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build.gradle
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build.gradle
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buildscript {
dependencies {
classpath 'org.postgresql:postgresql:42.2.18'
}
}
plugins {
id "org.liquibase.gradle" version "2.1.1"
}
apply plugin: 'java'
apply plugin: 'groovy'
apply from: 'agr.gradle'
apply from: 'console.gradle'
//apply from: file('setupTestsReports.gradle')
sourceCompatibility = 17
targetCompatibility = 17
//apply from : '../zfinGradle/build.gradle'
def env = System.getenv()
def dbname = env['DBNAME']
def sourceroot = env['SOURCEROOT']
def pgbindir = env['PGBINDIR']
def pgdata = env['PGDATA']
def pghost = env['PGHOST']
def dbunloadspath = env['DB_UNLOADS_PATH']
def solrunloadspath = env['SOLR_UNLOADS_PATH']
def downloaddirectory = env['DOWNLOAD_DIRECTORY']
String targetroot = env['TARGETROOT']
/*
dependencies {
implementation 'org.liquibase:liquibase-core:3.4.1'
implementation "org.liquibase:liquibase-gradle-plugin:1.1.1"
implementation gradleApi()
implementation localGroovy()
}
*/
task deployPostgres(dependsOn: ['deployPostgresFunctions',
'deployPostgresTrigger']) {
description "Deploy all postgres code"
}
defaultTasks 'make'
project.ext.set("dbname", dbname)
project.ext.set("sourceroot", sourceroot)
project.ext.set("pgdata", pgdata)
project.ext.set("pgbindir", pgbindir)
task loadDatabase() {
doLast {
File unloads = file(dbunloadspath)
String unloadPath
if (unloads.exists()) {
def files = unloads.listFiles()
Arrays.sort(files, new Comparator<File>() {
int compare(File f1, File f2) {
return Long.valueOf(f2.lastModified()).compareTo(f1.lastModified())
}
})
File latest = files[0]
File latestBakDump = latest.listFiles().last()
unloadPath = latestBakDump.getPath()
}
//use -DB=... path if specified, also, yes, I'm being cute so that it will be -DB=...
//rather than -Ddb=...
if (System.getProperty("B")) {
unloadPath = System.getProperty("B")
}
//might as well support -Dunload also
if (System.getProperty("unload")) {
unloadPath = System.getProperty("unload")
}
println "Loading $unloadPath into $dbname"
exec {
ignoreExitValue = true
commandLine "bash", "-c", "echo 'select pg_terminate_backend(pg_stat_activity.pid) from pg_stat_activity where pid <> pg_backend_pid();' | psql -v ON_ERROR_STOP=1 $dbname"
}
exec {
ignoreExitValue = true
commandLine 'dropdb', dbname
}
exec {
ignoreExitValue = true
commandLine 'createdb', dbname
}
exec {
ignoreExitValue = true
commandLine "bash", "-c", "pg_restore -j 8 -d $dbname $unloadPath"
}
exec {
ignoreExitValue = true
commandLine "bash", "-c", "echo 'vacuum (analyze)' | psql -v ON_ERROR_STOP=1 $dbname"
}
exec {
// do an "upsert" in the developer_data table to record the time of the last loaddb
ignoreExitValue = true
commandLine "bash", "-c", "echo \$'insert into developer_data (dd_key, dd_value)" +
" values (\\'loaddb completed\\', \\'$unloadPath\\') ON CONFLICT (dd_key) " +
"DO UPDATE SET dd_value = EXCLUDED.dd_value;' | psql -v ON_ERROR_STOP=1 $dbname"
}
}
}
task loadDb(type: GradleBuild) {
tasks = ['loadDatabase']
}
task downloadDB(type: GradleBuild) {
tasks = ['getLatestDatabaseUnload']
}
task downloadSolrIndex(type: GradleBuild) {
tasks = ['getLatestSolrUnload']
}
task loadSolrIndex(type: GradleBuild) {
tasks = ['getLatestSolrIndex']
}
task getdb(dependsOn: downloadDB) //alias for downloadDB (aka getLatestDatabaseUnload)
task loaddb(dependsOn: loadDb) //just an alias, since we're used to loaddb.pl
task buildDatabase(type: GradleBuild) {
tasks = ['liquibasePreBuild']
}
task buildPostGmakeDatabase(type: GradleBuild) {
tasks = ['liquibasePostBuild']
}
task reload(type: GradleBuild) {
tasks = ['loadDatabase', 'liquibasePreBuild', 'liquibasePostBuild']
}
String preChangeLog = "source/org/zfin/db/load/db.changelog.master.xml"
task liquibasePreBuild() {
doLast {
liquibase {
activities {
main {
println preChangeLog
changeLogFile preChangeLog
url 'jdbc:postgresql://' + pghost + ':5432/' + dbname
}
}
}
}
}
liquibasePreBuild.finalizedBy(update)
String postChangeLog = "source/org/zfin/db/postGmakePostloaddb/db.changelog.master.xml"
task liquibasePostBuild() {
doLast {
liquibase {
activities {
main {
changeLogFile preChangeLog
Properties properties = new Properties()
properties.setProperty("SOURCEROOT", ".")
