version 1.3.2 boosteting term and subTopic bug fixed

COPYRIGHT.md

@@ -1,42 +1,31 @@
-# BVS-InfoButton licenses
-
-BVS-InfoButton © Pan American Health Organization, 2018.
-
-BVS-InfoButton software is licensed under the terms available at https://github.com/bireme/BVS-InfoButton/blob/master/LICENSE.txt
-
-Follows a list of the Open Source Softwares and their respective applicable Open Source licenses and copyright notices.
-
-Observation: Information may be subject to alteration.
+# bvs-infobutton-licenses
 
 Category | License | Dependency | Notes
 --- | --- | --- | ---
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | joda-time # joda-time # 2.9.9 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-analyzers-common # 7.5.0 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-backward-codecs # 7.5.0 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-core # 7.5.0 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-queries # 7.5.0 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-queryparser # 7.5.0 | <notextile></notextile>
-Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-sandbox # 7.5.0 | <notextile></notextile>
+Apache | [Apache 2](https://www.apache.org/licenses/LICENSE-2.0.txt) | joda-time # joda-time # 2.10.1 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-analyzers-common # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-backward-codecs # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-core # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-queries # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-queryparser # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.lucene # lucene-sandbox # 8.0.0 | <notextile></notextile>
+Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0) | org.scalaj # scalaj-http_2.12 # 2.4.1 | <notextile></notextile>
 Apache | [Apache 2](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.typelevel # macro-compat_2.12 # 1.1.1 | <notextile></notextile>
-Apache | [Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.scala-logging # scala-logging_2.12 # 3.9.0 | <notextile></notextile>
-Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | commons-codec # commons-codec # 1.10 | <notextile></notextile>
-Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.httpcomponents # httpclient # 4.5.6 | <notextile></notextile>
-Apache | [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | org.apache.httpcomponents # httpcore # 4.4.10 | <notextile></notextile>
-Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-http-core_2.12 # 10.1.5 | <notextile></notextile>
-Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-http_2.12 # 10.1.5 | <notextile></notextile>
-Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-parsing_2.12 # 10.1.5 | <notextile></notextile>
-Apache | [Apache-2.0](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.play # play-functional_2.12 # 2.6.10 | <notextile></notextile>
-Apache | [Apache-2.0](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.play # play-json_2.12 # 2.6.10 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-annotations # 2.8.11 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-core # 2.8.11 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-databind # 2.8.11.1 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.datatype # jackson-datatype-jdk8 # 2.8.11 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.datatype # jackson-datatype-jsr310 # 2.8.11 | <notextile></notextile>
-Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | commons-logging # commons-logging # 1.2 | <notextile></notextile>
-Apache | [the Apache License, ASL Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | org.scalactic # scalactic_2.12 # 3.0.5 | <notextile></notextile>
-Apache | [the Apache License, ASL Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | org.scalatest # scalatest_2.12 # 3.0.5 | <notextile></notextile>
-BSD | [BSD 3-Clause](http://www.scala-lang.org/license.html) | org.scala-lang # scala-library # 2.12.7 | <notextile></notextile>
-BSD | [BSD 3-Clause](http://www.scala-lang.org/license.html) | org.scala-lang # scala-reflect # 2.12.7 | <notextile></notextile>
+Apache | [Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.scala-logging # scala-logging_2.12 # 3.9.2 | <notextile></notextile>
+Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-http-core_2.12 # 10.1.7 | <notextile></notextile>
+Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-http_2.12 # 10.1.7 | <notextile></notextile>
+Apache | [Apache-2.0](https://opensource.org/licenses/Apache-2.0) | com.typesafe.akka # akka-parsing_2.12 # 10.1.7 | <notextile></notextile>
+Apache | [Apache-2.0](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.play # play-functional_2.12 # 2.7.2 | <notextile></notextile>
+Apache | [Apache-2.0](http://www.apache.org/licenses/LICENSE-2.0.html) | com.typesafe.play # play-json_2.12 # 2.7.2 | <notextile></notextile>
+Apache | [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) | org.scala-lang # scala-library # 2.12.8 | <notextile></notextile>
+Apache | [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) | org.scala-lang # scala-reflect # 2.12.8 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-annotations # 2.9.8 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-core # 2.9.8 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.core # jackson-databind # 2.9.8 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.datatype # jackson-datatype-jdk8 # 2.9.8 | <notextile></notextile>
+Apache | [The Apache Software License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt) | com.fasterxml.jackson.datatype # jackson-datatype-jsr310 # 2.9.8 | <notextile></notextile>
+Apache | [the Apache License, ASL Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | org.scalactic # scalactic_2.12 # 3.0.7 | <notextile></notextile>
+Apache | [the Apache License, ASL Version 2.0](http://www.apache.org/licenses/LICENSE-2.0) | org.scalatest # scalatest_2.12 # 3.0.7 | <notextile></notextile>
 BSD | [BSD 3-clause](http://opensource.org/licenses/BSD-3-Clause) | org.scala-lang.modules # scala-xml_2.12 # 1.1.1 | <notextile></notextile>
 BSD | [BSD 3-clause New License](https://github.com/dom4j/dom4j/blob/master/LICENSE) | org.dom4j # dom4j # 2.1.1 | <notextile></notextile>
 LGPL | [GNU Lesser General Public License](http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html) | ch.qos.logback # logback-classic # 1.2.3 | <notextile></notextile>

