EDIT Project Management: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852024-01-24T10:17:25ZEDIT Project Management
Redmine EDIT - bug #10461 (Closed): Duplicate user name not handled correctly during registrationhttps://dev.e-taxonomy.eu/redmine/issues/104612024-01-24T10:17:25ZAndreas Müller
<pre>java.util.concurrent.ExecutionException: eu.etaxonomy.cdm.api.service.security.AccountSelfManagementException: This user name is already being used by someone else.
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at eu.etaxonomy.cdm.vaadin.view.AccountRegistrationPresenter.onRegisterAccountEvent(AccountRegistrationPresenter.java:108)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.vaadin.spring.events.internal.MethodListenerWrapper.publish(MethodListenerWrapper.java:78)
at org.vaadin.spring.events.internal.ListenerCollection.publish(ListenerCollection.java:167)
at org.vaadin.spring.events.internal.ScopedEventBus.publish(ScopedEventBus.java:116)
at org.vaadin.spring.events.internal.ScopedEventBus.publish(ScopedEventBus.java:109)
at eu.etaxonomy.cdm.vaadin.view.AccountRegistrationViewBean.lambda$initContent$61446b05$1(AccountRegistrationViewBean.java:85)
at sun.reflect.GeneratedMethodAccessor1348.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:510)
at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:200)
at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:163)
at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:1015)
at com.vaadin.ui.Button.fireClick(Button.java:377)
at com.vaadin.ui.Button$1.click(Button.java:54)
at sun.reflect.GeneratedMethodAccessor1347.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:158)
at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:119)
at com.vaadin.server.communication.ServerRpcHandler.handleInvocation(ServerRpcHandler.java:437)
at com.vaadin.server.communication.ServerRpcHandler.handleInvocations(ServerRpcHandler.java:402)
at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:273)
at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:90)
at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41)
at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1435)
at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:380)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:755)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1617)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)
at ...
Caused by: eu.etaxonomy.cdm.api.service.security.AccountSelfManagementException: This user name is already being used by someone else.
at eu.etaxonomy.cdm.api.service.security.AccountRegistrationService.createUserAccount(AccountRegistrationService.java:113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
</pre> EDIT - feature request #10459 (Closed): Add taxon-specimen association filter for taxon pageshttps://dev.e-taxonomy.eu/redmine/issues/104592024-01-20T17:30:34ZAndreas Müller
<p>The webservices have been adapted in <a class="issue tracker-5 status-3 priority-13 priority-high13" title="feature request: Make taxon-specimen relation for taxon pages configurable in webservice (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/10400">#10400</a>. The filter parameter still needs to be implemented in dataportal.</p>
<p>Discuss, in which format the parameter should be passed to the webservice.</p>
EDIT - feature request #10448 (Closed): Implement WFO Backbone export in TaxEditorhttps://dev.e-taxonomy.eu/redmine/issues/104482024-01-10T10:05:18ZAndreas Müller
<p>see <a class="issue tracker-5 status-3 priority-10 priority-lowest" title="feature request: WFO Backbone export (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/10446">#10446</a> for details</p>
EDIT - bug #10441 (Closed): LIE in logfiles for DefinedTermBase.includeshttps://dev.e-taxonomy.eu/redmine/issues/104412023-12-11T10:00:04ZAndreas Müller
<p>The logfiles (at least for eFloraMex, but also for our servers) are full of LIE loggs for DefinedTermBase.includes. We need to find out why this happens, if it is critical and/or how to avoid this exception being thrown and logged.</p>
<pre>Caused by: org.hibernate.LazyInitializationException: failed to lazily initialize a collection of role: eu.etaxonomy.cdm.model.term.DefinedTermBase.includes, could not initialize proxy - no Session
at org.hibernate.collection.internal.AbstractPersistentCollection.throwLazyInitializationException(AbstractPersistentCollection.java:606)
