Start legiolist mine

.gitignore

+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
+

build.gradle

+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"
+}

dbmodel/build.gradle

+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 = ""
+}

dbmodel/resources/class_keys.properties

+# 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

dbmodel/resources/genomic_precompute.properties

+# 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_)
+

dbmodel/resources/genomic_priorities.properties

+#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, *
+
+

dbmodel/resources/keyword_search.properties

+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

dbmodel/resources/objectstoresummary.config.properties

+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

dbmodel/resources/so_terms

+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

gradle.properties

+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

gradle/wrapper/gradle-wrapper.properties

+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

gradlew

+#!/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 "$@"

gradlew.bat

+@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.xml

+<project type="bio">
+  <property name="target.model" value="genomic"/>
+  <property name="common.os.prefix" value="common"/>
+  <sources>
+
+
+
+  </sources>
+
+  <post-processing>
+
+
+
+  </post-processing>
+
+</project>
+

settings.gradle

+rootProject.name = 'legiomine'
+
+include ':dbmodel',':webapp'
+
+project(':dbmodel').projectDir = new File(settingsDir, './dbmodel')
+project(':webapp').projectDir = new File(settingsDir, './webapp')

webapp/build.gradle

+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'
+    description "Create the war from the build/explodedWebAppDir directory"
+    from "${explodedWebAppDir}"