EDIT Project Management: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852023-12-19T13:47:45ZEDIT Project Management
Redmine EDIT - discussion #10445 (New): [Master] Upgrade architecturehttps://dev.e-taxonomy.eu/redmine/issues/104452023-12-19T13:47:45ZAndreas Müller
<p>The EDIT platform architekture needs to be generally upgraded. This ticket is for reporting and linking ideas.</p>
<ul>
<li><p>Composable Web Architecture / Microservices / Hexagonale Architektur</p>
<ul>
<li><a href="https://www.bigcommerce.com/articles/ecommerce-website-development/composable-architecture/">https://www.bigcommerce.com/articles/ecommerce-website-development/composable-architecture/</a></li>
<li><a href="https://www.heise.de/hintergrund/Buchbesprechung-Get-Your-Hands-Dirty-on-Clean-Architecture-9289270.html">https://www.heise.de/hintergrund/Buchbesprechung-Get-Your-Hands-Dirty-on-Clean-Architecture-9289270.html</a></li>
<li><a href="https://www.happycoders.eu/de/software-craftsmanship/hexagonale-architektur/">https://www.happycoders.eu/de/software-craftsmanship/hexagonale-architektur/</a> <a href="https://www.happycoders.eu/de/software-craftsmanship/hexagonale-architektur-java/">https://www.happycoders.eu/de/software-craftsmanship/hexagonale-architektur-java/</a> <a href="https://github.com/SvenWoltmann/hexagonal-architecture-java">https://github.com/SvenWoltmann/hexagonal-architecture-java</a></li>
<li><a href="https://blog.getambassador.io/microservice-orchestration-best-practices-f32314dd6a12">https://blog.getambassador.io/microservice-orchestration-best-practices-f32314dd6a12</a></li>
</ul></li>
<li><p>techniques on job descriptions</p></li>
<li><p>reactive:</p>
<ul>
<li><a href="https://vertx.io/introduction-to-vertx-and-reactive/">https://vertx.io/introduction-to-vertx-and-reactive/</a></li>
</ul></li>
<li><p>Cloud native: <a href="https://www.enterpriseintegrationpatterns.com/patterns/messaging/PublishSubscribeChannel.html">https://www.enterpriseintegrationpatterns.com/patterns/messaging/PublishSubscribeChannel.html</a></p></li>
</ul>
EDIT - task #10444 (New): Add integration test with dockerhttps://dev.e-taxonomy.eu/redmine/issues/104442023-12-19T13:39:31ZAndreas Müller
<p>"Als Werkzeug für Integrationstests mit Docker hat sich die Java-Bibliothek Testcontainers in den vergangenen Jahren einen festen Platz in der Developer-Community erobert. Nachdem das Projekt laut der Docker-Verantwortlichen im laufenden Jahr zu den wachstumsstärksten auf Docker Hub avanciert war, hat Docker die Übernahme von AtomicJar angekündigt – dem Unternehmen hinter Testcontainers."</p>
<p><a href="https://www.docker.com/blog/docker-whale-comes-atomicjar-maker-of-testcontainers/">https://www.docker.com/blog/docker-whale-comes-atomicjar-maker-of-testcontainers/</a></p>
EDIT - task #10052 (New): Check if JReleaser could be helpfulhttps://dev.e-taxonomy.eu/redmine/issues/100522022-05-02T07:54:56ZAndreas Müller
<p><a href="https://www.heise.de/news/JReleaser-1-0-0-Release-Automatisierung-fuer-Java-und-andere-Projekte-6669624.html">https://www.heise.de/news/JReleaser-1-0-0-Release-Automatisierung-fuer-Java-und-andere-Projekte-6669624.html</a></p>
EDIT - task #9909 (New): Think about using the checker framework to avoid e.g. NPEshttps://dev.e-taxonomy.eu/redmine/issues/99092022-01-05T09:16:05ZAndreas Müller
<p><a href="https://checkerframework.org/manual/">https://checkerframework.org/manual/</a></p>
EDIT - task #8559 (Worksforme): Revision of the technical concept for the demositeshttps://dev.e-taxonomy.eu/redmine/issues/85592019-09-19T16:31:23ZAndreas Kohlbecker
<p>from <a class="wiki-page new" href="https://dev.e-taxonomy.eu/redmine/projects/edit/wiki/Meeting_2019-09-02">Meeting_2019-09-02</a></p>
<ul>
<li><p>"AK entwickelt Konzept für die Demo-Sites und damit den technischen Hintergrund von Workshops und Training events sowie das Selbststudium."*</p></li>
<li><p>Docker?</p></li>
<li><p>reuse workshop server setup scripts</p></li>
</ul>
EDIT - feature request #6942 (New): Authors in EDIT - How to handle IPNI additional author datahttps://dev.e-taxonomy.eu/redmine/issues/69422017-09-12T14:35:50ZWolf-Henning Kusber
<p>State of the art (EDITor)<br>
Example:<br>
Title Cache - Metzeltin, D.M.<br>
Abbrev. Title - Metzeltin [Comment: better Name]<br>
Firstname - Ditmar <br>
Initials - D.M.<br>
Lastname - Metzeltin<br>
Prefix<br>
Suffix </p>
<p>PhycoBank will compare PhycoBank author information with IPNI author information (<a href="http://www.ipni.org/ipni/authorsearchpage.do):">http://www.ipni.org/ipni/authorsearchpage.do):</a><br>
For many authors IPNI has entries under an IPNI-ID, including a standard abbreviation, life span or fl.=flowerish date, Alternative Name (such as Boye-Petersen, Boye Petersen), Information Source (such as "R.Jahn (B)." OR "CMI, Berkeley Algal list"), Country [Comment: Country related to the working place of the author such as L.=Sweden], Name Notes (such as "later Cleve-Euler, A." for A.Cleve), Example of Name Published.</p>
<p>These data are from IPNI. For the “master” entry of an author additional information within the EDIT database might be useful. These additional data could be imported into a notes field or into a structure to be implemented into EDIT.<br>
Discussion points:<br>
Necessary for PhycoBank: possibility to enter life span data (possible according to model) and fl. Date (new).<br>
Necessary for PhycoBank: Track IPNI-ID (in a way which is easy-to-use): should be possible<br>
Which projects (beside PhycoBank) need more author information?<br>
It was agreed that we will not synchronize EDIT-authors and IPNI-authors. The question is how much additional information is needed/is useful in EDIT.</p>
<p>In PhycoBank we have to construct new standard entries for algal names authors not in IPNI yet and we plan to deliver them to IPNI. To achive this, additional data could be stored in EDIT (Extension necessary) or in another data structure (not easy to handle).</p>
EDIT - task #6901 (New): Test if Polygone is a possible alternative in architecture (Composite or...https://dev.e-taxonomy.eu/redmine/issues/69012017-08-09T13:06:14ZAndreas Müller
<p>See <a href="https://polygene.apache.org/java/latest/intro.html">https://polygene.apache.org/java/latest/intro.html</a> </p>
<p>And the tutorials at <a href="https://polygene.apache.org/java/latest/tutorials.html">https://polygene.apache.org/java/latest/tutorials.html</a> </p>
EDIT - feature request #6884 (New): Use stable UUIDs for CoL importhttps://dev.e-taxonomy.eu/redmine/issues/68842017-08-04T07:21:11ZAndreas Müller
<p>We should try to keep UUIDs from one CoL version to the next.</p>
<p>Stable IDs could be mapped against CoL LSIDs (without version part) or name strings (including authors and maybe including higher taxonomy if duplicates exist).</p>
<p>External services that use CoL:</p>
<p>UTIS: currently stable IDs not required</p>
<p>GFBio: ??</p>
EDIT - task #6696 (New): Improve architecture for Model updateshttps://dev.e-taxonomy.eu/redmine/issues/66962017-06-06T23:30:45ZAndreas Müller
<p>Some issues make model update work intensive and should be improved:</p>
<ul>
