Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-01-13T17:37:32ZEcoinformatics Redmine
Redmine Bug #5273 (Resolved): docs with inline-data allow invalid xml into metacathttps://projects.ecoinformatics.org/ecoinfo/issues/52732011-01-13T17:37:32ZChad Berkleyberkley@nceas.ucsb.edu
<p>If you insert a document with inline-data, the data is stripped out of the document before it is validated. However, when you do a GET on the document, it is read off of the disk. So if you insert a doc with inline-data that has invalid characters in it (like unescaped ampersands), metacat will not recognize that it is invalid, but when you try to get the document, you will get a parser error if you try to parse it.</p>
<p>We should be validating the document first before stripping inline-data out of it.</p> Bug #3415 (Resolved): metacat prints namespace attributes in opposite order of original documenthttps://projects.ecoinformatics.org/ecoinfo/issues/34152008-06-24T22:06:18ZChad Berkleyberkley@nceas.ucsb.edu
<p>When you serialize a document from metacat, the xmlns attributes come out in the opposite order from which the original document had them. This should be fixed so that what you put in comes back out again.</p> Bug #3413 (Resolved): Sort order of returned resultsets needs to be standardhttps://projects.ecoinformatics.org/ecoinfo/issues/34132008-06-23T21:59:06ZChad Berkleyberkley@nceas.ucsb.edu
<p>Metacat seems to sort the returned search results in different ways, which causes problems with paged query returns. Either the search results should always be sorted by docid or the search criteria should be included with the request.</p> Bug #3403 (Resolved): xmlns without a : is serialized incorrectlyhttps://projects.ecoinformatics.org/ecoinfo/issues/34032008-06-19T18:54:10ZChad Berkleyberkley@nceas.ucsb.edu
<p>if you upload a document with an xmlns=xxx instead of xmlns:y=xxx to metacat, it uploads correctly, but when you read the document, metacat erroneously puts a ":" into the xmlns, which makes the document invalid.</p> Bug #3402 (In Progress): internal dtds are not handledhttps://projects.ecoinformatics.org/ecoinfo/issues/34022008-06-19T18:52:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>XML documents with internal DTDs are not handled by metacat. The internal dtd entity callback in the sax parser is blank and doesn't do anything when presented with an internal dtd.</p> Bug #3397 (Resolved): metacat needs server side sort mechanismhttps://projects.ecoinformatics.org/ecoinfo/issues/33972008-06-16T23:38:50ZChad Berkleyberkley@nceas.ucsb.edu
<p>in the past, we've been using xslt to sort search results going to a browser or client. This works fine until you use paged search results when you need the results sorted before the paging takes place. we need to add functionality to give the server an attribute to sort on before it pages the results. this should probably work similar to the returnfields mechanism (or with the returnfields mechanism).</p> Bug #3395 (Closed): allow private access via indexed "shortcut" urlhttps://projects.ecoinformatics.org/ecoinfo/issues/33952008-06-12T20:03:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>Currently you can read documents using the url <a class="external" href="http://server.com/metacat/metacat/docid.1.1">http://server.com/metacat/metacat/docid.1.1</a>. This only works for public documents. I understand it was originally intended to allow search engines to index the public metacat documents, but I find no reason why this url should not be able to perform access control just like the other url (docid=docid.1.1&action=read). They should behave identically. This will allow for more succinct urls to be sent between people and machines.</p> Bug #3394 (Resolved): can't upload xml documents via multiparthttps://projects.ecoinformatics.org/ecoinfo/issues/33942008-06-12T20:00:30ZChad Berkleyberkley@nceas.ucsb.edu
<p>You can only upload a binary file via the action=upload functionality. This should be changed to allow xml documents as well since you may want to use multipart encoding to upload an xml file from a web form instead of having to send the entire text of the document with the action=insert function.</p> Bug #3367 (New): Harvester stores passwords in clear texthttps://projects.ecoinformatics.org/ecoinfo/issues/33672008-06-05T20:18:24ZChad Berkleyberkley@nceas.ucsb.edu
<p>The harvester stores the user's password in clear text in the database. Passwords need to be stored as md5s or use some other secure form of encryption.</p> Bug #3084 (Resolved): Need to be able to set filenames on data uploadshttps://projects.ecoinformatics.org/ecoinfo/issues/30842008-01-22T19:47:04ZChad Berkleyberkley@nceas.ucsb.edu