build.sbt

@@ -19,7 +19,7 @@ val logbackVersion = "1.2.3"
 val scalaTestVersion = "3.0.7" // "3.0.5"
 val hairyfotrVersion = "0.1.17"
 val luceneVersion = "8.0.0" // "7.5.0"
-val httpComponentsVersion = "4.5.7" //"4.5.6"
+val scalajHttpVersion = "2.4.1"
 
 libraryDependencies ++= Seq(
   "com.typesafe.akka" %% "akka-http" % akkaVersion,
@@ -36,7 +36,7 @@ libraryDependencies ++= Seq(
   "org.apache.lucene" % "lucene-queryparser" % luceneVersion,
   "org.apache.lucene" % "lucene-queries" % luceneVersion,
   "org.apache.lucene" % "lucene-backward-codecs" % luceneVersion,
-  "org.apache.httpcomponents" % "httpclient" % httpComponentsVersion
+  "org.scalaj" %% "scalaj-http" % scalajHttpVersion
 )
 
 logBuffered in Test := false

src/main/scala/org/bireme/infob/InfoServer.scala

@@ -8,20 +8,14 @@
 package org.bireme.infob
 
 import java.net.{URL, URLDecoder, URLEncoder}
-import java.nio.charset.Charset
 
 import ch.qos.logback.classic.{Level, Logger => xLogger}
 import com.typesafe.scalalogging.Logger
-import org.apache.http.HttpEntity
-import org.apache.http.client.entity.UrlEncodedFormEntity
-import org.apache.http.client.methods.HttpPost
-import org.apache.http.impl.client.HttpClients
-import org.apache.http.message.BasicNameValuePair
-import org.apache.http.util.EntityUtils
 import org.bireme.infob.parameters._
 import org.dom4j.Element
 import org.slf4j.LoggerFactory
 import play.api.libs.json._
+import scalaj.http.{Http, HttpResponse}
 
 import scala.collection.JavaConverters._
 import scala.reflect._
@@ -292,34 +286,16 @@ class InfoServer(
     * error occurred
     */
   private def post(params: Seq[(String, String)]): Either[String, String] = {
-//println(s"post: params=$params")
-    val paramSeq: Seq[BasicNameValuePair] = params.map(elem => new BasicNameValuePair(elem._1, elem._2))
-    val httpclient = HttpClients.createDefault()
-    val httpPost = new HttpPost(iahxUrl)
-    httpPost.addHeader("Accept-Charset", "UTF-8")
-    httpPost.addHeader("Accept", "application/json")
-    httpPost.setEntity(new UrlEncodedFormEntity(paramSeq.asJava, Charset.forName("utf-8")))
-//println(s"httpPost=$httpPost")
-    val response = httpclient.execute(httpPost)
-    val statusLine = response.getStatusLine
-//println("status Code=" + statusLine.getStatusCode)
-    if (statusLine.getStatusCode == 200) {
-//println(s"response=$response")
-      try {
-        val entity: HttpEntity = response.getEntity
-        val content: String = EntityUtils.toString(entity)
-  //println(s"content=$content entity=$entity")
-        response.close()
+    //println(s"post: params=$params")
+
+    val response: HttpResponse[String] = Http(iahxUrl)
+      .headers(Seq("Accept-Charset" ->"UTF-8", "Accept" -> "application/json")).postForm(params).asString
+
+    if (response.code == 200) {
+        val content: String = response.body
         Right(content)
-      } catch {
-        case ex: Throwable =>
-  //println("Throwable=${ex.toString}")
-          response.close()
-          Left(ex.toString)
-      }
     } else {
-      val reason: String = statusLine.getReasonPhrase
-      Left(if (reason.isEmpty) s"errCode:${statusLine.getStatusCode}" else reason)
+      Left(s"errCode:${response.code}")
     }
   }
 
@@ -487,7 +463,7 @@ object InfoServer extends App {
       ".administrativeGenderCode.c=M&age.v.v=45&age.v.u=a&informationRecipient" +
       "=PAT&performer=PROV&performer.languageCode.c=en&performer.healthCarePro" +
       "vider.c.c=163W00000X&knowledgeResponseType=application/json"*/
-     "http://bvsinfobutton.homolog.bvsalud.org/infobutton/search?mainSearchCriteria.v.ot=zika virus&knowledgeResponseType=text/xml&knowledgeResponseType=text/xml&explain=true"
+     "http://bvsinfobutton.homolog.bvsalud.org/infobutton/search?mainSearchCriteria.v.ot=zika virus&subTopic.v.c=79899007&subTopic.v.cs=2.16.840.1.113883.6.96&knowledgeResponseType=text/xml&explain=true"
   } else {
     args(0)
   }

src/main/scala/org/bireme/infob/parameters/MainSearchCriteria.scala

@@ -55,13 +55,12 @@ class MainSearchCriteria(conv: MeshConverter,
 //println(s"strOriginalText=$strOriginalText strOriginalTextStatus=$strOriginalTextStatus")
 
