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Merge branch 'hotfix-2.1.2'
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René Meier committed Mar 11, 2020
2 parents 3af6745 + ec84b19 commit 31619b8
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25 changes: 17 additions & 8 deletions MassBank-Project/MassBank-lib/pom.xml
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@@ -1,26 +1,27 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>de.ipb-halle.msbi</groupId>
<artifactId>MassBank-Project</artifactId>
<groupId>de.ipb-halle.msbi</groupId>
<version>2.1.2</version>
</parent>

<artifactId>MassBank-lib</artifactId>
<name>MassBank lib</name>
<url>http://maven.apache.org</url>
<!-- <packaging>jar</packaging> -->

<dependencies>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.13.0</version>
<version>2.13.1</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>4.0.1</version>
<version>${servlet-api-version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
Expand Down Expand Up @@ -85,7 +86,7 @@
<dependency>
<groupId>com.github.petitparser</groupId>
<artifactId>petitparser-core</artifactId>
<version>2.2.0</version>
<version>${petitparser-version}</version>
</dependency>
<dependency>
<groupId>edu.ucdavis.fiehnlab.splash</groupId>
Expand All @@ -104,10 +105,18 @@
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources-filtered</directory>
<filtering>true</filtering>
</resource>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<finalName>MassBank-lib</finalName>
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230 changes: 55 additions & 175 deletions MassBank-Project/MassBank-lib/src/main/java/massbank/Validator.java
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@@ -1,10 +1,16 @@
package massbank;

import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import java.util.concurrent.atomic.AtomicBoolean;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
Expand All @@ -14,167 +20,11 @@
/**
* This class validates a record file or String by using the syntax of {@link RecordParserDefinition}.
* @author rmeier
* @version 01-03-2019
* @version 05-03-2020
*/
public class Validator {
private static final Logger logger = LogManager.getLogger(Validator.class);

