Commit 0ed86b58 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

Merge branch 'dev' into 'master'

Dev

See merge request unlock/interface!1
parents 6c5b0738 423dc429
Pipeline #34517 passed with stage
in 2 minutes and 53 seconds
plugins {
id 'org.springframework.boot' version '2.2.4.RELEASE'
id 'io.spring.dependency-management' version '1.0.9.RELEASE'
id 'org.springframework.boot' version '2.6.1'
id 'io.spring.dependency-management' version '1.0.11.RELEASE'
id 'java'
id 'com.vaadin' version '0.14.6.0'
}
......@@ -10,6 +10,12 @@ defaultTasks("clean", "build")
group = 'nl.munlock'
version = '1.0.1'
java {
toolchain {
languageVersion.set(JavaLanguageVersion.of(11))
}
}
repositories {
mavenCentral()
mavenLocal()
......@@ -19,7 +25,8 @@ repositories {
}
ext {
set('vaadinVersion', "14.7.0")
set('vaadinVersion', "14.8.0")
set('log4j2Version', "2.16.0")
}
configurations {
......@@ -27,12 +34,21 @@ configurations {
runtimeClasspath {
extendsFrom developmentOnly
}
// all {
// exclude group: 'org.springframework.boot', module: 'spring-boot-starter-logging'
// }
all {
resolutionStrategy.eachDependency { details ->
if (details.requested.group == 'org.apache.logging.log4j') {
details.useVersion '2.16.0'
details.because 'zero-day-exploits'
}
}
exclude group: 'log4j'
}
}
// Function to download and include URL jar files, now in testing versus using a bash script to prepare the files (still included)
// Function to download and include URL jar files
def urlFile = { url, name ->
File file = new File("$buildDir/download/${name}.jar")
file.parentFile.mkdirs()
......@@ -52,28 +68,27 @@ test {
dependencies {
implementation('com.vaadin:vaadin-spring-boot-starter') {
// Webjars are only needed when running in Vaadin 13 compatibility mode
["com.vaadin.webjar", "org.webjars.bowergithub.insites",
// Webjars are only needed when running in Vaadin 13 compatibility mode
["spring-boot-starter-logging", "com.vaadin.webjar", "org.webjars.bowergithub.insites",
"org.webjars.bowergithub.polymer", "org.webjars.bowergithub.polymerelements",
"org.webjars.bowergithub.vaadin", "org.webjars.bowergithub.webcomponents"]
.forEach { group -> exclude(group: group) }
}
// implementation 'org.springframework.boot:spring-boot-starter-web'
// implementation 'org.springframework.boot:spring-boot-starter-log4j2'
developmentOnly 'org.springframework.boot:spring-boot-devtools'
testImplementation('org.springframework.boot:spring-boot-starter-test') {
exclude group: 'org.junit.vintage', module: 'junit-vintage-engine'
}
implementation 'org.springframework.boot:spring-boot-starter-web'
implementation 'org.springframework.boot:spring-boot-starter-log4j2'
implementation 'org.vaadin.olli:file-download-wrapper:3.0.1'
// Use JUnit test framework.
testImplementation 'junit:junit:4.13.2'
// This dependency is used by the application.
implementation 'com.google.guava:guava:29.0-jre'
implementation 'com.google.guava:guava:31.0.1-jre'
// irods dependency obtained locally
// implementation 'jargon:core:4.3.0.2' // now using direct download versus build.sh script
......@@ -84,14 +99,14 @@ dependencies {
implementation urlFile('http://download.systemsbiology.nl/unlock/UnlockOntology.jar', 'UnlockOntology')
// kubernetes api
implementation 'io.kubernetes:client-java:5.0.0'
implementation 'io.kubernetes:client-java:14.0.0'
// Excel parsers
implementation 'org.apache.poi:poi:4.1.1'
implementation 'org.apache.poi:poi-ooxml:4.1.1'
implementation 'org.apache.poi:poi:5.0.0'
implementation 'org.apache.poi:poi-ooxml:5.0.0'
// Checker implementation
implementation 'org.checkerframework:checker-qual:2.5.6'
implementation 'org.checkerframework:checker-qual:3.18.1'
implementation group: 'com.esotericsoftware.yamlbeans', name: 'yamlbeans', version: '1.14'
// https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-validation
......@@ -100,7 +115,9 @@ dependencies {
// Download button functionality
implementation 'org.vaadin.stefan:lazy-download-button:1.0.0'
// implementation group: 'org.slf4j', name: 'slf4j-simple', version: '1.7.21'
// https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core
implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.16.0'
}
......
