Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-11-17T21:32:46ZEcoinformatics Redmine
Redmine Bug #3675 (Resolved): Change morpho code repository from CVS to SVNhttps://projects.ecoinformatics.org/ecoinfo/issues/36752008-11-17T21:32:46ZJing Taotao@nceas.ucsb.edu
<p>More and more projects were transfered from CVS to SVN. Morpho need to this too.</p> Bug #3596 (Resolved): morpho couldn't display some ldap user names correctly.https://projects.ecoinformatics.org/ecoinfo/issues/35962008-11-06T01:01:13ZJing Taotao@nceas.ucsb.edu
<p>No matter the encoding method of getPrincipal in metacat is ASCII or iso-8859-1, morpho couldn't display some ldap user names correctly. In lib/accesslist.xml, it shows:<br /><user> <username>uid=redbc,o=unaffiliated,dc=ecoinformatics,dc=org</username><br /><name>Zulay M←ndez</name></p>
<p>However, firefox can display it correctly. So i think there is bug in morpho.</p> Bug #3565 (Resolved): hangs up loading data packagehttps://projects.ecoinformatics.org/ecoinfo/issues/35652008-10-24T19:15:44ZMargaret O'Brienmob@msi.ucsb.edu
<p>I've been trying to use morpho for updates on data packages that were created manually, but are valid eml201. At least 2 have hung up when loading the data package (searches work fine). Note that morpho is searching the catalog at data.piscoweb.org/catalog/metacat, not the knb.</p>
<p>packages that hang up: knb-lter-sbc.23, knb-lter-sbc.21</p>
<p>Here is the text from the .morpho/.../sdterr.log:<br />Name: qformat => xml<br />removed from window list<br /><?xml version="1.0"?><br /><pathquery version="1.2"><br /> <local_search>false</local_search><br /> <network_search>true</network_search><br /> <querytitle>Untitled-Search-5</querytitle><br /> <returndoctype>-//ecoinformatics.org//eml-dataset-2.0.0beta4//EN</returndoctype><br /> <returndoctype>-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN</returndoctype><br /> <returndoctype>-//NCEAS//eml-dataset-2.0//EN</returndoctype><br /> <returndoctype>-//NCEAS//resource//EN</returndoctype><br /> <returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype><br /> <returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype><br /> <returnfield>dataset/title</returnfield><br /> <returnfield>individualName/surName</returnfield><br /> <returnfield>keyword</returnfield><br /> <returnfield>entityName</returnfield><br /> <querygroup operator="INTERSECT"><br /> <querygroup operator="UNION"><br /> <querygroup operator="UNION"><br /> <queryterm searchmode="starts-with" casesensitive="false"><br /> <value>SBC</value><br /> <pathexpr>title</pathexpr><br /> </queryterm><br /> </querygroup><br /> </querygroup><br /> </querygroup><br /></pathquery></p>
<p>Adding window: Untitled-Search-5<br />(3) Executing metacat query...<br />(2.1) Executing metacat query...<br />Sending data to: <a class="external" href="http://data.piscoweb.org/catalog/metacat">http://data.piscoweb.org/catalog/metacat</a><br />HTTP Handler class is: HTTPClient.HttpURLConnection<br />Name: action => squery<br />Name: query => <?xml version="1.0"?><br /><pathquery version="1.2"><br /> <local_search>false</local_search><br /> <network_search>true</network_search><br /> <querytitle>Untitled-Search-5</querytitle><br /> <returndoctype>-//ecoinformatics.org//eml-dataset-2.0.0beta4//EN</returndoctype><br /> <returndoctype>-//ecoinformatics.org//eml-dataset-2.0.0beta6//EN</returndoctype><br /> <returndoctype>-//NCEAS//eml-dataset-2.0//EN</returndoctype><br /> <returndoctype>-//NCEAS//resource//EN</returndoctype><br /> <returndoctype>eml://ecoinformatics.org/eml-2.0.0</returndoctype><br /> <returndoctype>eml://ecoinformatics.org/eml-2.0.1</returndoctype><br /> <returnfield>dataset/title</returnfield><br /> <returnfield>individualName/surName</returnfield><br /> <returnfield>keyword</returnfield><br /> <returnfield>entityName</returnfield><br /> <querygroup operator="INTERSECT"><br /> <querygroup operator="UNION"><br /> <querygroup operator="UNION"><br /> <queryterm searchmode="starts-with" casesensitive="false"><br /> <value>SBC</value><br /> <pathexpr>title</pathexpr><br /> </queryterm><br /> </querygroup><br /> </querygroup><br /> </querygroup><br /></pathquery></p>
