EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852022-09-12T11:58:43ZEDIT Project Management
Redmine bug #10151 (Closed): Creating a field unit with a given taxon filter does not create a taxon-seci...https://dev.e-taxonomy.eu/redmine/issues/101512022-09-12T11:58:43ZAndreas Müller
<p>AM:</p>
<p>"... Taxon Navigator –> Open in ... –> Specimen Editor (tree) ... Ich habe das gerade mal ausprobiert und es scheint überhaupt nicht zu funktionieren. Wenn ich so ein Specimen anlege wird die Verknüpfung zwischen Taxon und Specimen (ich würde hier insbesondere mit einer IndividualsAssocitation rechnen, die also in den Taxon Facts sichtbar sein müsste; evtl. zusätzlich eine Determination auf FieldUnit oder Specimenebene) gar nicht angelegt. Das mag eine Regression sein, da das glaube ich schon mal funktioniert hat"</p>
bug #10137 (Closed): Compressed table does not show derivates anymorehttps://dev.e-taxonomy.eu/redmine/issues/101372022-09-06T10:49:04ZAndreas Müller
<p>e.g. Campanula polyclada (<a href="https://campanula.e-taxonomy.net/cdm_dataportal/taxon/2e3aa801-7307-409c-bd39-d825f5f1e031/specimens">https://campanula.e-taxonomy.net/cdm_dataportal/taxon/2e3aa801-7307-409c-bd39-d825f5f1e031/specimens</a>) does not show tissue sample, DNA sample, consensu sequence and single read information anymore</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2209/clipboard-202209061247-ngjnp.png" alt="" /></p>
<p>It should show the following:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/2210/clipboard-202209061248-dkxev.png" alt="" /></p>
feature request #9474 (New): Creating a new Specimen/FieldUnit in Specimen Tree Editor with taxon...https://dev.e-taxonomy.eu/redmine/issues/94742021-02-24T14:35:10ZKatja Luther
<p>When a taxon is selected in specimen tree editor and a new fieldunit/specimen is created, the specimen should have an association to the selected taxon.<br>
Maybe we should add a dialog whether the taxon association should be added or not?</p>
feature request #9447 (New): Allow editing derivation events with multiple originals in specimen ...https://dev.e-taxonomy.eu/redmine/issues/94472021-02-02T17:50:11ZAndreas Müller
<p>Currently the specimen tree editor only allows derivation hierarchies with derivation events having only 1 "original" (parent).<br>
This covers most usecases but e.g. ICN Art. 9 Ex. 4 (<a href="https://www.iapt-taxon.org/nomen/pages/main/art_8.html">https://www.iapt-taxon.org/nomen/pages/main/art_8.html</a>) gives an example for a unit that has 2 field numbers and therefore exact modelling with given classes requires to allow to combining 2 field units to a single derived unit to model this case exactly.</p>
<p>Also in zoology such cases exists where e.g. fossils are combined from multiple bones to a single specimen.</p>
<p>A possible implementation could look like the following:</p>
<ul>
<li>keep the current tree structure</li>
<li>add menu item to add a given unit to an additional "parent" (could be similar to copy&paste functionality and, even better, multi select should be allowed when adding a new derivation to a parent)</li>
<li>once added to a second parent the child should show up at 2 places in the tree (so no unique constraint for the tree nodes anymore)</li>
<li>visual support should be given to indicate that a child has >1 parents by
<ul>
<li>textual information in DetailsView (similar to the text in red indicating that an objects is referred to multiple times)</li>
<li>by color or symbol in the tree </li>
<li>and maybe also by textual label support in the tree</li>
</ul></li>
<li>removing a parent being part of such a derivation should not be allowed, deleting the child first should be a requirement; alternatively a more sophisticated method is possible</li>
</ul>
<p>Maybe we need to adapt cache strategies for this usecase as the UnitFacade cache strategies do not allow multiple parents </p>
feature request #9446 (New): Define possible derivation paths in SpecimenOrObservationTypehttps://dev.e-taxonomy.eu/redmine/issues/94462021-02-02T17:27:14ZAndreas Müller
<p>Even in theory, not all specimenOrObservation types can be derived from all specimenOrObservation types.</p>
