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Commit ed4973ba authored by Piotr Gawron's avatar Piotr Gawron
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dependency conflicts resolved

parent b5de2ac6
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1 merge request!782Resolve "Replace deprecated APIs"
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annotation/pom.xml
+ 26
− 6
View file @ ed4973ba
......@@ -143,10 +143,6 @@
<groupId>org.glassfish.jaxb</groupId>
<artifactId>txw2</artifactId>
</exclusion>
<exclusion>
<groupId>org.jvnet.staxex</groupId>
<artifactId>stax-ex</artifactId>
</exclusion>
</exclusions>
</dependency>
......@@ -215,20 +211,44 @@
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<artifactId>poi</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<!-- mockito used for testing -->
<dependency>
<groupId>org.mockito</groupId>
......
annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
+ 9
− 8
View file @ ed4973ba
......@@ -19,16 +19,17 @@ import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.*;
import org.apache.poi.poifs.filesystem.NPOIFSFileSystem;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.poi.poifs.filesystem.NotOLE2FileException;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellType;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.ss.usermodel.WorkbookFactory;
import org.apache.poi.ss.usermodel.Row.MissingCellPolicy;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
......@@ -269,7 +270,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
//if downloaded file is corrupted download it again
try {
NPOIFSFileSystem element = new NPOIFSFileSystem(new ByteArrayInputStream(sourceInputStream.toByteArray()));
POIFSFileSystem element = new POIFSFileSystem(new ByteArrayInputStream(sourceInputStream.toByteArray()));
element.close();
} catch (NotOLE2FileException e) {
bigFileCache.removeFile(URL_SOURCE_DATABASE);
......@@ -324,9 +325,9 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
Map<String, MiRNA> miRNAs = new HashMap<>();
List<MiRNA> result = new ArrayList<>();
NPOIFSFileSystem fileInputStream = null;
POIFSFileSystem fileInputStream = null;
try {
fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
fileInputStream = new POIFSFileSystem(getSourceInputStream());
Workbook workbook = WorkbookFactory.create(fileInputStream);
Sheet sheet = workbook.getSheetAt(0);
Iterator<Row> rows = sheet.rowIterator();
......@@ -499,11 +500,11 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
}
if (targets.size() > 0) {
NPOIFSFileSystem fileInputStream = null;
POIFSFileSystem fileInputStream = null;
String value = null;
try {
fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
fileInputStream = new POIFSFileSystem(getSourceInputStream());
Workbook workbook = WorkbookFactory.create(fileInputStream);
Sheet sheet = workbook.getSheetAt(0);
Iterator<Row> rows = sheet.rowIterator();
......
commons/pom.xml
+ 7
− 0
View file @ ed4973ba
......@@ -34,7 +34,14 @@
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${apache.commons-text.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
......
converter-sbml/pom.xml
+ 12
− 0
View file @ ed4973ba
......@@ -162,6 +162,18 @@
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${apache.commons-text.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${apache.commons-lang3.version}</version>
</dependency>
<dependency>
......
pom.xml
+ 4
− 2
View file @ ed4973ba
......@@ -28,8 +28,10 @@
<apache.httpcomponents.version>4.5.8</apache.httpcomponents.version>
<apache.httpcomponents-core.version>4.4.11</apache.httpcomponents-core.version>
<!-- version 4.x has conflict on dependencies with jsbml 1.4 -->
<apache.poi.version>3.16</apache.poi.version>
<commons-codec.version>1.11</commons-codec.version>
<mockito.version>2.27.0</mockito.version>
<springframework.version>4.3.19.RELEASE</springframework.version>
......@@ -55,7 +57,7 @@
<hibernate.version>5.4.2.Final</hibernate.version>
<jboss-logging.version>3.4.0.Final</jboss-logging.version>
<byte-buddy.version>1.9.12</byte-buddy.version>
<byte-buddy.version>1.9.10</byte-buddy.version>
<pathvisio.version>3.2.0</pathvisio.version>
......
service/pom.xml
+ 20
− 2
View file @ ed4973ba
......@@ -71,7 +71,7 @@
<version>1.0</version>
</dependency>
<!-- Log4J2-->
<!-- Log4J2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
......@@ -117,12 +117,30 @@
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>${apache.poi.version}</version>
</dependency>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.unboundid/unboundid-ldapsdk -->
<dependency>
......
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