NPE after grails clean - grails

Question

The application works just fine, but after grails clean it starts throwing an error if I execute grails war or grail web-app:
|Loading Grails 2.4.3
|Configuring classpath
.
|Environment set to production
.................................
|Packaging Grails application
..
|Compiling 18 source files
.Error
|
Compilation error: startup failed:
General error during class generation: NPE while processing BcvjobService.groovy
groovy.lang.GroovyRuntimeException: NPE while processing BcvjobService.groovy
at org.codehaus.groovy.classgen.AsmClassGenerator.visitClass(AsmClassGenerator.java:252)
at org.codehaus.groovy.control.CompilationUnit$16.call(CompilationUnit.java:805)
at org.codehaus.groovy.control.CompilationUnit.applyToPrimaryClassNodes(CompilationUnit.java:1047)
at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:583)
at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:561)
at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:538)
at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:517)
at org.codehaus.groovy.tools.FileSystemCompiler.compile(FileSystemCompiler.java:59)
at org.codehaus.groovy.tools.FileSystemCompiler.doCompilation(FileSystemCompiler.java:215)
at org.codehaus.groovy.ant.Groovyc.runCompiler(Groovyc.java:1161)
at org.codehaus.groovy.ant.Groovyc.compile(Groovyc.java:1212)
at org.codehaus.groovy.grails.compiler.Grailsc.compile(Grailsc.java:78)
at org.codehaus.groovy.ant.Groovyc.execute(Groovyc.java:827)
...
Googling didn't help in the least, so I can't even understand where to start, and any help would be greatly appreciated.
Here is BcvjobService.groovy:
package bcvapp
import grails.transaction.Transactional
import groovy.lang.Closure;
import groovy.io.FileType
import groovy.util.AntBuilder
import java.awt.event.ItemEvent;
import java.util.List;
import java.util.regex.Pattern;
import grails.util.Mixin
import grails.util.Holders
import org.codehaus.groovy.grails.web.context.ServletContextHolder as SCH
#Transactional
#Mixin(ServiceCategory)
class BcvjobService {
def mailService
def holderService
def servletContext = SCH.servletContext
def String absPath = getAbsPath()
def String configPath = servletContext.getRealPath("/pipeline/bcvrun.prj.xml")
def outputMap = [:]
def prepareDirectory(Bcvjob job, String sessionId, List fileList, List directionList, Integer queueSize){
def configFile = new File (configPath)
def defaultConfig = new XmlParser().parse(configFile)
// Create directory structure
def inputLine = defaultConfig.BCV_Input
def input = inputLine.text().replaceAll(Pattern.compile('[\\.\\/\\\\]'), '')
def outputLine = defaultConfig.BCV_Output
def output = outputLine.text().replaceAll(Pattern.compile('[\\.\\/\\\\]'), '')
def folderPath = "${absPath}${sessionId}"
def inputPath = folderPath + "/" + input
def outputPath = folderPath + "/" + output
addResultsPath(sessionId, outputPath)
inputLine[0].value = inputPath
outputLine[0].value = outputPath
def inpath = defaultConfig.InPath // why there are two almost identical lines in bcv config?
inpath[0].value = inputPath
new File (inputPath).mkdirs()
new File (outputPath).mkdir()
new File(outputPath + "/simple_results.html").createNewFile()
File res = new File(outputPath + "/simple_results.html")
if (queueSize > 2 ){
res << ("Your task was submitted at ${new Date()}<p>")
res << ("Waiting in queue..<p>")
res << ("Please, bookmark this page to see the results later. Refresh the page to check if they are ready.")
}
else {
res << ("Your task was submitted at ${new Date()}<p>")
res << ("Running..<p>")
res << ("Please, bookmark this page to see the results later. Refresh the page to check if they are ready.")