changeLogFile postChangeLog
url 'jdbc:postgresql://' + pghost + ':5432/' + dbname
}
}
}
}
}
liquibasePostBuild.finalizedBy(update)
// variables used for translation of keys in files in SOURCEROOT copied into TARGETROOT
def translateVariableSet = [
'CATALINA_HOME',
'CGI_BIN_DIR_NAME',
'DB_NAME',
'PGHOST',
'DEFAULT_EMAIL',
'ENVIRONMENT',
'FTP_ROOT',
'GBROWSE_PATH_FROM_ROOT',
'GENBANK_DAILY_EMAIL',
'GO_EMAIL_ERR',
'GO_EMAIL_CURATOR',
'GROOVY_CLASSPATH',
'INSTANCE',
'JAVA_HOME',
'JBROWSE_PATH_FROM_ROOT',
'LOADUP_FULL_PATH',
'MOVE_BLAST_FILES_TO_DEVELOPMENT',
'MUTANT_NAME',
'PARTNER_DBNAME',
'PARTNER_INTERNAL_INSTANCE',
'ROOT_PATH',
'SHARED_DOMAIN_NAME',
'SOURCEROOT',
'SQLHOSTS_FILE',
'SWISSPROT_EMAIL_REPORT',
'SWISSPROT_EMAIL_CURATOR',
'SWISSPROT_EMAIL_ERR',
'TARGETROOT',
'USER',
'VALIDATION_EMAIL_DBA',
'WEBHOST_BLASTDB_TO_COPY',
'WEBHOST_FASTA_FILE_PATH',
]
//These are the only files that need to be searched and replaced (<!--|KEY|-->)
//Let's whittle this list down over time
//Other
def whitelistTemplateFiles = [
'**/CreateMarkerSearchPage.sql', //server_apps/data_transfer/ExternalSearch
'**/CreateMarkerSearchPage.pl',
'**/OMIM.pl', //server_apps/data_transfer/OMIM
'**/loadOMIM.sql',
'**/NCBIStartEnd.pl', //server_apps/data_transfer/NCBIStartEnd
'**/gpad.pl', //server_apps/data_transfer/GO
'**/gofile2_all.sql',
'**/gofile.sql',
'**/gofile2.sql',
'**/gpad2.0.sql',
'**/go.pl',
'**/gp2protein.pl',
'**/validateUniprotIDsZFIN.pl',
'**/checkRNAConsequenceTerm.groovy', //server_apps/data_transfer/maintainTermDisplay
'**/insert_eco_go_map.sql', //server_apps/data_transfer/eco_go_mapping
'**/zfishbook.pl', //server_apps/data_transfer/zfishbook
'**/preprocess_zfishbook.pl',
'**/zfishbook.sh',
'**/sp_load.sql', //server_apps/data_transfer/SWISS-PROT
'**/load_protein_domain_info.sql',
'**/sp_load_ec2gopart.sql',
'**/referenceProteome.sql',
'**/sp_delete_ec2gopart.sql',
'**/loadTranscriptSequences.sql', //server_apps/data_transfer/RNACentral
'**/runTscriptSequenceLoad.pl',
'**/loadTscriptSeq.pl',
'**/preLoadTranscriptSequence.sql',
'**/blast_withdrawn.pl', //server_apps/data_transfer/Load
'**/generate_special_Sanger_uniprot_nomenclature_run.sh', //server_apps/data_transfer/Load/ReNo/Nomenclature
'**/load_run_report_hit.sh', //server_apps/data_transfer/Load/ReNo
'**/fetch_ensembl_agp.sh', //server_apps/data_transfer/Ensembl
'**/notifyStaleIds.sh',
'**/fetch_ensdarT_dbacc.sh',
'**/fetch_sangerMutantInfo.sh',
'**/reportEnsembleStatistics.sh',
'**/pullFromBioMart.pl',
'**/fetch_ensdarg.sh',
'**/fetch_ensdargOttdargTable.sh',
'**/loadNewSNPs.sql', //server_apps/data_transfer/SNP
'**/loadNewSNPAttrs.sql',
'**/addNewClonesJSmith.pl',
'**/addTalbotSNPAttr.sql',
'**/dbSNP.pl',
'**/parseObo.pl', //server_apps/data_transfer/LoadOntology
'**/parseHeader.pl',
'**/meow.pl', //server_apps/data_transfer/MEOW
'**/insertJournalAlias.sql', //server_apps/data_transfer/PUBMED/Journal
'**/checkAndUpdateJournals.sql',
'**/load_complete_author_names.sql', //server_apps/data_transfer/PUBMED
'**/loadNewPubs.sql',
'**/updatePublicationDate.groovy',
'**/pubActivation.groovy',
