@hbasaric, another clean up that needs to happen is the JavaDoc errors that pop up when compiling with Java 17. It is not urgent but it's rewarding work at the end of the day.
Here is a subset of errors:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:3.4.0:jar (attach-javadocs) on project org.bridgedb: MavenReportException: Error while generating Javadoc:
[ERROR] Exit code: 1 - Loading source files for package buildsystem...
[ERROR] Loading source files for package org.bridgedb...
[ERROR] Loading source files for package org.bridgedb.impl...
[ERROR] Loading source files for package org.bridgedb.resolvers...
[ERROR] Loading source files for package org.bridgedb.file...
[ERROR] Loading source files for package org.bridgedb.webservice...
[ERROR] Constructing Javadoc information...
[ERROR] Building index for all the packages and classes...
[ERROR] Standard Doclet version 17.0.3+7-Debian-1deb11u1
[ERROR] Building tree for all the packages and classes...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:54: error: reference not found
[ERROR] Definitions for common DataSources can be found in {@link org.bridgedb.bio.BioDataSource}.
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/package.html:19: warning: empty <p> tag
[ERROR] <p>
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/AbstractIDMapper.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/AbstractIDMapperCapabilities.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/AttributeMapper.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/resolvers/BioregistryResolver.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/IResolver.java:31: warning: no @param for xref
[ERROR] public String getURL(Xref xref);
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/BioregistryResolver.java:19: warning: no comment
[ERROR] public class BioregistryResolver implements IResolver {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/BioregistryResolver.java:25: warning: no comment
[ERROR] public static IResolver getInstance() {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/BridgeDb.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/DataSource.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:785: error: unknown tag: Since
[ERROR] * @Since Version 2.0.0
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:810: error: unknown tag: Since
[ERROR] * @Since Version 2.0.0
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:945: error: unknown tag: returns
[ERROR] * @returns the DataSource for a given urn base, or null if the base is invalid or unknown.
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:947: warning: no @return
[ERROR] public static DataSource getByMiriamBase(String base)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:960: error: unknown tag: returns
[ERROR] * @returns the DataSource for a given base, or null if the base is invalid or unknown.
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:962: warning: no @return
[ERROR] public static DataSource getByIdentiferOrgBase(String base) {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:978: error: unknown tag: returns
[ERROR] * @returns the compact identifier
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:980: warning: no @return
[ERROR] public String getCompactIdentifierPrefix() {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:60: warning: no comment
[ERROR] public static final String UNKOWN = "unknown";
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:816: warning: no comment
[ERROR] public static DataSource getByAlias(String alias)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:937: warning: no comment
[ERROR] public static DataSource getByCompactIdentifierPrefix(String prefix)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:186: warning: no comment
[ERROR] public String[] getCategories()
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:258: warning: no comment
[ERROR] public String getIdentifiersOrgUri(String id) {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:738: warning: no comment
[ERROR] public void registerAlias(String alias)
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/DataSource.Builder.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:615: warning: no description for @param
[ERROR] * @param alternative
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:637: error: @param name not found
[ERROR] * @param alternative
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:637: warning: no description for @param
[ERROR] * @param alternative
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:641: warning: no @param for description
[ERROR] public Builder description(String description){
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:586: warning: no comment
[ERROR] public Builder bioregistryPrefix(String prefix) {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:463: warning: no comment
[ERROR] public Builder categories (String categories)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:448: warning: no comment
[ERROR] public Builder categories (String[] categories)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:599: warning: no comment
[ERROR] public Builder compactIdentifierPrefix(String prefix) {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/DataSource.java:571: warning: no comment
[ERROR] public Builder miriamBase(String base){
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/DataSourcePatterns.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/Driver.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/resolvers/IdentifiersDotOrgResolver.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/IdentifiersDotOrgResolver.java:19: warning: no comment
[ERROR] public class IdentifiersDotOrgResolver implements IResolver {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/IdentifiersDotOrgResolver.java:25: warning: no comment
[ERROR] public static IResolver getInstance() {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/IDMapper.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/IDMapperCapabilities.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/IDMapperException.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/file/IDMapperFile.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMapperFile.java:39: warning: no comment
[ERROR] protected final IDMapperFileCapabilities cap;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMapperFile.java:40: warning: no comment
[ERROR] protected final IDMappingReader reader;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMapperFile.java:176: warning: no comment
[ERROR] protected IDMappingReader getIDMappingReader() {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/IDMapperStack.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/IDMapperStack.java:490: error: malformed HTML
[ERROR] * @param index in the range 0 <= index < getSize()
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/IDMapperStack.java:490: error: malformed HTML
[ERROR] * @param index in the range 0 <= index < getSize()
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/IDMapperStack.java:616: warning: no @return
[ERROR] public List<IDMapper> getMappers()
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/file/IDMapperText.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/webservice/IDMapperWebservice.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/file/IDMappingReader.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/file/IDMappingReaderFromDelimitedReader.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromDelimitedReader.java:47: warning: no comment
[ERROR] protected boolean dsValid, idMappingValid;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromDelimitedReader.java:47: warning: no comment
[ERROR] protected boolean dsValid, idMappingValid;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromDelimitedReader.java:45: warning: no comment
[ERROR] protected String regExDataSourceDelimiter;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromDelimitedReader.java:46: warning: no comment
[ERROR] protected String regExIDDelimiter;
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/file/IDMappingReaderFromText.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromText.java:37: warning: no comment
[ERROR] protected final URL url;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/file/IDMappingReaderFromText.java:144: warning: no comment
[ERROR] protected static String strs2regex(final char[] chs) {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/impl/InternalUtils.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:114: error: semicolon missing
[ERROR] * expected to have a formatting like @code{base?arg1=val&arg2=val}.