}
res << ("<script>")
res << ("var interval = setInterval('location.reload()', '30000');")
res << ("</script>")
for (f in fileList){
new File (outputPath + "/" + f.getOriginalFilename().replaceAll(Pattern.compile('\\..*'), '').replaceAll("\\s+", "_")).mkdir()
}
uploadFiles(inputPath, fileList)
// Write custom configuration file
def vocabulary = defaultConfig.Vocabulary
def vocabularyPath = vocabulary[0].text().substring(0, vocabulary[0].text().lastIndexOf("/")+1)
def vocabularyName = job.vocabulary.replaceAll(/\s+/, "_")
vocabulary[0].value = vocabularyPath + vocabularyName + ".seq.fas"
def reads = defaultConfig.READS.find{'READS'}
reads.children.clear()
def counter = 0
for (f in fileList){
def stringDirection
if (directionList.get(counter) == "r"){
stringDirection = "reverse"
}
else stringDirection = "forward"
reads.appendNode('Read', [name:f.getOriginalFilename().replaceAll("\\s+", "_")]).appendNode('Direction', stringDirection)
counter++
}
def taxdb = defaultConfig.Database
if (job.taxdb == "full"){
taxdb[0].value = "all"
}
else if (job.taxdb == "named isolates"){
taxdb[0].value = "named"
}
def distance = defaultConfig.DistanceThreshold
distance[0].value = job.distance.toFloat()
def email = defaultConfig.Email
email[0].value = job.email
def mode = defaultConfig.Mode
mode[0].value = "PIPELINE"
def writer = new StringWriter()
def printer = new XmlNodePrinter(new PrintWriter(writer))
printer.with {
preserveWhitespace = true
expandEmptyElements = true
}
printer.print(defaultConfig)
def result = writer.toString()
new File(folderPath + "/bcvrun.prj.xml").write(result)
return outputPath
}
def Closure getWaitingPipeline = {Bcvjob job ->
def queueSize = Bcvjob.countByDateCreatedLessThanEquals(job.dateCreated) + Stapjob.countByDateCreatedLessThanEquals(job.dateCreated)
if(queueSize > 2){
println (" bcv waiting in queue; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
while (queueSize > 2){ // 1 running task + our task
sleep(5000)
queueSize = Bcvjob.countByDateCreatedLessThanEquals(job.dateCreated) + Stapjob.countByDateCreatedLessThanEquals(job.dateCreated)
}
println (" bcv finished waiting in queue; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
def res = new File(getResults(job.sessionId)).newWriter()
res.write("Your task was submitted at ${new Date()}<p>")
res.write("Running..<p>")
res.write("Please, bookmark this page to see the results later. Refresh the page to check if they are ready.")
res.close()
}
def returnCode = runPipeline(job.sessionId)
println (" bcv waiting pipeline finished; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
if (returnCode != 143){
zipResults(job.sessionId)
println (" bcv waiting results zipped; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
if (returnCode == 0){
if (job.email) {
sendResults(job.email, job.sessionId)
println (" bcv waiting results sent; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
}
else {
if (job.email) {
sendLogs(job.email, job.sessionId)
println (" bcv bad news sent; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
else if (returnCode != 143) {
sendLogs(job.sessionId) // send to weidewind
}
else {
println (" user left; sessionId ${job.sessionId} ")
}
}
def sessionId = job.sessionId
job.delete(flush:true)
holderService.setDone(sessionId)
}
def Closure getPipeline = {Bcvjob job ->
def returnCode = runPipeline(job.sessionId)
println (" bcv pipeline finished; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
if (returnCode != 143){
zipResults(job.sessionId)
