EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852020-01-15T10:08:05ZEDIT Project Management
Redmine feature request #8803 (Closed): Add "per mm²" to measurement unitshttps://dev.e-taxonomy.eu/redmine/issues/88032020-01-15T10:08:05ZAndreas Müller
<p>This is needed for some Cactaceae characters</p>
task #8786 (Resolved): Display of mean value with min max https://dev.e-taxonomy.eu/redmine/issues/87862019-12-19T16:08:22ZAndreas Kohlbecker
<blockquote>
<p>abgesehen davon, dass die Mittelwertangabe zwischen Min und Max unüblich ist, ... Eine bessere Darstellung wäre ", mean = xx hinter Min+Max .</p>
</blockquote>
<p>Wir haben wir diese kompaktere Darstellung implementiert, die zudem auf Angaben zu den TypicalBounds erlaubst. Das Schema hierzu sieht erkklärt anhand eines Beispiels folgendermaßen aus</p>
<pre>
(1.0)-1.2-2.2-3.1-(3.3)
(1.0)= Min (Extremwert)
1.2 = TypicalLowerBound
2.2. = Mittelwert
3.1 = TypicalUpperBound
(3.3) = Max (Extremwert)
</pre>
<p>Ich bin bisher davon ausgegangen, dieses Schema so in Additivity besprochen und beschlossen worden ist.<br>
Vielleicht könnt Ihr das nochmal im Projektteam klären.</p>
<p>Als Ergebnis der unterstehenden Diskussion haben wir uns auf folgendes <strong>neues Schema</strong> geeinigt:</p>
<pre>
(1.0–)1.2–3.1(–3.3)[9;x̄=2.2]
(1.0)= Min (Extremwert)
1.2 = TypicalLowerBound
3.1 = TypicalUpperBound
(3.3) = Max (Extremwert)
Use the n-dash "–"
in brackets []:
9 = Sample Size
x̄ (x-bar) denotes the mean value
all other values like variance and standard deviation follow the mean value, see #8766
</pre>
<p>As caption for the aggregated description and for the description table <em>"A single or the first number in square brackets denotes sample size"</em> </p>
feature request #8781 (Closed): Descriptions (aggregated): futher improvementshttps://dev.e-taxonomy.eu/redmine/issues/87812019-12-18T11:08:26ZAndreas Kohlbecker
<p>Hallo Andreas,</p>
<ol>
<li>am Ende der aggregated descriptions gibt es derzeit im noch ein überflüssiges Komma. Könntest du das löschen? - <strong>DONE</strong></li>
<li>... und ich denke der erste Character sollte immer mit einem Großbuchstaben beginnen.</li>
</ol>
<p>Viele Grüße,<br>
Andreas M.</p>
bug #8779 (Closed): Description page: use render_taxon_or_name() for creating the page and descri...https://dev.e-taxonomy.eu/redmine/issues/87792019-12-17T14:20:20ZAndreas Kohlbecker
<p>in <code>compose_description_table()</code> the <code>render_taxon_or_name()</code> method must be used for portal wide consistend display of taxa and names </p>
feature request #8771 (Resolved): display of average value with precision so that it differs from...https://dev.e-taxonomy.eu/redmine/issues/87712019-12-17T08:07:24ZAndreas Kohlbecker
<p>The display of decimal place for average value should be adjusted so that it differs from the values on min and max (typical upper and lower bound) by one digit. The number of visible decimal places should not be lower than that of the least precise min or max value</p>
<p>e.g (min - mean - max).:</p>
<ul>
<li>12.23 - 13.2345 - 14.2 => <strong>12.23 - 13.2 - 14.2</strong></li>
<li>5 - 4.234325 - 6 => <strong>5 - 4 - 6</strong></li>
<li>6.3467 - 6.3477 - 6.3482 => <strong>6.3467 - 6.347 - 6.3482</strong> </li>
<li>0.00000001 - 0.500000001 - 1 => <strong>0.00000001 - 0.5 - 1</strong></li>
<li>0.123457- 0.1234565 - 0.123456 => <strong>0.123457- 0.1234565 - 0.123456</strong></li>
</ul>
bug #8765 (Resolved): defined weight for feature and pseudo feature blocks and position "Descript...https://dev.e-taxonomy.eu/redmine/issues/87652019-12-12T14:45:35ZAndreas Kohlbecker
<p><em>recovery from accidentally deleted previous ticket #8658</em></p>
<hr>
<p>copied from <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Add a list of descriptions to the taxon page (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8596#note-8">#8596#note-8</a></p>
<ul>