'**/addMeshTermsToAllPubs.groovy',
'**/addPMCidsToAllPubs.groovy',
'**/gbaccession.pl', //server_apps/data_transfer/Genbank
'**/loadHumanSynonyms.sql', //server_apps/data_transfer/ORTHO
'**/updateZebrafishGeneNames.sql',
'**/runOrthology.pl',
'**/emailOrthologyReports.pl',
'**/reportOrthoNameChanges.pl',
'**/parseOrthoFile.pl',
'**/downloadFiles.pl',
'**/parseHumanData.pl',
'**/updateZebrafishGeneNames.pl',
'**/loadAndUpdateNCBIOrthologs.sql',
'**/E_unload_ensembl_contig.sql', //server_apps/data_transfer/Downloads/GFF3
'**/pullFromEZRC.pl', //server_apps/data_transfer/ResourceCenters
'**/pushToZirc.sql',
'**/pullFromZIRC.pl',
'**/pushToZirc.pl',
'**/fx_permission_check.pl', //server_apps/DB_maintenance
'**/loadExternalNotes.pl',
'**/checkVarcharOctetLength.pl',
'**/loadExternalNotes.sql',
'**/disable_updates.pl',
'**/set_unload_timestamp.sql',
'**/rotateInformixLog.sh',
'**/check_undefined_environment.pl',
'**/pushDataToPublic.sh',
'**/backupBlastDbsAndRsyncAlmostBlastDbs.sh',
'**/compareTables.groovy', //server_apps/DB_maintenance/postgres
'**/dailyExtentCheck.sh', //server_apps/DB_maintenance/extentMonitoring
'**/dailyQueryCostCheck.sh', //server_apps/DB_maintenance/queryMonitoring
'**/regenExpressionMart.sh', //server_apps/DB_maintenance/warehouse
'**/who_is.sh',
'**/regenPhenotypeMart.sh',
'**/regenChromosomeMart.sh',
'**/who_is_not.sh',
'**/switch.sh',
'**/runPhenotypeMart.sh', //server_apps/DB_maintenance/warehouse/phenotypeMart
'**/runExpressionMart.sh', //server_apps/DB_maintenance/warehouse/expressionMart
'**/runChromosomeMart.sh', //server_apps/DB_maintenance/warehouse/chromosomeMartPostgres
'**/rsync.pl', //server_apps/DB_maintenance/loadUp
'**/README_loadUp',
'**/signsoflife.sh', //server_apps/WebSiteTools
'**/gen-meetings-rss.r',
'**/gen-jobs-rss.r',
'**/gen-news-rss.r',
'**/inc-redirect', //server_apps/apache
'**/crontab.production', //server_apps/cron
'**/elsevier_report.pl', //server_apps/Reports
'**/reportPubsForGeneAndFeature.pl',
'**/runStats.sh', //server_apps/Reports/AnnualStats
'**/betterFish.sql', //server_apps/Reports/BetterFish
'**/runAverageTimeInBinsCumulative.sh', //server_apps/Reports/PubTracking
'**/runLongestBinResidents.sh',
'**/runPaperlessPubTrackingDailyIndexedMetrics.sh',
'**/runMonthlyBinLengthReport.sh',
]
// load properties into gradle
task setup {
project.ext.ttNameMap = new Properties()
file("home/WEB-INF/zfin.properties").withInputStream {
ttNameMap.load(it)
}
Map filteredMap = new HashMap()
project.ext.ttNameMap.each { name, value ->
if (translateVariableSet.contains(name)) {
filteredMap.put(name, value)
}
}
project.ext.ttNameMap = filteredMap
}
/*
allprojects.findAll { it.path.startsWith(":server_apps:data_transfer:") }.each { p ->
println p.path
}
*/
task printProp() {
doLast {
println 'All Properties'
ttNameMap.each { name, value ->
println name + ' = ' + value
}
}
}
project(':home') {
task "deployFiles"(type: ZfinTargetCopy) {
from file('robots.txt')
from file('favicon.ico')
into targetroot + pName
}
}
project(':home:zf_info') {
task "deployGenericFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.html'