<p>We may want to define those combination which are allowed / forbidden in theory and maybe we want also define a default for a given context (e.g. in theory it may be allowed to derive OtherSpecimen from any of the given types but in practice we want to avoid the usage of OtherSpecimen and therefore it should not be allowed by default).</p>
<p>Some rules for derivations not allowed in theory are:</p>
<ul>
<li>"real" material units can not be derived from media based units and from pure observations</li>
<li>field units can not be derived from preserved specimen and most other types</li>
<li>... </li>
</ul>
<p>In a next step we should make the possible combinations configurable in TaxEditor which is another ticket.</p>
<p>The base default should be defined by the requirements for classical higher vascular plant treatments as these are the most common usecases for the CDM.</p>
task #9445 (New): [DISCUSS] Should GatheringEvent have descriptive datahttps://dev.e-taxonomy.eu/redmine/issues/94452021-02-02T17:06:10ZAndreas Müller
<p>Currently descriptive data on the gathering site such as ecology data, site images or water quality parameters for water samples are stored with the field unit.</p>
<p>However, this data may be shared among field units if multiple field units have been collected at the same place and date and with the same method (and even by the same team as required by GatheringEvent for simplification of the model).</p>
<p>Pro: reduce reduncancy; semantically more exact<br>
Con: more complex when unifying data, e.g. for creating a single specimen string including all data; additional implementation work; a 4. DescriptionBase class is needed</p>
<p>Complexity in implementation is reduced by UnitFacade where only smaller changes are needed to handle the new situation accordingly.</p>
<p>May make more sense once explicit handling of GahteringEvents is implemented in TaxEditor <a class="issue tracker-5 status-1 priority-11 priority-default" title="feature request: Allow showing, editing and reusing GatheringEvent in specimen tree editor (New)" href="https://dev.e-taxonomy.eu/redmine/issues/9444">#9444</a>. </p>
<p>TODO: </p>
<ul>
<li>compare with ABCD and other standards</li>
</ul>
feature request #9444 (New): Allow showing, editing and reusing GatheringEvent in specimen tree e...https://dev.e-taxonomy.eu/redmine/issues/94442021-02-02T16:54:17ZAndreas Müller
<p>Currently the highes level of units in the derivative tree editor is the field unit. However, in the model and in reality field units sometimes share the same GatheringEvent (currently holds data on where, who and how, maybe extended in future <a class="issue tracker-6 status-1 priority-11 priority-default" title="task: [DISCUSS] Should GatheringEvent have descriptive data (New)" href="https://dev.e-taxonomy.eu/redmine/issues/9445">#9445</a>).<br>
We should therefore extend the specimen tree editor in the way that GatheringEvent may become the root element.</p>
<p>This functionality should be configurable 1.) by CdmPreferences and 2.) by selection in the search UI (e.g. by a checkbox). The CdmPreferences should define the default value for the searchUI configuration value. The default value for the CdmPreference should be not to show the GatheringEvent (to keep the UI simple for default usecases, and for now as this may change in future).</p>
bug #8760 (New): Presentation and linking of molecular data in specimen table too unclear https://dev.e-taxonomy.eu/redmine/issues/87602019-12-11T12:41:20ZPatrick Plitzner
<p>Hallo,</p>
<p>mir ist auf <a href="http://test.e-taxonomy.eu/dataportal/preview/campanulaceae/cdm_dataportal/taxon/48249487-e921-4185-aed9-50a5bf0e86e1">http://test.e-taxonomy.eu/dataportal/preview/campanulaceae/cdm_dataportal/taxon/48249487-e921-4185-aed9-50a5bf0e86e1</a> (Rhipsalis mesembryanthemoides) gerade folgendes in der Specimentabelle aufgefallen:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1781/picture770-1.png" alt="" /></p>
<p>Das "no provider" sieht nicht schön aus und ist für den Normaluser (in dem Fall auch mich) unverständlich. Welche Daten „fehlen“ denn da? Und muss das so angezeigt werden. Die Information scheint mir wenig Sinn zu machen. Sie sollte entweder entfernt oder mit mehr Inhalt versehen werden.</p>
feature request #8451 (New): Link specimen to taxon via Drag and Drophttps://dev.e-taxonomy.eu/redmine/issues/84512019-08-08T07:07:10ZPatrick Plitzner
