https://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-12-14T23:58:55ZEcoinformatics RedmineKepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155622009-12-14T23:58:55ZDerik Barseghianbarseghian@nceas.ucsb.edu
<ul></ul><p>The problem in comment <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need more extensive element documentation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1">#1</a> was fixed some time ago.</p>
<p>Things seem to be working fine, but I notice the way the tags are serialized in a workflow vs the workflowRun are different.</p>
<p>E.g. <br />inside WorkflowRun:<br /> <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:lsid.ecoinformatics.org:onto:8:1#AboveGroundBiomassMeasurement"></p>
<p>inside workflow:<br /><property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:lsid.ecoinformatics.org:onto:8:1#AboveGroundBiomassMeasurement#AboveGroundBiomassMe..."></p>
<p>Which one is right?</p> Kepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155632010-01-05T18:09:01Zben leinfelderleinfelder@nceas.ucsb.edu
<ul></ul><p>this looks wrong:<br /><property name="semanticType" class="org.kepler.sms.SemanticType" <br />value="urn:lsid:lsid.ecoinformatics.org:onto:8:1#AboveGroundBiomassMeasurement#AboveGroundBiomassMe..."></p>
<p>It appears that the class is being double appended to the URI of the ontology (before the first #).<br />There should only be one # - used to delimit the ontology from the class name</p> Kepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155642010-01-05T19:31:43ZSean Riddleswriddle@gmail.com
<ul></ul><p>(In reply to comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: attribute editing for EMPTY elements doesn't work (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2">#2</a>)</p>
<blockquote>
<p>this looks wrong:<br /><property name="semanticType" class="org.kepler.sms.SemanticType" <br />value="urn:lsid:lsid.ecoinformatics.org:onto:8:1#AboveGroundBiomassMeasurement#AboveGroundBiomassMe..."></p>
<p>It appears that the class is being double appended to the URI of the ontology<br />(before the first #).<br />There should only be one # - used to delimit the ontology from the class name</p>
</blockquote>
<p>That's a result of the way we're handling 'orphaned' concepts. Even if the ontology vanished completely, we still wanted to be able to search on its label, rather than just on the anchor/concept ID. Even though the concept ID is usually the same or closely related to the label, there is no guarantee that this will be true in all cases. I had tags added through the tagging interface have the following value:</p>
<p>ontology_uri#concept_id#concept_label</p>
<p>As long as no one tries to take the string representation of the semantic type and treat it directly as a URI, it should be fine. But please post replies to here if errors of that nature are found.</p> Kepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155652010-01-25T19:14:13ZDerik Barseghianbarseghian@nceas.ucsb.edu
<ul></ul><p>Things had changed and the concept_label was no longer in the tags in the workflowRun. Sean added the concept_label back in r22469.</p> Kepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155662010-01-28T00:21:46ZSean Riddleswriddle@gmail.com
<ul></ul><p>Seems like this got fixed a while back. Closing unless there are any objections.</p> Kepler - Bug #4538: problems with KARs that contain tags from default ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/4538?journal_id=155672013-03-27T21:27:12ZRedmine Admin
<ul></ul><p>Original Bugzilla ID was 4538</p>