Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362006-02-28T20:02:49ZEcoinformatics Redmine
Redmine Bug #2371 (Resolved): Replication problem with links with '&'https://projects.ecoinformatics.org/ecoinfo/issues/23712006-02-28T20:02:49ZDan Higginshiggins@nceas.ucsb.edu
<p>There seems to be problem in replicating datapackages with links that contain<br />the '&' character.<br />In particular, consider the knb-lter-gce.232.5 package. Using morpho and KNB, the<br />Online Distribution element is:</p>
<p><a class="external" href="http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?name=metacat-user&ail=none&filiation=LNO&tify=0&cession=INV-GCEM-0412b1&lename=INV-GCEM-0412b1_1_0.TXT">http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?name=metacat-user&ail=none&filiation=LNO&tify=0&cession=INV-GCEM-0412b1&lename=INV-GCEM-0412b1_1_0.TXT</a></p>
<p>while in ecogrid it is:</p>
<p><a class="external" href="http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?name=metacat-user&il=none&iliation=LNO&ify=0&ession=INV-GCEM-0412b1&ename=INV-GCEM-0412b1_1_0.TXT">http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?name=metacat-user&il=none&iliation=LNO&ify=0&ession=INV-GCEM-0412b1&ename=INV-GCEM-0412b1_1_0.TXT</a></p>
<p>Note the loss of characters after the '&'s !!!</p>
<p>This is making it impossible to retreive data in Kepler (and in Morpho)</p> Bug #1538 (Resolved): Entity/Character Refeference Conversion Problemshttps://projects.ecoinformatics.org/ecoinfo/issues/15382004-04-28T16:29:39ZDan Higginshiggins@nceas.ucsb.edu
<p>In Morpho, we have run into some problem with the use of special, non-ascii<br />characters (like the 'degree' symbol or greek 'mu'). [Any character represented<br />by a byte with a decimal value > 127 is in this class of special characters.]<br />These characters have been copied from Word or PDF documents into Morpho fields<br />and then put into eml xml docs. Unfortunately, they are not not necessarily in<br />the correct format for xml documents and have caused parser problems.</p>
<p>The solution that was implemented in Morpho was to use entity/character<br />references. Any character with a value greater than 127 is written as '&#xxx;'<br />where 'xxx' is the decimal value of the character. On a Windows machine, the<br />'deg' symbol becomes '°' and 'mu' becomes 'μ'. XML parsers<br />automatically convert these character entities to the character for display, but<br />the conversion depends on the assumed character set.</p>
<p>The metacat problem is that when one submits a document containing such<br />character references (&#xxx;) and then reads the document back, one does not get<br />the character refenence, but rather the character itself! I assume this is due<br />to the XML parser. This is a violation of the idea that metacat should return<br />exactly the same data given it.</p>
<p>Morpho already handles this by converting back to character references any info<br />sent it by Metacat with character values greater than 127. But metacat actually<br />sends back the wrong character for some symbols! (e.g. a 'mu' becomes a '1/4'<br />symbol. I assume this is due to different character set assumption under linux<br />and windows. In any case, there is some data corruption here that we should<br />figureout how to avoid.</p> Bug #1186 (Resolved): query returning invalid UTF-8 sequencehttps://projects.ecoinformatics.org/ecoinfo/issues/11862003-10-10T18:12:30ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently, if one runs a "%" query on the default metacat server from Morpho,<br />Morpho reports the exception "(2.431) Exception creating result set ...(2.432)<br />java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence.<br />(2.433) Exception is: java.io.UTFDataFormatException"</p>
<p>The error stops the ResultSet parsing so that not all the results are displayed<br />in Morpho. Apparently, Metacat is generating invalid UTF data in the returned XML</p>
<p>Apparently, the package that triggers this problem has the id "redemm.4.1". The<br />web display from Metacat works and shows that this package is in Spanish with<br />lots of special symbols (which may explain the UTF-8 error).</p> Bug #1053 (Resolved): 'ampersand' (&) problem in ResultSethttps://projects.ecoinformatics.org/ecoinfo/issues/10532003-04-30T23:54:28ZDan Higginshiggins@nceas.ucsb.edu
<p>One of Christy's students entered an ampersnaf ('&') in the dataPackage name<br />field for a package and discovered that this created a problem. '&' is cinverted<br />to & by Morpho and submission to metacat works OK as do purely local<br />rearches on Morpho.</p>
<p>An error message about 'not having entity info following the &' occurs, however<br />when Metacat tries to build a resultsSet document from the package with the '&'<br />in the package name! This keeps a user from doing any searches for their own<br />docs on metacat!</p> Bug #929 (Resolved): Occasionally, deletes are VERY slowhttps://projects.ecoinformatics.org/ecoinfo/issues/9292002-12-30T22:12:47ZDan Higginshiggins@nceas.ucsb.edu
<p>Sometimes, deleting a data package is very slow (> 1 min), although most of the<br />time metacat response to a delete in a few seconds</p> Bug #916 (Resolved): bug with 'less-than' query when usng a numberhttps://projects.ecoinformatics.org/ecoinfo/issues/9162002-11-20T19:39:52ZDan Higginshiggins@nceas.ucsb.edu
<p>When one uses the 'less-than' operator with a squery action and the comparison<br />is made to a number (e.g. '<field> less-than 90'), the metacat system reports NO<br />hits, even though there is data.</p>
