EDIT Project Management: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852021-01-20T18:08:46ZEDIT Project Management
Redmine EDIT - feature request #9406 (Rejected): Open issue for Edaphobase rank web servicehttps://dev.e-taxonomy.eu/redmine/issues/94062021-01-20T18:08:46ZAndreas Müller
<p>follow up for <a class="issue tracker-5 status-5 priority-10 priority-lowest closed child" title="feature request: Improve Rank Webservice (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6133">#6133</a></p>
<p>Open issue:</p>
<ul>
<li>representations are not mapped to a language</li>
</ul>
EDIT - bug #7823 (Closed): User Persons are not deduplicatedhttps://dev.e-taxonomy.eu/redmine/issues/78232018-10-14T12:55:48ZAndreas Müller
<p>Persons related to users are often the same as they are only for different sec's.</p>
<p>We may want to deduplicate them.</p>
<p>===</p>
<p>Also we could deduplicate the users themselves as the rights management is differnt in CDM.</p>
EDIT - bug #7445 (Closed): Empty term uri and isoXXX fields should be nullhttps://dev.e-taxonomy.eu/redmine/issues/74452018-06-03T10:09:58ZAndreas Müller
<p>Term URIs are currently loaded as empty strings, not as NULL by DefinedTermBase.readCsv. This should be changed. Also existing data should be updated.</p>
<p>Update script will run in <a class="issue tracker-4 status-2 priority-12 priority-high14" title="bug: TermVocabularies of OrderedTerms must be OrderedVocabularies (In Progress)" href="https://dev.e-taxonomy.eu/redmine/issues/6343">#6343</a></p>
EDIT - bug #5284 (Duplicate): [UML] Replace Scope by DefinedTerm in PolytomousKey UMLhttps://dev.e-taxonomy.eu/redmine/issues/52842015-09-21T18:36:57ZAndreas Müller
<p>Replace Scope by DefinedTerm in PolytomousKey UML</p>
EDIT - bug #4915 (Closed): Abbrev title for person should never be orangehttps://dev.e-taxonomy.eu/redmine/issues/49152015-05-19T15:00:12ZAndreas Müller
<p>the abbreviated title of a person should never become orange as it is not a cache field. However it sometimes becomes orange.</p>
<p>What I did:</p>
<ul>
<li><p>Open Person or Team Bulk editor</p></li>
<li><p>create new Person (right click New-Author) => the new person is shown with protected white title cache and white abbrev. title</p></li>
<li><p>do any change in title cache => the abbrev. title becomes orange !!</p></li>
</ul>
<p>You may go further and unprotect the title cache => everything becomes white and then protect it and again everything incluging abbrev title becomes orange</p>
<p>related to <a class="issue tracker-4 status-5 priority-13 priority-high13 closed child" title="bug: "Protected" indication for references needs to be improved (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/4944">#4944</a>, for general implementation issues see there.</p>
<p>see also #4912</p>
EDIT - bug #4821 (Closed): Changing order of terms not possiblehttps://dev.e-taxonomy.eu/redmine/issues/48212015-04-24T08:46:42ZAndreas Müller
<p>When trying to change the order of an ordered term vocabulary (e.g. Presence Absence Term) by moving an existing term in between 2 other terms the term is added as a child to the above term instead of just changing the order.</p>
EDIT - bug #4773 (Worksforme): Lampranthus throws IndexOutOfRange exceptionhttps://dev.e-taxonomy.eu/redmine/issues/47732015-04-01T15:21:13ZAndreas Müller
<p>Opening Lampranthus in Caryophyllales results in an IndexOutOfRange exception. </p>
<p>Reason was: Aristanthus Schwantes had a "Generic" nom. ref. with a Journal as in-reference. The results in null when calling inRef.getNomenclaturalCitation(String).</p>
<p>Error was:</p>
<pre>java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(Unknown Source)
at eu.etaxonomy.cdm.strategy.cache.reference.NomRefDefaultCacheStrategyBase.replaceMicroRefToken(NomRefDefaultCacheStrategyBase.java:165)
at eu.etaxonomy.cdm.strategy.cache.reference.NomRefDefaultCacheStrategyBase.getNomenclaturalCitation(NomRefDefaultCacheStrategyBase.java:151)
at eu.etaxonomy.cdm.model.reference.Reference.getNomenclaturalCitation(Reference.java:1010)
at eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy.getTaggedFullTitle(NonViralNameDefaultCacheStrategy.java:449)
at eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy.getFullTitleCache(NonViralNameDefaultCacheStrategy.java:190)
at eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy.getFullTitleCache(NonViralNameDefaultCacheStrategy.java:201)
at eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy.getFullTitleCache(NonViralNameDefaultCacheStrategy.java:1)
at eu.etaxonomy.cdm.model.name.NonViralName.generateFullTitle(NonViralName.java:719)
at eu.etaxonomy.taxeditor.model.NameHelper.getDisplayNameWithRef(NameHelper.java:55)
at eu.etaxonomy.taxeditor.editor.name.container.AbstractGroupedContainer.initTextViewer(AbstractGroupedContainer.java:289)
at eu.etaxonomy.taxeditor.editor.name.container.SynonymContainer.initializeComposite(SynonymContainer.java:68)
...
