diff --git a/app-openbis-installer/build.gradle b/app-openbis-installer/build.gradle index 51f1bc31c22b4172884a5bff5fb059230ad57f80..f99ac40e38d97659bdea3cac1523ba70c4096641 100644 --- a/app-openbis-installer/build.gradle +++ b/app-openbis-installer/build.gradle @@ -61,7 +61,7 @@ task copyResources(type: Copy, dependsOn: [compileJava, ':core-plugin-openbis:zi into installerDistDir from zipTree(project(':core-plugin-openbis').zipBdlServer.archivePath) into installerDistDir - from("${installerDistDir}/../BUILD-installation.INFO") { + from("${installerDistDir}/../BUILD-app-openbis-installer.INFO") { into 'bin' } from("${buildDir}/classes/java/main/InstallerVariableAccess.class") { diff --git a/build/settings.gradle b/build/settings.gradle index baf43e1571612a1619ada41f4bf8c95c7674b7b1..a9305bae9e63d025fcf19f5c2b2ddc256de711a4 100644 --- a/build/settings.gradle +++ b/build/settings.gradle @@ -1,4 +1,4 @@ includeFlat 'lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'lib-authentication', 'lib-dbmigration', 'server-application-server', 'server-original-data-store', 'server-screening', 'core-plugin-openbis', 'app-openbis-installer', 'lib-image-readers', 'test-ui-core', 'test-api-openbis-javascript', 'server-external-data-store', 'ui-admin', - 'lib-microservice-server', 'lib-transactional-file-system', 'server-data-store' \ No newline at end of file + 'lib-microservice-server', 'lib-transactional-file-system', 'server-data-store', 'ui-eln-lims' \ No newline at end of file diff --git a/core-plugin-openbis/build.gradle b/core-plugin-openbis/build.gradle index d79096d2eef9e4f1ae1303a1c4fa09ce4cd31ef5..d8f5d7045edf96568b8ae31b66610eeec62638c1 100644 --- a/core-plugin-openbis/build.gradle +++ b/core-plugin-openbis/build.gradle @@ -39,6 +39,7 @@ evaluationDependsOn(':server-original-data-store') evaluationDependsOn(':server-screening') evaluationDependsOn(':server-external-data-store') evaluationDependsOn(':ui-admin') +evaluationDependsOn(':ui-eln-lims') apply from: '../build/javaproject.gradle' @@ -57,6 +58,7 @@ configurations.create('zipping') configurations.create('server_original_data_store') configurations.create('javadoc_sources') configurations.create('javadoc_compilation') +configurations.create('blast_tar') def jettyVersion = '9.4.44' def jettyDistributionVersion = '9.4.44.v20210927' @@ -79,6 +81,8 @@ dependencies { zipping "eclipse:jetty-distribution:${jettyVersion}@zip" + blast_tar "blast:blast:2.2.30@tar.gz" + server_original_data_store project(':server-screening'), 'bioformats:bioformats:6.5.1', 'imagej:ij:1.43u', @@ -348,6 +352,9 @@ task zipCorePlugins(type: SymZip) { from fileTree(dir: 'targets/downloads/obit_shared_core_technology-release-20.x/core-plugins', includes: ['shared/**']) from 'dist/core-plugins' from 'dist/server/core-plugins.properties' + from(configurations.blast_tar.collect { tarTree(it) }) { + into 'eln-lims' + } into 'core-plugins' } @@ -503,7 +510,17 @@ task copyOpenbisNgUiToCorePlugins(type: Copy, dependsOn: [deleteOpenbisNgUi, ':u into file('dist/core-plugins') } +task deleteOpenbisElnLims(type: Delete) { + delete 'dist/core-plugins/eln-lims' +} + +task copyOpenbisElnLimsCorePlugins(type: Copy, dependsOn: [deleteOpenbisNgUi, ':ui-eln-lims:copyCorePlugins']) { + from project(':ui-eln-lims').file('build/core-plugins') + into file('dist/core-plugins') +} + zipCorePlugins.dependsOn copyOpenbisNgUiToCorePlugins +zipCorePlugins.dependsOn copyOpenbisElnLimsCorePlugins task generateJavadoc(type: Javadoc) { source = configurations.javadoc_sources.collect { diff --git a/core-plugin-openbis/settings.gradle b/core-plugin-openbis/settings.gradle index df7724ce0359ace7d89fe754342a537380c209a6..2ce594f05ee8fbc34111e3ded1b316b100974d57 100644 --- a/core-plugin-openbis/settings.gradle +++ b/core-plugin-openbis/settings.gradle @@ -1,3 +1,3 @@ includeFlat 'lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'lib-authentication', 'lib-dbmigration', 'server-application-server', 'server-original-data-store', 'server-screening', 'server-external-data-store', - 'ui-admin', 'lib-microservice-server' + 'ui-admin', 'lib-microservice-server', 'ui-eln-lims' diff --git a/server-original-data-store/build.gradle b/server-original-data-store/build.gradle index 8a41bcea224a3800bb80db69cc3a2f5193dc25f0..5b46693006fb834978b86226f2239ff1a21e5eba 100644 --- a/server-original-data-store/build.gradle +++ b/server-original-data-store/build.gradle @@ -42,18 +42,18 @@ dependencies { runtimeOnly 'bioformats:bioformats:6.5.1' // eln-lims Jython APIs dependencies - datastoreExecRuntime files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/zip4j_1.3.2.