diff --git a/openbis_standard_technologies/build.gradle b/openbis_standard_technologies/build.gradle
index fb17d04db0308bfe3b24428083f4767bb117d331..94b70ce0b995130f966b4c9a6c9761eca0cc6881 100644
--- a/openbis_standard_technologies/build.gradle
+++ b/openbis_standard_technologies/build.gradle
@@ -61,9 +61,9 @@ def jettyVersion = '9.4.30'
dependencies {
compile project(':screening')
-
+
providedCompile 'google:gwt-user:2.4'
-
+
providedRuntime "eclipse:jetty-deploy:${jettyVersion}.v20200611@jar",
"eclipse:jetty-xml:${jettyVersion}.v20200611@jar",
"eclipse:jetty-webapp:${jettyVersion}.v20200611@jar",
@@ -71,12 +71,12 @@ dependencies {
"eclipse:jetty-security:${jettyVersion}.v20200611@jar",
"eclipse:jetty-server:${jettyVersion}.v20200611@jar",
"eclipse:jetty-continuation:${jettyVersion}.v20200611@jar"
-
+
gwt 'reveregroup:gwt-image-loader:1.1.4',
'google:gwt-dev:2.4'
-
+
zipping "eclipse:jetty-distribution:${jettyVersion}@zip"
-
+
datastore_server project(':deep_sequencing_unit'),
project(':rtd_yeastx'),
project(':screening'),
@@ -88,7 +88,7 @@ dependencies {
'slf4j:slf4j:1.6.2',
'slf4j:slf4j-log4j12:1.6.2',
'sybit:image-viewer:0.3.6'
-
+
javadoc_sources project(path:':commonbase', configuration: 'archives'),
project(path:':common', configuration: 'archives'),
project(path:':openbis_api', configuration: 'archives'),
@@ -126,22 +126,22 @@ def gwtArchiveFileName = 'gwt.tar.gz'
task compileGwt (dependsOn: classes, type: JavaExec) {
ext.buildDir = gwtBuildDir
def extraDir = "${project.buildDir}/extra"
-
+
// inputs.source
sourceSets.main.java.srcDirs
// inputs.dir
sourceSets.main.output.resourcesDir
outputs.dir buildDir
-
+
doFirst {
file(buildDir).mkdirs()
}
-
+
main = 'com.google.gwt.dev.Compiler'
-
+
classpath {
[
- sourceSets.main.java.srcDirs,
+ sourceSets.main.java.srcDirs,
project(":openbis").sourceSets.main.java.srcDirs,
project(":openbis").sourceSets.main.output.resourcesDir,
project(":openbis").sourceSets.main.output.classesDirs,
@@ -151,21 +151,21 @@ task compileGwt (dependsOn: classes, type: JavaExec) {
project(":screening").sourceSets.main.java.srcDirs,
project(":screening").sourceSets.main.output.resourcesDir,
configurations.gwt
- ]
+ ]
}
-
+
args =
[
gwtModuleName,
'-war', buildDir,
'-logLevel', 'INFO',
'-localWorkers', '2',
- '-compileReport',
+ '-compileReport',
'-extra', extraDir,
]
-
+
maxHeapSize = '1024m'
-
+
systemProperty "javax.xml.parsers.SAXParserFactory", "org.apache.xerces.jaxp.SAXParserFactoryImpl"
}
@@ -212,7 +212,7 @@ ext.zipEntries = files(
project(':openbis').file('dist/server/export-master-data.sh'),
project(':openbis').file('dist/server/install.sh'),
project(':openbis').file('dist/server/openBIS.keystore'),
- project(':openbis').file('dist/server/openbis.conf'),
+ project(':openbis').file('dist/server/openbis.conf'),
project(':openbis').file('dist/server/passwd.sh'),
project(':openbis').file('dist/server/register-master-data.sh'),
project(':openbis').file('dist/server/setup-env'),
@@ -223,7 +223,7 @@ ext.zipEntries = files(
project(':openbis').file('dist/server/watchdog.sh'),
project(':openbis').fileTree(dir: 'dist/server').matching {
include 'base/**'
- },
+ },
file('dist/server/service.properties'),
file('dist/server/web-client.properties')
)
@@ -236,7 +236,7 @@ task checkFilesExist {
}
zipEntries.each {
x -> assert x.exists()
- }
+ }
}
}
@@ -247,7 +247,7 @@ war.dependsOn checkFilesExist
war.dependsOn signWebStartJars
war {
rootSpec.eachFile { file ->
- if (file.name.startsWith('cisd-cifex')
+ if (file.name.startsWith('cisd-cifex')
|| file.name.startsWith('datastore_server')
|| file.name.startsWith('bioformats')
|| file.name.startsWith('cisd-image-readers')
@@ -266,34 +266,34 @@ war {
file('resource/server/jetty-web.xml'),
project(':common').file('resource/server/web-common.xml')
}
-
+
from (classpathEntries) {
- into("WEB-INF/classes")
+ into("WEB-INF/classes")
}
- from('dist/server'){
- into("WEB-INF/classes")
- include "etc/log.xml"
- }
+ from('dist/server'){
+ into("WEB-INF/classes")
+ include "etc/log.xml"
+ }
- from('targets/dist'){
- into("WEB-INF/classes")
- include 'BUILD*INFO'
+ from('targets/dist'){
+ into("WEB-INF/classes")
+ include 'BUILD*INFO'
rename 'BUILD.*INFO', 'BUILD-openbis.INFO'
- }
+ }
- from('../screening/source'){
- into("WEB-INF/classes")
- include "sql/**/*.sql"
- exclude "sql/imaging/postgresql/_ERD"
- }
+ from('../screening/source'){