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:321: warning: no @param for is
[ERROR] public static void readXmlConfig(InputSource is) throws ParserConfigurationException, SAXException, IOException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:321: warning: no @throws for javax.xml.parsers.ParserConfigurationException
[ERROR] public static void readXmlConfig(InputSource is) throws ParserConfigurationException, SAXException, IOException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:321: warning: no @throws for org.xml.sax.SAXException
[ERROR] public static void readXmlConfig(InputSource is) throws ParserConfigurationException, SAXException, IOException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:321: warning: no @throws for java.io.IOException
[ERROR] public static void readXmlConfig(InputSource is) throws ParserConfigurationException, SAXException, IOException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/InternalUtils.java:166: warning: no comment
[ERROR] public static InputStream getInputStream(String source) throws IOException {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/resolvers/IResolver.html...
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/buildsystem/Measure.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/buildsystem/Measure.java:10: warning: no comment
[ERROR] public class Measure
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/buildsystem/Measure.java:14: warning: no comment
[ERROR] public Measure(String fileName)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/buildsystem/Measure.java:19: warning: no comment
[ERROR] public void add(String key, String value, String unit)
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/resolvers/Names2ThingsResolver.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/Names2ThingsResolver.java:19: warning: no comment
[ERROR] public class Names2ThingsResolver implements IResolver {
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/resolvers/Names2ThingsResolver.java:25: warning: no comment
[ERROR] public static IResolver getInstance() {
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/impl/TransitiveGraph.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:45: warning: no @param for gdbs
[ERROR] public TransitiveGraph(List<IDMapper> gdbs) throws IDMapperException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:45: warning: no @throws for org.bridgedb.IDMapperException
[ERROR] public TransitiveGraph(List<IDMapper> gdbs) throws IDMapperException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:126: warning: no @param for map
[ERROR] public void printMap(Map<DataSource, Set<Path> > map)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:335: warning: no comment
[ERROR] public boolean isTransitiveMappingSupported(DataSource src, DataSource tgt) throws IDMapperException
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:349: warning: no comment
[ERROR] public Set<Xref> mapIDtransitiveTargetted(Xref ref, Set<DataSource> dsFilter)
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/impl/TransitiveGraph.java:373: warning: no comment
[ERROR] public Set<Xref> mapIDtransitiveUntargetted(Xref ref) throws IDMapperException
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/Xref.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/Xref.java:167: warning: no description for @param
[ERROR] * @param urn
[ERROR] ^
[ERROR] Generating /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/target/apidocs/org/bridgedb/XrefIterator.html...
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:8: warning: no @param for ds
[ERROR] Iterable<Xref> getIterator(DataSource ds) throws IDMapperException;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:8: warning: no @return
[ERROR] Iterable<Xref> getIterator(DataSource ds) throws IDMapperException;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:8: warning: no @throws for org.bridgedb.IDMapperException
[ERROR] Iterable<Xref> getIterator(DataSource ds) throws IDMapperException;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:13: warning: no @return
[ERROR] Iterable<Xref> getIterator() throws IDMapperException;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:13: warning: no @throws for org.bridgedb.IDMapperException
[ERROR] Iterable<Xref> getIterator() throws IDMapperException;
[ERROR] ^
[ERROR] /home/egonw/var/Projects/hub/bridgedb/org.bridgedb/src/main/java/org/bridgedb/XrefIterator.java:3: warning: no comment
[ERROR] public interface XrefIterator {
[ERROR] ^
hbasaric
commented
2 years ago
@hbasaric, another clean up that needs to happen is the JavaDoc errors that pop up when compiling with Java 17. It is not urgent but it's rewarding work at the end of the day.
Here is a subset of errors: