EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852024-01-12T16:27:18ZEDIT Project Management
Redmine task #10450 (New): Handle zip-files consistent in list exportshttps://dev.e-taxonomy.eu/redmine/issues/104502024-01-12T16:27:18ZAndreas Müller
<p>The handling of zip-files differs in the list exports (cdm-light, coldp, wfo-classification and dwc-a export).</p>
<p>For coldp (and maybe the coming wfo-classification) export it allows selecting a folder and defines a default file name for the zip-file while only at the second page of the assistant one can choose to create a zip-file or not. This should be at the same page. Also when selecting "Create zip-file" it should show the "Select folder for exported files" option while when unselecting "create zip-file" it should show the file selection dialogue which then possibly opens the a browser and allows to choose a filename using OS functionality for this.</p>
<p>We should keep the default for zip-creation as "don't" for cdmlight but "do" for the others as dwc-a and coldp by default are handled as zip-files.</p>
<p>For the ordinary dwc-a export we need to check if it is easy to implement to also allow creation of an unzipped version.</p>
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>
task #10443 (New): Develop NFDI-API with Open APIhttps://dev.e-taxonomy.eu/redmine/issues/104432023-12-19T13:21:59ZAndreas Müller
<p><a href="https://openapi.tools/#gui-editors">https://openapi.tools/#gui-editors</a></p>
task #10438 (New): Check if reported Win10 performance issue for eclipse is relevant for TaxEditorhttps://dev.e-taxonomy.eu/redmine/issues/104382023-12-07T09:25:29ZAndreas Müller
<p><a href="https://bugs.eclipse.org/bugs/show_bug.cgi?id=548443">https://bugs.eclipse.org/bugs/show_bug.cgi?id=548443</a></p>
task #10432 (Resolved): Cora importhttps://dev.e-taxonomy.eu/redmine/issues/104322023-11-23T13:24:46ZAndreas Müller
<p>for use in lichenes database and in integrated taxonomy course</p>
<p>open issues:</p>
<ul>
<li>e-Publication year (-> new ticket and request)</li>
<li>URI for Index Fungorum in term loading (<a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Add Index Fungorum name identifier type (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10433">#10433</a>)</li>
<li>general parser for in-authors (<a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: Implement in-authors in name parser and formatter for zoological and fungi names (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/7443">#7443</a>)</li>
</ul>
task #10359 (New): Integrate Vienna common names into E+Mhttps://dev.e-taxonomy.eu/redmine/issues/103592023-06-23T14:29:16ZAndreas Müller
<p>Waiting for API link...</p>
<p>Reconciliation service avaiable at: <a href="https://bioling.acdh.oeaw.ac.at/reconcile">https://bioling.acdh.oeaw.ac.at/reconcile</a> . Many names come from PESI here. We need to avoid circles.</p>
<p>He:</p>
<p>hier Beispiele für den Aufruf:</p>
<p><a href="http://openup.nhm-wien.ac.at/commonNames/?query=%7b%22type%22:%22/name/common%22,%22query%22:%22Platalea+leucorodia%22%7d">http://openup.nhm-wien.ac.at/commonNames/?query=%7b%22type%22:%22/name/common%22,%22query%22:%22Platalea+leucorodia%22%7d</a></p>
<p>Außerdem noch die Landung Page die einen wissenschaftlichen Namen:<br>
<a href="http://openup.nhm-wien.ac.at/commonNames/references/scientificName/163889">http://openup.nhm-wien.ac.at/commonNames/references/scientificName/163889</a></p>
<p>und der direkt Aufruf eines CNames<br>
<a href="http://openup.nhm-wien.ac.at/commonNames/651207">http://openup.nhm-wien.ac.at/commonNames/651207</a></p>