<li>weight value for all blocks, increment by 2 or more</li>
<li>place "Description (aggregated)" after "Description" if both exists</li>
<li>assure the same order is applied to the toc</li>
</ul>
feature request #8758 (Closed): Aggregated Descriptions: order states by frequencyhttps://dev.e-taxonomy.eu/redmine/issues/87582019-12-11T12:10:01ZAndreas Kohlbecker
<p>Most frequent states should be displayed first.</p>
<p>Another option to order the stated would be the term order as defined in the db. According to the users, implementing this order is not explicitly wanted, so we will only implement order by ferquency by now. </p>
bug #8745 (Closed): Type designations of synonyms missing on specimen pagehttps://dev.e-taxonomy.eu/redmine/issues/87452019-12-05T15:31:34ZKatja Luther
<p>Type designations of synonyms are missing in the compressed specimen page.</p>
<p>mail NK:</p>
<p>Es geht darum, dass von den sechs auf <a href="http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/216b08ec-2088-49c7-b3e5-37d3e0eaf546/synonymy">http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/216b08ec-2088-49c7-b3e5-37d3e0eaf546/synonymy</a> aufgeführten Typen, nur der des akzeptierten Namens im Specimen-Tab(!) aufgeführt wird. </p>
<p>Ich habe gestern schon mit Patrick darüber gesprochen: Es wäre zu prüfen, ob beim Einsammeln der Specimens zu einem Taxon eventuell die Typen der heterotypischen Synonyme nicht (mehr?) eingesammelt werden. Da Patrick in seinen wenigen letzten Arbeitstagen noch genug mit dem Projektabschluss zu tun hat, kann er sich darum nicht mehr kümmern.</p>
bug #8739 (Closed): remaining issues for description detail pagehttps://dev.e-taxonomy.eu/redmine/issues/87392019-12-03T11:17:06ZPatrick Plitzner
<p>Copied from <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Create description detail page (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8595">#8595</a></p>
<ul>
<li>Evtl. will man auf aggr. Description von höheren Taxa nicht die Specimen als Quellen anzeigen, sondern die niedrigeren aggr. Description.</li>
</ul>
<p>AM: Generally all descriptive data should be shown, not only structured descriptions. E.g. distribution data is still missing. => <a class="issue tracker-4 status-1 priority-12 priority-high14" title="bug: Description page must show all DescriptionElement subclasses (New)" href="https://dev.e-taxonomy.eu/redmine/issues/8687">#8687</a></p>
<hr>
<a name="TODOs-from-Code-review"></a>
<h2 >TODOs from Code review:<a href="#TODOs-from-Code-review" class="wiki-anchor">¶</a></h2>
<p><strong>1.</strong></p>
<p><strong>DONE</strong></p>
<p>description.inc#1179 : </p>
<pre><code class="php syntaxhl"><span class="nv">$enclosing_tag</span> <span class="o">=</span> <span class="nf">cdm_feature_block_element_tag_name</span><span class="p">(</span><span class="nv">$feature_block_settings</span><span class="p">);</span>
</code></pre>
<p>is unused, this breaks the feature block setting as_list (old bug)</p>
<p><strong>2.</strong> Don't use <code><i></code> and <code><br></code> etc to apply styling, all styling must be applied through css</p>
<p><strong>DONE</strong> <a class="changeset" title="ref #8739 labels of CategoricalData and QuatitativeData stylable" href="https://dev.e-taxonomy.eu/redmine/projects/edit/repository/cdm-dataportal/revisions/bea708138e1c882a1551164f13b189a3ddb2ec4c">cdm-dataportal|bea70813</a> & <a class="changeset" title="ref #8739 description page better and stylable DOM" href="https://dev.e-taxonomy.eu/redmine/projects/edit/repository/cdm-dataportal/revisions/753a8083c89db261fe98babe4e10eb2fd1e2301e">cdm-dataportal|753a8083</a> </p>
<ol>
<li>pages.inc: <code>render_cdm_description_link()</code> ...</li>
<li>pages.inc: <code>$render_array[] = markup_to_render_array("Aggregation source from ".$description->created.'<br><br>');</code></li>
<li>pages.inc: render_cdm_description() - <code>$detail_html = (empty($description_string)?$link_text:$description_string).$iconlink."<br><br>";</code></li>