// just a test String
public static String recordstringExample =
"ACCESSION: BSU00002\n" +
"RECORD_TITLE: Veratramine; LC-ESI-QTOF; MS2; CE: 50 V\n" +
"DATE: 2016.01.19 (Created 2012.12.18, modified 2013.07.16)\n" +
"AUTHORS: Chandler, C. and Habig, J. Boise State University\n" +
"LICENSE: CC BY-SA\n" +
"COPYRIGHT: Chandler, C., Habig, J. and McDougal O. Boise State University\n" +
"PUBLICATION: Iida T, Tamura T, et al, J Lipid Res. 29, 165-71 (1988). [PMID: 3367086]\n" +
"COMMENT: Data obtained from a veratramine standard purchased from Logan Natural Products, Logan, Utah USA.\n" +
"COMMENT: Data obtained from a veratramine standard purchased from Logan Natural Products, Logan, Utah USA.\n" +
"CH$NAME: Veratramine\n" +
"CH$NAME: {(3beta,23R)-14,15,16,17-Tetradehydroveratraman-3,23-diol\n" +
"CH$COMPOUND_CLASS: N/A; Environmental Standard; grr\n" +
"CH$FORMULA: C27H41NO2\n" +
"CH$EXACT_MASS: 409.29807\n" +
"CH$SMILES: CC1CC2C(C(C3(O2)CCC4C5CC=C6CC(CCC6(C5CC4=C3C)C)O)C)NC1\n" +
"CH$IUPAC: InChI=1S/C27H41NO2/c1-15-11-24-25(28-14-15)17(3)27(30-24)10-8-20-21-6-5-18-12-19(29)7-9-26(18,4)23(21)13-22(20)16(27)2/h5,15,17,19-21,23-25,28-29H,6-14H2,1-4H3/t15-,17+,19-,20-,21-,23-,24+,25-,26-,27-/m0/s1\n" +
"CH$LINK: INCHIKEY 60-70-8\n" +
"CH$LINK: CAS 60-70-8\n" +
"CH$LINK: CHEBI 9951\n" +
"CH$LINK: CHEMSPIDER 5845\n" +
"CH$LINK: KEGG C10829\n" +
"CH$LINK: KNAPSACK C00002270\n" +
"CH$LINK: PUBCHEM 13012\n" +
"SP$SCIENTIFIC_NAME: Mus musculus\n" +
"SP$LINK: NCBI-TAXONOMY 10090\n" +
"SP$LINK: NCBI-TAXONOMY 10090\n" +
"SP$SAMPLE: Liver extracts\n" +
"SP$SAMPLE: Liver extracts\n" +
"AC$INSTRUMENT: Bruker maXis ESI-QTOF\n" +
"AC$INSTRUMENT_TYPE: LC-ESI-QTOF\n" +
"AC$MASS_SPECTROMETRY: MS_TYPE MS2\n" +
"AC$MASS_SPECTROMETRY: ION_MODE POSITIVE\n" +
"AC$MASS_SPECTROMETRY: COLLISION_ENERGY 50 eV\n" +
"AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE CID\n" +
"AC$MASS_SPECTROMETRY: IONIZATION ESI\n" +
"AC$MASS_SPECTROMETRY: RESOLUTION 35000\n" +
"AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um, 2.1x100mm, Thermo\n" +
"AC$CHROMATOGRAPHY: FLOW_GRADIENT 99/1 at 0-1 min, 61/39 at 3 min, 0.1/99.9 at 14-16 min, 99/1 at 16.1-20 min\n" +
"AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min at 0-3 min, 400 uL/min at 14 min, 480 uL/min at 16-19 min, 200 uL/min at 19.1-20 min\n" +
"AC$CHROMATOGRAPHY: NAPS_RTI 100\n" +
"AC$CHROMATOGRAPHY: RETENTION_TIME 6.2 min\n" +
"AC$CHROMATOGRAPHY: SOLVENT A 90:10 water:methanol with 0.01% formic acid and 5mM ammonium formate\n" +
"AC$CHROMATOGRAPHY: SOLVENT B methanol with 0.01% formic acid and 5mM ammonium formate\n" +
"MS$FOCUSED_ION: PRECURSOR_M/Z 410.3\n" +
"MS$FOCUSED_ION: PRECURSOR_TYPE [M+2H]2+\n" +
"PK$SPLASH: splash10-0002-0960000000-77302b0326a418630a84\n" +
"PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)\n" +
" 134.0594 C8H8NO+ 2 134.0600 -4.77\n" +
" 135.0618 C7[13]CH8NO+ 2 135.0632 10.37\n" +
" 140.016 C6H6NOS+ 1 140.0165 -3.22\n" +
"PK$NUM_PEAK: 100\n" +
"PK$PEAK: m/z int. rel.int.\n" +
" 84.1 12461 32\n" +
" 105.1 2208 6\n" +
" 107.1 2394 6\n" +
" 114.1 40390 105\n" +
" 115.1 2816 7\n" +
" 119.1 3122 8\n" +
" 121.1 2233 6\n" +
" 124.1 31739 82\n" +
" 125.1 2905 8\n" +
" 129.1 2850 7\n" +
" 131.1 49572 129\n" +
" 132.1 4865 13\n" +
" 133.1 81554 212\n" +
" 134.1 8725 23\n" +
" 141.1 1570 4\n" +
" 144.1 1940 5\n" +
" 145.1 41441 108\n" +
" 146.1 4421 11\n" +
" 147.1 5354 14\n" +
" 151.1 3257 8\n" +
" 154.1 1568 4\n" +
" 155.1 10003 26\n" +
" 156.1 6505 17\n" +
" 157.1 143020 372\n" +
" 158.1 17481 45\n" +
" 159.1 82905 215\n" +
" 160.1 11221 29\n" +
" 161.1 2347 6\n" +
" 167.1 2176 6\n" +
" 168.1 2768 7\n" +
" 169.1 46331 120\n" +
" 170.1 6508 17\n" +
" 171.1 134721 350\n" +
" 172.1 18235 47\n" +
" 173.1 3731 10\n" +
" 175.1 2015 5\n" +
" 179.1 1858 5\n" +
" 180.1 1535 4\n" +
" 181.1 10257 27\n" +
" 182.1 4717 12\n" +
" 183.1 41396 108\n" +
" 184.1 7101 18\n" +
" 185.1 6914 18\n" +
" 192.1 1409 4\n" +
" 193.1 6170 16\n" +
" 194.1 2234 6\n" +
" 195.1 14163 37\n" +
" 196.1 4474 12\n" +
" 197.1 15633 41\n" +
" 198.1 2557 7\n" +
" 199.1 1506 4\n" +
" 206.1 3117 8\n" +
" 207.1 10875 28\n" +
" 208.1 3128 8\n" +
" 209.1 8959 23\n" +
" 210.1 1778 5\n" +
" 211.1 19727 51\n" +
" 212.2 3417 9\n" +
" 219.1 2485 6\n" +
" 220.1 4278 11\n" +
" 221.1 13267 34\n" +
" 222.1 5170 13\n" +
" 223.1 4101 11\n" +
" 225.2 1653 4\n" +
" 233.1 6156 16\n" +
" 234.1 3148 8\n" +
" 235.2 13261 34\n" +
" 236.2 4846 13\n" +
" 237.2 4596 12\n" +
" 247.2 6331 16\n" +
" 248.2 6908 18\n" +
" 249.2 6605 17\n" +
" 251.2 2136 6\n" +
" 261.2 1339 3\n" +
" 262.2 16113 42\n" +
" 263.2 4055 11\n" +
" 265.2 1366 4\n" +
" 277.2 29461 77\n" +
" 278.2 6409 17\n" +
" 280.2 6501 17\n" +
" 281.2 8268 21\n" +
" 282.2 1857 5\n" +
" 295.2 384391 999\n" +
" 296.2 86672 225\n" +
" 297.2 10146 26\n" +
" 309.2 2642 7\n" +
" 319.2 3763 10\n" +
" 320.2 2207 6\n" +
" 333.2 3370 9\n" +
" 362.3 1851 5\n" +
" 363.3 1716 4\n" +
" 375.3 2380 6\n" +
" 376.3 1392 4\n" +
" 377.3 1755 5\n" +
" 392.3 23807 62\n" +
" 393.3 6937 18\n" +
" 396.3 2914 8\n" +
" 410.3 6059 16\n" +
" 411.3 1871 5\n" +
" 414.3 9233 24\n" +
"//";

