fixes #57: upgrade jchem to version 17.24.1

.env

@@ -0,0 +1,2 @@
+CHEMAXON_USERNAME=<username>
+CHEMAXON_PASSWORD=<api key>

Dockerfile

@@ -1,10 +1,18 @@
 FROM mcneilco/tomcat-maven:openjdk8
+ARG CHEMAXON_USERNAME
+ARG CHEMAXON_PASSWORD
+ENV CHEMAXON_USERNAME ${CHEMAXON_USERNAME}
+ENV CHEMAXON_PASSWORD ${CHEMAXON_PASSWORD}
 WORKDIR /src
 ENV CATALINA_HOME /usr/local/tomcat
 ENV PATH $CATALINA_HOME/bin:$PATH
+ADD 	settings.xml /src/settings.xml
+#ADD 	lib/jchem-16.4.25.0.jar /lib/jchem-16.4.25.0.jar
+#RUN 	["mvn", "install:install-file","-Dfile=/lib/jchem-16.4.25.0.jar","-DartifactId=jchem","-DgroupId=com.chemaxon","-Dversion=16.4.25.0","-Dpackaging=jar","-DgeneratePom=true","-DcreateChecksum=true"]
+#RUN 	["mvn", "dependency:get","-s","./settings.xml","-DrepoUrl=https://hub.chemaxon.com/artifactory/libs-release","-Dartifact=com.chemaxon:jchem-main:17.24.1","-Dtransitive=true"]
+#RUN 	["mvn", "dependency:get","-s","./settings.xml","-DrepoUrl=https://hub.chemaxon.com/artifactory/libs-release","-DartifactId=jchem-main","-DgroupId=com.chemaxon","-Dversion=17.24.1","-Dpackaging=jar","-DgeneratePom=true","-DcreateChecksum=true","-Dtransitive=true"]
+RUN		mvn dependency:get -s ./settings.xml -DrepoUrl=https://hub.chemaxon.com/artifactory/libs-release -Dartifact=com.chemaxon:jchem-main:17.24.1 -Dtransitive=true
 ADD 	pom.xml /src/pom.xml
-ADD 	lib/jchem-16.4.25.0.jar /lib/jchem-16.4.25.0.jar
-RUN 	["mvn", "install:install-file","-Dfile=/lib/jchem-16.4.25.0.jar","-DartifactId=jchem","-DgroupId=com.chemaxon","-Dversion=16.4.25.0","-Dpackaging=jar","-DgeneratePom=true","-DcreateChecksum=true"]
 RUN 	["mvn", "dependency:resolve", "-P default"]
 RUN		["mvn", "clean"]
 ADD		. /src

pom.xml

@@ -43,7 +43,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.]]>
 		<gvnix.version>1.4.1.RELEASE</gvnix.version>
 		<querydsl.version>3.4.3</querydsl.version>
 		<spring-security.version>3.1.0.RELEASE</spring-security.version>
-		<jchem.version>16.4.25.0</jchem.version>
+		<jchem.version>17.24.1</jchem.version>
 		<indigo.version>1.2.3.r0</indigo.version>
 		<git-sha-1>${buildNumber}</git-sha-1>
 		<BuildScmBranch>${scmBranch}</BuildScmBranch>
@@ -118,7 +118,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.]]>
 			<dependencies>
 				<dependency>
 					<groupId>com.chemaxon</groupId>
-					<artifactId>jchem</artifactId>
+					<artifactId>jchem-main</artifactId>
 					<version>${jchem.version}</version>
 				</dependency>
 			</dependencies>	

settings.xml

@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<settings xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd" xmlns="http://maven.apache.org/SETTINGS/1.1.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <servers>
+    <server>
+      <username>${CHEMAXON_USERNAME}</username>
+      <password>${CHEMAXON_PASSWORD}</password>
+      <id>central</id>
+    </server>
+    <server>
+      <username>${CHEMAXON_USERNAME}</username>
+      <password>${CHEMAXON_PASSWORD}</password>
+      <id>snapshots</id>
+    </server>
+  </servers>
+  <profiles>
+    <profile>
+      <repositories>
+        <repository>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <id>central</id>
+          <name>libs-release</name>
+          <url>https://hub.chemaxon.com/artifactory/libs-release</url>
+        </repository>
+        <repository>
+          <snapshots />
+          <id>snapshots</id>
+          <name>libs-snapshot</name>
+          <url>https://hub.chemaxon.com/artifactory/libs-snapshot</url>
+        </repository>
+      </repositories>
+      <pluginRepositories>
+        <pluginRepository>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <id>apache</id>
+          <name>repo.maven.apache.org</name>
+          <url>https://repo.maven.apache.org/maven2</url>
+        </pluginRepository>
+        <pluginRepository>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <id>central</id>
+          <name>plugins-release</name>
+          <url>https://hub.chemaxon.com/artifactory/plugins-release</url>
+        </pluginRepository>
+        <pluginRepository>
+          <snapshots />
+          <id>snapshots</id>
+          <name>plugins-release</name>
+          <url>https://hub.chemaxon.com/artifactory/plugins-release</url>
+        </pluginRepository>
+      </pluginRepositories>
+      <id>artifactory</id>
+    </profile>
+  </profiles>
+  <activeProfiles>
+    <activeProfile>artifactory</activeProfile>
+  </activeProfiles>
+</settings>