at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:218)
at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:585)
at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:149)
at org.hibernate.collection.internal.PersistentSet.iterator(PersistentSet.java:188)
at eu.etaxonomy.cdm.model.term.DefinedTermBase.getIncludes(DefinedTermBase.java:303)
</pre> EDIT - feature request #10436 (Closed): Make state modifiers invisible if no recommended term col...https://dev.e-taxonomy.eu/redmine/issues/104362023-12-05T11:29:56ZAndreas Müller
<p>... for the given future.</p>
<p>Only show the modifiers if either a recommended term collection is available for the feature or if the data already has modifiers.</p>
<p>Implement in details view and in matrix dialogue.</p>
EDIT - bug #10397 (Closed): Moving a specimen imported via ABCD to a new taxon does not show the ...https://dev.e-taxonomy.eu/redmine/issues/103972023-09-19T10:09:50ZAndreas Müller
<p>This is because ABCD imports determinations/identifications. Also moving a specimen to a new taxon does not automatically create a new determination. Also taxon pages do not show (at least in table view) the associated (via individualsAssociation) specimen if it has a determination (to another name/taxon).</p>
<p>This can be handled by various alternatives:</p>
<ul>
<li><del>make import of determinations configurable in ABDC import</del>(<a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Make it configurable in ABCD import if identifications should be imported as determinations or in... (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10398">#10398</a>)</li>
<li>allow (semi-)automated creation of new current determinations when a specimen is moved to another taxon (in TaxEditor)</li>
<li><del>disable filtering of individuals association if specimen has another determination</del> (see also note-5 and <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: Compressed table does not show derivates anymore (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10137">#10137</a>)</li>
<li><del>allow configuration for dataportal which taxon-specimen relationship types should be shown on taxon pages</del> (<a class="issue tracker-5 status-3 priority-13 priority-high13" title="feature request: Make taxon-specimen relation for taxon pages configurable in webservice (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/10400">#10400</a>) </li>
<li>...?</li>
</ul>
EDIT - feature request #10367 (Closed): Add citationMicroReference to description of sources in R...https://dev.e-taxonomy.eu/redmine/issues/103672023-07-07T09:23:26ZAndreas Müller
<p>This is helpful when e.g. cleaning up references used as nomenclatural references</p>
EDIT - feature request #10336 (Closed): Allow defining the "et al." position in name formatters f...https://dev.e-taxonomy.eu/redmine/issues/103362023-05-28T13:23:16ZAndreas MüllerEDIT - task #10236 (Rejected): Import data from caucasus DB to E+Mhttps://dev.e-taxonomy.eu/redmine/issues/102362023-01-25T17:48:19ZAndreas Müller
<p>for details see <a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Create database for Caucasus distribution editing (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/7921">#7921</a></p>
<p>Maybe not needed. Wait for final decision.</p>
EDIT - task #10222 (Closed): Use DTOs for portal taxon page - first implementation for E+Mhttps://dev.e-taxonomy.eu/redmine/issues/102222023-01-09T18:31:06ZAndreas Müller
<p>... to improve performance and simplify dataportal rendering. If possible formatting should take place server side.</p>
<p>Open issues: how to pass configuration?</p>
<ul>
<li>huge number of parameters</li>
<li>json configuration</li>
</ul>
<p>Discussion about data, contained in DTO(s): </p>
<ul>
<li>taxonName: <del>should everything be handled in typedLabel or in own DTO?</del> => typedLabel or taggedText should be enough
<ul>
<li><del>if we have an own dto, we can add rank and rankorder index, but maybe we only need the rank string if all ordering is done serverside</del> => ordering is done serverside</li>
<li><del>nomenclatural source is missing</del></li>
<li><del>to create a link to the name page the uuid is needed.</del> => added</li>
</ul></li>
<li><del>name relationships</del> => implemented -> <del>ruleConsidered is missing</del> => added</li>