}
into targetroot + pName
}
task "deployStaticFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
exclude '**/*.html'
exclude '**/Makefile'
}
into targetroot + pName
}
task "deployFiles"(type: GradleBuild) {
tasks = ['deployGenericFiles', 'deployStaticFiles']
}
}
project(':home:ZFIN') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile'
}
into targetroot + pName
}
}
project(':server_apps:sysexecs') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile', '**/build.gradle'
}
into targetroot + pName
}
}
project(':server_apps:apache') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile', '**/build.gradle'
}
into targetroot + pName
}
}
project(':server_apps:Reports') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile', '**/build.gradle'
}
into targetroot + pName
}
}
project(':server_apps:DB_maintenance') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile', '**/build.gradle', '**/postgres/liquibase/*'
}
into targetroot + pName
}
}
project(':cgi-bin') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
exclude '**/Makefile', '**/build.gradle'
}
into targetroot + pName
}
}
project(':server_apps:perl_lib') {
task "deployFiles"(type: ZfinTargetCopy) {
from project.projectDir
into targetroot + pName
}
}
task deployGitInfoFile() {
description 'Deploy git-info.txt file into TARGETROOT'
group 'ZFIN Deployment'
def packageFiles = 'git-info.txt'
doLast {
exec {
commandLine 'bash', './generate-git-info.sh'
}
copy {
from(packageFiles)
into(targetroot + "/home/WEB-INF/classes")
}
}
}
project(':server_apps:data_transfer') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
// Apply the search and replace logic only for files that need it
filesMatching(whitelistTemplateFiles) { fileCopyDetails ->
// println("Processing template rules for file: " + fileCopyDetails.file)
ttNameMap.each { name, value ->
fileCopyDetails.filter { String line -> line.replaceAll("<!--\\|${name}\\|-->", value) }
}
}
exclude '**/Makefile', '**/build.gradle', '**/SangerMutants/*', '**/Ensembl'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:Ensembl') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:PUBMED') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:GPAD') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:GPI') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:ExpressionAtlas') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:RNASeqCuration') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:ResourceCenters') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:GO') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:ORTHO') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:eco_go_mapping') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.pl', '**/*.xml', '**/*.txt'
}
into targetroot + pName
}
}
project(':server_apps:data_transfer:Downloads') {
task "createSymlink"() {
doLast {
if (!file(downloaddirectory).exists()) {
exec {
commandLine "mkdir", "-p", downloaddirectory
}
}
String datatransferpath = targetroot + "/home/data-transfer"
if (!file(datatransferpath).exists()) {
exec {
commandLine "ln", "-s", downloaddirectory, datatransferpath