<p>It would be a nice feature to be able to link a specimen to a taxon via drag&drop. This could be done from the specimen tree editor when dragging a specimen to the taxon navigator and dropping on a taxon. This would generate an IndividualsAssociation between the two CDM objects.</p>
bug #7686 (Closed): Specimen title cache issues in data portal specimen tablehttps://dev.e-taxonomy.eu/redmine/issues/76862018-08-27T11:31:27ZPatrick Plitzner
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1344/picture727-1.png" alt="" /></p>
<p>Walter: </p>
<ul>
<li>Der Name nach Holotype of wird doppelt ausgegeben.</li>
<li>Vor dem Link zum Herbarbeleg sollte ein Promt stehen “Link(s) to specimens:”</li>
<li>Warum steht eine Leerzeile vor den Links? </li>
</ul>
<p>Beim folgenden Beispiel stehen die folgenden Daten im Cache:</p>
<pre>Philippines, Panay, Antique Prov., Mariliso (= Malalison) Island., male infl or. May–Aug. 1918, McGregor 32313 (holotype: US, isotype: B, photo K, photo PNH)
</pre>
<p>Das muss auch erstmal so stehen bleiben, da wir noch kein Specimen-unabhängiges Feld für das Originalzitat des Typus und die Typendiskussion haben. Damit aber unter der Überschrift Specimens etwas steht, habe ich Sammler und Nummer (sozusagen der Field Unit) eingetragen, dann kommt folgendes heraus:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1345/picture248-1.png" alt="" /></p>
<p>Offenbar wird die Zeile “xType of” nur ausgegeben, wenn die Typuskategorie eingegeben wurde? Das ist bei mehrere Specimens umfassenden Cache-Angaben natürlich nicht möglich.<br>
Der unschöne Link wäre ja mit entsprechendem Prompt noch akzeptabel – aber auf der Specimen Seite wird dann der Cache nicht angezeigt:</p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1346/picture248-2.png" alt="" /></p>
<p>Ich gehe davon aus, dass die Specimen-Daten, die aus der Literatur hereinkommen, zunächst meist im Cache zitiert werden (besonders die Typen, solange es noch kein unabhängiges Typus-Diskussionsfeld gibt). Da wäre es gut, wenn man sich die Daten auch anzeigen lassen könnte. </p>
feature request #7685 (Closed): Add Selenium tests for specimen table in data portalhttps://dev.e-taxonomy.eu/redmine/issues/76852018-08-27T11:28:01ZPatrick Plitzner
<ul>
<li>add test data to 160.45.63.201/cdm_integration_reference</li>
<li>create new dump which needs to be stored in edit-integration /var/lib/cdm/testdb/{RELEASE} </li>
<li>create <code>SpecimenTaxonPage</code> class which <code>extends PortalPage</code> in <code>cdm-dataportal/src/main/java/eu/etaxonomy/dataportal/pages/</code></li>
<li>create test class in <code>cdm-dataportal/src/test/java/eu/etaxonomy/dataportal/selenium/tests/reference/</code> with</li>
</ul>
<pre><code class="java syntaxhl"><span class="nd">@DataPortalContexts</span><span class="o">(</span> <span class="o">{</span> <span class="nc">DataPortalSite</span><span class="o">.</span><span class="na">reference</span> <span class="o">})</span>
<span class="kd">public</span> <span class="kd">class</span> <span class="nc">SpecimenTableTest</span> <span class="kd">extends</span> <span class="nc">CdmDataPortalTestBase</span><span class="o">{</span>
<span class="o">...</span>
<span class="o">}</span>
</code></pre> task #7562 (Closed): Specimen table "Associated with" taxon is irritating and needs to be removed...https://dev.e-taxonomy.eu/redmine/issues/75622018-07-18T14:59:33ZAndreas Kohlbecker
<p>see issues <a class="issue tracker-4 status-5 priority-11 priority-default closed" title="bug: [Dataportal] Specimen table issues (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6816">#6816</a>, <a class="issue tracker-6 status-5 priority-11 priority-default closed" title="task: OccurrencePortalController and FieldUnitDTO should not allow passing the determintation, associat... (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/7561">#7561</a> for older information on this.</p>
feature request #6870 (New): Further specimen table issueshttps://dev.e-taxonomy.eu/redmine/issues/68702017-08-01T12:34:31ZAndreas Müller
<p>A couple of smaller issues with the specimen table has already been fixed in <a class="issue tracker-4 status-5 priority-11 priority-default closed" title="bug: [Dataportal] Specimen table issues (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6816">#6816</a>. There are few more.</p>
