Commit 1eec94c4 authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Start legiolist mine

parents
bin/
dist/
client-dist/
build/
client-build/
*.log
*.log.*
.settings
.eclipse
executeLog*
*.pyc
*.class
productionLog
*~
# IDEs
nbproject/
nb-build.xml
.idea/
apache-tomcat*
prefixed
failures.list
*.jks
*.iml
out/
.gradle/
*.code-workspace
buildscript {
repositories {
mavenLocal()
jcenter()
maven {
url "https://oss.jfrog.org/artifactory/oss-snapshot-local"
}
}
dependencies {
classpath group: 'org.intermine', name: 'plugin', version: System.getProperty("imVersion")
classpath 'com.bmuschko:gradle-cargo-plugin:2.3'
}
}
ext {
mineRelease = project.hasProperty('release') ? "." + release : ''
mineName = "legiomine"
minePropertyFileName = "${mineName}.properties$mineRelease"
minePropertyFile = "${System.env.HOME}/.intermine/$minePropertyFileName"
println "Using properties file: '$minePropertyFile'"
}
subprojects {
apply plugin: 'java'
apply plugin: 'maven'
sourceCompatibility = 1.8
targetCompatibility = 1.8
repositories {
mavenLocal()
jcenter()
maven { url 'https://clojars.org/repo' }
maven {
url "https://oss.jfrog.org/artifactory/oss-snapshot-local"
}
maven {
url 'http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/'
}
}
dependencies {
compile group: "org.intermine", name: "intermine-resources", version: System.getProperty("imVersion")
compile('ant:ant:1.6.5')
testCompile group: 'junit', name: 'junit', version: '4.8.2'
}
task copyMineProperties(type: Copy) {
description "Copies mine specific intermine.properties file (from .intermine directory) into resources output to be included in the war"
dependsOn 'processResources'
from (minePropertyFile)
into sourceSets.main.output.resourcesDir
rename { fileName -> fileName.replace("$minePropertyFileName", "intermine.properties") }
inputs.sourceFiles.stopExecutionIfEmpty()
}
}
task clean(type: Delete) {
println "cleaning"
delete "idresolver.cache"
println "deleting idresolver cache"
delete "datasources.xml"
println "deleting datasources.xml"
delete "organisms.xml"
println "deleting organisms.xml"
delete "publications.xml"
println "deleting publications.xml"
delete fileTree('.') {
include '*.log'
}
println "deleted log files"
}
apply plugin: 'dbmodel'
apply plugin: 'mine-dbmodel'
apply plugin: 'integrate'
apply plugin: 'postprocess'
sourceSets {
main {
java {
srcDirs = ['build/gen']
}
resources {
srcDirs = ['resources']
}
}
}
dependencies {
compile group: "org.intermine", name: "bio-core", version: System.getProperty("bioVersion"), transitive: false
compile group: "org.intermine", name: "intermine-integrate", version: System.getProperty("imVersion")
compile group: "org.intermine", name: "intermine-resources", version: System.getProperty("imVersion") // for log4j
compile fileTree(dir: 'libs', include: '*.jar')
bioModel group: "org.intermine", name: "bio-model", version: System.getProperty("bioVersion"), transitive: false
}
dbModelConfig {
mineName = "legiomine"
objectStoreName = "os.production"
modelName = "genomic"
defaultInterminePropertiesFile = "default.intermine.production.properties"
userProfileObjectStoreName = "os.userprofile-production"
userProfileModelName = "userprofile"
soTermListFilePath = "dbmodel/resources/so_terms"
soAdditionFilePath = "dbmodel/build/so_additions.xml"
}
mineDBModelConfig {
modelName = "genomic"
extraModelsStart = "so_additions.xml genomic_additions.xml global_additions.xml"
extraModelsEnd = ""