</pre> 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 #2925 (Worksforme): [DISCUSS]Do we need newly created objects for EntityCollectionSec...https://dev.e-taxonomy.eu/redmine/issues/29252012-06-20T11:21:07ZAndreas Müller
<p>In AbstractEntityCollectionSection.createToolbar the add-Action requries createNewElement().</p>
<p>Is this really needed?</p>
<p>It creates strange looking result e.g. for adding a Scope to a DescriptionBase</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>
EDIT - feature request #2584 (Worksforme): Show loading information for "Referencing Objects"https://dev.e-taxonomy.eu/redmine/issues/25842011-09-06T13:01:23ZAndreas Müller
<p>Currently it is impossible to know if the referencing objects view is empty because there are no referencing objects or because it is still loading.</p>
<p>Some info like "loading..." whould be nice.</p>
<p>see also #4537</p>
EDIT - feature request #1080 (Closed): Model changes for references, taxonBase, OriginalSourcehttps://dev.e-taxonomy.eu/redmine/issues/10802009-09-21T00:02:15ZAndreas Müller
<p>Dear All,</p>
<p>I would like to inform you that I was working on some model changes the last days. I committed them to the trunk so you will find the changes in the svn.</p>
<p>The changes are:</p>
<p>1) References: </p>
<p>1a) I added a new field "refererenceAbstract" to the referenceBase class</p>
<p>1b) I deleted the BibtexReference class -> as a result I merged the StrictReferenceBase class into the referenceBase class and deleted StrictReferenceBase</p>
<p>1c) I deleted BibTexEntryType and it's DefinedTerm csv file</p>
<p>1d) I moved all attributes of referenceBase subclasses to referenceBase. The according methods in the subclasses are passed through to the base class. At the same time created an Enum ReferenceType the represents all the subclasses an is an attribute in referenceBase.</p>
<p>This is the first step to remove the subclasses completedly (at least for persistence) which makes e.g. casting much easier. The type check will probably removed by hibernate validation later.</p>
<p>1e) I removed the attributes inSeries, inProceedings, inBook, inJournal by the one attribute inReference.</p>
<p>1f) I removed the "Publisher" class (this was an old class not in use anymore)</p>
<p>2) TaxonBase: I added an string field "appendedPhrase" and a boolean field "useNameCache". The first is used to add a concept related phrase like "sensu latu" to the pure name used for the taxon. The second is used to use only the names name cache instead the title cache. This is sometimes needed in combination with the appended phrase attribute.</p>
<p>I still have to adapt the according cache strategy!</p>
<p>3) I changed the molecular.Sequence.dataSequenced field from Calendar to joda times DateTime. Now all Calendar types should be removed by joda time types.</p>
<p>4) I added a boolean field "isTechnical" to MarkerType. This way we can differentiate between markers for user defined content (to be shown in applications) and markers that are just to be read by machines and define e.g. a role of on object (e.g. a FeatureTree may have different, these roles may be defined by markers, this is not an information a user needs but usually just a machine).</p>
<p><img alt="" /></p>
<p>Problems to be solved:</p>
<p>=============================</p>
<p>1) Most tests are running. The only test I know that it is not running (except for cdmlib-remote tests) is in io.jaxb.ReferenceTest.</p>
<p>@Anahit, Katja, Ben: <del>Could you please try to fix this test? Also the JAXB import and export or at least the schema may be broken. This should be fixed too.</del></p>
<p><del>The cdmlib-remobe tests also seem to be broken. Andreas K. & Ben could you please try to fix them?</del> </p>
<p>2) ReferenceBase.inReference: I deleted the @IndexedEmbedded annotation because I just hadn't time to check how to use it correctly. I will try tomorrow.</p>
<p>@Ben: Do you have a hint? I think you added this annotation to the in-references</p>
<p>I hadn't have time to test the new model intensively yet (except for unit and integeration tests). A first try with diptera seems to be successful. But please be aware that some problems could appear when updating (please just let me know immidiately)</p>
<p>Cheers,</p>
<p>Andreas M.</p>
EDIT - feature request #922 (Closed): Implement compareTo method in IdentifiableEntity properlyhttps://dev.e-taxonomy.eu/redmine/issues/9222009-08-17T11:02:01ZAndreas Müller
<p>At the moment there is just one method that uses case differentiation instead of using the inheritance.</p>
<p>Either overwrite compoareTo or use abstract methods to get relevant information from subclasses</p>
EDIT - task #615 (Closed): remove suns repositoryhttps://dev.e-taxonomy.eu/redmine/issues/6152009-02-26T15:26:12ZAndreas Müller
<p><a href="http://raibledesigns.com/rd/entry/upgrading_hibernate_to_3_4:">http://raibledesigns.com/rd/entry/upgrading_hibernate_to_3_4:</a> </p>
<p>... <a href="http://repository.jboss.com/maven2">http://repository.jboss.com/maven2</a> as a permanent repository. As a bonus, you can remove <a href="http://download.java.net/maven/2">http://download.java.net/maven/2</a> since JTA is in JBoss's repo.</p>
<p>see also #4779</p>