<p>There needs to be functionality in metacat to allow the setting of a filename for data uploads. Currently, when you upload a data file, it is stored on disc as it's docid. When you go to download it, the MIME filename attribute is set as "data". There needs to be an interface added to set the MIME filename on upload so that when you download the file, the correct filename can be put into the MIME encoding.</p>
<p>This will probably require adding a field to xml_documents to store the filename. The appropriate interfaces on the ecogrid also need to be updated so that this functionality is available via the grid.</p> Bug #2847 (Resolved): returnfields need full xpath supporthttps://projects.ecoinformatics.org/ecoinfo/issues/28472007-05-17T18:01:07ZChad Berkleyberkley@nceas.ucsb.edu
<p>the current implementation of xpath used in metacat for the purpose of returning specific fields of an xml document within a returnset is not sufficient for highly structured documents. more or full xpath support needs to be implemented. currently, if you specify "/x/y" as a return field and the document is structured<br /><x><br /> <y><br /> <z>...</z><br /> <z>...</z><br /> </y><br /></x></p>
<p>metacat will return nothing. metacat seems to require that you specify the exact xpath to a node or it just returns null. This really doesn't work for any document that contains formatting (such as <p>, <i>, <b>, etc) within the xml.</p> Bug #2675 (Resolved): column "infinity" does not existhttps://projects.ecoinformatics.org/ecoinfo/issues/26752006-11-22T17:29:45ZChad Berkleyberkley@nceas.ucsb.edu
<p>When uploading certain xml files to metacat via the ecogrid, I get a message that says:<br /><error><br />ERROR: column "infinity" does not exist<br /></error></p>
<p>I'm not sure why it's looking for this column. You can reproduce it from kepler by trying to upload the Current Time actor to the library. Here is a full error from kepler:</p>
<p>Here's the full error:</p>
<p>[java] got lsid client<br /> [java] checking if lsid urn:lsid:kepler-project.org:actor:2:1 is already registered<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] is registered? false<br /> [java] Creating transport KAR file at /Users/berkley/.kepler/cache/tmp/tmp.kar<br /> [java] done writing KAR file to /Users/berkley/.kepler/cache/tmp/tmp.kar<br /> [java] uploading kar file with id urn:lsid:kepler-project.org:kar:7:1<br /> [java] session id: 4EB5CA645287A4E729BCD30072EBCABA<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] uploaded kar file with id urn:lsid:kepler-project.org:kar:7:1<br /> [java] uploading actor metadata with id urn:lsid:kepler-project.org:actor:2:1<br /> [java] session id: 4EB5CA645287A4E729BCD30072EBCABA<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] repository: name=keplerRepository, repository=localhost:8080, username=uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org<br /> [java] org.kepler.objectmanager.repository.RepositoryException: java.rmi.RemoteException: <?xml version="1.0"?><br /> [java] <error><br /> [java] ERROR: column "infinity" does not exist<br /> [java] </error></p>
<pre><code>[java] at org.kepler.objectmanager.repository.EcogridRepository.put(EcogridRepository.java:176)<br /> [java] at org.kepler.gui.UploadToRepository.upload(UploadToRepository.java:273)<br /> [java] at org.kepler.gui.UploadToRepository.access$000(UploadToRepository.java:75)<br /> [java] at org.kepler.gui.UploadToRepository$UploadSwingWorker.construct(UploadToRepository.java:449)<br /> [java] at util.SwingWorker$2.run(SwingWorker.java:122)<br /> [java] at java.lang.Thread.run(Thread.java:613)</code></pre> Bug #421 (In Progress): create simple turnkey installer for metacat Phase IIhttps://projects.ecoinformatics.org/ecoinfo/issues/4212002-02-13T18:32:47ZChad Berkleyberkley@nceas.ucsb.edu
<p>we need to use the previously protyped metacat installer to build a robust, one<br />click installer for metacat that includes Tomcat, Ant, Metacat, PostgresSQL and<br />any other tools that are necessary.</p>
<p>We should do this for the next release of Metacat.</p> Bug #131 (Resolved): add doctype identifier to returnfieldshttps://projects.ecoinformatics.org/ecoinfo/issues/1312000-09-20T20:07:46ZChad Berkleyberkley@nceas.ucsb.edu
<p>a returnfield should not only include the path to an element but also the<br />doctype from which it should be selected. This will allow for a more precise<br />way to specify the fields that should be returned and remove any ambiguity<br />between two documents that might have the same path to a field that each have<br />different symantic meaning.</p> Bug #129 (Closed): Metacat Performance: paged Query Returnshttps://projects.ecoinformatics.org/ecoinfo/issues/1292000-09-20T20:02:40ZChad Berkleyberkley@nceas.ucsb.edu
<p>If a query returns more than n results, then only n results should be shown to<br />the user at a time. This functionality is similar to a commercial search engine<br />that only shows the user "results 1-25" then you click a "next 25" button to get<br />to the next page of results.</p>