<li>Vaadin and TaxEditor still have their own dataset.dtd. They replace it by dataset.dtd from cdmlib-test (maybe same for 001-cdm.h2.sql</li>
<li>Tests in Vaadin and/or Editor are too big. Many redundant test data.</li>
<li>TaxEdtior (also Vaadin??) has its own hibernate.cfg.xml, should be replaced by cdmlib-test or cdmlib-persistence hibernate.cfg.xml</li>
<li>CdmModelCacher <del>should be moved to cdmlib and should be started automatically with each build,</del> stored either in model, persistence, service or io (?); maybe used by cdmlib itself; <del>also it needs some dependency to lucene etc which doesn't exist in TaxEditor. We could also use a simplified configuration without lucene(?).</del></li>
<li><del>001-cdm.h2.sql should be created automatically (there is still an issue with the envers part)</del> => <a class="issue tracker-6 status-5 priority-12 priority-high14 closed" title="task: Create 001-cdm.h2.sql automatically (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6714">#6714</a></li>
<li>ClearDB_with_Terms_DataSet.xml, ClearDBDataSet.xml and TermsDataSet.xml is still required in each project. Should only be in cdmlib-test.</li>
<li><del>remove getNextUpdater()</del></li>
<li>...</li>
</ul>
EDIT - feature request #4922 (New): GrantedAuthorities not reusable anymorehttps://dev.e-taxonomy.eu/redmine/issues/49222015-05-21T11:36:56ZKatja Luther
<p>Currently granted authorities are reusable. We want to make them group/user specific. Whenever a GA is removed from its owner it should be completely deleted from the DB.</p>
<p>GAs which are to be used by multiple owners need to be cloned.</p>
<p>We need to remove the unique index from the authority string and make he sets orphanRemoval = true.</p>
<p>During later processing or selection existing strings need to be deduplicated. => create new ticket for TaxEditor and cdmlib-security</p>
<p>see also #3785</p>
EDIT - feature request #4182 (New): use elasticsearch as search engine [DISCUSS]https://dev.e-taxonomy.eu/redmine/issues/41822014-04-10T06:15:59ZAndreas Kohlbecker
<p><strong>Links:</strong> </p>
<ul>
<li><p><a href="http://www.elasticsearch.org/" class="external">elasticsearch</a></p></li>
<li><p>on how to let hibernate send modified entities to a different search backend, slor in this case: <a href="http://anotherjavaday.blogspot.co.il/2012/01/combining-power-of-hibernate-search-and.html">http://anotherjavaday.blogspot.co.il/2012/01/combining-power-of-hibernate-search-and.html</a></p></li>
<li><p><a href="https://github.com/55social/hibernate-search-elasticsearch-connector">https://github.com/55social/hibernate-search-elasticsearch-connector</a></p></li>
</ul>
<p><strong>Questions</strong> </p>
<ul>
<li><p>We need to run searches across multiple indexes, is elasticsearch supporting this? Currently we have our own implementation for this: <code>LuceneMultiSearch</code> </p></li>
<li><p>Our own <code>LucenSearch</code> class is capable of returning lucene documents together with cdm entities in the same response. With elastic search this will no longer be possible. So we would have to send two requests: One request to do the search and a second one to fetch cdm entities, if necessary.</p></li>
<li><p>It will be necessary to install a separate Elasticsearch server in parallel to the cdmserver. This makes the initial installation more complex. Can we bundle the cdm server and elastic search together in a single install package. How will this work in workshops. Simple HQL based search as fall back? </p></li>
</ul>
EDIT - feature request #3958 (Closed): Handle CDMPreference tablehttps://dev.e-taxonomy.eu/redmine/issues/39582014-01-14T21:42:47ZAndreas Müller