<p>Die Doku zum Service wird gerade von confluence in eine knowledge base überführt, ist aktuell in einem internen confluence System vergraben.</p>
<p>Open issue: </p>
<ul>
<li>discussion on approriate filter (e.g. geo-filter, time filter - there are names used only in the past -, and language filter - e.g. for Netherlands there are many names that differ only in dialect-, ...)</li>
<li>source handling: we want to show the original source and Vienna as broker</li>
</ul>
task #10338 (New): Think about using GraphQL (graphQL-java and spring GraphQL)https://dev.e-taxonomy.eu/redmine/issues/103382023-05-29T15:03:21ZAndreas Müller
<p><a href="https://www.graphql-java.com/documentation/getting-started/">https://www.graphql-java.com/documentation/getting-started/</a></p>
<p>Goes <a href="https://spring.io/projects/spring-graphql">https://spring.io/projects/spring-graphql</a></p>
task #10326 (In Progress): EuroMed mosses remaining issueshttps://dev.e-taxonomy.eu/redmine/issues/103262023-05-27T19:18:00ZAndreas Müller
<p>copied from #10229 </p>
<ul>
<li>Dataportal:
<ul>
<li>Condensed Distribution String handling EUR area</li>
<li>maps (or comment) for the separate mosses areas, shapefile needed for Russian areas (urgent) and Gr+Ae(Gr) (not urgent) => <a class="issue tracker-5 status-1 priority-11 priority-default" title="feature request: Add Gr+AE(G) und Russian aereas for mosses to the E+M shapefile (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10349">#10349</a><br></li>
<li><del>Condensed Distribution String for IUCN data</del> <a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: IUCN condensed distribution configuration (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10327">#10327</a></li>
<li>Advanced search does not look nice anymore <a class="issue tracker-4 status-1 priority-11 priority-default" title="bug: Adapt advanced search to use area tree (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10366">#10366</a> </li>
</ul></li>
<li>Data:
<ul>
<li>synonyms (still unclear were to take from)</li>
<li>Mediterranean data (still unclear were to take from)</li>
<li>Nomencl. authors for higher taxa</li>
<li>Ireland: Discuss with authors if mapping to Hb(E) is correct</li>
<li>move endemisim data to E+M Areal once possible</li>
<li>decision by ERS, if IUCN status NA should map to a distribution status native or introduced, currently it is mapped to native but probably introduced is correct (mail sent)</li>
<li>Check with ERS if Status Notes and/or Taxon Details tables were considered (in the same Excel files), see #10229#note-11, also author comparison (Tropicos - import file) </li>
</ul></li>
<li>TaxEditor
<ul>
<li>see how the mosses areas can be handled best in TaxEditor (don't show them usually, but allow the possibility to edit them in case a change is needed)</li>
<li>Handling of IUCN status in TaxEditor - preference needed <a class="issue tracker-5 status-2 priority-10 priority-lowest" title="feature request: Preference for IUCN status list states (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/10323">#10323</a></li>
<li>Maybe move It subareas to main vocabulary</li>
</ul></li>
<li><del>Handle EUR as alternative root as long as mediterranean data is missing</del></li>
<li>Correct handling of Tu and its childs in hierarchy and cond. distr. (see also <a class="issue tracker-5 status-3 priority-10 priority-lowest" title="feature request: Implement subarea preference rule and fallback areas for areas with complex hierarchy (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/9502">#9502</a>)</li>
<li>Discuss: should EUR be shown in condensed distribution for status "not endemic" for mosses?