......@@ -10,18 +10,5 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
git -C $DIR pull
# ////////////////////////////////////////////////////////////////////////////////////
# Jargon dependency
# ////////////////////////////////////////////////////////////////////////////////////
# wget --timestamping https://github.com/DICE-UNC/jargon/releases/download/4.3.0.2-RELEASE/jargon-core-4.3.0.2-RELEASE-jar-with-dependencies.jar -O $DIR/jargon-core-4.3.0.2-RELEASE-jar-with-dependencies.jar
# mvn install:install-file -Dfile=$DIR/jargon-core-4.3.0.2-RELEASE-jar-with-dependencies.jar -DgroupId=jargon -DartifactId=core -Dversion=4.3.0.2 -Dpackaging=jar
# ////////////////////////////////////////////////////////////////////////////////////
# // UNLOCK API
# ////////////////////////////////////////////////////////////////////////////////////
# wget --timestamping http://download.systemsbiology.nl/unlock/UnlockOntology.jar -O $DIR/UnlockOntology.jar
# mvn install:install-file -Dfile=$DIR/UnlockOntology.jar -DgroupId=nl.munlock -DartifactId=unlockapi -Dversion=1.0.1 -Dpackaging=jar
# ////////////////////////////////////////////////////////////////////////////////////
$DIR/gradlew build -Dvaadin.productionMode=true -x test
vaadinVersion=14.7.3
\ No newline at end of file
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.1-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
#!/usr/bin/env sh
#!/bin/sh
#
# Copyright 2015 the original author or authors.
# Copyright ? 2015-2021 the original authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
......@@ -17,67 +17,101 @@
#
##############################################################################
##
## Gradle start up script for UN*X
##
#
# Gradle start up script for POSIX generated by Gradle.
#
# Important for running:
#
# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
# noncompliant, but you have some other compliant shell such as ksh or
# bash, then to run this script, type that shell name before the whole
# command line, like:
#
# ksh Gradle
#
# Busybox and similar reduced shells will NOT work, because this script
# requires all of these POSIX shell features:
# * functions;
# * expansions ?$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
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
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
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >/dev/null
APP_HOME="`pwd -P`"
cd "$SAVED" >/dev/null
APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
APP_NAME="Gradle"
APP_BASE_NAME=`basename "$0"`
APP_BASE_NAME=${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"
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
;;
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
......@@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
if [ -n "$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"
JAVACMD=$JAVA_HOME/jre/sh/java
else
JAVACMD="$JAVA_HOME/bin/java"
JAVACMD=$JAVA_HOME/bin/java
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
......@@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD="java"
JAVACMD=java
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
......@@ -106,80 +140,95 @@ location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
if [ "$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: $MAX_FD_LIMIT"
fi
if ! "$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
# 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
# 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 [ "$cygwin" = "true" -o "$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
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
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\""
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
i=`expr $i + 1`
# Roll the args list around exactly as many times as the number of
# args, so each arg winds up back in the position where it started, but
# possibly modified.
#
# NB: a `for` loop captures its iteration list before it begins, so
# changing the positional parameters here affects neither the number of
# iterations, nor the values presented in `arg`.
shift # remove old arg
set -- "$@" "$arg" # push replacement arg
done
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;
# * $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 "$CLASSPATH" \
org.gradle.wrapper.GradleWrapperMain \
"$@"
# 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.
#
# 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"
eval "set -- $(
printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
xargs -n1 |
sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
tr '\n' ' '
)" '"$@"'
exec "$JAVACMD" "$@"
......@@ -92,8 +92,9 @@ public class ApplicationServiceInitListener implements VaadinServiceInitListener
}
}
if (config.getDebug())
logger.info("DEBUG MODE ACTIVATED");
if (config.getDebug()) {
logger.debug("DEBUG MODE ACTIVATED");
}
}
......
......@@ -113,7 +113,7 @@ public class Credentials {
System.setProperty("javax.net.ssl.trustStore", this.certificateTrustStore);
System.setProperty("javax.net.ssl.trustStorePassword", this.certificateTrustStorePassword);
System.getProperties().forEach((o, o2) -> {
System.err.println(o + "\t" + o2);
logger.info("System property: " + o + "\t" + o2);
});
} else if (this.authenticationScheme.matches("STANDARD")) {
irodsAccount.setAuthenticationScheme(AuthScheme.STANDARD);
......