<li><del>name facts</del> => added</li>
<li><del>protologue links</del> => added</li>
<li><del>currently the facts are merged into the feature tree (see _mergeFeatureTreeDescriptions in cdm_api.module of the dataportal code), we should handle this similar when creating the dto</del> => implemented, see <a href="#note-27">#note-27</a></li>
<li><del>the distribution facts are handled separately in dataportal, maybe we should handle them in a separate item in the dto as well.</del></li>
<li><del>error in distribution string (<a href="#note-52">#note-52</a>)</del> => fixed when passing the statusOrderPreference param to the service</li>
<li><del>include description sources in description element sources</del></li>
<li><del>fallback areas not yet handled correctly in long text distributions, e.g. Caucasia (Ab+...) in Crepis</del> => seems to be fixed in the meanwhile</li>
<li><del>IUCN status missing in DTO (for A. alba)</del> => seems to be fixed in the meanwhile</li>
</ul>
<p>Issues on portal side:</p>
<ul>
<li>bibliographie
<ul>
<li><del>links in bibliographie (<a href="https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/newtaxon/6a8e85bd-5e52-4ae2-9444-99128c87a672">https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/newtaxon/6a8e85bd-5e52-4ae2-9444-99128c87a672</a>, Mitarbeiter 2013: Florenliste von Deutschland - Gefäßpflanzen, Version 5 (July 2013) – <a href="http://www.kp-buttler.de">http://www.kp-buttler.de</a>)</del></li>
<li><del>name used in source is missing (Andreev, N. , Ančev, M. , Kožuharov, S. I. , Markova, M. , Peev, D. & Petrova, A. 1992: Opredelitel na visšite rastenija v Bălgarija <strong>(as Abies alba Mill. subsp. alba)</strong> )</del></li>
</ul></li>
<li><del>breadcrumbs do not work</del></li>
<li><del>open classification at current taxon position does not work</del></li>
<li><del>namerelationships (Abies nobilis A. Dietr., Fl. Berlin: 793. 1824, nom. illeg. [is earlier homonym of Abies nobilis (D. Don) Lindl. 1833] in synonymy of Abies alba)</del></li>
<li><del>adapt portal code that the default feature tree does not has a default uuid.</del></li>
<li><del>name facts</del></li>
<li><del>add setting to switch between dto usage and standard pages.</del></li>
<li><del>unnecessary additional webservice calls</del></li>
<li><del>combining misapplied name records which refer to the same name (example in Abies alba)</del>
<ul>
<li><del>open new issue: biblio footnote for second sensu reference</del></li>
</ul></li>
<li>IUCN "distributions" not shown correctly</li>
<li><del>correct handling of textual distributions</del></li>
<li><del>annotatins on names: <a href="https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/taxon/a17ab06c-07ba-4743-9851-ce692e15f91b">https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/taxon/a17ab06c-07ba-4743-9851-ce692e15f91b</a> (but this is the only one in E+M)</del></li>
</ul>
<p>issues not relevant for E+M handled in <a class="issue tracker-5 status-2 priority-10 priority-lowest" title="feature request: Use DTOs for portal taxon page (cont.) (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/10322">#10322</a></p>
<p><a href="https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/newtaxon/6a8e85bd-5e52-4ae2-9444-99128c87a672">https://test.e-taxonomy.eu/dataportal/preview/euromed/cdm_dataportal/newtaxon/6a8e85bd-5e52-4ae2-9444-99128c87a672</a> (Abies alba)</p>
EDIT - task #9359 (Closed): Update cdmlib, taxeditor, cdmserver etc. dependencieshttps://dev.e-taxonomy.eu/redmine/issues/93592020-12-18T22:17:24ZAndreas Müller
<p>A lot of version updates and updates to how dependencies are handled in TaxEditor has been done already in <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Update cdmlib and taxeditor dependencies (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9204">#9204</a>.</p>
<p>However, further cleanup and update is needed.</p>
<pre>mvn versions:display-dependency-updates
mvn dependency:tree (better use "Dependency Hierarchy" view in eclipse)
mvn dependency:tree -Dscope=compile
mvn org.apache.maven.plugins:maven-dependency-plugin:2.10:tree -Dverbose=true (verbose flag has been removed in 3.0 (https://maven.apache.org/plugins/maven-dependency-plugin/examples/resolving-conflicts-using-the-dependency-tree.html)
mvn dependency:analyze
mvn versions:display-plugin-updates (upgrade required maven version from time to time!)
* also try https://github.com/basepom/duplicate-finder-maven-plugin
* for checking newer versions: https://javalibs.com/artifact/xpp3/xpp3 (more info then in maven repo)
</pre>
<p>also all other maven projects (CDM Server, cdm-vaadin (<a class="issue tracker-6 status-1 priority-11 priority-default" title="task: Upgrade vaadin to latest version (New)" href="https://dev.e-taxonomy.eu/redmine/issues/9955">#9955</a>, <a class="issue tracker-6 status-2 priority-10 priority-lowest" title="task: updadte vaadin to latets 7.* version (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/9837">#9837</a>), webapp, utis(2/3x) need dependency updates</p>
<p>TODO:</p>
<ul>
<li>spring</li>
<li><del>lucene</del> (<a class="issue tracker-6 status-5 priority-12 priority-high14 closed behind-schedule" title="task: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5 (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10067">#10067</a>)</li>
<li>others</li>
<li>remove cdmlib-persistence from taxeditor dependencies (also removes hibernate dependencies) (<a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Move cdmlib-print and cdmib-remote to taxeditor.printpublisher (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9208">#9208</a>, <a class="issue tracker-6 status-5 priority-12 priority-high14 closed behind-schedule" title="task: Cleanup dependencies in TaxEditor (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10009">#10009</a>, ...)</li>
<li><del>upgrade to hibernate</del> >5.1 (<a class="issue tracker-6 status-5 priority-12 priority-high14 closed behind-schedule" title="task: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5 (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10067">#10067</a>)</li>
<li>hibernate-validation ( <del>also move to new artefact org.hibernate.validator</del> )</li>
<li><del>remove apache-log4j-extras from taxeditor</del> <a class="issue tracker-6 status-5 priority-12 priority-high14 closed" title="task: Remove apache-log4j-extras from TaxEditor dependencies (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9205">#9205</a></li>
<li>update maven-compiler-plugin to 3.x in cdmlib <a class="issue tracker-4 status-1 priority-12 priority-high14" title="bug: Upgrade maven compiler plugin to latest version (New)" href="https://dev.e-taxonomy.eu/redmine/issues/6407">#6407</a>/#9919</li>
<li>update maven-resources-plugin to 3.2.0 in cdmlib-remote (see comment in pom)</li>
<li>jgitflow (<a class="issue tracker-6 status-1 priority-11 priority-default" title="task: Update or remove jgitflow (New)" href="https://dev.e-taxonomy.eu/redmine/issues/9946">#9946</a>)</li>
<li>Vaadin needs to be migrated: free support for V8 is over (<a href="https://vaadin.com/blog/free-vaadin-8-support-is-over.-what-happens-next">https://vaadin.com/blog/free-vaadin-8-support-is-over.-what-happens-next</a>)</li>
<li>updated jboss-logging to 3.5.0.Final once we use java11</li>
<li>check new group-id com.opencsv for OpenCSV</li>
</ul>
<p>===</p>
<p>Open issues from older tickets:</p>
<p>#3403: Update remaining libraries:</p>
<ul>
<li><del>Try to remove springmodules dependency in remote and remote-web-app and maybe also in vaadin</del> : <a class="issue tracker-6 status-2 priority-12 priority-high14" title="task: replace spring-modules-cache by up to date implementation (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/3408">#3408</a>, <a class="issue tracker-6 status-1 priority-12 priority-high14" title="task: upgrade ehcache to 3.x (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10077">#10077</a> </li>
<li>Try to remove json-lib (and dependent xom, xmlParserAPIs) dependency and replace by jackson: <a class="issue tracker-6 status-1 priority-12 priority-high14 child parent" title="task: consider using jackson as json library (New)" href="https://dev.e-taxonomy.eu/redmine/issues/4009">#4009</a></li>
<li><del>Don't forget to update dependencies in Taxonomic Editor and CDM Server (e.g. <a href="http://dev.e-taxonomy.eu/trac/changeset/17582/trunk/cdm-server/pom.xml?old=17396&old_path=trunk%2Fcdm-server%2Fpom.xml">http://dev.e-taxonomy.eu/trac/changeset/17582/trunk/cdm-server/pom.xml?old=17396&old_path=trunk%2Fcdm-server%2Fpom.xml</a>)</del></li>
</ul>
<p>#3344: Migrate to hibernate 4</p>
<ul>
<li><del>check if exclusion in parent.pom for hibernate-search-engine is still needed</del> => has been removed in the meanwhile</li>
<li>check all applicationContexts.xml (xxx-test.xml) for redundant data</li>
<li>check preliminary hardcoded type in CdmEntityDaoBase.addOrder
<ul>
<li>AK: Ich denke das können wir vorerst mal so lassen, da ohnehin fast alles als String indiziert ist. Mit dem neuen hibernate search könnte da nun anders sein. Das würde dann eventuell id und date betreffen. Diese Freetext Methoden auf dao ebene werden bisher ohnehin nicht verwendet insofern besteht eh keine gefahr.</li>
</ul></li>
<li><del>remove deprecated new FlatXmlDataSet by DataSetBuilder</del> -> not sure what is meant here, maybe fixed already, I can't find a deprecated FlatXmlDataSet</li>
<li>uncomment _c3p0ConnectionTest in src/test/resource/cp30-config.xml and remove this file in test (still exists in main)</li>
<li>check all errors when running in commandline (e.g. all locks on index updating and others) - index locking problem solved r17458</li>
<li>check @Ignore necessary for all tests (especially in service layer)</li>
</ul>
<p>#2031 Update Hibernate to latest stable 4.1.1:</p>
<ul>
<li><del>All open issues in ticket, kept open for now, including OrderedColumn ticket</del> (see <a class="issue tracker-6 status-5 priority-12 priority-high14 closed behind-schedule" title="task: Using @OrderColumn does not work in trees (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/3722">#3722</a>) => ticket closed in the meanwhile</li>
</ul>
<p><a class="issue tracker-5 status-5 priority-11 priority-default closed parent" title="feature request: Other dependencies to be updated (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/4716">#4716</a> Other dependencies to be updated</p>
<ul>
<li>remove and solve ignore from DescriptionServiceImplTest.testMoveDescriptionElementsToTaxon => see comment <a class="issue tracker-5 status-5 priority-11 priority-default closed parent" title="feature request: Other dependencies to be updated (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/4716#note-6">#4716#note-6</a></li>
<li>AK: fix hibernate search related issues
<ul>
<li>8096b11 : IndexDocValue relates issues solved, indexing now without exceptions, most tests in TaxonServiceSearchTest successful</li>
<li>remove <code>Index annotations from abstract classes, hibernate search seems not capable of indexing polymorph classes. This will remove the @HSEARCH000044</code> warings.</li>
</ul></li>
<li><p>AK: use the encrypto Passwordencoder in UserService instead of the deprecated one</p></li>
<li><p>move remoting-services.xml and httpInvokerServices.xml to remoting</p></li>
<li><p>try to remove exclusions where possible</p></li>
<li><p>check if the postcommit handler were set correctly in CdmPostDataChangeObservableListener and ValidationEventListenerBase</p></li>
<li><p>fix EntityValidationCrudJdbcImplTest and remove ignore</p></li>
<li><p>move TableGeneratorGlobalOverride back to cdmlib-test (see r27338)</p></li>
<li><p>remove dependsOn=tableGeneratorGlobalOverride from sessionFactory in persistence.xml and security_base.xml in production mode. It should be used only for test. </p></li>
<li><p>find a solution for dbunitModul to load datasets also from jars and other packages to avoid duplication of standard dataset files (TODO create ticket with detailed information)</p></li>
</ul>
<p>TODO</p>
<ul>
<li><p>aspectj-main anttask in model-pom still uses org.springframework.aspects and not sring-aspects (?) and aspectjtools version 1.7.1 => moved to #4608 if still open</p></li>
<li><p>we may concider removing commons-dbcp.commons-dbcp by org.apache.commons.commons-dbcp2 (maybe only used by unitils-database)</p></li>
<li><p>AK: what is with json-lib, <del>why does it have [classifier]jdk15[/classifier] and is the dependency net.sf.json-lib:json-lib:jar:jdk15:2.4 still required</del> => see <a class="issue tracker-6 status-6 priority-12 priority-high14 closed" title="task: remove jdk15 classifier from json-lib (Rejected)" href="https://dev.e-taxonomy.eu/redmine/issues/9887">#9887</a></p></li>
<li><p>do we want to move xpp3.xpp3 (1.1.4c) to org.ogce.xpp3 (1.1.6) ?</p></li>
<li><p>do we want to move xom.xom (1.2.5) to com.io7m.xom.xom (1.2.10) ? Already upgraded from 1.0 to 1.2.5</p></li>
<li><p><del>do we still need hibernate-parent (last version was 3.6.)?</del> => can't find this anymore, probably removed some time ago</p></li>
<li><p>decide which oracle driver to use</p></li>
<li><p><del>check if usertype.jodatime has been replaced by usertype.core</del> => yes, and changed in pom with b82005b408a86 (<a class="issue tracker-6 status-5 priority-12 priority-high14 closed behind-schedule" title="task: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5 (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10067">#10067</a>)</p></li>
<li><p><del>check how to upgrade to jena-tdb 3.0.0 (also check if commonsRDF is an alternative: <a href="https://commonsrdf.incubator.apache.org/">https://commonsrdf.incubator.apache.org/</a> )</del> => new ticket <a class="issue tracker-6 status-1 priority-11 priority-default" title="task: Upgrade jena dependency (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10125">#10125</a></p></li>
<li><p><del>resolve those spring configuration files which still do have a spring-beans-3.0.xsd schema location</del> => all changed to spring-beans-4.3.xsd some time ago</p></li>
<li><p><del>remove apache snapshot repository (for jena) and others</del> => removed JBoss and apache incubating repos, maybe still open "OSGeo Repository" (<a class="issue tracker-6 status-1 priority-10 priority-lowest" title="task: Updates, upgrades and cleanup 2023 (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10055">#10055</a>)</p></li>
<li><p><del>check if we can upgrade hibernate tooling with dependencies to hibernate 3.2.4 in persistence pom (tooling 5 is not yet released)</del> => seems to be fixed in the meanwhile</p></li>
<li><p><del>Check if SpringModule dependencies can be fully removed (it is only used in AbstractOaiPmhController for Caching, this could probably handled by other caching frameworks like EhCacheCache from spring-context-support) .</del> <a class="issue tracker-6 status-2 priority-12 priority-high14" title="task: replace spring-modules-cache by up to date implementation (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/3408">#3408</a></p></li>
<li><p>we may want to further normalize spring config files: #5380</p></li>
<li><p>check if TaxonNodeByNameComparator is needed as spring bean as it is currently the case</p></li>
<li><p>Try to fix the HHH90000003 warnings (thrown in org.hibernate.boot.model.source.internal.hbm.ModelBinder line 2416, probably related to hibernate-envers, can be switched off by log4j.logger.org.hibernate.orm.deprecation=error) (related but not <a class="issue tracker-4 status-5 priority-11 priority-default closed" title="bug: hibernate warning HHH90000003 pollutes log files (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/7289">#7289</a>)</p></li>