<p>Name: qformat => xml<br />(2.3) Metacat output is:<br />HTTPClient.RespInputStream@109099d<br />(2.4) Done Executing metacat query...<br />Parser created is: org.apache.xerces.parsers.SAXParser<br />(2.43) Creating result set ...<br />(2.44) Creating result set ...<br />(2.3) Metacat output is:<br />HTTPClient.RespInputStream@192c4c<br />(2.4) Done Executing metacat query...<br />Parser created is: org.apache.xerces.parsers.SAXParser<br />(2.43) Creating result set ...<br />(2.44) Creating result set ...<br />selectedId is: knb-lter-sbc.23.2<br />the package name is: knb-lter-sbc.23<br />the number of previous version is: 1<br />selectedId is: knb-lter-sbc.23.2<br />the package name is: knb-lter-sbc.23<br />the number of previous version is: 1<br />DataPackage: Got service request to open: knb-lter-sbc.23.2 from metacat.<br />MetacatDataStore: getting cached file<br />the second line string is: ?xml-stylesheet type="text/xsl" href="eml2esa.xsl" ?<br />Adding window: Data Package: knb-lter-sbc.23.2<br />ViewContainer startUp time: 114<br />Exception in thread "Thread-49" java.lang.NullPointerException<br /> at edu.ucsb.nceas.morpho.datapackage.DataViewContainerPanel.<init>(DataViewContainerPanel.java:272)<br /> at edu.ucsb.nceas.morpho.datapackage.DataPackagePlugin.openDataPackage(DataPackagePlugin.java:805)<br /> at edu.ucsb.nceas.morpho.query.OpenPackageCommand$1.construct(OpenPackageCommand.java:142)<br /> at edu.ucsb.nceas.morpho.framework.SwingWorker$2.run(SwingWorker.java:140)<br /> at java.lang.Thread.run(Thread.java:619)</p> Bug #3548 (Resolved): import data table hangs up on large tableshttps://projects.ecoinformatics.org/ecoinfo/issues/35482008-10-22T18:17:03ZMargaret O'Brienmob@msi.ucsb.edu
<p>This table is ~18k lines long (7 columns):<br /><a class="external" href="http://sbcdata.lternet.edu/external/Ocean/Data/SantaBarbaraHarbor_longTermTemperature/sbManualShoreSta_temperature_1955ongoing.txt">http://sbcdata.lternet.edu/external/Ocean/Data/SantaBarbaraHarbor_longTermTemperature/sbManualShoreSta_temperature_1955ongoing.txt</a><br />I have gotten the table import wizard to hang up twice when auto-detecting. <br />1. during the attribute description at about column 3<br />2. at the beginning, if you use the back button to reset the number of lines to skip or check the box specifying that the first line contains the attribute names.</p>
<p>I did not try manually describing the attributes. Auto descriptions are preferred, so that these data descriptions could be entered by people with little formal training.</p> Bug #2996 (Resolved): Check if RELEASE_EML_2_0_1_UPDATE_5 eml stylesheets works for morphohttps://projects.ecoinformatics.org/ecoinfo/issues/29962007-11-06T01:35:36ZJing Taotao@nceas.ucsb.edu
<p>Callie did some eml stylesheets work and they were checked in eml cvs module and tagged as RELEASE_EML_2_0_1_UPDATE_5. We need to make sure it doesn't break morpho.</p> Bug #2900 (Resolved): Morpho Ubuntu install needs Java 1.5.0 or greaterhttps://projects.ecoinformatics.org/ecoinfo/issues/29002007-08-07T19:04:09ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>The Morpho install for Ubuntu contains a zip file that installs a Morpho.1.6.1 directory containing the files needed to run Morpho. This program can be started by using the terminal and typing in ./morpho in that directory. When an older version of Java was previously loaded and has the JAVA_HOME path set there is a problem. This is the error: Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/ucsb/nceas/morpho/Morpho (Unsupported major.minor version 49.0)</p>
<p>Here is the command for the version and the version that my computer was set to: java version "1.4.2_12".</p>