......@@ -10,6 +10,7 @@ public class Biom {
private String assay;
private String folder;
private String job;
private String sample;
public String getProject() {
return project;
......@@ -74,4 +75,12 @@ public class Biom {
public String getJob() {
return job;
}
public void setSample(String sample) {
this.sample = sample;
}
public String getSample() {
return sample;
}
}
......@@ -3,8 +3,7 @@ package nl.fairbydesign.backend.irods;
import nl.fairbydesign.backend.data.objects.Biom;
import nl.fairbydesign.backend.data.objects.DiskUsage;
import nl.fairbydesign.backend.data.objects.Process;
import org.apache.commons.lang.StringUtils;
import org.jboss.logging.Logger;
import org.apache.commons.lang3.StringUtils;
import org.irods.jargon.core.checksum.ChecksumValue;
import org.irods.jargon.core.checksum.LocalChecksumComputerFactory;
import org.irods.jargon.core.checksum.LocalChecksumComputerFactoryImpl;
......@@ -19,13 +18,17 @@ import org.irods.jargon.core.pub.IRODSGenQueryExecutor;
import org.irods.jargon.core.pub.io.IRODSFile;
import org.irods.jargon.core.pub.io.IRODSFileFactory;
import org.irods.jargon.core.query.*;
import org.jboss.logging.Logger;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
public class Data {
public static final Logger logger = Logger.getLogger(Data.class);
......@@ -126,7 +129,7 @@ public class Data {
} else if (unit.equals("finished")) {
processHash.setFinished(count);
} else if (unit.equals("failed")) {
System.err.println(process.getPath() +" " + workflow +" " + unit + " " + count);
logger.error(process.getPath() +" " + workflow +" " + unit + " " + count);
processHash.setFailed(count);
} else if (unit.equals("queue")) {
processHash.setQueue(count);
......@@ -305,7 +308,7 @@ public class Data {
}
public static ArrayList<Biom> getJobOutputs(IRODSAccount irodsAccount, String search) {
logger.info("Searching with " + search);
try {
// Obtain all projects via metadata
IRODSGenQueryBuilder queryBuilder = new IRODSGenQueryBuilder(true, null);
......@@ -333,14 +336,27 @@ public class Data {
// assayPath = assayPath.replaceAll(root, "");
String[] pathSplit = assayPath.split("/");
if (pathSplit.length == 11) {
biom.setProject(pathSplit[3].replaceFirst("P_",""));
biom.setInvestigation(pathSplit[4].replaceFirst("I_",""));
biom.setStudy(pathSplit[5].replaceFirst("S_",""));
biom.setObservationUnit(pathSplit[6].replaceFirst("O_",""));
biom.setAssay(pathSplit[8].replaceFirst("A_",""));
biom.setProject(pathSplit[3].split("_", 1)[0]);
biom.setInvestigation(pathSplit[4].split("_", 1)[0]);
biom.setStudy(pathSplit[5].split("_", 1)[0]);
biom.setObservationUnit(pathSplit[6].split("_", 1)[0]);
// 7 = assay type
biom.setAssay(pathSplit[8].split("_", 1)[0]);
biom.setJob(pathSplit[9]);
biom.setFolder(assayPath);
bioms.add(biom);
} else if (pathSplit.length == 12) {
// New formatting with /SampleID/ folder added
biom.setProject(pathSplit[3].replaceFirst("PRJ_",""));
biom.setInvestigation(pathSplit[4].replaceFirst("INV_",""));
biom.setStudy(pathSplit[5].replaceFirst("STU_",""));
biom.setObservationUnit(pathSplit[6].replaceFirst("OBS_",""));
biom.setSample(pathSplit[7].replaceFirst("SAM_", ""));
// 8 = assay type
biom.setAssay(pathSplit[9].replaceFirst("ASY_",""));
biom.setJob(pathSplit[10]);
biom.setFolder(assayPath);
bioms.add(biom);
}
}
}
......
package nl.fairbydesign.backend.kubernetes;
import io.kubernetes.client.ApiClient;
import io.kubernetes.client.Configuration;
import io.kubernetes.client.apis.BatchV1Api;
import io.kubernetes.client.custom.Quantity;
import io.kubernetes.client.models.*;
import io.kubernetes.client.openapi.ApiClient;
import io.kubernetes.client.openapi.Configuration;
import io.kubernetes.client.openapi.apis.BatchV1Api;
import io.kubernetes.client.openapi.models.*;
import io.kubernetes.client.util.Config;
import nl.fairbydesign.backend.data.yaml.Workflow;
import nl.fairbydesign.backend.irods.Connection;
......@@ -47,8 +47,8 @@ public class Kubernetes {
// Submit the job to nl.wur.ssb.kubernetes
log.info("Dispatching kubernetes job");
batchV1Api.createNamespacedJob("unlock", v1Job, false, null, null);
batchV1Api.createNamespacedJobCall("unlock", v1Job, null, null, null, null, null);