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/plasmapper.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/htmlcleaner-2.23.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docx4j-3.3.3.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/ascii-table-1.1.0.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docxbuilder.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/jsoup-1.11.3.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/serializer-2.7.2.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/slf4j-api-1.7.21.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/xalan-2.7.2.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/lib/job-scheduler.jar"), - files("../core-plugin-openbis/dist/core-plugins/eln-lims/1/dss/reporting-plugins/password-reset-api/lib/persistentkeyvaluestore.jar"), + datastoreExecRuntime files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/zip4j_1.3.2.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/plasmapper.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/eln-lims-api/lib/htmlcleaner-2.23.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docx4j-3.3.3.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/ascii-table-1.1.0.jar"), + files("../ui-eln-lims/src/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docxbuilder.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/jsoup-1.11.3.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/serializer-2.7.2.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/slf4j-api-1.7.21.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/xalan-2.7.2.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/lib/job-scheduler.jar"), + files("../ui-eln-lims/src/core-plugins/eln-lims/1/dss/reporting-plugins/password-reset-api/lib/persistentkeyvaluestore.jar"), files("../../../openbis-hvl.ethz.ch/deployed/core-plugins/hvl-dropbox/1/dss/dropboxes/hvl-dropbox/lib/jmatio-1.5.jar") testImplementation project(path: ':lib-commonbase', configuration: 'tests'), diff --git a/ui-eln-lims/build.gradle b/ui-eln-lims/build.gradle new file mode 100644 index 0000000000000000000000000000000000000000..0ff8270be88ec96e4b3c8c8402f950800d8be237 --- /dev/null +++ b/ui-eln-lims/build.gradle @@ -0,0 +1,8 @@ +task cleanBuild(type: Delete) { + delete 'build' +} + +task copyCorePlugins(type: Copy) { + from file('src/core-plugins') + into file('build/core-plugins') +} diff --git a/ui-eln-lims/gradle/wrapper/gradle-wrapper.jar b/ui-eln-lims/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000000000000000000000000000000000000..5c2d1cf016b3885f6930543d57b744ea8c220a1a Binary files /dev/null and b/ui-eln-lims/gradle/wrapper/gradle-wrapper.jar differ diff --git a/ui-eln-lims/gradle/wrapper/gradle-wrapper.properties b/ui-eln-lims/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000000000000000000000000000000000000..7745c4ec463c7bb1c4ff6a5e58db239890345152 --- /dev/null +++ b/ui-eln-lims/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/ui-eln-lims/gradlew b/ui-eln-lims/gradlew new file mode 100755 index 0000000000000000000000000000000000000000..83f2acfdc319a24e8766cca78f32474ad7a22dd6 --- /dev/null +++ b/ui-eln-lims/gradlew @@ -0,0 +1,188 @@ +#!/usr/bin/env sh + +# +# Copyright 2015 the original author or 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 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 "$0"` + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD="maximum" + +warn () { + echo "$*" +} + +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 or MSYS, switch paths to Windows format before running java +if [ "$cygwin" = "true" -o "$msys" = "true" ] ; 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" "$@" diff --git a/ui-eln-lims/gradlew.bat b/ui-eln-lims/gradlew.bat new file mode 100644 index 0000000000000000000000000000000000000000..9618d8d9607cd91a0efb866bcac4810064ba6fac --- /dev/null +++ b/ui-eln-lims/gradlew.bat @@ -0,0 +1,100 @@ +@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 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%" == "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