<p>Java has been updated on this computer but the JAVA_HOME path has not been changed with the update. End users will get the above error if the path has not been updated. They do not get the helpful screen for people who do not have a path set.</p>
<p>Here is the screen that comes up for people who do not have the JAVA_HOME path set.</p>
<p>----------------------------------------------------------------------<br />----------------------------------------------------------------------<br />---------------------------- N O T E ---------------------------------<br />---- YOU MUST SET THE JAVA_HOME ENVIRONMENT VARIABLE TO POINT TO -----<br />--- YOUR JDK OR JRE INSTALLATION DIRECTORY BEFORE RUNNING MORPHO! ----<br />----- Note that Morpho may not work correctly with non-SUN JVMs, -----<br />--------------------- such as gcj or kafee. --------------------------<br />----------------------------------------------------------------------<br />----------------------------------------------------------------------</p>
<p>There are two problems that need to be addressed.</p>
<p>One is the README file says that Java 1.3 or greater will work and recommends 1.4. (1.4 does not work with this Ubuntu version of Morpho). The README needs to be changed to reflect this. I wonder if we should give direction on updating the JAVA_HOME environment variable in the readme file as well.</p>
<p>The other problem is that users need to be told to update their JAVA_HOME environment variable path if they have an earlier version set with it. The error that users get when the variable is not set right might not be clear to many users.</p>
<p>something like this needs to be run at the command line<br />export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun/ and be set in the users .bashrc file.</p> Bug #2799 (Resolved): Access List doesn't include groups at LDAP roothttps://projects.ecoinformatics.org/ecoinfo/issues/27992007-03-14T18:58:38ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>Currently, the Morpho access list in the Access Information wizard screen doesn't include groups located at the root of the LDAP tree (e.g. kepler, seek, esa-moderate). This is a problem if the user wants to grant privileges on a dp to a root-level group (esa-moderate, for example).</p> Bug #2768 (Resolved): http://knb.ecoinformatics.org/knb/servlet/metacat preference setting problemhttps://projects.ecoinformatics.org/ecoinfo/issues/27682007-02-12T21:00:24ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>The default preference setting in Morpho is not working. Unless the "servlet" part is removed login does not go through. An error box says Login failed. Please check the Caps Lock key and try again. This might be new since the last changes that were made to other metacat related files.</p> Bug #2529 (Resolved): Add Morpho Version/Date info to KNB websitehttps://projects.ecoinformatics.org/ecoinfo/issues/25292006-08-28T18:44:10ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>The date and version number of the most recent version of morpho should be displayed by the "Quick download" links on index.jsp of the KNB website, and well as on the morphpoportal.jsp page</p> Bug #2508 (Resolved): Incorrect example for relative attribute given in table wizardhttps://projects.ecoinformatics.org/ecoinfo/issues/25082006-08-02T17:00:39ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>In the new data table wizard, the example for the attribute category "relative" is currently "12.2 meters". However, meter measurements are generally absolute measurements, not relative measurements. The example of a relative attribute should instead be something like "12 degrees Celsius". This should be a quick fix, but it's important to have good examples here since the distinction between the categories is already confusing to many users.