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genbank001

This commit is contained in:
yanggang 2018-11-01 17:33:40 +08:00
parent 06bdb859d2
commit 1d623d70b7
8 changed files with 14 additions and 24 deletions
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9
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/LoadFromFtpUrl.scala → piflow-bundle/src/main/scala/cn/piflow/bundle/ftp/LoadFromFtpUrl.scala
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@ -1,19 +1,16 @@
package cn.piflow.bundle.genBankParse
package cn.piflow.bundle.ftp
import java.io._
import java.net.URL
import java.util
import java.util.ArrayList
import cn.piflow.conf.bean.PropertyDescriptor
import cn.piflow.conf.util.{ImageUtil, MapUtil}
import cn.piflow.conf.{ConfigurableStop, PortEnum, StopGroupEnum}
import cn.piflow.{JobContext, JobInputStream, JobOutputStream, ProcessContext}
import org.apache.spark.sql.{DataFrame, SparkSession}
import org.apache.spark.sql.SparkSession
import org.jsoup.Jsoup
import org.jsoup.select.Elements
import shapeless.ops.hlist.Unzip
import sun.net.ftp.FtpProtocolException
@ -162,7 +159,7 @@ class LoadFromFtpUrl extends ConfigurableStop{
}
override def getGroup(): List[String] = {
List(StopGroupEnum.GenBankParseGroup.toString)
List(StopGroupEnum.FtpGroup.toString)
}
def initialize(ctx: ProcessContext): Unit = {

11
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/UnGz.scala → piflow-bundle/src/main/scala/cn/piflow/bundle/ftp/UnGz.scala
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@ -1,8 +1,4 @@
package cn.piflow.bundle.genBankParse
import java.io._
import java.net.URL
import java.util.ArrayList
package cn.piflow.bundle.ftp
import cn.piflow.bundle.util.UnGzUtil
import cn.piflow.conf.bean.PropertyDescriptor
@ -10,9 +6,6 @@ import cn.piflow.conf.util.{ImageUtil, MapUtil}
import cn.piflow.conf.{ConfigurableStop, PortEnum, StopGroupEnum}
import cn.piflow.{JobContext, JobInputStream, JobOutputStream, ProcessContext}
import org.apache.spark.sql.{Row, SparkSession}
import org.jsoup.Jsoup
import org.jsoup.select.Elements
import sun.net.ftp.FtpProtocolException
class UnGz extends ConfigurableStop{
@ -80,7 +73,7 @@ class UnGz extends ConfigurableStop{
}
override def getGroup(): List[String] = {
List(StopGroupEnum.GenBankParseGroup.toString)
List(StopGroupEnum.FtpGroup.toString)
}
def initialize(ctx: ProcessContext): Unit = {

8
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/GenBankParse.scala → piflow-bundle/src/main/scala/cn/piflow/bundle/microorganism/GenBankParse.scala
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@ -1,4 +1,4 @@
package cn.piflow.bundle.genBankParse
package cn.piflow.bundle.microorganism
import java.io._
import java.net.URL
@ -7,8 +7,8 @@ import java.util
import java.util.ArrayList
import java.util.zip.GZIPInputStream
import cn.piflow.bundle.genBankParse.util.CustomIOTools
import cn.piflow.bundle.genBankParse.util.Process
import cn.piflow.bundle.microorganism.util.CustomIOTools
import cn.piflow.bundle.microorganism.util.Process
import cn.piflow.conf.bean.PropertyDescriptor
import cn.piflow.conf.util.{ImageUtil, MapUtil}
import cn.piflow.conf.{ConfigurableStop, PortEnum, StopGroupEnum}
@ -204,7 +204,7 @@ class GenBankParse extends ConfigurableStop{
}
override def getGroup(): List[String] = {
List(StopGroupEnum.GenBankParseGroup.toString)
List(StopGroupEnum.MicroorganismGroup.toString)
}
def initialize(ctx: ProcessContext): Unit = {

2
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/util/CustomGenbankFormat.java → piflow-bundle/src/main/scala/cn/piflow/bundle/microorganism/util/CustomGenbankFormat.java
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@ -1,4 +1,4 @@
package cn.piflow.bundle.genBankParse.util;
package cn.piflow.bundle.microorganism.util;

2
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/util/CustomIOTools.java → piflow-bundle/src/main/scala/cn/piflow/bundle/microorganism/util/CustomIOTools.java
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@ -1,4 +1,4 @@
package cn.piflow.bundle.genBankParse.util;
package cn.piflow.bundle.microorganism.util;
import org.biojava.bio.BioError;

2
piflow-bundle/src/main/scala/cn/piflow/bundle/genBankParse/util/Process.java → piflow-bundle/src/main/scala/cn/piflow/bundle/microorganism/util/Process.java
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@ -1,4 +1,4 @@
package cn.piflow.bundle.genBankParse.util;
package cn.piflow.bundle.microorganism.util;

2
piflow-bundle/src/main/scala/cn/piflow/conf/StopGroup.scala
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@ -18,7 +18,7 @@ case object KafkaGroup extends StopGroup
case object ESGroup extends StopGroup
case object UrlGroup extends StopGroup
case object HdfsGroup extends StopGroup
case object GenBankParseGroup extends StopGroup
case object MicroorganismGroup extends StopGroup

2
piflow-bundle/src/main/scala/cn/piflow/conf/StopGroupEnum.scala
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@ -22,6 +22,6 @@ object StopGroupEnum extends Enumeration {
val RDFGroup = Value("RDFGroup")
val UrlGroup= Value("UrlGroup")
val HdfsGroup= Value("HdfsGroup")
val GenBankParseGroup= Value("GenBankParseGroup")
val MicroorganismGroup= Value("MicroorganismGroup")
}