}
# Specify keys for classes in the data model. These define which types can be
# stored in 'object' bags and are used for porting those bags to new releases.
BioEntity = primaryIdentifier, secondaryIdentifier
SequenceFeature = symbol, name
Protein = primaryAccession
OntologyTerm = identifier, name
Organism = name, shortName, taxonid
Publication = pubMedId
Author = name
DataSource = name
DataSet = name
# keys used to generate permanent navigable URL and URI
# primaryIdentifier is used as default values
DataSet_URI = name
Protein_URI = primaryAccession
OntologyTerm_URI = identifier
Organism_URI = taxonId
Publication_URI = pubMedId
# Bag upload queries
precompute.query.1 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE a1_.synonyms CONTAINS a2_
precompute.query.3 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a1_.organism CONTAINS a5_)
# gene/protein --> organism [used by some widgets]
precompute.query.5 = SELECT a1_.id as a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Gene AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_
precompute.query.6 = SELECT a1_.id AS a3_, a2_.name AS a4_ FROM org.intermine.model.bio.Protein AS a1_, org.intermine.model.bio.Organism AS a2_ WHERE a1_.organism CONTAINS a2_
# chromosome distribution widget
precompute.query.7 = SELECT a2_.id as a4_, a1_.primaryIdentifier AS a5_, a2_.primaryIdentifier AS a6_, a3_.name as a7_ FROM org.intermine.model.bio.Chromosome AS a1_, org.intermine.model.bio.SequenceFeature AS a2_, org.intermine.model.bio.Organism AS a3_ WHERE (a2_.chromosome CONTAINS a1_ AND a2_.organism CONTAINS a3_)
#contains only classes that come from more than one source
#for each class contained every source for that class must be listed
# priority for fields declared in superclass are not overridden by different order in subclass
# e.g. identfier and organism always have priority as defined in BioEntity
# For example, to give interpro prioritiy over uniprot for the 'shortName' field of ProteinDomain:
#
# ProteinDomain.shortName = interpro, uniprot
# To give flybase priority over all other sources for Gene name:
#
# Gene.name = flybase, *
index.temp.directory = /tmp
index.references.BioEntity = synonyms organism crossReferences
index.references.OntologyTerm = synonyms
#index.references.Gene = pathways proteins.proteinDomains goAnnotation.ontologyTerm
#index.references.Protein = proteinDomains
index.ignore = Comment CrossReference Location OntologyAnnotation OntologyRelation Sequence Synonym
index.facet.single.Category = Category
index.facet.single.Organism = organism.shortName
#index.facet.multi.Pathway = pathways.name
index.boost.Gene = 1.5
index.boost.Protein = 1.2
search.debug = false
index.solrurl = http://localhost:8983/solr/intermine-search
index.batch.size = 1000
max.field.values = 200
# autocomplete = in forms on the webapp, these fields will offer suggestions to the user as they type
# index is created in post process create-autocomplete-index
org.intermine.model.bio.OntologyTerm.autocomplete = name
org.intermine.model.bio.SOTerm.autocomplete = name
autocomplete.solrurl = http://localhost:8983/solr/autocomplete
allele
binding_site
cDNA_clone
CDS
CRM
chromosomal_deletion
chromosomal_duplication
chromosomal_inversion
chromosomal_translocation
chromosomal_transposition
chromosome
chromosome_band
chromosome_structure_variation
EST
enhancer
exon
five_prime_UTR
forward_primer
gene
golden_path_fragment
intergenic_region
intron
mRNA
miRNA
microarray_oligo
natural_transposable_element
ncRNA
oligo
overlapping_EST_set
PCR_product
point_mutation
primer
rRNA
regulatory_region
reverse_primer
sequence_collection
sequence_feature
sequence_variant
snRNA
snoRNA
TF_binding_site
tRNA
three_prime_UTR
transcript
transposable_element
transposable_element_insertion_site
UTR
# many-to-many part_of relationships (default is many-to-one)
exon.transcript
intron.transcript
UTR.transcript
EST.overlapping_EST_set
systemProp.imVersion=4.1.+
systemProp.bioVersion=4.1.+
systemProp.blueGenesVersion=0.9.9-SNAPSHOT
systemProp.javax.xml.stream.XMLOutputFactory=com.sun.xml.internal.stream.XMLOutputFactoryImpl
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-4.9-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
#!/usr/bin/env bash
##############################################################################
##
## 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 "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS=""
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn ( ) {
echo "$*"
}
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, switch paths to Windows format before running java
if $cygwin ; then
APP_HOME=`cygpath --path --mixed "$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
# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
function splitJvmOpts() {
JVM_OPTS=("$@")
}
eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then
cd "$(dirname "$0")"
fi
exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
@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=
@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
<project type="bio">
<property name="target.model" value="genomic"/>
<property name="common.os.prefix" value="common"/>
<sources>
</sources>
<post-processing>
</post-processing>
</project>
rootProject.name = 'legiomine'
include ':dbmodel',':webapp'
project(':dbmodel').projectDir = new File(settingsDir, './dbmodel')
project(':webapp').projectDir = new File(settingsDir, './webapp')
apply plugin: "war"
apply plugin: "webapp"
apply plugin: "com.bmuschko.cargo"
sourceSets {
main {
java {
srcDirs = ["src/main/java"]
}
resources {
srcDirs = ["src/main/resources"]
}
}
}
configurations {
onlyRunTime
}
def explodedWebAppDir = "$buildDir/explodedWebApp"
def mergePropsDir = "$buildDir/props"
dependencies {
compile (project(":dbmodel")) {transitive = false}
compile group: "org.intermine", name: "bio-core", version: System.getProperty("bioVersion"), transitive: false
compile group: "org.intermine", name: "intermine-api", version: System.getProperty("imVersion")
compile group: "org.intermine", name: "intermine-webapp", version: System.getProperty("imVersion"), classifier: "classes"
compile group: "org.intermine", name: "intermine-webtasks", version: System.getProperty("imVersion")
onlyRunTime group: 'org.intermine', name: 'bluegenes', version: System.getProperty("blueGenesVersion")
}
war {
dependsOn 'mergeProperties', 'summariseObjectStore', 'unwarBioWebApp', 'addStrutsConfig'
finalizedBy 'warWebApp'
}
task warWebApp(type: War) {
dependsOn 'copyWebappContent'