<p>It is implemented in model but not yet used and not filled with any data. Methods in Service layer are also missing.</p>
<p>Keep in UML milestone as we may need a data updater (e.g. <a class="issue tracker-4 status-5 priority-13 priority-high13 closed" title="bug: Update Nomenclatural code for datasources (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/3658">#3658</a>). Move otherwise.</p>
<p>Decisions for the syntax of the different fields:</p>
<p>subject:</p>
<ul>
<li><p>/ (Database wide)</p></li>
<li><p>/TaxonNode<img src="for a classification or subtree" alt="#c1#33#44#35#55" /></p></li>
<li><p>/editor (??) for purely TaxEditor related preferences (e.g. show ID in supplemental data view)</p></li>
<li><p>TBC</p></li>
</ul>
<p>predicate: No required structure, but package like structure with dot separators makes sence</p>
<ul>
<li><p>aaaa.bbb.ccc.MATCH_MODE</p></li>
<li><p>aaaa.ee.ff.abc</p></li>
<li><p>allows starts with search to return lists of values</p></li>
<li><p>Case insensitive (?)</p></li>
<li><p>each predicate might be defined by as a constant of an enum</p></li>
</ul>
<p>object: up to the predicate to implement</p>
<p>Difficulties may occur when trying to match filters (subjects). An object that requires a preference (e.g. a TaxonName requires a list of available ranks) may match to multiple filters which map to different values (e.g. because the name is used in multiple classifications)</p>
<p>for details see: #3555, see also open issues there</p>
<p>related #5004, #3773, <a class="issue tracker-5 status-5 priority-10 priority-lowest closed child" title="feature request: Implement CdmPreference reading for database preferences (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/5969">#5969</a></p>
EDIT - feature request #3702 (Closed): WaterbodyOrCountry ISO 3166 alpha-3 code should be availab...https://dev.e-taxonomy.eu/redmine/issues/37022013-09-04T15:21:13ZAndreas Müller
<p>Currently the ISO alpha-3 code is only available as abbreviated label of the english representation. We should have an own attribute instead.</p>
<p>Separated <strong>this</strong> ticket from <a class="issue tracker-5 status-1 priority-14 priority-high12" title="feature request: Include ISO-3166 numeric codes to Country (New)" href="https://dev.e-taxonomy.eu/redmine/issues/2302">#2302</a> as <strong>this</strong> became fixed by #3479</p>
EDIT - task #3547 (In Progress): Remove size of test data where possiblehttps://dev.e-taxonomy.eu/redmine/issues/35472013-06-21T07:47:30ZAndreas Müller
<p>Remove size of test data where possible</p>
<p>e.g in <br>
<del>TaxonDaoHibernateImplTest.testDelete-result.xml</del><br>
<del>TaxonDaoHibernateImplTest.testDelete-result1.xml</del> => deleted<br>
<del>TaxonDaoHibernateImplTest.testFind.xml</del><br>
<del>TaxonDaoHibernateImplTest.testFindDeleted.xml</del><br>
<del>TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml</del> => did delete only few, maybe more possible<br>
<del>TaxonDaoHibernateImplTest.xml</del><br>
ConcurrentSessionTest.xml<br>
<del>TaxonNameDaoHibernateImplTest.xml</del><br>
DescriptionDaoHibernateImplTest.xml<br>
DefinedTermDaoImplTest.xml !!<br>
TermVocabularyDaoImplTest.xml !!<br>
FreeTextSearchIntegration.xml<br>
BeanInitializerIntegration.xml</p>
<p>some vaadin tests</p>
EDIT - feature request #2854 (Closed): Implement part of other title for part of articles and par...https://dev.e-taxonomy.eu/redmine/issues/28542012-03-13T14:52:37ZAndreas Müller
<p>duplicate for #2853 to have it in both milestones</p>