<li><p>fix open issues for cdmlib-db (<a class="issue tracker-4 status-1 priority-11 priority-default" title="bug: Remaining open issues for cdmlib-db (New)" href="https://dev.e-taxonomy.eu/redmine/issues/6025">#6025</a>)</p></li>
<li><p>see if we can do more cross-project version management using toolchain plugin (<a href="https://maven.apache.org/plugins/maven-toolchains-plugin/index.html">https://maven.apache.org/plugins/maven-toolchains-plugin/index.html</a>) or enforcer plugin or similar solutions. => see <a href="https://maven.apache.org/pom.html#Quick_Overview">https://maven.apache.org/pom.html#Quick_Overview</a> inheritance and aggregation section for all required base information on this. We may create a "cdm_base.pom" for all cdm wide inherited information and maybe another "edit_platform.pom" for all widely shared information (such as the EDIT platform repository and maybe some maven-plugin versioning). Cdmlib-parent will then primarily become an aggregation.pom </p></li>
</ul>
EDIT - task #9207 (Duplicate): update ehcache dependency and handle hibernate-ehcachehttps://dev.e-taxonomy.eu/redmine/issues/92072020-08-25T15:56:48ZAndreas Müller
<p>The latest version of ehcache-core is 3.8.1 but has a different groupId since version 3.0 so we need to check if this is still working together.</p>
<p><del>Also we should check if cdmlib-remote dependency hibernate-ehcache is really needed. It relates to the similar library ehcache (not -core) and therefore many classes are duplicated.<br>
Removing hibernate-ehcache from maven pom does not create any compile problems.</del> => seems to be fixed in the meanwhile, hibernate-ehcache is not a dependency anymore</p>
EDIT - feature request #9197 (Rejected): Handle caucasus conspectus data in E+M and caucasus portalhttps://dev.e-taxonomy.eu/redmine/issues/91972020-08-18T11:11:43ZAndreas Müller
<p>Distribution data for caucasus taxa from "Konspekt flory Kavkaza" has been entered into a seperate database (euromed-caucasus) some time ago (<a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Create database for Caucasus distribution editing (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/7921">#7921</a>).</p>
<p>On 2020-08-18 we (ERS, NK, AK, AM) had a meeting to discuss how to handle these data which are using areas which differ from the typical E+M caucasus areas. The following is the outcome of this meeting:</p>
<ol>
<li>for the E+M dataportal only the existing E+M areas should be shown, data needs to be aggregated to these areas</li>
<li>where data is ambigous as the E+M area hierarchie and the conspectus areas are ambigous sometimes (conspectus areas may have 2 parent areas in the E+M hierarchy) aggregated data need to be flaged doubtful if no other data exists which is not doubtful. Question: what if the distribution status differs in the later case.</li>
<li><p>there are 5 conspectus areas which are ambigous when mapped to E+M areas:</p>
<p>a. VK which belongs mostly to Nothern Caucasus but the subarea Kubinsky belongs belongs to Azerbaidjan<br>
b. The Eastern Transcaucasus areas Alazan-Agrichay, Iori-Sheki, Murghuz-Murovdagh: they belong partly to Georgia and partly to Azerbaidjan<br>
c. The nothern border of Central and parts of Eastern Transcaucasia seems to be a bit more south then the country borders between Georgia and Russia</p></li>
<li><p>issue 3c will be checked by NK if the border really differs from the country border or if the map is inaccurate at this point</p></li>
<li><p>data in 3b needs to be aggregated in the way that doubtful distribution data will be created for Geogia and Azerbaidjan</p></li>
<li><p>data in 3a needs to be doubfully aggregated to Northern Caucasus and Azerbaijan</p></li>