<li>pages.inc: render_description_string() </li>
</ol>
<pre><code class="php syntaxhl"> <span class="nv">$descriptionString</span> <span class="mf">.</span><span class="o">=</span> <span class="s1">'<i>'</span> <span class="mf">.</span> <span class="nv">$element</span><span class="o">-></span><span class="n">feature</span><span class="o">-></span><span class="n">representation_L10n</span> <span class="mf">.</span> <span class="s1">'</i>: '</span> <span class="mf">.</span> <span class="nv">$state_data</span> <span class="mf">.</span> <span class="s2">"; "</span><span class="p">;</span>
<span class="p">}</span>
<span class="k">break</span><span class="p">;</span>
<span class="k">case</span> <span class="s1">'QuantitativeData'</span><span class="o">:</span>
<span class="nv">$descriptionString</span> <span class="mf">.</span><span class="o">=</span> <span class="s1">'<i>'</span> <span class="mf">.</span> <span class="nv">$element</span><span class="o">-></span><span class="n">feature</span><span class="o">-></span><span class="n">representation_L10n</span> <span class="mf">.</span> <span class="s1">'</i>: '</span> <span class="mf">.</span> <span class="nf">compose_quant_stats</span><span class="p">(</span><span class="nv">$element</span><span class="p">)</span> <span class="mf">.</span> <span class="s2">"; "</span><span class="p">;</span>
</code></pre>
<ol>
<li>pages.inc: compose_cdm_description()</li>
</ol>
<pre><code class="php syntaxhl"><span class="k">if</span> <span class="p">(</span><span class="k">isset</span><span class="p">(</span><span class="nv">$description</span><span class="o">-></span><span class="n">describedSpecimenOrObservation</span><span class="p">))</span> <span class="p">{</span>
<span class="nv">$render_array</span><span class="p">[]</span> <span class="o">=</span> <span class="nf">markup_to_render_array</span><span class="p">(</span><span class="s2">"<b>Specimen</b><br>"</span><span class="p">);</span>
<span class="nv">$render_array</span><span class="p">[]</span> <span class="o">=</span> <span class="nf">markup_to_render_array</span><span class="p">(</span><span class="nf">render_cdm_specimen_link</span><span class="p">(</span><span class="nv">$description</span><span class="o">-></span><span class="n">describedSpecimenOrObservation</span><span class="p">));</span>
<span class="p">}</span>
<span class="k">if</span> <span class="p">(</span><span class="k">isset</span><span class="p">(</span><span class="nv">$description</span><span class="o">-></span><span class="n">taxon</span><span class="p">))</span> <span class="p">{</span>
<span class="nv">$render_array</span><span class="p">[]</span> <span class="o">=</span> <span class="nf">markup_to_render_array</span><span class="p">(</span><span class="s2">"<b>Taxon</b><br>"</span><span class="p">);</span>
<span class="nv">$render_array</span><span class="p">[]</span> <span class="o">=</span> <span class="nf">markup_to_render_array</span><span class="p">(</span><span class="nf">render_cdm_taxon</span><span class="p">(</span><span class="nv">$description</span><span class="o">-></span><span class="n">taxon</span><span class="p">));</span>
<span class="p">}</span>
</code></pre>
<p><strong>SampleSize:</strong></p>
<p>diese Sache mit der SampleSize, die überall auftaucht, ist das schnell zu fixen? Das ist ziemlich irritierend. </p>
<ul>
<li>warum werden die nur bei einem Teil der Characters in Klammern (wie es sein sollte), bei den anderen aber als "92 Sample Size" ausgegeben?</li>
<li>wir sollten in der Tabelle im Header hinter "States" erklärend anfügen: "(bracketed numbers denote sample size)" oder so, ähnlich bei der Description ...</li>
</ul>
<p>===> <a class="issue tracker-4 status-5 priority-11 priority-default closed" title="bug: Aggregated Descriptions: show Sample size as [$SAMPLE_SIZE] (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8766">#8766</a></p>
