From f2c83f25321acf41c46bcd83cfe6ba679ce62b3f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Wed, 19 Feb 2025 08:56:35 +0100
Subject: [PATCH] checkstyle issues
---
.../annotation/services/MiriamConnectorImpl.java | 10 ++++------
.../converter/model/sbgnml/SbgnmlXmlExporterTest.java | 2 +-
.../main/java/lcsb/mapviewer/model/map/MiriamType.java | 5 ++---
.../wikipathway/model/biopax/BiopaxFactory.java | 5 ++---
4 files changed, 9 insertions(+), 13 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
index f60eb7ad87..fcf345ef25 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
@@ -83,8 +83,8 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn
public String getUrlString(final MiriamData miriamData) {
if (miriamData.getDataType() == null) {
throw new InvalidArgumentException("Data type cannot be empty.");
- } else if (miriamData.getDataType().getUris().size() == 0) {
- throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
+ } else if (miriamData.getDataType().getUris().isEmpty()) {
+ throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retrieved.");
}
String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
String result = getCacheValue(query);
@@ -162,8 +162,7 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn
* @param string identifier in the format NAME:IDENTIFIER. Where NAME is the name
* from {@link MiriamType#getCommonName()} and IDENTIFIER is resource
* identifier.
- * @return <code>true</code> if identifier can be transformed into
- * {@link MiriamData}
+ * @return <code>true</code> if identifier can be transformed into {@link MiriamData}
*/
@Override
public boolean isValidIdentifier(final String string) {
@@ -179,8 +178,7 @@ public class MiriamConnectorImpl extends CachableInterface implements MiriamConn
* Checks if {@link MiriamType} is valid.
*
* @param type type to be checked
- * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code>
- * otherwise
+ * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code> otherwise
*/
@Override
public boolean isValidMiriamType(final MiriamType type) {
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 2b34837e9d..34655cfe5d 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -172,7 +172,7 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
assertTrue(SbgnUtil.isValid(tempFile));
}
- isDescribedBy
+
@Test
public void importExportZ() throws Exception {
Compartment compartment = createCompartment();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 9d9bb94a7d..ce6428dd06 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -6700,7 +6700,7 @@ public enum MiriamType {
* @param uris {@link #uris}
* @param classes {@link #validClass}
* @param registryIdentifier {@link #registryIdentifier}
- * @param requiredClasses {@link #requiredClasses}
+ * @param requiredClasses {@link #requiredClass}
*/
MiriamType(final String commonName, final String dbHomePage, final String[] uris, final Class<?>[] classes, final String registryIdentifier,
final Class<?>[] requiredClasses, final String namespace, final String exampleIdentifier) {
@@ -6772,8 +6772,7 @@ public enum MiriamType {
* @param generalIdentifier identifier in the format NAME:IDENTIFIER. Where NAME is the name
* from {@link MiriamType#commonName} and IDENTIFIER is resource
* identifier.
- * @return {@link MiriamData} representing generalIdentifier, when identifier is
- * invalid InvalidArgumentException is thrown
+ * @return {@link MiriamData} representing generalIdentifier, when identifier is invalid InvalidArgumentException is thrown
*/
public static MiriamData getMiriamDataFromIdentifier(final String generalIdentifier) {
int index = generalIdentifier.indexOf(":");
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
index 6b289f3310..7702778bf1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java
@@ -29,7 +29,7 @@ public class BiopaxFactory {
*/
public MiriamData createMiriamData(final BiopaxPublication publication) {
if ("PubMed".equals(publication.getDb())) {
- if (publication.getId() == null || publication.getId().equals("")) {
+ if (publication.getId() == null || publication.getId().isEmpty()) {
return null;
} else {
if (StringUtils.isNumeric(publication.getId().trim())) {
@@ -50,8 +50,7 @@ public class BiopaxFactory {
* @param biopaxData {@link BiopaxData} where annotations are stored
* @param biopaxReference list of references (to data in {@link BiopaxData}) that we want to
* convert into {@link MiriamData}
- * @return list of {@link MiriamData} that are referenced in {@link BiopaxData}
- * with identifier given in biopaxReference.
+ * @return list of {@link MiriamData} that are referenced in {@link BiopaxData} with identifier given in biopaxReference.
*/
public Collection<MiriamData> getMiriamData(final BiopaxData biopaxData, final Collection<String> biopaxReference) {
List<MiriamData> result = new ArrayList<>();
--
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