/**
* Returns <code>true</code> if there is any suspicious character in <code>recordstring</code>.
*/
Expand Down Expand Up @@ -244,28 +94,58 @@ public static Record validate(String recordstring, String contributor, boolean s
return record;
}

public static void main(String[] arguments) throws Exception {
boolean haserror = false;
if (arguments.length==0) {
Record record = validate(recordstringExample, "");
if (record == null) logger.fatal("Error.");
else logger.trace(record.toString());
}
else {
System.out.println("Validating " + arguments.length + " files");
for (String filename : arguments) {
String recordstring = FileUtils.readFileToString(new File(filename), StandardCharsets.UTF_8);
hasNonStandardChars(recordstring);
Record record = validate(recordstring, "");
if (record == null) {
logger.error("error in " + filename);
haserror = true;
public static void main(String[] arguments) {
final Properties properties = new Properties();
try {
properties.load(ClassLoader.getSystemClassLoader().getResourceAsStream("project.properties"));
System.out.println("Validator version: " + properties.getProperty("version"));

if (arguments.length==0) {
System.out.println("usage: Validator <FILE|DIR> [<FILE|DIR> ...]");
System.exit(1);
}

// validate all files in arguments and all *.txt files in directories and subdirectories
// specified in arguments
List<File> recordfiles = new ArrayList<>();
for (String argument : arguments) {
File argumentf = new File(argument);
if (argumentf.isFile() && FilenameUtils.getExtension(argument).equals("txt")) {
recordfiles.add(argumentf);
}
else if (argumentf.isDirectory()) {
recordfiles.addAll(FileUtils.listFiles(argumentf, new String[] {"txt"}, true));
}
else {
logger.trace("validation passed for " + filename);
logger.warn("Argument " + argument + " could not be processed.");
}
}

logger.trace("Validating " + recordfiles.size() + " files");