<li><p>generally data was entered on sub-area level, however it looks like main-areas were used if data existed for ALL subareas (we tested this for Dianthus barbatus which has data "Eastern Caucasus" and in the book it has data for all 4 sub-areas, while Atriplex fominii has data only for the Eastern Caucasus sub-areas Kubinsky and Manas-Samur but no data for the main area itself. This rule still needs to be further validated. Also it needs to be checked what has been edited if all sub-areas existed but with different status.</p></li>
<li><p>as the handling described in 7. differs from the typical handling in E+M (and from best practice) where data for all sub-areas is entered if it exists in all sub-areas we may need a script that creates the sub-area data for these cases (and deletes the main area data)<br>
). </p></li>
<li><p>for the caucasus dataportal the sub-area data should be shown if it exists, in some cases this may lead to overlapping area information as data may come from different sources (conspectus and other sources, using the E+M areas), generally this is not a problem for the maps (but maybe for the textual representation which requires hierarchical areas), problems here will be discussed later</p></li>
<li><p>the shapefile does not need hierarchical information and therefore can be created straight forward (<a class="issue tracker-6 status-6 priority-13 priority-high13 closed" title="task: E+M shapefile with Kaukasus regions (Rejected)" href="https://dev.e-taxonomy.eu/redmine/issues/9161">#9161</a>) </p></li>
</ol>
<p>The map:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1917/picture541-1.png" alt="" /></p>
<p>and <a href="https://www.binran.ru/upload/caucasian/images/%D0%A0%D0%B0%D0%B9%D0%BE%D0%BD%D0%B8%D1%80%D0%BE%D0%B2%D0%B0%D0%BD%D0%B8%D0%B5_html_181329b1.jpg">https://www.binran.ru/upload/caucasian/images/%D0%A0%D0%B0%D0%B9%D0%BE%D0%BD%D0%B8%D1%80%D0%BE%D0%B2%D0%B0%D0%BD%D0%B8%D0%B5_html_181329b1.jpg</a> </p>
<p>Tervuren geoserver: <a href="http://edit.africamuseum.be/geoserver/topp/wms?service=WMS&version=1.1.0&request=GetMap&layers=topp:euromed_2013&styles=&bbox=-1600072.75,-1800000.0,5600000.0,5850093.0&width=481&height=512&srs=EPSG:7777777&format=application/openlayers">http://edit.africamuseum.be/geoserver/topp/wms?service=WMS&version=1.1.0&request=GetMap&layers=topp:euromed_2013&styles=&bbox=-1600072.75,-1800000.0,5600000.0,5850093.0&width=481&height=512&srs=EPSG:7777777&format=application/openlayers</a> </p>
EDIT - feature request #8930 (Closed): Publishable objects should show icon if they are unpublishedhttps://dev.e-taxonomy.eu/redmine/issues/89302020-04-03T08:17:10ZAndreas Müller
<p>To avoid that someone accidentally switches the publish flag of and generally to immediately now that a taxon is not published.<br>
Maybe we should show these icons also in the name editor and/or the bulk editor (or whereever a taxon is shown, e.g. search results, etc.)</p>
<p>The same should be implemented for doubtful taxa (see comment #1)</p>
<p>Also we should implement it similarly for Descriptions (see also <a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: Add publish flag to description base (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10206">#10206</a>, <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Make publish flag editable for DescriptionBase (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10333">#10333</a>) and SpecimeOrObservation (see also #7444)</p>
EDIT - feature request #7443 (Closed): Implement in-authors in name parser and formatter for zool...https://dev.e-taxonomy.eu/redmine/issues/74432018-05-30T05:47:12ZAndreas Müller
<p>For now we implement it only for fungi and zoological names. Need to check first if it exists for botanical names, too.</p>