000000000000000..a69d9cb6c20655813e44515156e7253a2a239138 --- /dev/null +++ b/lib-json/gradlew @@ -0,0 +1,240 @@ +#!/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/master/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 + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit + +APP_NAME="Gradle" +APP_BASE_NAME=${0##*/} + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&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: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$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 + +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$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 "$JAVACMD" "$@" diff --git a/lib-json/gradlew.bat b/lib-json/gradlew.bat new file mode 100644 index 0000000000000000000000000000000000000000..f127cfd49d4024c3e1e0d08ba56399221b4fb25d --- /dev/null +++ b/lib-json/gradlew.bat @@ -0,0 +1,91 @@ +@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=. +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. +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 execute + +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 + +: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 diff --git a/lib-json/src/main/java/ch/ethz/sis/afsjson/JsonObjectMapper.java b/lib-json/src/main/java/ch/ethz/sis/afsjson/JsonObjectMapper.java new file mode 100644 index 0000000000000000000000000000000000000000..a826a6f627a7efbafbc198d967223110f423bb7b --- /dev/null +++ b/lib-json/src/main/java/ch/ethz/sis/afsjson/JsonObjectMapper.java @@ -0,0 +1,28 @@ +/* + * Copyright ETH 2023 Zürich, Scientific IT Services + * + * 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 + * + * http://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. + * + */ + +package ch.ethz.sis.afsjson; + +import java.io.InputStream; + +public interface JsonObjectMapper +{ + <T> T readValue(InputStream src, Class<T> valueType) throws Exception; + + byte[] writeValue(Object value) throws Exception; + +} diff --git a/lib-json/src/main/java/ch/ethz/sis/afsjson/jackson/JacksonObjectMapper.java b/lib-json/src/main/java/ch/ethz/sis/afsjson/jackson/JacksonObjectMapper.java new file mode 100644 index 0000000000000000000000000000000000000000..45fff2e94374fbf8d58f0e2191b08f702f2e1ac1 --- /dev/null +++ b/lib-json/src/main/java/ch/ethz/sis/afsjson/jackson/JacksonObjectMapper.java @@ -0,0 +1,70 @@ +/* + * Copyright ETH 2023 Zürich, Scientific IT Services + * + * 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 + * + * http://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. + * + */ + +package ch.ethz.sis.afsjson.jackson; + +import ch.ethz.sis.afsjson.JsonObjectMapper; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializationFeature; +import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule; + +import java.io.InputStream; + +public class JacksonObjectMapper implements JsonObjectMapper +{ + // + // Singleton + // + private static final JacksonObjectMapper jacksonObjectMapper; + + static + { + jacksonObjectMapper = new JacksonObjectMapper(); + } + + public static JsonObjectMapper getInstance() + { + return jacksonObjectMapper; + } + + // + // Class implementation + // + + private final ObjectMapper objectMapper; + + public JacksonObjectMapper() + { + objectMapper = new ObjectMapper(); + objectMapper.registerModule(new JavaTimeModule()); // new module, NOT JSR310Module + objectMapper.enable(SerializationFeature.INDENT_OUTPUT); + objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false); + objectMapper.enableDefaultTyping(); + } + + @Override + public <T> T readValue(final InputStream src, final Class<T> valueType) throws Exception + { + return objectMapper.readValue(src, valueType); + } + + @Override + public byte[] writeValue(final Object value) throws Exception + { + return objectMapper.writeValueAsBytes(value); + } +}