<p>The query returned data on Jing's version of Metacat, however.</p>
<p>Problem can be reproduced when a field being compared to a number has string<br />data that CANNOT be converted to a number. Error keeps metacat from retruning<br />any hits rather than just skipping node with invalid string data!</p> Bug #445 (Resolved): getprincipals action not workinghttps://projects.ecoinformatics.org/ecoinfo/issues/4452002-03-21T00:27:13ZDan Higginshiggins@nceas.ucsb.edu
<p>The getprincipals action, which is supposed to "Get all users and groups in the<br />current authentication schema" is apparently not working. All I get is an error<br />message containing null. (Dan Higgins)</p>
<p>(This did work at one point, but has not been tried for some time.)</p> Bug #441 (Resolved): Unable to increment data id revision numbershttps://projects.ecoinformatics.org/ecoinfo/issues/4412002-03-05T23:28:31ZDan Higginshiggins@nceas.ucsb.edu
<p>In an attempt to let the Morpho user update a data file (NOT a metadata doc), it<br />was discovered that Metacat returns the following when an attempt is made to<br />insert a revised data document, eg 801.1 --> 801.2</p>
<p>Same code works when a new id is used rather than one with incremented version #.</p>
<p><error><br />ORA-00001: unique constraint (TAO.XML_DOCUMENTS_PK) violated</p> Bug #417 (Resolved): Is sequential numbering of versions needed?https://projects.ecoinformatics.org/ecoinfo/issues/4172002-02-08T17:06:50ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently, version changes of documents must be sequentially numbered. This<br />means that someone working locally in Morpho might make 6 changes to a document<br />and 6 versions must be sent to Metacat in order, even though only the last one<br />is meant to be submitted. Also, if any of the early version is invalid then the<br />whole submission fails. Likewise, a download of any datapackage requires the<br />download of all version, even if only the most recent is needed.</p>
<p>Therefore, I suggest that submission of new versions only require that the new<br />version number be greater than the current one, not exactly one greater.</p> Bug #398 (Resolved): error in handling '&' in response to querieshttps://projects.ecoinformatics.org/ecoinfo/issues/3982002-01-15T04:49:23ZDan Higginshiggins@nceas.ucsb.edu
<p>There appears to be a problem in how Metacat handles entities like '&' in<br />responding to queries. If a data file name contains a '&' that gets encoded into<br />the triple linking the datafile to the datapackage. It get encoded as '&' in<br />the text, but when one looks at the response to an 'squery' the triple shows up as</p>
<p>"><subject>higgins.498</subject><relationship>isDataFileFor(96l</relationship><object>higgins.497</object></triple><triple><subject>higgins.498</subject><relationship>&</relationship><object>higgins.497</object></triple>"</p>
<p>actually, the relationship should have & after the "(961..." <br />Apparently, entities are not created when characters like '&' are pulled from<br />the database as the result of an 'squery'</p> Bug #298 (Resolved): Problem with Export functionhttps://projects.ecoinformatics.org/ecoinfo/issues/2982001-10-16T18:29:20ZDan Higginshiggins@nceas.ucsb.edu
<p>If a dataset which includes a data document is inserted into production Metacat<br />context and then 'Exported' the export of the data document appears to work<br />(because there is also a local copy?) However, if local dataset is deleted and<br />then one 'Exports' from Metacat, the data document contains an error message<br />rather than the data!</p>
<p>It is currently not clear whether this is a Morpho or a Metacat problem. Thus,<br />this error has been entered to both.</p> Bug #291 (Resolved): knb context of Metacat fails to find eml-attribute dtdhttps://projects.ecoinformatics.org/ecoinfo/issues/2912001-10-03T17:04:45ZDan Higginshiggins@nceas.ucsb.edu
<p>Inserting a new datapackage to Metacat from Morpho fails with message about not<br />being able to find eml-attribute dtd.</p> Bug #180 (Resolved): return of DTD comments with documents should be eliminatedhttps://projects.ecoinformatics.org/ecoinfo/issues/1802001-01-08T20:07:31ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently, if I submit an XML metadata document to Metacat and then retrieve <br />that document, the retrieved document contains<br />comment fields from its DTD that were NOT present in the original document. A <br />user should retrieve a document<br />from metacat that is a duplicate of the one submitted and comments in the DTD <br />should remain in the DTD only. Putting them into a returned<br />document tends to confuse the user into thinking that the retrieved document is <br />not the same one as submitted.</p> Bug #40 (Resolved): Search Refinement Capabilityhttps://projects.ecoinformatics.org/ecoinfo/issues/402000-07-25T20:49:43ZDan Higginshiggins@nceas.ucsb.edu
<p>There is a need to consider the ability to refine a search, perhaps by sending a<br />list of previously found documents to the MetaCat for further searcing. [Simply<br />repeating the first search may be OK if performance hit is not too large.]</p> Bug #31 (Resolved): need dataset id reference from metadatahttps://projects.ecoinformatics.org/ecoinfo/issues/312000-06-21T18:40:21ZDan Higginshiggins@nceas.ucsb.edu
<p>Need update to relations tag in order to obtain data id from metadata</p>