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 #3601 (Resolved): Transform demo eml document from eml 2.0.1 to eml 2.1.0https://projects.ecoinformatics.org/ecoinfo/issues/36012008-11-06T23:44:18ZJing Taotao@nceas.ucsb.edu
<p>Currently, the demo eml document of morpho (jscientist.7.2) is eml 2.0.1. We need to transform it to eml 2.1.0.</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 #3550 (Resolved): no way to enter a missingValueCodehttps://projects.ecoinformatics.org/ecoinfo/issues/35502008-10-22T18:31:25ZMargaret O'Brienmob@msi.ucsb.edu
<p>My data has a missing value code, but morpho did not have a form field for it, and it does not appear in the tree editor. <br />Perhaps this field is auto-filled, and since this file was big, morpho missed it. The first error flag appears at about line 25. Here is the file:<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></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 #3479 (Resolved): Syanptic Package Manager distribution for Morpho?https://projects.ecoinformatics.org/ecoinfo/issues/34792008-08-28T00:31:37ZRick Reevesreeves@nceas.ucsb.edu
<p>Having worked too hard recently to install Morpho on NCEAS Ubuntu machines, I am logging a formal request for someone to set up distribution of Morpho (and its supporting packages such as JRE) through the Synaptic Package Manager.</p>
<p>Just imagine how good that would be for all past, present, future Morpho users. <br />Esp considering NCEAS' strident advocacy of Open-source scientific software.</p>
<p>Catch my drift? :}</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 #2798 (Resolved): The Morpho Linux install file no longer works with current Ubuntu 6.10https://projects.ecoinformatics.org/ecoinfo/issues/27982007-03-13T23:15:56ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>It looks like the installAnywhere installer for linux is out of date. When the file is executed errors come up. Here is a sample of what the consle returns when the file at <a class="external" href="http://knb.ecoinformatics.org/software/dist/morpho-1.6.1-linux.bin">http://knb.ecoinformatics.org/software/dist/morpho-1.6.1-linux.bin</a> is executed.</p>
<p>Preparing to install...<br />Extracting the installation resources from the installer archive...<br />Configuring the installer for this system's environment...<br />nawk: error while loading shared libraries: libm.so.6: cannot open<br />shared object file: No such file or directory<br />dirname: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory<br />/bin/ls: error while loading shared libraries: librt.so.1: cannot open<br />shared object file: No such file or directory<br />basename: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory<br />dirname: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory<br />basename: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory<br />hostname: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory</p>
<p>Launching installer...</p>
<p>grep: error while loading shared libraries: libc.so.6: cannot open<br />shared object file: No such file or directory<br />/usr/lib/jvm/java-1.5.0-sun/jre/bin/java: error while loading shared<br />libraries: libpthread.so.0: cannot open shared object file: No such<br />file or directory</p>
<p>There are some workarounds for this but I do not think they are very easy to follow. Nick has tested them. However, if we can not get a new install file for this version we probably need to test and document the workaround.</p>
<p>Nick Brand was able to install Morpho with these directions:</p>
<p>1. Download the installer</p>
<p>2. copy the installer</p>
<p>cp morpho-1.6.1-linux.bin morpho-1.6.1-linux.bak</p>
<p>3. run the fix (put everything on one line)</p>
<p>cat morpho-1.6.1-linux.bak | sed "s/export LD_ASSUME_KERNEL/#xport<br />LD_ASSUME_KERNEL/" > morpho-1.6.1-linux.bin</p>
<p>4. now run the installer and move the the install dir</p>
<p>./morpho-1.6.1-linux.bin<br />cd Morpho-1.6.1/</p>
<p>Here are some alternate instructions, after installing morpho, cd to the<br />Morpho-1.6.1 directory, then run:</p>
<p>dos2unix morpho</p>
<p>export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun/jre/</p>
<p>./morpho</p>
<p>You may need to install "tofrodos" to get the dos2unix program.</p> Bug #2795 (Resolved): The delete selected row feature does not always work.https://projects.ecoinformatics.org/ecoinfo/issues/27952007-03-09T20:04:46ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>The Morpho table feature that allow for adding and deleting rows is hard to work with. Once the rows have been added it is hard to delete the empty row that is sometimes created. The delete selected row feature does not always work. When the table file is saved there are extra "," (commas) to mark the empty cells in the table. There is the option to Revert Entity to Saved Version (off of the edit menu) but this is not helpful if changes have been made.</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>