}
}
}
}
}
project(':server_apps:data_transfer:Downloads:GFF3') {
task "deployFiles"(type: ZfinTargetCopy) {
from(project.projectDir) {
ttNameMap.each { name, value ->
filter { it.replaceAll('<!--\\|' + name + '\\|-->', value) }
}
include '**/*.sh', '**/*.sql', '**/*.groovy', '**/*.xml'
}
into targetroot + pName
}
}
task make(type: GradleBuild) {
tasks = ['deployPostgresFunctions',
'deployPostgresTriggers',
'createEmptyDirsIfNotExists',
':home:deployFiles',
':home:zf_info:deployFiles',
':home:ZFIN:deployFiles',
':server_apps:apache:deployFiles',
':server_apps:sysexecs:deployFiles',
':server_apps:DB_maintenance:deployFiles',
':server_apps:data_transfer:deployFiles',
':server_apps:data_transfer:Downloads:createSymlink',
':server_apps:data_transfer:Ensembl:deployFiles',
':server_apps:data_transfer:PUBMED:deployFiles',
':server_apps:data_transfer:ResourceCenters:deployFiles',
':server_apps:data_transfer:GO:deployFiles',
':server_apps:data_transfer:ORTHO:deployFiles',
':server_apps:data_transfer:eco_go_mapping:deployFiles',
':server_apps:Reports:deployFiles',
'deployGitInfoFile',
':cgi-bin:deployFiles',
':server_apps:perl_lib:deployFiles',
]
}
task createEmptyDirsIfNotExists() {
doLast {
exec {
commandLine "mkdir", "-p", targetroot + "/home/data_transfer/Downloads/"
}
exec {
commandLine "mkdir", "-p", targetroot + "/server_apps/data_transfer/Downloads/GFF3/knockdown_reagents/"
}
exec {
commandLine "mkdir", "-p", downloaddirectory + "/current/"
}
}
}
task getLatestSolrUnload() {
doLast {
if (solrunloadspath != '/research/zunloads/solr/zfindb') {
def command = "ssh " + env['SSH_USER'] + "@thorax.zfin.org " + 'ls -d /research/zunloads/solr/zfindb/20??.??.??-??:?? | sort -n |tail -n 1'
def filepath = command.execute().text
println "Getting " + filepath
exec {
ignoreExitValue = true
commandLine "scp", "-r", env['SSH_USER'] + "@thorax.zfin.org:" + filepath, solrunloadspath
}
} else {
println 'SOLR_UNLOADS_PATH is set to ' + solrunloadspath + '. Please change before attempting to copy.'
}
}
}
task getLatestSolrIndexFilesTrunk() {
doLast {
exec {
ignoreExitValue = true
commandLine "bash", "-c", "scp -r " + env['USER'] + "@thorax.zfin.org:/research/zunloads/solr/trunkdb/current current.solr.dump"
}
}
}
task getLatestDatabaseUnload() {
doLast {
if (dbunloadspath != '/research/zunloads/databases/zfindb') {
def command = "ssh " + env['SSH_USER'] + "@thorax.zfin.org " + 'ls -d /research/zunloads/databases/zfindb/20??.??.??.? | sort -n |tail -n 1'
def filepath = command.execute().text
println "Getting " + filepath
exec {
ignoreExitValue = true
commandLine "scp", "-r", env['SSH_USER'] + "@thorax.zfin.org:" + filepath, dbunloadspath
}
} else {
println 'DB_UNLOADS_PATH is set to ' + dbunloadspath + '. Please change before attempting to copy.'
}
}
}
task getLatestPostgresFilesTrunk() {
doLast {
exec {
ignoreExitValue = true
commandLine "bash", "-c", "scp " + env['USER'] + "@thorax.zfin.org:/research/zunloads/databases/trunkdb/current current.postgres.dump"
}
}
}
task getLatestSolrIndex() {
doLast {
println 'Upgrade Solr index to the latest production one...'
