EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852022-05-12T10:19:52ZEDIT Project Management
Redmine bug #10059 (Closed): Link for stored under and identification on specimen page does not work corr...https://dev.e-taxonomy.eu/redmine/issues/100592022-05-12T10:19:52ZAndreas Müller
<p><strong>Stored under</strong> links to e.g. <a href="https://portal.cybertaxonomy.org/salvador/cdm_dataportal/occurrence/cdm_dataportal/name/7b7c2239-3836-4772-9bb4-0f9a9b17fd41/null/null/">https://portal.cybertaxonomy.org/salvador/cdm_dataportal/occurrence/cdm_dataportal/name/7b7c2239-3836-4772-9bb4-0f9a9b17fd41/null/null/</a></p>
<p>instead of linking to <a href="https://portal.cybertaxonomy.org/salvador/cdm_dataportal/name/7b7c2239-3836-4772-9bb4-0f9a9b17fd41/null/null/">https://portal.cybertaxonomy.org/salvador/cdm_dataportal/name/7b7c2239-3836-4772-9bb4-0f9a9b17fd41/null/null/</a></p>
<p>So the duplicated occurrence/cdm_dataportal/ needs to be removed.</p>
<p>An example for <strong>identification</strong> mislinking can be found here: <a href="https://int.e-taxonomy.eu/dataportal/integration/reference/cdm_dataportal/occurrence/8259122c-7140-44f3-980e-1a6506ce8f50">https://int.e-taxonomy.eu/dataportal/integration/reference/cdm_dataportal/occurrence/8259122c-7140-44f3-980e-1a6506ce8f50</a></p>
feature request #10058 (New): Further improve specimen page (factual data, extensions, https://dev.e-taxonomy.eu/redmine/issues/100582022-05-12T10:17:47ZAndreas Müller
<p>follow up for <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Improve specimen page (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6866">#6866</a></p>
<p>In <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Improve specimen page (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6866">#6866</a> data has been atomized and structured already. However, there are datatypes missing. Some of them important.</p>
<p>Important:</p>
<ul>
<li>facts (<a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: specimen page: character data displayed in details section (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9584">#9584</a>)</li>
<li>original label Info</li>
<li>sex</li>
<li>identifiers (supplemental data)</li>
</ul>
<p>Less important:</p>
<ul>
<li>extensions (supplemental data)</li>
<li>credits (supplemental data)</li>
<li>rights (supplemental data)</li>
</ul>
<p>Usage information:</p>
<ul>
<li>from taxon descriptions (individuals associations)</li>
<li>from specimen descriptions (individuals associations) - rare usecase</li>
<li>from name descriptions (individuals associations) - rare usecase</li>
</ul>
<p>Please also test </p>
<ul>
<li>preservation method, life stage and typification as I did not test them.</li>
</ul>
<p>For field units the following (additional) fields are missing:</p>
<ul>
<li>Colecting Method</li>
<li>Gathering Event Description</li>
<li>All(?) supplemental data (tested for annotations and extensions)</li>
<li>Ecology and plant Description (specific factual data used in field unit facade)</li>
<li>Field notes</li>
<li>Individual count</li>
<li>Not tested: kind-of-unit, life stage</li>
</ul>
<p>I only tested specimens (derived units) and field units. Improvements for media specimens are handled in <a class="issue tracker-5 status-1 priority-10 priority-lowest" title="feature request: Missing data and layout improvements for MediaSpecimen in data portal (New)" href="https://dev.e-taxonomy.eu/redmine/issues/3756">#3756</a>. Dna samples still need to be tested (<a class="issue tracker-6 status-2 priority-12 priority-high14" title="task: Check if all molecular data is shown correctly in data portal [also DISCUSS] (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/3749">#3749</a>).</p>
