#!/usr/bin/groovy

@GrabResolver(name='glycoinfo', root='https://nexus.glycoinfo.org/content/groups/public/')
@GrabResolver(name='glycoinfo-snapshots', root='https://nexus.glycoinfo.org/content/repositories/snapshots/')
//@Grab('org.glytoucan:client:1.2.5-TOCO-SNAPSHOT')
@Grab( group='org.glytoucan',
       module='client',
       version='1.2.11-TOCO-SNAPSHOT',
       changing=true )
@Grab('org.apache.commons:commons-csv:1.2')
import org.glytoucan.client.AntiSpringJavaRest

def cli = new CliBuilder(
   usage: 'gtc -s sequence or -c csvFileName -u contributorId -a apiKey -o outputFormat -m uaf',
   header: '\nAvailable options (use -h for help):\n',
   footer: '\nInformation provided via above options is used to generate printed string.\n')
import org.apache.commons.cli.Option
cli.with
{
   h(longOpt: 'help', 'usage information', required: false)
   s(longOpt: 'sequence', 'glycan structure sequence', args: 1, required: false)
   c(longOpt: 'csvFileName', 'CSV file name', args: 1, required: false)
   u(longOpt: 'contributorId', 'Contribuor Id', args: 1, required: true)
   a(longOpt: 'apiKey', 'API Key', args: 1, required: true)
   p(longOpt: 'partnerId', 'partner accession number', args: 1, required: false)
   // '-o tsv'' or '-o csv''
   o(longOpt: 'outputFormat', 'output format: tsv or csv', args: 1, required: false)
   t(longOpt: 'tsvFileName', 'TSV file name', args: 1, required: false)
   r(longOpt: 'remove', 'remove partner accession number. if use data in a file, -r file', args: 1, required: false)
   // '-m uaf'; u: contributorId, a: apiKey, f: csvFileName or tsvFileName, h: header
   // header = partnerId,Accession Number, sequence
   m(longOpt: 'output metadata', 'u: contributorId, a: apiKey, f: csvFileName or tsvFileName, h: header', args: 1, required: false)
}
def opt = cli.parse(args)
if (!opt) return
if (opt.h) cli.usage()
def sequence = opt.s
def csvFileName = opt.c
def contributorId = opt.u
def apiKey = opt.a
def partnerId = opt.p
def oFormat = opt.o
def tsvFileName = opt.t
def metadata = opt.m
def removePartnerId = opt.r
def asjr = new AntiSpringJavaRest()

// check contributorId and apiKey
if (contributorId){
}
else {
    println "Please check contributorId."
    return
}

if (apiKey){
}
else {
    println "Please check apiKey."
    return
}

// check input format
if (sequence){
    if (tsvFileName){
        println "Please check input format."
        return
    }
    if (csvFileName){
        println "Please check input format."
        return
    }
}
if (tsvFileName){
    if (sequence){
        println "Please check input format."
        return
    }
}
if (csvFileName){
    if (sequence){
        println "Please check input format."
        return
    }
}


// start

if (metadata){
    if (metadata.contains('u')) {    
    println "User ID: ${contributorId}"
    }
    if (metadata.contains('a')) {
    println "Api Key: ${apiKey}"
    }
}

if (sequence) {
    if (oFormat != 'tsv' && oFormat != 'csv') {
        println "Registering sequence: ${sequence}"
    }
    String result;
    if (partnerId) {
        if (oFormat != 'tsv' && oFormat != 'csv') {
            println "Partner Accession Number: ${partnerId}"
        }

        try {
          result = asjr.register(sequence, partnerId, contributorId, apiKey)
        }
        catch (Exception e) {
          e.printStackTrace();
        }

    } else {
        try {
            result = asjr.register(sequence, contributorId, apiKey)
        } 
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    if (removePartnerId) {
      if (oFormat != 'tsv' && oFormat != 'csv') {
         println "Removing partner Accession Number: ${removePartnerId}"
      }
      try {
        result = asjr.removeId(sequence, removePartnerId, contributorId, apiKey)
      }
      catch (Exception e) {
        e.printStackTrace();
      }
    }

    if (oFormat == 'tsv') {
        if (partnerId) {
            println "${result}\t${partnerId}\t${sequence}"
        }
        else {
            println "${result}\t${sequence}"
        }
    }
    else if (oFormat == 'csv') {
        if (partnerId) {
            println "\"${result}\",\"${partnerId}\",\"${sequence}\""
        }
        else {
            println "\"${result}\",\"${sequence}\""
        }
    }
    else {
        if (partnerId) {  
            println "Complete list of all submissions can be found at https://glytoucan.org/Users/structure\nRegistration of sequence:>${sequence}< using id:>${partnerId}< output:>${result}<" // TODO: check if the result is an accession number (starts with G and 8 characters) and if so display https://glytoucan.org/Structures/Glycans/${result}.  Otherwise display https://glytoucan.org/Structures/Submission/${result}.
        }
        else {
            println "Complete list of all submissions can be found at https://glytoucan.org/Users/structure\nRegistration of sequence:>${sequence}< output:>${result}<"  
        }
    }
}
import org.apache.commons.csv.CSVParser
import org.apache.commons.csv.CSVFormat
import org.apache.commons.csv.CSVRecord
import static org.apache.commons.csv.CSVFormat.*
import java.nio.file.Paths
import java.io.IOException
import java.nio.charset.Charset
import java.nio.file.Path
import java.util.List


final def TAB = '\t'
def bPartnerId = false
if ((csvFileName) || (tsvFileName)) {