println (" bcv results zipped; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
if (returnCode == 0){
if (job.email) {
sendResults(job.email, job.sessionId)
println (" bcv results sent; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
}
else {
if (job.email) {
sendLogs(job.email, job.sessionId, returnCode)
println (" bcv bad news sent; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
else if (returnCode != 143) {
sendLogs(job.sessionId) // send to weidewind
}
else {
println (" user left; sessionId ${job.sessionId} ")
}
}
def sessionId = job.sessionId
job.delete(flush:true)
holderService.setDone(sessionId)
}
private def addResultsPath(String sessionId, String outputPath){
outputMap.putAt(sessionId, outputPath)
}
def runPipeline(String sessionId){
println (" going to run bcv pipeline, sessionId ${sessionId}")
def command = "perl /store/home/popova/Programs/BCV_pipeline/pipeline.pl ${absPath}${sessionId} bcvrun.prj.xml >${absPath}pipelinelog.txt >2${absPath}pipelinerr.txt"// Create the String
holderService.procs[sessionId] = command.execute() // Call *execute* on the string
holderService.procs[sessionId].consumeProcessOutput( System.out, System.err ) //31.10
holderService.procs[sessionId].waitFor() // Wait for the command to finish
def exitValue = holderService.procs[sessionId].exitValue()
println "return code " + exitValue
holderService.deleteProc(sessionId)
return exitValue
}
def uploadFiles(String uploadPath, List fileList){
for (f in fileList){
if(f instanceof org.springframework.web.multipart.commons.CommonsMultipartFile){
def fileName = f.getOriginalFilename().replaceAll("\\s+", "_")
new FileOutputStream(uploadPath + "/" + fileName).leftShift( f.getInputStream() )
} else {
log.error("wrong attachment type [${f.getClass()}]");
}
}
}
def uploadSequenceFiles(String uploadPath, List fileList){
for (f in fileList){
if(f instanceof org.springframework.web.multipart.commons.CommonsMultipartFile){
def fileName = f.getOriginalFilename().replaceAll("\\s+", "_")
new FileOutputStream(uploadPath + "/" + fileName.replaceAll(Pattern.compile('\\..*'), '') + "/" + fileName).leftShift( f.getInputStream() )
} else {
log.error("wrong attachment type [${f.getClass()}]");
}
}
}
def sendResults(String email, String sessionId) {
def results = getZipResults(sessionId)
println "going to send files, sessionID ${sessionId} resultsPath ${results} time ${System.currentTimeMillis()}"
mailService.sendMail {
multipart true
to email
subject "BCV results"
body "Thanks for using BCV!\n Here are your results. \n Have a nice day!"
attachBytes 'results.zip','application/zip', new File(results).readBytes()
}
}
def sendExampleResults(String email, String folderName){
def results = getStorePath() + folderName + "/results.zip"
println "going to send files, folderName ${folderName} resultsPath ${results} time ${System.currentTimeMillis()}"
mailService.sendMail {
multipart true
to email
subject "Example BCV results"
body "Thanks for using BCV!\n Here are your example results. \n Have a nice day!"
attachBytes 'results.zip','application/zip', new File(results).readBytes()
}
}
def sendLogs(String email, String sessionId) {
//def logs = "${absPath}${sessionId}logfile"
def results = getZipResults(sessionId)
println "going to send logs, sessionID ${sessionId} logPath ${logs} time ${System.currentTimeMillis()}"
mailService.sendMail {
multipart true
to email
subject "BCV failed"
body "We are very sorry, but something has gone amiss. Here are some of your results, though."