<ul>
<li>Also improve handling of derivation events (currently shown "Accessioning" should be removed, maybe it can be included into the tree in some way)</li>
</ul>
<p>Also the layout/display for Media could be improved and dicussion is needed if the general layout could be improved (see examples from <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Improve specimen page (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6866">#6866</a> for comparison).</p>
<p>For stored under we may not want the fullTitleCache but titleCache might be enough as the name is linked.</p>
feature request #10003 (Closed): Implement specimen status in Data portalhttps://dev.e-taxonomy.eu/redmine/issues/100032022-03-28T11:19:01ZAndreas Müller
<p>see <a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: (Type-) Specimens may need status (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/2506">#2506</a> for information on the "status" attribute</p>
<p>The information is already shown in long labels but not for atomized data everywhere where atomized data is shown (Derivate tree, Derivate path and Compressed derivate table). Needs probably discussion on details where and how to show it.</p>
<p>Write tests!</p>
feature request #9879 (New): Short title for field and derived unitshttps://dev.e-taxonomy.eu/redmine/issues/98792021-11-22T20:57:57ZAndreas Müller
<p>WGB:</p>
<p>Der <strong>Titel</strong> mit seinem langen Text ist sehr groß – folgt vermutlich dem normalen Titelformat – kann man das kleiner setzen? <br>
Und die alte Frage nach der Konkatenation des Aufsammlungsstrings. In der Botanik wird eine Aufsammlung in der Regel durch Sammler und Sammelnummer identifiziert – normalerweise gefolgt vom Ort. Ort ist hier unpraktisch, da der Bezug nicht unbedingt klar ist (es sind ja nicht nur Herbarbelege, aber Sammler + Sammelnummer als erstes im Titel wäre doch möglich? Noch schöner wäre nur Sammler und Sammelnummr als <strong>Titel und der Rest als Daten</strong>:</p>
<a name="T-Leyens-CV-94-124"></a>
<h1 >T. Leyens CV-94-124<a href="#T-Leyens-CV-94-124" class="wiki-anchor">¶</a></h1>
<a name="Cape-Verde-Republic-of-Brava-Road-Vila-n-Cintra-NS-do-Monte-Before-bifurcation-with-road-to-Faja-da-Agua-alt-540-m-14524N-244224W-30-Jan-1994"></a>
<h2 >Cape Verde, Republic of, Brava, Road Vila n. Cintra, N.S. do Monte, Before bifurcation with road to Faja da Agua, alt. 540 m, 14°52'4"N, 24°42'24"W, 30 Jan 1994.<a href="#Cape-Verde-Republic-of-Brava-Road-Vila-n-Cintra-NS-do-Monte-Before-bifurcation-with-road-to-Faja-da-Agua-alt-540-m-14524N-244224W-30-Jan-1994" class="wiki-anchor">¶</a></h2>
<p>====</p>
<p>Note: this is not a duplicate for <a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Specimen Tree View: option to choose summaryLabel or collectingString for fieldUnit label (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9715">#9715</a> but is about the title of specimen and field unit pages. <a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Specimen Tree View: option to choose summaryLabel or collectingString for fieldUnit label (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9715">#9715</a> implements the label used e.g. in the derivation tree. </p>
<p>====</p>
<p>Similar to the implementation in <a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Specimen Tree View: option to choose summaryLabel or collectingString for fieldUnit label (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9715">#9715</a> it should be configurable if </p>
<ul>
<li>only the short title is shown</li>
<li>the short title is shown and additionally the long title is shown as subtitle or ordinary "citation" text</li>