AtomicBoolean haserror = new AtomicBoolean(false);
recordfiles.parallelStream().forEach(filename -> {
String recordstring;
Record record=null;
try {
recordstring = FileUtils.readFileToString(filename, StandardCharsets.UTF_8);
hasNonStandardChars(recordstring);
record = validate(recordstring, "");
if (record == null) {
logger.error("error in " + filename);
haserror.set(true);
}
else {
logger.trace("validation passed for " + filename);
}
} catch (IOException e) {
e.printStackTrace();
System.exit(1);
}
});
} catch (IOException e) {
e.printStackTrace();
System.exit(1);
}
if (haserror) System.exit(1);
}
}
1 change: 1 addition & 0 deletions MassBank-Project/MassBank-lib/src/main/resources-filtered/project.properties
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@@ -0,0 +1 @@
version=${project.version}
9 changes: 6 additions & 3 deletions MassBank-Project/MassBank-lib/src/main/resources/log4j2.xml
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@@ -1,14 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE xml>
<Configuration status="WARN">
<Appenders>
<Console name="Console" target="SYSTEM_OUT">
<!-- <PatternLayout -->
<!-- pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n" /> -->
<PatternLayout
pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n" />
pattern="%d{HH:mm:ss.SSS} %-5level %logger{36} - %msg%n" />
</Console>
</Appenders>
<Loggers>
<!-- <Logger name="massbank.Validator" level="trace"/> -->
<Root level="debug">
<!-- <Logger name="massbank.Validator" level="trace"/> -->
<Root level="error">
<AppenderRef ref="Console" />
</Root>
</Loggers>
Expand Down
3 changes: 1 addition & 2 deletions MassBank-Project/MassBank-lib/src/main/scripts/AddMetaData
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Expand Up @@ -4,7 +4,6 @@ JAVA_EXECUTABLE="`which java`"

DIST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/../" && pwd )"
LIB_DIR="$DIST_DIR/lib"
CONF_DIR="$DIST_DIR/conf"

$JAVA_EXECUTABLE -cp "$CONF_DIR:$LIB_DIR/*" \
$JAVA_EXECUTABLE -cp "$LIB_DIR/*" \
massbank.AddMetaData "$@"
3 changes: 1 addition & 2 deletions MassBank-Project/MassBank-lib/src/main/scripts/Inspector
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Expand Up @@ -4,7 +4,6 @@ JAVA_EXECUTABLE="`which java`"

DIST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/../" && pwd )"
LIB_DIR="$DIST_DIR/lib"
CONF_DIR="$DIST_DIR/conf"

$JAVA_EXECUTABLE -cp "$CONF_DIR:$LIB_DIR/*" \
$JAVA_EXECUTABLE -cp "$LIB_DIR/*" \
massbank.Inspector "$@"
3 changes: 1 addition & 2 deletions MassBank-Project/MassBank-lib/src/main/scripts/RefreshDatabase
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ JAVA_EXECUTABLE="`which java`"

DIST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/../" && pwd )"
LIB_DIR="$DIST_DIR/lib"
CONF_DIR="$DIST_DIR/conf"

$JAVA_EXECUTABLE -cp "$CONF_DIR:$LIB_DIR/*" \
$JAVA_EXECUTABLE -cp "$LIB_DIR/*" \
massbank.RefreshDatabase "$@"
3 changes: 1 addition & 2 deletions MassBank-Project/MassBank-lib/src/main/scripts/Validator
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Expand Up @@ -4,7 +4,6 @@ JAVA_EXECUTABLE="`which java`"

DIST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/../" && pwd )"
LIB_DIR="$DIST_DIR/lib"
CONF_DIR="$DIST_DIR/conf"

$JAVA_EXECUTABLE -cp "$CONF_DIR:$LIB_DIR/*" \
$JAVA_EXECUTABLE -cp "$LIB_DIR/*" \
massbank.Validator "$@"
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