   // set data form file
    List<List<String>> glycanList = new ArrayList<ArrayList<String>>()
    try {

        if (csvFileName) { 
            Paths.get(csvFileName).withReader { reader ->
            CSVParser csv = new CSVParser(reader, DEFAULT.withHeader())

                for (record in csv.iterator()) {
                    if (record.size() == 2) {
                        glycanList.push( [record.get(0), record.get(1) ] )
                    }
                    else if (record.size() == 1) {
                        glycanList.push( [record.get(0) ] )
                    }
                }
            }
        }
        if (tsvFileName) { 
            new File(tsvFileName).eachWithIndex {
                String line, int i -> 
                if (i == 0) { return }
                else {

                    contents = line.split(TAB) 
                    if (contents.size() == 2) {
                        glycanList.push( [ contents[0], contents[1] ])
                        bPartnerId = true
                    }
                    else if (contents.size() == 1) {
                        glycanList.push( [ contents[0] ])
                    }
                }
            }
        }

    } catch (IOException e) {
      e.printStackTrace();
    }

    if (metadata){
        if (metadata.contains('f')) { 
            if (csvFileName) {
                println "Reading file: ${csvFileName}"
            }
            else if (tsvFileName) {
                println "Reading file: ${tsvFileName}"
            }
        }
        if (metadata.contains('h')) {
            if (oFormat == 'tsv') {
                if (bPartnerId == true) {
                    println "partnerId\tAccession Number\tsequence"
                }
                else if (bPartnerId == false) {
                    println "Accession Number\tsequence"
                }
            }
            else if (oFormat == 'csv') {
                if (bPartnerId == true) {
                    println "\"partnerId\",\"Accession Number\",\"sequence\""
                }
                else if (bPartnerId == false) {
                    println "\"Accession Number\",\"sequence\""
                }
            }
        }
    }

    if (removePartnerId == "file") {
        for (List<String> glycan : glycanList) {

            if (glycan.size() == 2) {
                partnerId = glycan[0]
                sequence = glycan[1]

                if (sequence) {
                    if (partnerId) {
                        //if (oFormat != 'tsv' && oFormat != 'csv') {
                        //    println "Removing partner Accession Number:" + partnerId + "\tsequence: " + sequence
                        //}
                        try {
                            result = asjr.removeId(sequence, partnerId, contributorId, apiKey)
                            
                            if (oFormat == 'tsv') {
                                    if (partnerId) {
                                        println "Removing partner Accession Number:\t${partnerId}\t${sequence}\t${result}"
                                    }
                            }
                            else if (oFormat == 'csv') {
                                if (partnerId) {
                                        println "\"Removing partner Accession Number\",\"${partnerId}\",\"${sequence}\",\"${result}\""
                                }
                            }
                            else {
                                println "Removing partner Accession Number of ${partnerId}.  Please check status at Entries page: https://glytoucan.org/Users/structure"
                            }
                        }
                        catch (Exception e) {
                            println "problem: partner Accession Number:" + partnerId + "\tsequence: " + sequence
                            e.printStackTrace();
                        }
                    }
                }
            }
            else if (glycan.size() == 1) {
                println "Please use your database id in a file."
                return;
            }
        }

    }
    else {

        for (List<String> glycan : glycanList) {

            if (glycan.size() == 2) {
                partnerId = glycan[0]
                sequence = glycan[1]
            }
            else if (glycan.size() == 1) {
                sequence = glycan[0]
            }

            if (sequence) {

                if (oFormat != 'tsv' && oFormat != 'csv') {
                    println "Registering sequence: " + sequence
                }  

                if (partnerId) {
                    if (oFormat != 'tsv' && oFormat != 'csv') {
                        println "Partner Id: ${partnerId}"
                    }

                    try {
                        result = asjr.register(sequence, partnerId, contributorId, apiKey)
                    }
                    catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                else {
                    try {
                        result = asjr.register(sequence, contributorId, apiKey)
                    } 
                    catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                
                if (oFormat == 'tsv') {
                        if (partnerId) {
                            println "${partnerId}\t${result}\t${sequence}"
                        }
                        else {
                            println "${result}\t${sequence}"
                        }
                }
                else if (oFormat == 'csv') {
                    if (partnerId) {
                            println "\"${partnerId}\",\"${result}\",\"${sequence}\""
                    }
                    else {
                            println "\"${result}\",\"${sequence}\""
                    }
                }
                else {
                    if (partnerId) {
                        println "Complete list of all submissions can be found at https://glytoucan.org/Users/structure\nRegistration of sequence:>${sequence}< using id:>${partnerId}< output:>${result}<"  
                    }
                    else {
                        println "Complete list of all submissions can be found at https://glytoucan.org/Users/structure\nRegistration of sequence:>${sequence}< output:>${result}<"  
                    }
                }
            }
            partnerId = false
            sequence = false
        }
    }




}