<li>only the long title is shown</li>
</ul>
feature request #9584 (Closed): specimen page: character data displayed in details section https://dev.e-taxonomy.eu/redmine/issues/95842021-04-21T09:33:09ZAndreas Kohlbecker
<p>In the specimen page character data is shown as link which points again to the same specimen. This is OK for the specimen tree view which uses the same code. In the Specimen page, character data should be instead displayed in the details section. This always should point to the details view of the character data otherwise the character data are never shown.</p>
<p>Actually the character data only displayed in derivate path view!</p>
<p>Suggestion:</p>
<p>Create an extra part for the character data like for media and identification</p>
bug #9580 (New): more symbols for record basis (and kind of unit) in derivation tree - coninuationhttps://dev.e-taxonomy.eu/redmine/issues/95802021-04-14T15:15:24ZAndreas Kohlbecker
<p>this is a continuation ticket for <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: symbols for record basis (and kind of unit) in derivation tree (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/9555">#9555</a></p>
<p>show symbols with the units-header per record basis and kind of unit if needed</p>
<p>Icon fonts:</p>
<ul>
<li><a href="https://feathericons.com/">https://feathericons.com/</a></li>
<li><a href="https://fontawesome.com/icons">https://fontawesome.com/icons</a></li>
</ul>
<p>A quickly assembled list:</p>
<p><strong>record basis</strong></p>
<ul>
<li>DerivedUnit</li>
<li>DnaSample: <a href="https://fontawesome.com/icons/dna?style=solid">https://fontawesome.com/icons/dna?style=solid</a></li>
<li>FieldUnit: <a href="https://fontawesome.com/icons/mountain?style=solid">https://fontawesome.com/icons/mountain?style=solid</a> or <a href="https://fontawesome.com/icons/map-marker-alt?style=solid">https://fontawesome.com/icons/map-marker-alt?style=solid</a></li>
<li>Fossil: <a href="https://fontawesome.com/icons/bone?style=solid">https://fontawesome.com/icons/bone?style=solid</a></li>
<li>HumanObservation: <a href="https://fontawesome.com/icons/eye?style=solid">https://fontawesome.com/icons/eye?style=solid</a></li>
<li>LivingSpecimen: <a href="https://fontawesome.com/icons/tree?style=solid">https://fontawesome.com/icons/tree?style=solid</a></li>
<li>MachineObservation: <a href="https://fontawesome.com/icons/binoculars?style=solid">https://fontawesome.com/icons/binoculars?style=solid</a></li>
<li>MaterialSample</li>
<li>Media</li>
<li>MovingImage: <a href="https://fontawesome.com/icons/film?style=solid">https://fontawesome.com/icons/film?style=solid</a></li>
<li>Multimedia: <a href="https://fontawesome.com/icons/photo-video?style=solid">https://fontawesome.com/icons/photo-video?style=solid</a></li>
<li>Observation: <a href="https://fontawesome.com/icons/binoculars?style=solid">https://fontawesome.com/icons/binoculars?style=solid</a></li>
<li>OtherSpecimen</li>
<li>PreservedSpecimen: <a href="https://fontawesome.com/icons/pagelines?style=brands">https://fontawesome.com/icons/pagelines?style=brands</a> or <a href="https://fontawesome.com/icons/leaf?style=solid">https://fontawesome.com/icons/leaf?style=solid</a> or <a href="https://feathericons.com/">https://feathericons.com/</a> 'archive'?</li>
<li>SoundRecording: <a href="https://fontawesome.com/icons/microphone?style=solid">https://fontawesome.com/icons/microphone?style=solid</a></li>
<li>StillImage: <a href="https://fontawesome.com/icons/image?style=solid">https://fontawesome.com/icons/image?style=solid</a></li>
<li>TissueSample: <a href="https://fontawesome.com/icons/cut?style=solid">https://fontawesome.com/icons/cut?style=solid</a>,</li>