   override def toSrcExpression(env: Seq[SearchParameter]): Option[String] = {
-    val circ = "ˆ"
     val ret = code match {
       case Some(_) =>
         strCodeStatus match {
           case "exact"  =>
             val code2: String = codeSet.head.toLowerCase
-            Some("(mh:\"" + code2 + circ + "2\" OR ti:\"" + code2 + circ + "1\")")
+            Some("(mh:\"" + code2 + "\"^2 OR ti:\"" + code2 + "\"^1)")
             //                     "\" OR ab:\"" + code2 + "\")")
           case "synonym"  => Some("(" +
                                   andOrExpression("mh", codeSet, 2) + " OR " +
@@ -147,9 +146,7 @@ class MainSearchCriteria(conv: MeshConverter,
         }
     }
 
-    val circ = "ˆ"
-    val words2 = if (boost == 1) words.map(word => s"$index:$word")
-      else words.map(word => s"$index:$word$circ$boost")
+    val words2 = words.map(word => s"$index:$word^$boost")
 
     val words3 = if (words2.size > 5) {
       words2.mkString(" OR ")

src/main/scala/org/bireme/infob/parameters/SubTopic.scala

@@ -29,9 +29,9 @@ class SubTopic(
   )
 
   override def toSrcExpression(env: Seq[SearchParameter]): Option[String] = {
-    val codeSrcExpr: Option[String] = code.flatMap(x => getSrcExpr(x))
-    lazy val dplNameSrcExpr = displayName.flatMap(x => getSrcExpr(x))
-    lazy val oTextSrcExpr = originalText.flatMap(x => getSrcExpr(x))
+    val codeSrcExpr: Option[String] = code.flatMap(getSrcExpr)
+    lazy val dplNameSrcExpr = displayName.flatMap(getSrcExpr)
+    lazy val oTextSrcExpr = originalText.flatMap(getSrcExpr)
 
     codeSrcExpr orElse dplNameSrcExpr orElse oTextSrcExpr
   }
@@ -52,8 +52,9 @@ class SubTopic(
       }
     }.map {
       case (qual, expr) =>
-        val index = if (qual) "sh" else "mh"
-        s"($index:${'"'}$expr${'"'} OR ti:${'"'}$expr${'"'} OR ab:${'"'}$expr${'"'})"
+        val index = if (qual) "sh" else "mh"  // sh - sub headings.  mh - mesh headings
+        s"($index:${'"'}$expr${'"'} OR ti:${'"'}$expr${'"'})" +
+        s" OR ab:${'"'}$expr${'"'})"
     }
   }
 
@@ -63,7 +64,7 @@ class SubTopic(
       Category("subTopic.v.cs", codeSystem.get),
       Category("subTopic.v.dn", displayName.getOrElse("")),
       Category("subTopic.v.ot", originalText.getOrElse(""))
-    ).filter(!_.term.isEmpty)
+    ).filter(_.term.nonEmpty)
   }
 
   override def toString: String =

web/BVSInfoButton/build/web/index.html

@@ -310,7 +310,7 @@ <h1>BVS - Infobutton (version 1.0.0)</h1>
    <option value="Q000633">Q000633 - toxicity (MeSH)</option>
    <option value="Q000506">Q000506 - poisoning (MeSH)</option>
 
-   <option value="79899007">79899007 - Drug Interactions (SNOMED_CT)</option>
+   <option value="79899007">79899007 - Drug Interaction (SNOMED_CT)</option>
    <option value="47965005">47965005 - Diagnosis, Differential (SNOMED_CT)</option>
    <option value="404204005">404204005 - Drug interaction with drug (SNOMED_CT)</option>
    <option value="95907004">95907004 - Drug interaction with food (SNOMED_CT)</option>

web/BVSInfoButton/src/java/org/bireme/binfo/BVSInfoButton.java

@@ -96,7 +96,7 @@ private String getRequestInfo(HttpServletRequest request,
         final long now = Calendar.getInstance().getTimeInMillis();
 
         builder.append("date=" + now);
-        builder.append("\tremote_address==" + raddr);
+        builder.append("\tremote_address=" + raddr);
         builder.append("\treferer=" + referer);
         builder.append("\tdocs_found=" + total);
 

web/BVSInfoButton/web/index.html

@@ -310,7 +310,7 @@ <h1>BVS - Infobutton (version 1.0.0)</h1>
    <option value="Q000633">Q000633 - toxicity (MeSH)</option>
    <option value="Q000506">Q000506 - poisoning (MeSH)</option>
 
-   <option value="79899007">79899007 - Drug Interactions (SNOMED_CT)</option>
+   <option value="79899007">79899007 - Drug Interaction (SNOMED_CT)</option>
    <option value="47965005">47965005 - Diagnosis, Differential (SNOMED_CT)</option>
    <option value="404204005">404204005 - Drug interaction with drug (SNOMED_CT)</option>
    <option value="95907004">95907004 - Drug interaction with food (SNOMED_CT)</option>