println "latest index: " + "find ./* -type d -prune -exec ls -d ".execute().text
def folder = solrunloadspath
def baseDir = new File(folder)
def files = baseDir.listFiles()
Arrays.sort(files, new Comparator<File>() {
int compare(File f1, File f2) {
return Long.valueOf(f2.lastModified()).compareTo(f1.lastModified())
}
})
def latestIndex = files[0]
println latestIndex
def sout = new StringBuilder(), serr = new StringBuilder()
def procString = "ant restore-solr-core -DRESTORE_FROM=" + latestIndex.getAbsolutePath()
def proc = procString.execute()
def b = new StringBuffer()
proc.consumeProcessErrorStream(b)
println proc.text
println b.toString()
}
}
//getsolr as alias for getLatestSolrUnload
task getsolr(dependsOn: getLatestSolrUnload)
//loadsolr as alias for getLatestSolrIndex
task loadsolr(dependsOn: getLatestSolrIndex)
task getBlastAllDatabases() {
doLast {
exec {
ignoreExitValue = true
commandLine "rsync", "-av", env['SSH_USER'] + "@thorax.zfin.org:/research/zfin.org/blastdb/Current", "/opt/zfin/blastdb/"
}
}
}
task getBlastSmallDatabases() {
doLast {
exec {
ignoreExitValue = true
commandLine "rsync", "-av", "--max-size=100m", env['SSH_USER'] + "@thorax.zfin.org:/research/zfin.org/blastdb/Current", "/opt/zfin/blastdb/"
}
}
}
task getBlastBinaries() {
doLast {
exec {
ignoreExitValue = true
commandLine "rsync", "-av", env['SSH_USER'] + "@thorax.zfin.org:/opt/ab-blast", "/opt/zfin/blastdb/"
}
}
}
task getBlast(type: GradleBuild) {
tasks = ['getBlastSmallDatabases',
'getBlastBinaries'
]
}
task createSchemaSpy() {
doLast {
println 'Creating ER diagram for ' + ttNameMap.get('DB_NAME') + ' ...'
javaexec {
main = "-jar"
args = [
"lib/Java/schemaSpy_5.0.0.jar",
"-t",
"pgsql",
"-db",
ttNameMap.get('DB_NAME'),
"-u",
ttNameMap.get('USER'),
"-host",
pghost,
"-dp",
"lib/Java/postgresql-42.2.18.jar",
"-s",
"public",
"-o",
ttNameMap.get('TARGETROOT') + "/home/schemaSpy",
]
}
}
}
repositories {
mavenCentral()
}
dependencies {
liquibaseRuntime("org.liquibase:liquibase-core:4.7.1")
liquibaseRuntime("info.picocli:picocli:4.6.3")
liquibaseRuntime("org.postgresql:postgresql:42.2.18")
implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.11'
implementation group: 'commons-collections', name: 'commons-collections', version: '3.2.1'
implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.17.1'
implementation group: 'net.bytebuddy', name: 'byte-buddy', version: '1.12.7'
implementation group: 'org.hibernate', name: 'hibernate-core', version: '5.6.5.Final'
implementation group: 'org.hibernate', name: 'hibernate-validator', version: '6.0.13.Final'
implementation group: 'org.hibernate.search', name: 'hibernate-search-engine', version: '6.1.0.Final'
implementation group: 'org.hibernate.search', name: 'hibernate-search-mapper-pojo-base', version: '6.1.0.Final'
implementation group: 'org.springframework', name: 'spring-orm', version: '4.3.30.RELEASE'
implementation group: 'org.springframework', name: 'spring-core', version: '4.3.30.RELEASE'
implementation group: 'org.springframework.security', name: 'spring-security-core', version: '4.2.20.RELEASE'
implementation group: 'org.springframework', name: 'spring-webmvc', version: '4.3.30.RELEASE'
implementation group: 'org.springframework', name: 'spring-web', version: '4.3.30.RELEASE'
implementation group: 'org.springframework', name: 'spring-context-support', version: '4.3.30.RELEASE'
implementation group: 'org.springframework.security', name: 'spring-security-web', version: '4.2.20.RELEASE'
implementation group: 'org.springframework.security', name: 'spring-security-crypto', version: '4.2.20.RELEASE'
implementation group: 'javax.validation', name: 'validation-api', version: '2.0.1.Final'
implementation group: 'javax.el', name: 'javax.el-api', version: '3.0.0'
implementation group: 'org.glassfish.web', name: 'javax.el', version: '2.2.4'
implementation group: 'commons-lang', name: 'commons-lang', version: '2.6'
implementation 'org.junit.jupiter:junit-jupiter:5.4.2'
runtimeOnly group: 'com.google.gwt', name: 'gwt-servlet', version: '2.9.0'
implementation('com.google.gwt:gwt-user:2.9.0')
implementation group: 'org.jboss.resteasy', name: 'resteasy-client', version: '3.9.1.Final'