<li>Unknown: DEFAULT-Symbol: <a href="https://fontawesome.com/icons/archive?style=solid">https://fontawesome.com/icons/archive?style=solid</a> ?? <a href="https://fontawesome.com/icons/cube?style=solid">https://fontawesome.com/icons/cube?style=solid</a></li>
</ul>
<p><strong>kind of unit</strong></p>
<ul>
<li>Culture: <a href="https://fontawesome.com/icons/flask?style=solid">https://fontawesome.com/icons/flask?style=solid</a></li>
</ul>
bug #9557 (Closed): implement occurrence/{uuid}/rootUnitDTOs https://dev.e-taxonomy.eu/redmine/issues/95572021-03-25T16:54:47ZAndreas Kohlbecker
<p>see <a href="http://int.e-taxonomy.eu/cdmserver/integration_reference/occurrence/8259122c-7140-44f3-980e-1a6506ce8f50/fieldUnitDTOs.json">http://int.e-taxonomy.eu/cdmserver/integration_reference/occurrence/8259122c-7140-44f3-980e-1a6506ce8f50/fieldUnitDTOs.json</a></p>
<hr>
<p><strong>UPDATE</strong>:</p>
<p>Subject changed from "<em>ccurrence/{uuid}/fieldUnitDTOs returns null element when fieldUnit is missing</em>"</p>
bug #9556 (Closed): occurrence/{uuid}/fieldUnitDTOs web service adds duplicate units to responsehttps://dev.e-taxonomy.eu/redmine/issues/95562021-03-25T16:52:18ZAndreas Kohlbecker
<p>see <a href="http://localhost:8080/occurrence/8585081c-b73b-440b-b349-582845cf3fb4/fieldUnitDTOs.json">http://localhost:8080/occurrence/8585081c-b73b-440b-b349-582845cf3fb4/fieldUnitDTOs.json</a> </p>
<p>the response data may be filtered with </p>
<pre>http http://localhost:8080/occurrence/8585081c-b73b-440b-b349-582845cf3fb4/fieldUnitDTOs.json | jq '.' | grep 'XKCD MASKS 2X (Masks)'
</pre>
<p>to see duplicates easily</p>
bug #9555 (Closed): symbols for record basis (and kind of unit) in derivation treehttps://dev.e-taxonomy.eu/redmine/issues/95552021-03-25T16:22:47ZAndreas Kohlbecker
<p>show symbols with the units-header per record basis and kind of unit if needed</p>
<p>A quickly assembled list:</p>
<p><strong>record basis</strong></p>
<ul>
<li>DerivedUnit</li>
<li>DnaSample: <a href="https://fontawesome.com/icons/dna?style=solid">https://fontawesome.com/icons/dna?style=solid</a></li>
<li>FieldUnit: <a href="https://fontawesome.com/icons/mountain?style=solid">https://fontawesome.com/icons/mountain?style=solid</a> or <a href="https://fontawesome.com/icons/map-marker-alt?style=solid">https://fontawesome.com/icons/map-marker-alt?style=solid</a></li>
<li>Fossil: <a href="https://fontawesome.com/icons/bone?style=solid">https://fontawesome.com/icons/bone?style=solid</a></li>
<li>HumanObservation: <a href="https://fontawesome.com/icons/eye?style=solid">https://fontawesome.com/icons/eye?style=solid</a></li>
<li>LivingSpecimen: <a href="https://fontawesome.com/icons/tree?style=solid">https://fontawesome.com/icons/tree?style=solid</a></li>
<li>MachineObservation: <a href="https://fontawesome.com/icons/binoculars?style=solid">https://fontawesome.com/icons/binoculars?style=solid</a></li>
<li>MaterialSample</li>
<li>Media</li>
<li>MovingImage: <a href="https://fontawesome.com/icons/film?style=solid">https://fontawesome.com/icons/film?style=solid</a></li>
<li>Multimedia: <a href="https://fontawesome.com/icons/photo-video?style=solid">https://fontawesome.com/icons/photo-video?style=solid</a></li>
<li>Observation: <a href="https://fontawesome.com/icons/binoculars?style=solid">https://fontawesome.com/icons/binoculars?style=solid</a></li>
<li>OtherSpecimen</li>
<li>PreservedSpecimen: <a href="https://fontawesome.com/icons/pagelines?style=brands">https://fontawesome.com/icons/pagelines?style=brands</a> or <a href="https://fontawesome.com/icons/leaf?style=solid">https://fontawesome.com/icons/leaf?style=solid</a></li>
