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shrine-medco/commons/ont-support/src/main/scala/net/shrine/ont/data/ShrineSqlOntologyDao.scala
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ShrineSqlOntologyDao.scala
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package net.shrine.ont.data
import net.shrine.log.Loggable
import net.shrine.ont.messaging.Concept
import scala.io.Source
import scala.util.matching.Regex
import scala.util.matching.Regex.Match
import java.io.InputStream
/**
* @author Clint Gilbert
* @since Feb 8, 2012
*
*/
final class ShrineSqlOntologyDao(val file: InputStream) extends OntologyDao with Loggable {
require(file != null)
override def ontologyEntries: Iterable[Concept] = {
//Matches VALUES (99, '<full term>', 'synonym', '<is_synonym>'
//where is_synonym is 'Y' or 'N'
val pathAndSynonymRegex = """VALUES\s+\(\d+,\s+'(.+?)',\s+'(.+?)',\s+'(\w)',\s+'(.+?)',\s+(NULL|'.*?'),\s+(NULL|'(.*?)')""".r
def mungeBaseCode(rawBaseCode: String): Option[String] = {
val icd9BaseCodePrefix = """SHRINE|ICD9:"""
def isNotNull(s: String) = s != "NULL"
def isNotEmpty(s: String) = !s.isEmpty
def isAcceptable(s: String): Boolean = !s.isEmpty && s != "NULL" && s.startsWith(icd9BaseCodePrefix)
Option(rawBaseCode).filter(isAcceptable).map(_.drop(icd9BaseCodePrefix.size))
}
def toConcept(termMatch: Match): Concept = {
/*val synonym = termMatch.group(3) match {
case "Y" => Option(termMatch.group(2))
case "N" => None
}*/
//Ignore synonym_cd (y/n) field.
//NB: Do this because medications are stored as coded names (..\CV000\CV350\203144\, etc)
//but with synonyms containing human-readable names for the drugs ('pravastatin sodium', etc).
//Crucially, synonym_cd is 'N' in this case (not sure why), and we don't want those synonyms to
//be ignored. This has the effect of making medications' names available when searching an index
//of terms, and also makes the relevance ranking "better", in that simple terms "male", "female"
//are higher up the list. Some terms now have a redundant synonym now, but this is an ok tradeoff.
val synonym = Option(termMatch.group(2))
val rawPath = termMatch.group(1)
val rawBaseCode = termMatch.group(7)
//Need to add '\\SHRINE' that's missing from the SQL file, but needed by i2b2
Concept("""\\SHRINE""" + rawPath, synonym, mungeBaseCode(rawBaseCode))
}
parseWith(pathAndSynonymRegex, toConcept)
}
private def parseWith(regex: Regex, parser: Match => Concept): Iterable[Concept] = {
def parseLine(line: String): Option[Concept] = {
val result = regex.findFirstMatchIn(line).map(parser)
if(result.isEmpty) warn("Failed to parse line: " + line)
result
}
def noEmptyLines(line: String) = line != null && line.trim != ""
def mungeSingleQuotes(line: String) = line.replace("''", "'")
val source = Source.fromInputStream(file)
source.getLines.filter(noEmptyLines)/*.map(mungeSingleQuotes)*/.flatMap(parseLine).toIterable
}
}
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