<ul>
<li>Pro: being not endemic in EUR does not mean being not endemic in E+M. So showing EUR explicitly clearifies that endemism is about EUR not E+M here</li>
<li>The area of scope is shown in the long representation as Europe. This at least indicates that the data is about EUR, not E+M </li>
</ul></li>
</ul>
task #10321 (In Progress): WFO name matching for Cichorioideaehttps://dev.e-taxonomy.eu/redmine/issues/103212023-05-16T14:32:10ZAndreas Müller
<p>NoK:</p>
<p>Backbone + Content nur des Standard View</p>
<p>How to:</p>
<ul>
<li>Run cache updater</li>
<li>Take template from Casearia/NameMatching</li>
<li>Use below queries (with short select) to create original data</li>
<li>Use the normalized names put in WFO name matcher at <a href="https://list.worldfloraonline.org/matching.php">https://list.worldfloraonline.org/matching.php</a></li>
<li>Use default parameters and run match</li>
<li>Copy results (output and candidates) to same folder as template</li>
<li>Import output and candidate results via text import (comma separated, UNICODE-8, Format:Text, add data to data model)</li>
<li>filter matching and unmatching names via "wfo-id field is empty"</li>
<li>Run the same for synonyms</li>
</ul>
<p>TODO:</p>
<ul>
<li>filter out hybrid formulas (and aggregates if not yet done)</li>
</ul>
task #10317 (New): Think about flyway or liquibase for database migrationhttps://dev.e-taxonomy.eu/redmine/issues/103172023-05-05T14:02:19ZAndreas Müller
<p><a href="https://flywaydb.org/">https://flywaydb.org/</a> </p>
<p><a href="https://www.liquibase.org/">https://www.liquibase.org/</a></p>
task #10314 (New): Cleanup authors that differ only in collationhttps://dev.e-taxonomy.eu/redmine/issues/103142023-04-29T08:43:37ZAndreas Müller
<p>The following SQL finds such cases, but index should be set on nomenclaturalTitleCache for performance reasons.</p>
<pre>SELECT ab.id, ab.titleCache, ab.nomenclaturalTitleCache, ab2.id, ab2.titleCache, ab2.nomenclaturalTitleCache -- , ab.nomenclaturalTitle, ab.protectedTitleCache, ab.protectedNomenclaturalTitleCache, ab.familyName, ab.initials, ab.givenName
FROM AgentBase ab INNER JOIN AgentBase ab2 ON ab.nomenclaturalTitleCache = ab2.nomenclaturalTitleCache AND ab2.id>ab.id
AND BINARY ab.nomenclaturalTitleCache <> BINARY ab2.nomenclaturalTitleCache
WHERE ab.DTYPE = 'Person' -- AND ab.protectedNomenclaturalTitleCache = 0
ORDER BY ab.nomenclaturalTitleCache
</pre> task #10285 (New): Catch hibernate search exception so hibernate search dependencies are not need...https://dev.e-taxonomy.eu/redmine/issues/102852023-03-22T16:54:16ZAndreas Müller
<p>copied from <a class="issue tracker-4 status-5 priority-13 priority-high13 closed" title="bug: HibernateSystemException and BridgeException not in taxeditor dependencies (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10277">#10277</a> </p>
<p>If hibernate search indexing throws an exception this may result in a HibernateSystemException. This is not nice as it requires that spring-orm and hibernate-search-engine are on the taxeditor classpath just to be able to handle HibernateSystemException and BridgeException.</p>
<p>We should try to find a way to avoid this.</p>
task #10283 (New): Add mapping for non-mexican areas for eFloraMexhttps://dev.e-taxonomy.eu/redmine/issues/102832023-03-22T15:03:12ZAndreas Müller
<p>... as technical annotations for areas</p>
task #10268 (In Progress): Selecting an existing name as basionymhttps://dev.e-taxonomy.eu/redmine/issues/102682023-03-10T10:17:34ZWolf-Henning Kusber
<p>Rights: User<br>
Action: User provides a new combination and wants to select a basionym or replaced synonym already in the system:<br>
Here: in Testsystem:102794 new name: Naviuladitoides brekkaensoides <br>
Basionym: Navicula brekkaensoides (the reference should be available as <a href="http://phycobank.org/103528">http://phycobank.org/103528</a>)<br>
The Basionym can be selected, but the reference is not shown for the user.<br>
It is possibel to save the basionym, but the error is shown, that the basionym is lacking a reference.<br>
See blocking registration: 102795</p>
<p>The idea was that users use a (by other users or curator or admin) inserted pubished name "as is" without further editing</p>
<p>There is another related issue.</p>
<p>related to <a class="issue tracker-4 status-5 priority-12 priority-high14 closed" title="bug: Selecting an existing name and adding a new journal does not work for phycobank registration (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10167">#10167</a> </p>
task #10249 (In Progress): Mapping for metadata labels of images in portalhttps://dev.e-taxonomy.eu/redmine/issues/102492023-02-10T12:04:45ZKatja Luther
<p>It should be possible to provide a mapping for the displayed meta data labels and the labels coming from apache imaging.</p>
<p>Actually we only convert from CamelCase to String with whitespaces.</p>
<p>Examples:</p>
<p>artist/credit? -> photographer<br>
sublocation -> locality<br>
tbc.</p>
<p>The simplest solution would be to create a mapping for all portals with an java enumeration or an xml file, another would be to move it to the dataportal configuration or the db preferences.</p>