<p><strong>Name der Description</strong></p>
<p>Da war ich ungenau. Wenn das Taxon einen TaxonName hat, sollte der TaxonName.titleCache genommen werden, sonst wird’s zu lang. Nur wenn taxon.getName() == null dann taxon.titleCache nehmen. Wäre jedenfalls mein Vorschlag und machen wir an vielen andere Stellen so. Auf der Seite kommt dann ja auch nochmal der Link, wenn man es genau haben will.</p>
<p>===> <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: Description page: use render_taxon_or_name() for creating the page and description title and taxo... (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8779">#8779</a> </p>
<hr>
<p>Hallo,</p>
<p>hier wie besprochen noch ein paar Anmerkungen zur Portaldarstellung<br>
zu <a href="http://test.e-taxonomy.eu/dataportal/preview/greece_bupleurum/cdm_dataportal/description/ff646ffe-0e6a-4edf-8aff-d3a5e0fdab11">http://test.e-taxonomy.eu/dataportal/preview/greece_bupleurum/cdm_dataportal/description/ff646ffe-0e6a-4edf-8aff-d3a5e0fdab11</a></p>
<ol>
<li>wir sollten in der Tabelle im Header hinter "States" erklärend anfügen: "(bracketed numbers denote sample size)" oder so, ähnlich bei der Description ... <strong>DONE</strong>: Note appears as caption below the table and feature block, the text is aligned right.</li>
<li>bei numerischen Characters wird immer noch am Ende die Specimen-Zahl ausgegeben als e.g. "10 SampleSize", auch hier sollte stehen "[10]" - <strong>DONE</strong></li>
<li><del>Bei "stem width" wird als Minimum "0" angegeben: wie kommt das? Dateneingabe- oder -ausgabe-Fehler?</del> <strong>REJETCED</strong>: this is a problem in the aggregation algorithm not in the dataportal.
<ul>
<li>es fehlt hier die Maßeinheit. Dateneingabe- oder -ausgabe-Fehler? - <strong>DONE</strong>: Problems solved by <a class="changeset" title="ref #8739 description page: solving problems with unit display, order and spacing" href="https://dev.e-taxonomy.eu/redmine/projects/edit/repository/cdm-dataportal/revisions/ad7fa57c0cb8bb61a5ac64bb19dfce2f87a85ffd">cdm-dataportal|ad7fa57c</a> but nothing visible yet due to missing data.</li>
<li>abgesehen davon, dass die Mittelwertangabe zwischen Min und Max unüblich ist, sind 4 Nachkommastellen mindestens 2 zuviel. Das lässt sich doch sicher angeben? ==> <a class="issue tracker-5 status-3 priority-10 priority-lowest" title="feature request: display of average value with precision so that it differs from min and max by one digit (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/8771">#8771</a></li>
<li>Eine bessere Darstellung wäre ", mean = xx hinter Min+Max . ==> <a class="issue tracker-6 status-3 priority-10 priority-lowest" title="task: Display of mean value with min max (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/8786">#8786</a></li>
</ul></li>
<li>Presence-Problematik: Hatten wir nicht mal eine Regel aufgestellt, wann die Angabe von Presence entfallen soll? Ganz schlimm: "Entire Plant present (28)"; siehe auch, im Gegensatz: "adventitious root presence present (2)"; spine presence present (2), absent(1)" ===> <a class="issue tracker-5 status-3 priority-11 priority-default" title="feature request: Description aggregation : suppress state present when more details are available (Resolved)" href="https://dev.e-taxonomy.eu/redmine/issues/8759">#8759</a></li>
<li>Die seq. Referenzen bei den Taxanahmen sollten in solchen Zusammenhängen unbedingt entfallen, das ist nur krude und völlig überflüssig, da es ja eine Link aufs Taxon gibt; eigentlich sind sogar die Taxonautoren entbehrlich. ==> <a class="issue tracker-4 status-5 priority-10 priority-lowest closed" title="bug: Description page: use render_taxon_or_name() for creating the page and description title and taxo... (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8779">#8779</a></li>
</ol>
<p>Schöne Grüße,<br>
Norbert</p>