attachBytes 'results.zip','application/zip', new File(results).readBytes()
}
//just in case there is no results at all and results.zip does not exist. Todo: catch mailService or zip exception
//else user left, auto-termination
mailService.sendMail {
multipart true
to "weidewind#gmail.com"
subject "BCV failed"
body "Achtung! email: ${email}, sessionId: ${sessionId}"
}
mailService.sendMail {
multipart true
to "weidewind#gmail.com"
subject "BCV failed"
body "Achtung! email: ${email}, sessionId: ${sessionId}"
attachBytes 'results.zip','application/zip', new File(results).readBytes()
}
println (" bcv bad news sent to webmaster; sessionId ${job.sessionId} time ${System.currentTimeMillis()}")
}
def sendLogs(String sessionId){
//just in case there is no results at all and results.zip does not exist. Todo: catch mailService or zip exception
mailService.sendMail {
multipart true
to "weidewind#gmail.com"
subject "BCV failed"
body "Achtung! sessionId: ${sessionId}"
}
println (" bcv bad news sent to webmaster; sessionId ${sessionId} time ${System.currentTimeMillis()}")
}
def zipResults(String sessionId){
def output = getOutput(sessionId)
def results = getZipResults(sessionId)
println "going to zip files, sessionID ${sessionId} time ${System.currentTimeMillis()}"
println (output)
def p = ~/.*\.(svg|html|with_names|cluster\.fasta)/
def filelist = []
def outputDir = new File(output)
outputDir.eachDir { chrom ->
def chromDir = new File(chrom.absolutePath)
chromDir.eachFileMatch(FileType.FILES, p){ tree ->
def splittedPath = tree.absolutePath.split('/')
println ("going to add ${splittedPath[splittedPath.size()-2]}/${splittedPath[splittedPath.size()-1]} from ${output} to zip list; sessionId ${sessionId}")
filelist.add("${splittedPath[splittedPath.size()-2]}/${splittedPath[splittedPath.size()-1]}")
}
}
filelist.add("simple_results.html")
println("results will be placed here ${results}")
def zipFile = new File("${results}")
new AntBuilder().zip( basedir: output,
destFile: zipFile.absolutePath,
includes: filelist.join( ' ' ) )
}
def getResults (String sessionId){
return outputMap.getAt(sessionId) + "/simple_results.html"
}
def getOutput(String sessionId){
return outputMap.getAt(sessionId)
}
def getZipResults(String sessionId){
return outputMap.getAt(sessionId) + "/results.zip"
}
def getExampleFolderName(List fileList){
def exampleFileNames = []
for (f in fileList){
exampleFileNames.add(f.name)
}
exampleFileNames.sort()
def folderName = ""
for (f in exampleFileNames){
folderName = folderName + (f.replaceAll(Pattern.compile('\\..*'), ''))
}
println folderName
return folderName
}
def checkInput(Bcvjob job, List fileList){
String errorMessage = ""
if (!job.validate()) {
errorMessage = "Some errors occured: "
job.errors.each {
errorMessage += "<p>" + it + "</p>"
}
//if (!isFloat(job.distance) || job.distance.toFloat() < 0 || job.distance.toFloat() > 0.1){
if ( job.distance < 0 || job.distance > 0.1){
errorMessage += "<p> Maximum distance must not be less than 0 or more than 0.1 </p>"
}
if (job.errors.hasFieldErrors("email")){
errorMessage += "<p>Your e-mail does not seem valid </p>"
}
if (job.errors.hasFieldErrors("files") || (fileList.size() == 0 & job.isExample == "false")){
errorMessage += "<p>Select at least one file </p>"
}
}
if (fileList.size() > 10){
errorMessage += "<p>Please, do not select more than 10 files at once. </p>"
}
if (job.isExample == "false"){
for (f in fileList) {
def name = f.getOriginalFilename()
int dot= name.lastIndexOf(".");
if (name.substring(dot+1) != "ab1"){
errorMessage += "<p>Unsupported extension: ${name} </p>"
}
def bytes = f.getBytes()
if (bytes[0] != 'A' || bytes[1] != 'B' || bytes[2] != 'I' || bytes[3] != 'F' || !(bytes[4]+bytes[5] >= 101)){
errorMessage += "<p>Not ABI: ${name} </p>"
}
}
}
return errorMessage
}
def isFloat(String value)
{
try
{
Float.parseFloat(value);
return true;
} catch(NumberFormatException nfe)
{
return false;
}
}
def getAbsPath(){
return Holders.config.absPath
}
def getStorePath(){
return Holders.config.storePath
}
def talkWork(){
ServiceCategory.talkWork()
}
def talkQueue(){
ServiceCategory.talkQueue()
}
}