+ into("WEB-INF/classes")
+ include "sql/**/*.sql"
+ exclude "sql/imaging/postgresql/_ERD"
+ }
- from('../openbis/source'){
- into("WEB-INF/classes")
- include "sql/**/*.sql"
+ from('../openbis/source'){
+ into("WEB-INF/classes")
+ include "sql/**/*.sql"
exclude "sql/generic/_ERD"
- duplicatesStrategy 'exclude'
- }
+ duplicatesStrategy 'exclude'
+ }
}
def downloadCorePlugin(url, pluginname) {
@@ -310,7 +310,7 @@ import org.paleozogt.gradle.zip.SymZip;
task zipCorePlugins(type: SymZip) {
includeEmptyDirs = false
archiveName 'core-plugins.zip'
-
+
downloadCorePlugin('https://github.com/aarpon/obit_flow_core_technology/archive/release/20.x.zip', 'flow')
downloadCorePlugin('https://github.com/aarpon/obit_microscopy_core_technology/archive/release/20.x.zip', 'microscopy')
downloadCorePlugin('https://github.com/aarpon/obit_shared_core_technology/archive/release/20.x.zip', 'shared')
@@ -348,7 +348,7 @@ task checksums {
destFile.delete()
}
destFile.createNewFile()
-
+
def configFiles = classpathEntries.filter({file -> file.name.endsWith('xml') || file.name.endsWith('.conf') || file.name.endsWith('.properties')})
configFiles.each {file ->
destFile.text += generateMD5(file)+" webapps/openbis/WEB-INF/classes/"+file.name+"\n"
@@ -357,7 +357,7 @@ task checksums {
configFiles = war.getSource().filter({file -> file.name.endsWith('xml') || file.name.endsWith('.conf') || file.name.endsWith('.properties')}).minus(classpathEntries)
configFiles.each {file ->
destFile.text += generateMD5(file)+" webapps/openbis/WEB-INF/"+file.name+"\n"
- }
+ }
}
}
checksums.dependsOn war
@@ -375,11 +375,11 @@ task zip(type: Zip, dependsOn: createJettyVersionFile) {
from war
from zipEntries
from checksums
- from configurations.zipping
+ from configurations.zipping
from zipCorePlugins.archivePath
from zipAdminConsole.archivePath
rename 'jetty-distribution(.*).zip', 'jetty.zip'
- rename 'openBIS(.*).war', 'openBIS.war'
+ rename 'openBIS(.*).war', 'openBIS.war'
}
zip.dependsOn war
zip.dependsOn zipCorePlugins
@@ -389,7 +389,7 @@ zip.dependsOn checksums
task zipDss(type: Zip, dependsOn: signWebStartJars) {
baseName 'datastore_server-standard-technologies'
includeEmptyDirs true
-
+
from (configurations.datastore_server) {
into 'datastore_server/lib'
exclude '**/antlr*.jar'
@@ -405,13 +405,13 @@ task zipDss(type: Zip, dependsOn: signWebStartJars) {
rename 'common-.*jar', 'common.jar'
rename 'commonbase-.*jar', 'commonbase.jar'
}
-
+
from (signedJarsFolder) {
into 'datastore_server/lib/dss_upload_gui'
exclude openbisClientJarName
exclude dssCliClientJarName
}
-
+
from (project(':datastore_server').fileTree(dir: 'dist', includes: ['**/*'], excludes:['dss_client.sh', 'etc/**'])) {
into 'datastore_server';
}
@@ -419,15 +419,15 @@ task zipDss(type: Zip, dependsOn: signWebStartJars) {
from (project(':datastore_server').files('dist/etc/datastore_server.conf', 'dist/etc/openBIS.keystore')) {
into 'datastore_server/etc';
}
-
+
from (fileTree(dir: 'dist', includes: ['etc/service.properties', 'etc/log.xml'])) {
into 'datastore_server'
}
-
+
from (project(':screening').file('dist/etc/tabular-data-graph.properties')) {
into 'datastore_server/etc';
}
-
+
}
task zipBdlServer(type: Zip, dependsOn: project(':big_data_link_server').tasks.distZip) {
@@ -454,10 +454,10 @@ task clientsAndApis(type: Zip, dependsOn: [dssClientZip, queryApiZip, apiV3Zip,
from pybisZip.archivePath
from obisZip.archivePath
from ('dist/client/readme.txt')
- rename { filename ->
+ rename { filename ->
if (filename.startsWith('pybis-')) {
def contentOfSetUpFile = zipTree(pybisZip.archivePath).getFiles().findAll {it.path.endsWith('src/python/setup.py') }.iterator().next().text
- def pybisVersion = ( contentOfSetUpFile =~ /version.*=.*'(.*)'/)[0][1]
+ def pybisVersion = ( contentOfSetUpFile =~ /version.*=.*"(.*)"/)[0][1]
'pybis-' + pybisVersion + '.zip'
} else {
filename
@@ -482,7 +482,7 @@ task generateJavadoc(type: Javadoc) {
include "**/ch/ethz/sis/openbis/generic/dssapi/**/*.java"
include "**/ch/systemsx/cisd/**/api/**/*.java"
include "**/ch/systemsx/cisd/common/annotation/*.java"
- include "**/ch/systemsx/cisd/base/**/*.java"
+ include "**/ch/systemsx/cisd/base/**/*.java"
include "**/OpenBISScreeningML.java"
include "**/ch/systemsx/cisd/**/etlserver/TopLevelDataSetRegistratorGlobalState.java"
include "**/ch/systemsx/cisd/**/etlserver/registrator/*.java"