</p> Bug #2498 (Resolved): Change default metacat URLhttps://projects.ecoinformatics.org/ecoinfo/issues/24982006-07-20T23:29:08ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>The default Metacat URL in the Morpho preferences should be <a class="external" href="http://knb.ecoinformatics.org/knb/metacat">http://knb.ecoinformatics.org/knb/metacat</a> instead of <a class="external" href="http://knb.ecoinformatics.org/knb/servlet/metacat">http://knb.ecoinformatics.org/knb/servlet/metacat</a></p> Bug #2428 (Resolved): Morpho incorrectly tries to update instead of insert when saving a dp to a ...https://projects.ecoinformatics.org/ecoinfo/issues/24282006-04-26T21:09:21ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>To recreate this bug:<br />Create a data package and save it to a metacat server, (and locally, if you'd like). Make at least one change and save it a second time locally (i.e., so you're on the second revision of the document). Then go to set preferences and change to a different metacat sever (which doesn't have the dp on it yet). Open the dp, and try to save it to the new metacat. You will get an error saying "Problem Saving Data: Document not found for Accession number!", and the save will fail. Looking at stderr.log you can see that morpho tried to do an update instead of an insert.</p>
<p>Name: action => update<br />Name: public => no<br />message from server: <?xml version="1.0"?><br /><error><br />Document not found for Accession number bowdish.46<br /></error></p>
<p>MetacatUpload Exception in EML200DataPackage!<br /><?xml version="1.0"?><br /><error><br />Document not found for Accession number bowdish.46<br /></error></p> Bug #2202 (Resolved): Displaying year only under Temporal Coveragehttps://projects.ecoinformatics.org/ecoinfo/issues/22022005-09-20T17:54:10ZVeronique Connollyconnolly@nceas.ucsb.edu
<p>When you choose "Enter Year Only" for Temporal Coverage (either in the NDPW or<br />from the Documentation menu), what gets displayed in the data package is 1<br />January of the year you entered (e.g., 2005-01-01). Only the year in the yyyy<br />format should be displayed.</p> Bug #2201 (Resolved): data not uploaded to metacat from morphohttps://projects.ecoinformatics.org/ecoinfo/issues/22012005-09-20T17:35:50ZMatt Jonesjones@nceas.ucsb.edu
<p>Kristin Vanderbilt reports a problem with Morpho in which her two data tables<br />that were described in Morpho are not properly uploaded to metacat along with<br />her EML file (the EML file is sev.129.2). Morpho has the data files listed<br />using ecogrid urls as ecogrid://knb/SEV.4.1 and ecogrid://knb/SEV.5.1</p>
<p>I'm not sure how, but somehow the ecogrid URLs uses uppercase letters in the SEV<br />prefix, while the eml file uses lowercase. Kristin is unclear how this<br />happened, as am I. The file was uploaded from windows, which does not<br />differentiate case, which probably means that Morpho had difficulty creating the<br />"sev" and "SEV" subdirectories in her profile. So one possibility is to see<br />what would happen when the prefix is changed on windows to be all upper case.</p> Bug #2096 (Resolved): Not all elements of attribute module displayed in tree editorhttps://projects.ecoinformatics.org/ecoinfo/issues/20962005-05-31T17:15:07ZVeronique Connollyconnolly@nceas.ucsb.edu
<p>Let's say you have a data package that contains a data table which in turn<br />contains several attributes. In the tree editor, when you click “Show all”, nine<br />elements of the attribute module (dataTable/attributeList) appear for the first<br />attribute of the table (attributeName, attributeLabel, attributeDefinition,<br />storageType, measurementScale, missingValueCode, accuracy, coverage, method),<br />but only four elements appear for the other attributes (attributeName,<br />attributeLabel, attributeDefinition, measurementScale). All elements should<br />appear for all attributes.</p>
<p>When there are several tables in the data package, only the first data table<br />displays the nine elements for the first attribute; the other tables display<br />only the four elements mentioned above for all attributes.</p>