src/main/java/com/labsynch/cmpdreg/db/migration/postgres/jchem/V1_2_2_2__Upgrade_Jchem_Tables.java

@@ -0,0 +1,55 @@
+package com.labsynch.cmpdreg.db.migration.postgres.jchem;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import org.flywaydb.core.api.migration.jdbc.JdbcMigration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import chemaxon.jchem.db.UpdateHandlerException;
+import chemaxon.jchem.db.Updater;
+import chemaxon.util.ConnectionHandler;
+
+public class V1_2_2_2__Upgrade_Jchem_Tables implements JdbcMigration {
+
+	Logger logger = LoggerFactory.getLogger(V1_2_2_2__Upgrade_Jchem_Tables.class);
+
+
+	public void migrate(Connection conn) throws Exception {
+		logger.info("ATTEMPTING TO UPGRADE JCHEM TABLES");
+		conn.setAutoCommit(true);
+		logger.info("connection autocommit mode: " + conn.getAutoCommit());
+		logger.info("getTransactionIsolation  " + conn.getTransactionIsolation());
+
+		recalculateJChemTable(conn);
+
+		conn.setAutoCommit(false);
+		logger.info("connection autocommit mode: " + conn.getAutoCommit());
+
+	}	
+
+	private boolean recalculateJChemTable(Connection conn) throws UpdateHandlerException, SQLException {
+		ConnectionHandler ch = new ConnectionHandler();
+		ch.setConnection(conn);
+
+		String message = "";
+		Updater ud = new Updater(ch);
+		Updater.UpdateInfo ui = null;
+		while ((ui = ud.getNextUpdateInfo()) != null) {
+			logger.info("\n" + ui.processingMessage + "\n");
+			logger.info("Is structure change required: " + ui.isStructuralChange);
+			message = ud.performCurrentUpdate();
+			logger.info(message);
+		}
+
+		logger.info("updated the Jchem structure tables " );
+
+		return false;
+	}
+
+
+
+
+}
+

src/main/java/com/labsynch/cmpdreg/db/migration/sqlserver/jchem/V1_0_4_4__Upgrade_Jchem_Tables.java

@@ -0,0 +1,55 @@
+package com.labsynch.cmpdreg.db.migration.sqlserver.jchem;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import org.flywaydb.core.api.migration.jdbc.JdbcMigration;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import chemaxon.jchem.db.UpdateHandlerException;
+import chemaxon.jchem.db.Updater;
+import chemaxon.util.ConnectionHandler;
+
+public class V1_0_4_4__Upgrade_Jchem_Tables implements JdbcMigration {
+
+	Logger logger = LoggerFactory.getLogger(V1_0_4_4__Upgrade_Jchem_Tables.class);
+
+
+	public void migrate(Connection conn) throws Exception {
+		logger.info("ATTEMPTING TO UPGRADE JCHEM TABLES");
+		conn.setAutoCommit(true);
+		logger.info("connection autocommit mode: " + conn.getAutoCommit());
+		logger.info("getTransactionIsolation  " + conn.getTransactionIsolation());
+
+		recalculateJChemTable(conn);
+
+		conn.setAutoCommit(false);
+		logger.info("connection autocommit mode: " + conn.getAutoCommit());
+
+	}	
+
+	private boolean recalculateJChemTable(Connection conn) throws UpdateHandlerException, SQLException {
+		ConnectionHandler ch = new ConnectionHandler();
+		ch.setConnection(conn);
+
+		String message = "";
+		Updater ud = new Updater(ch);
+		Updater.UpdateInfo ui = null;
+		while ((ui = ud.getNextUpdateInfo()) != null) {
+			logger.info("\n" + ui.processingMessage + "\n");
+			logger.info("Is structure change required: " + ui.isStructuralChange);
+			message = ud.performCurrentUpdate();
+			logger.info(message);
+		}
+
+		logger.info("updated the Jchem structure tables " );
+
+		return false;
+	}
+
+
+
+
+}
+