implementation group: 'org.jboss.resteasy', name: 'resteasy-jaxrs', version: '3.9.1.Final'
implementation group: 'org.jboss.resteasy', name: 'resteasy-jackson2-provider', version: '3.9.1.Final'
implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.0'
implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.13.0'
implementation group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.13.0'
implementation group: 'com.github.mmazi', name: 'rescu', version: '2.1.0'
//Thanks for using https://jar-download.com
/*
implementation group: 'org.jboss.resteasy', name: 'resteasy-jackson-provider', version: '3.15.2.Final'
implementation group: 'org.codehaus.jackson', name: 'jackson-core-asl', version: '1.9.13'
implementation group: 'org.codehaus.jackson', name: 'jackson-xc', version: '1.9.13'
implementation group: 'org.codehaus.jackson', name: 'jackson-jaxrs', version: '1.9.13'
implementation group: 'org.codehaus.jackson', name: 'jackson-mapper-asl', version: '1.9.13'
*/
implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.13.0'
/*
implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.0'
implementation group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.13.0'
implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.13.0'
//implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jdk8', version: '2.13.0'
*/
//implementation group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.13.0'
implementation group: 'org.eclipse.microprofile.openapi', name: 'microprofile-openapi-api', version: '2.0.1-RC1'
implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.3.1'
implementation group: 'org.projectlombok', name: 'lombok', version: '1.18.20'
implementation group: 'org.apache.httpcomponents', name: 'httpcore', version: '4.4.1'
implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.4.1'
implementation group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
implementation group: 'com.google.code.gson', name: 'gson', version: '2.2.4'
implementation group: 'org.fusesource.restygwt', name: 'restygwt', version: '2.2.0'
implementation group: 'org.jboss.spec.javax.ws.rs', name: 'jboss-jaxrs-api_2.1_spec', version: '2.0.1.Final'
// implementation group: 'javax.ws.rs', name: 'jsr311-api', version: '1.1.1'
implementation group: 'org.apache.solr', name: 'solr-solrj', version: '8.6.3'
implementation group: 'commons-beanutils', name: 'commons-beanutils', version: '1.9.1'
implementation group: 'commons-cli', name: 'commons-cli', version: '1.2'
implementation group: 'org.freemarker', name: 'freemarker', version: '2.3.20'
implementation group: 'org.apache.lucene', name: 'lucene-core', version: '2.3.1'
implementation group: 'javax.xml.bind', name: 'jaxb-api', version: '2.4.0-b180830.0359'
implementation('org.glassfish.jaxb:jaxb-runtime:2.3.0')
implementation group: 'com.mchange', name: 'c3p0', version: '0.9.5.5'
implementation group: 'javax.mail', name: 'mail', version: '1.4'
implementation group: 'org.apache.commons', name: 'commons-exec', version: '1.0'
implementation group: 'javax.servlet.jsp', name: 'jsp-api', version: '2.0'
implementation group: 'javax.servlet', name: 'jstl', version: '1.2'
implementation group: 'taglibs', name: 'standard', version: '1.1.2'
implementation files('home/WEB-INF/lib/agr_curation_api-v0.35.0.jar')
implementation files('home/WEB-INF/lib/patricia-trie-0.2.jar')
implementation files('home/WEB-INF/lib/confluence-soap-v2.jar')
implementation files('home/WEB-INF/lib/cvu.jar')
implementation files('home/WEB-INF/lib/commons-configuration-ant-task-0.9.6.jar')
implementation files('home/WEB-INF/lib/obo.jar')
implementation files('home/WEB-INF/lib/bbop.jar')
implementation files('home/WEB-INF/lib/blast-serialization-1.0.jar')
implementation files('home/WEB-INF/lib/text-table-formatter-1.0.jar')
implementation files('home/WEB-INF/lib/commons-collections4-4.4.jar')
implementation files('home/WEB-INF/lib/commons-lang3-3.1.jar')
// maven reference does not have version 1.0, so using the plain jar file
//implementation group: 'org.nocrala.tools.texttablefmt', name: 'text-table-formatter', version: '1.2.4'
implementation files('home/WEB-INF/lib/hibernate-c3p0-5.6.5.Final.jar')
implementation files('home/WEB-INF/lib/slf4j-api-1.7.26.jar')