<li>SoundRecording: <a href="https://fontawesome.com/icons/microphone?style=solid">https://fontawesome.com/icons/microphone?style=solid</a></li>
<li>StillImage: <a href="https://fontawesome.com/icons/image?style=solid">https://fontawesome.com/icons/image?style=solid</a></li>
<li>TissueSample: <a href="https://fontawesome.com/icons/cut?style=solid">https://fontawesome.com/icons/cut?style=solid</a>,</li>
<li>Unknown: DEFAULT-Symbol: <a href="https://fontawesome.com/icons/archive?style=solid">https://fontawesome.com/icons/archive?style=solid</a> ?? <a href="https://fontawesome.com/icons/cube?style=solid">https://fontawesome.com/icons/cube?style=solid</a></li>
</ul>
<p><strong>kind of unit</strong></p>
<ul>
<li>Culture: <a href="https://fontawesome.com/icons/flask?style=solid">https://fontawesome.com/icons/flask?style=solid</a></li>
</ul>
bug #9543 (New): Revise, harmonize media list in SpecimenOrObservationBaseDTO vs. DerivedUnitFaca...https://dev.e-taxonomy.eu/redmine/issues/95432021-03-22T13:38:01ZAndreas Kohlbecker
<p><code>DerivedUnitFacade.getMediaTextData()</code> is being used to provide the media lists for the <code>DerivedUnit</code> and <code>FieldUnit</code> represented by the <code>DerivedUnitFacade</code> This implementation only covers the media stored in the "ObservationImageGalleryTextData" <br>
A parallel implementation exist in <code>SpecimenOrObservationBaseDTO.collectMedia(SpecimenOrObservationBase<?> specimenOrObservation)</code> </p>
feature request #9388 (New): show media specimen source in all pageshttps://dev.e-taxonomy.eu/redmine/issues/93882021-01-14T12:27:54ZAndreas Kohlbecker
<p>By now the <code>MediaSpecimen.media.souces.citation</code> is only shown in the registration page:</p>
<p>Registration page for </p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1995/picture257-1.png" alt="" /></p>
<p>Name page (<a href="https://www.phycobank.org/cdm_dataportal/name/2e0dfdc0-1ec5-4e2c-a7c1-fe5882355c74/null/null/):">https://www.phycobank.org/cdm_dataportal/name/2e0dfdc0-1ec5-4e2c-a7c1-fe5882355c74/null/null/):</a></p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1996/picture257-2.png" alt="" /></p>
<p>Taxon page (<a href="https://www.phycobank.org/cdm_dataportal/taxon/af65a4f2-cf79-46ee-bac5-75b689ff8522):">https://www.phycobank.org/cdm_dataportal/taxon/af65a4f2-cf79-46ee-bac5-75b689ff8522):</a></p>
<p><img src="https://dev.e-taxonomy.eu/redmine/attachments/download/1997/picture257-3.png" alt="" /></p>
<p>It should be made visible in all places where specimens are to be displayed. This especially accounts for sources of the type <code>PrimaryMediaSource</code>, but a restrition to this type only might not necessary. </p>
<p>URLs are to be shown as external link icon.</p>
feature request #9250 (New): collection page implementedhttps://dev.e-taxonomy.eu/redmine/issues/92502020-10-12T12:48:15ZAndreas Kohlbecker
<p>also enable link rendering in <code>function render_collection($collection, $do_link = false )</code> by changing the default if the <code>$do_link</code> parameter</p>
feature request #9249 (Closed): compact display of collection informationhttps://dev.e-taxonomy.eu/redmine/issues/92492020-10-12T12:22:12ZAndreas Kohlbeckerbug #7606 (Duplicate): compact display of CDM Point datahttps://dev.e-taxonomy.eu/redmine/issues/76062018-07-31T09:08:58ZAndreas Kohlbecker
<p>Point data like the exact location in gathering events should be displayed in a compact form including the </p>
<ul>
<li>sexagesimalString</li>
<li>errorRadius as "+/- {errorRadius}m"</li>
<li>referenceSystem</li>
</ul>
<p>create the method <code>render_point($point){}</code> in common.inc</p>
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>