bug #8738 (Closed): CdmLink.startPos and .endPos should allow Nullhttps://dev.e-taxonomy.eu/redmine/issues/87382019-12-02T09:55:23ZAndreas Müller
<p>The table was IntextReference before. After using it for class CdmLinkSource also the originally NOT NULL columns must allow NULL.<br>
An update script is needed for DBs create before CdmLinkSource was added.</p>
feature request #8724 (Closed): Allow OriginalSource to link to Taxonhttps://dev.e-taxonomy.eu/redmine/issues/87242019-11-27T13:25:21ZAndreas Müller
<p>When aggregating (or moving) data one may want to link to the taxon the data originally comes from so we need a possibility to link OriginalSource to taxa. This is generally implemented in <a class="issue tracker-5 status-5 priority-11 priority-default closed" title="feature request: Allow OriginalSource to link to other CDM objects (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/8673">#8673</a> already but we need to add the Taxon class to the ICdmTarget interface for final implementation.</p>
<p>Also "Link to Taxon" should be added to the "source modes" of aggregation. </p>
bug #8719 (Closed): installation profile 'CDM_Portal' causes Integrity constraint violation: 1048...https://dev.e-taxonomy.eu/redmine/issues/87192019-11-26T07:23:31ZAndreas Kohlbecker
<p>this bug has been discovered in the process of automatic creation of workshop servers (<code>server-scripts/workshop-setup</code>) </p>
<pre>exception 'PDOException' with message 'SQLSTATE[23000]: Integrity constraint violation: 1048 Column 'pages' cannot be null' in /var/www/drupal-7.32/includes/database/database.inc:2227
Stack trace:
#0 /var/www/drupal-7.32/includes/database/database.inc(2227): PDOStatement->execute(Array)
#1 /var/www/drupal-7.32/includes/database/database.inc(697): DatabaseStatementBase->execute(Array, Array)
#2 /var/www/drupal-7.32/includes/database/mysql/query.inc(36): DatabaseConnection->query('INSERT INTO {bl...',
Array, Array)
#3
/var/www/drupal-7.32/sites/_dataportal-production/modules/cdm_dataportal/profile/CDM_Portal/CDM_Portal.install(338):
InsertQuery_mysql->execute()
</pre> bug #8718 (Closed): polytomousKey page: better handling of invalid uuids https://dev.e-taxonomy.eu/redmine/issues/87182019-11-22T11:53:42ZAndreas Kohlbecker
<p>ich habe gerade gesehen, dass ein PolyKey, wenn dessen uuid nicht stimmt unschöne Fehler schmeißt:</p>
<p><a href="http://test.e-taxonomy.eu/dataportal/preview/greece_bupleurum/cdm_dataportal/polytomousKey/2e37d588-16c9-4e57-8b77-c33d3a63990a">http://test.e-taxonomy.eu/dataportal/preview/greece_bupleurum/cdm_dataportal/polytomousKey/2e37d588-16c9-4e57-8b77-c33d3a63990a</a></p>
<p>Hier sollten wir, genauso wie bei den Taxa eine "PK does not exist" Meldung einbauen.</p>
bug #8702 (Closed): Remove Not null constraint for uuid in AUD tableshttps://dev.e-taxonomy.eu/redmine/issues/87022019-11-19T12:47:04ZAndreas Müller
<p>Some databases do have uuid NOT NULL contraints in some _AUD tables. In caryo_spp I found the following tables with this problem, which is probably created by the model update script for these tables:</p>
<p>AmplificationResult_AUD<br>
CdmLink_AUD<br>
DnaQuality_AUD<br>
Identifier_AUD<br>
Registration_AUD</p>
<p>In other DBs also:</p>
<p>SingleReadAlignment_AUD<br>
TaxonNodeAgentRelation_AUD</p>
<p><del>The strange thing is that for caryo_nepenthes CdmLink_AUD does allow NULL for CdmLink_AUD (a very new model update) while in caryo_spp it is NOT NULL. While it is not very likely that someone changed this manually already it is not clear why the 2 databases were updated in a different way.</del> This is not so strange as CdmLink_AUD was only renamed, it was IntextReference before.</p>
<p>The exception that is thrwon otherwise is:</p>
<p>com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Column 'uuid' cannot be null is thrown.</p>
task #8468 (Closed): Remove old InapplicableIf tableshttps://dev.e-taxonomy.eu/redmine/issues/84682019-08-16T09:35:48ZAndreas Müller