implementation files('home/WEB-INF/lib/jstl-1.1.jar')
implementation files('home/WEB-INF/lib/jackson-core-2.13.0.rc1.jar')
implementation files('home/WEB-INF/lib/javax.persistence-api-2.2.jar')
implementation files('home/WEB-INF/lib/log4j-api-2.17.1.jar')
implementation files('home/WEB-INF/lib/log4j-core-2.17.1.jar')
implementation files('home/WEB-INF/lib/log4j-web-2.17.1.jar')
implementation files('home/WEB-INF/lib/log4j-slf4j-impl-2.13.3.jar')
implementation group: 'net.sourceforge.htmlunit', name: 'htmlunit', version: '2.62.0'
implementation group: 'commons-configuration', name: 'commons-configuration', version: '1.6'
implementation group: 'commons-net', name: 'commons-net', version: '1.4.1'
implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.4'
implementation group: 'com.github.samtools', name: 'htsjdk', version: '2.20.3'
implementation group: 'org.jdom', name: 'jdom', version: '1.1'
implementation group: 'org.springframework.ws', name: 'spring-ws-core', version: '2.2.2.RELEASE'
implementation group: 'org.codehaus.castor', name: 'castor-xml', version: '1.3'
implementation group: 'com.googlecode.owasp-java-html-sanitizer', name: 'owasp-java-html-sanitizer', version: '20200713.1'
implementation group: 'org.imgscalr', name: 'imgscalr-lib', version: '4.2'
implementation group: 'org.biojava', name: 'core', version: '1.9.4'
//implementation group: 'org.apache.tomcat', name: 'tomcat-servlet-api', version: '9.0.39'
implementation group: 'org.apache.ant', name: 'ant', version: '1.8.2'
implementation group: 'javax.xml.rpc', name: 'javax.xml.rpc-api', version: '1.1.2'
implementation group: 'org.apache.logging.log4j', name: 'log4j-web', version: '2.17.1'
implementation group: 'org.postgresql', name: 'postgresql', version: '42.2.18'
implementation group: 'com.google.guava', name: 'guava', version: '27.1-jre'
implementation group: 'org.apache.cxf', name: 'cxf-rt-rs-client', version: '3.4.2'
implementation group: 'com.fasterxml.jackson.jaxrs', name: 'jackson-jaxrs-json-provider', version: '2.12.2'
implementation group: 'org.json', name: 'json', version: '20210307'
annotationProcessor 'org.projectlombok:lombok:1.18.20'
//implementation group: 'log4j', name: 'log4j', version: '1.2.15'
//Thanks for using https://jar-download.com
//implementation group: 'org.apache.commons', name: 'commons-collections4', version: '4.4'
implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.9.4")
implementation 'junit:junit:4.11'
implementation group: 'org.hibernate', name: 'hibernate-gradle-plugin', version: '5.6.5.Final'
testImplementation group: 'xerces', name: 'xercesImpl', version: '2.12.1'
testImplementation("org.junit.jupiter:junit-jupiter-api:5.4.2")
testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.4.2")
testRuntimeOnly("org.junit.vintage:junit-vintage-engine:5.4.2")
testImplementation group: 'org.junit.platform', name: 'junit-platform-suite-api', version: '1.7.0'
testImplementation group: 'commons-discovery', name: 'commons-discovery', version: '0.5'
testImplementation group: 'javax.xml.soap', name: 'javax.xml.soap-api', version: '1.4.0'
testImplementation group: 'wsdl4j', name: 'wsdl4j', version: '1.6.3'
testImplementation group: 'javax.jws', name: 'jsr181-api', version: '1.0-MR1'
implementation group: 'org.javassist', name: 'javassist', version: '3.27.0-GA'
implementation group: 'log4j', name: 'log4j', version: '1.2.17'
// testCompile group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.7.0'
testImplementation group: 'org.hamcrest', name: 'hamcrest-all', version: '1.3'
testImplementation group: 'net.sourceforge.jwebunit', name: 'jwebunit-core', version: '2.4'
implementation group: 'org.springframework', name: 'spring-test', version: '4.3.30.RELEASE'
testImplementation group: 'org.gebish', name: 'geb-spock', version: '0.9.2'
// testCompile group: 'org.openqa.selenium', name: 'selenium', version: '0.8.1'
//testImplementation('org.codehaus.groovy:groovy-all:3.0.6')
testImplementation group: 'org.spockframework', name: 'spock-junit4', version: '2.0-groovy-3.0'
testImplementation group: 'org.spockframework', name: 'spock-spring', version: '2.0-groovy-3.0'
//changed this from groovy-2.4
testImplementation('org.spockframework:spock-core:1.0-groovy-3.0')