<ol>
<li><p>The sort order for the specimen (when opening a single line) should be alphabetical (or any other that makes sense), currently there is no order (AM: probably fixed already, atleast here <a href="http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/98924180-7c12-453d-bcfc-f6f211b684e1/specimens">http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/98924180-7c12-453d-bcfc-f6f211b684e1/specimens</a> it is correct but was not in previous versions)</p></li>
<li><p>Alignement: currently the vertical alignement of each cell is centric. This looks not so nice if some cells have 1 line and some cells have 2 lines. E.g. <a href="http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/507e13f3-5db7-45a6-a41e-07f0de20348a/specimens">http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/507e13f3-5db7-45a6-a41e-07f0de20348a/specimens</a> . I suggest that we should have a top alignement.</p></li>
<li><p>Spacing: though we do not have much space available we should have at least 1 or 2 points spacing (inner margin, don't know what the correct term is), otherwise the text is to close to the border/grid lines which looks not nice</p></li>
<li><p>If possible it would be great if the width of the cells would be adaptable, either by the user or by automatic computation. In the given example <a href="http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/507e13f3-5db7-45a6-a41e-07f0de20348a/specimens">http://portal.cybertaxonomy.org/salvador/cdm_dataportal/taxon/507e13f3-5db7-45a6-a41e-07f0de20348a/specimens</a> we have many specimen from "El Salvador". With the given fixed width these all break after "El" and use a second line. With a little bit more space they could all go into 1 line. If this is difficult to implement we should copy it to a new ticket. </p></li>
<li><p>The cell width changes when expanding/collapsing a FieldUnit. This width should be fixed in both states</p></li>
</ol>
feature request #6866 (Closed): Improve specimen pagehttps://dev.e-taxonomy.eu/redmine/issues/68662017-08-01T11:21:14ZAndreas Müller
<p>The pure specimen pages in the data portal need to be improved. Currently they show only basic and concatenated information.</p>
<p>E.g. <a href="http://portal.cybertaxonomy.org/salvador/cdm_dataportal/specimen/d3d330b5-9de1-4fd9-ab17-8ec55d17810f">http://portal.cybertaxonomy.org/salvador/cdm_dataportal/specimen/d3d330b5-9de1-4fd9-ab17-8ec55d17810f</a> </p>
<p>For a single specimen page I don't think we need primarily to show the title cache but better show atomized data.</p>
<p>Also we should show more or less all data (including annotations, extensions, factual data, media, sources, used where, ....) similar to the way specimen data is shown on the specimen tab on the taxon page when not using the compressed table view (but with some improvements). </p>
<p>Examples of specimen and occurrence page in other systems:</p>
<ul>
<li>GBIF: <a href="https://www.gbif.org/occurrence/2244182979">https://www.gbif.org/occurrence/2244182979</a></li>
<li>ALA: <a href="https://biocache.ala.org.au/occurrences/85e8e3a4-3976-41a9-8841-fc48acd818eb">https://biocache.ala.org.au/occurrences/85e8e3a4-3976-41a9-8841-fc48acd818eb</a></li>
<li>GGBN: <a href="http://www.ggbn.org/algae_bgbm/sptool/query_sptool.php?sqlType=Detail&ID_Collection=1072">http://www.ggbn.org/algae_bgbm/sptool/query_sptool.php?sqlType=Detail&ID_Collection=1072</a></li>
</ul>
<p>GBIF offers the option to hide the diagnostic information which allows to layout the details tables in two rows when the browser window is wide enough.</p>
feature request #6865 (Closed): [DISCUSS] Separator for Code and Accession Numberhttps://dev.e-taxonomy.eu/redmine/issues/68652017-08-01T11:01:51ZAndreas Müller
<p>WGB:</p>
<p>TitleCache: Ich würde ein Satzzeichen zwischen Herbarangabe und die dortige ID setzen, also statt (B B 10 0018600) lieber etwas wie (B: B 10 0018600). Zumindest wenn dieser „Title Cache“ auch für die Webausgabe genutzt werden soll.</p>
<p>=== </p>
<p>An alternative could be to deduplicate the B's for Berlin Specimen. The 2 B's are a specific problem that does not occur often for other herbaria, at least not with a space after the second occurrence. For readability the B's could be deduplicated. (this approach is probably also discussed in some other ticket)</p>