Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-03-21T16:32:28ZEcoinformatics Redmine
Redmine Bug #7175 (New): The link for non-numeric attribute domains doesn't work on the exported eml filehttps://projects.ecoinformatics.org/ecoinfo/issues/71752017-03-21T16:32:28ZJing Taotao@nceas.ucsb.edu
<p>To Whom It May Concern:</p>
<p>I am trying to use Morpho to create metadata for a project (Morpho has been updated to the latest version). I have entered all the information (that I have at this time, at least) into Morpho and can view everything that I’ve entered within the software. When I export the metadata and view the html or pdf files, everything is great except with defining nominal codes. For these attributes, a link name “Domain Info” is provided and when clicked the link either returns to the top of the metadata file (clicked within the Morpho preview) or opens a browser window that says “No file exists at the address “/metacat” (clicked from html or pdf files). I have attached a file for example. I am not a coder and have not been able to figure out a way for the nominal/category codes to be listed directly in the metadata export files. I don’t like the thought of having to export all my work from Morpho into Metavist, so thought I’d check with KNB for a possible solution first.</p>
<p>Thanks for any guidance that you are able to provide.</p>
<p>Best,</p>
<p>Jayne</p>
<p>I looked at the html of page and it shows:<br /><td class="innercoleven" align="center" colspan="2"><a href="/metacat?action=read&qformat=export&sessionid=&docid=&displaymodule=attributedomain&entitytype=dataTable&entityindex=4&attributeindex=6"><b>Domain Info</b></a></td></p>
<p>The link looks like to use the metacat read action to read the attributedomain module. However, this link as imported html can't work since it can't have the complete metacat url. I also search the Metacat code and can't find it supporting to display the attribute domain.</p>
<p>I also looked at the eml xslt code. Here is the code to generate the link at the template attributenonnumericdomaincommon:<br /> <a><xsl:attribute name="href"><xsl:value-of select="$tripleURI"/><xsl:value-of select="$docid"/>&displaymodule=attributedomain&entitytype=<xsl:value-of select="$entitytype"/>&entityindex=<xsl:value-of select="$entityindex"/>&attributeindex=<xsl:value-of select="$attributeindex"/></xsl:attribute></p>
<p>It seems there are issues on the export feature of Morpho. So the link doesn't work. However, we have a way to work around the issues. First, you may save the package to a Metacat server from Morpho. Then you can open the package on the link from a browser. You may save the html file which shows up on your browser to replace the metadata.html on your exported package directory.</p>
<p>Here is the link of an eml on our KNB web site (which is our default Metacat server on Morpho):<br /><a class="external" href="https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=default&amp;displaymodule=printall">https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=default&amp;displaymodule=printall</a><br />When you click the link "Domain info", it will show up the information. After you save your eml into KNB, you can open your package by modifying the above link - replace "autogen.2017031514432105092.2" by your docid.</p>
<p>If you do want to use one html to show all the information, you may use this link:<br /><a class="external" href="https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=metacatui&amp;displaymodule=printall">https://knb.ecoinformatics.org/knb/metacat?action=read&amp;docid=autogen.2017031514432105092.2&amp;qformat=metacatui&amp;displaymodule=printall</a><br />As I said, when you try to open your eml, you need to replace the "autogen.2017031514432105092.2" by your docid.</p> Bug #6701 (New): Entity descriptions can't be added outside wizardhttps://projects.ecoinformatics.org/ecoinfo/issues/67012015-03-27T21:56:52ZJessica Couturecouture@nceas.ucsb.edu
<p>I was trying to add entity descriptions after my tables had been imported and found that there is no way to go back and access this. Can this function be added so that this can be edited outside the initial data wizard has been closed?</p> Bug #6700 (New): Pub date fieldhttps://projects.ecoinformatics.org/ecoinfo/issues/67002015-03-27T21:54:54ZJessica Couturecouture@nceas.ucsb.edu
<p>The publication data defaults to the current date and there is no way to manually set this in Morpho. Can we have one added for datasets that had been published in the past?</p> Bug #6112 (New): Use .morpho when we release the morphohttps://projects.ecoinformatics.org/ecoinfo/issues/61122013-10-01T23:53:37ZJing Taotao@nceas.ucsb.edu
<p>Currently the default morpho home is .morpho2. It is great for users to test morpho without change the file structure. But the real release will use .morpho as the default directory.</p> Bug #5902 (Resolved): Replace "Owner" with "Creator" in Morpho interfacehttps://projects.ecoinformatics.org/ecoinfo/issues/59022013-04-10T21:20:59Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Using the word 'Owner' in the Morpho UI was a mistake, and is misleading. We should not have used it in our web display either. In the US, data can not be owned, because neither copyright nor patent law applies to facts. EML does not have an owner field. There is no owner.</p> Bug #5898 (Resolved): Some issue in the RelicationPolicyPagehttps://projects.ecoinformatics.org/ecoinfo/issues/58982013-03-26T23:54:34ZJing Taotao@nceas.ucsb.edu
<p>Hi, ben:</p>
<p>When i finished the new data package wizard and click "add a new entity link", i got this error:<br /> [java] Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "" <br /> [java] at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)<br /> [java] at java.lang.Integer.parseInt(Integer.java:504)<br /> [java] at java.lang.Integer.valueOf(Integer.java:582)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.pages.ReplicationPolicyPage.getReplicationPolicy(ReplicationPolicyPage.java:229)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.pages.ReplicationPolicyPage.getPageData(ReplicationPolicyPage.java:336)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.pages.ReplicationPolicyPage.getPageData(ReplicationPolicyPage.java:319)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.WizardContainerFrame.addPageDataToResultsMap(WizardContainerFrame.java:1961)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.WizardContainerFrame.collectDataFromPages(WizardContainerFrame.java:1058)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.WizardContainerFrame.finishAction(WizardContainerFrame.java:906)<br /> [java] at edu.ucsb.nceas.morpho.plugins.datapackagewizard.pages.Summary$1.execute(Summary.java:248)<br /> [java] at edu.ucsb.nceas.morpho.util.GUIAction.actionPerformed(GUIAction.java:410)<br /> [java] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)<br /> [java] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)<br /> [java] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)<br /> [java] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)<br /> [java] at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)<br /> [java] at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)<br /> [java] at java.awt.Component.processMouseEvent(Component.java:6505)<br /> [java] at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)<br /> [java] at java.awt.Component.processEvent(Component.java:6270)<br /> [java] at java.awt.Container.processEvent(Container.java:2229)<br /> [java] at java.awt.Component.dispatchEventImpl(Component.java:4861)<br /> [java] at java.awt.Container.dispatchEventImpl(Container.java:2287)<br /> [java] at java.awt.Component.dispatchEvent(Component.java:4687)<br /> [java] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)<br /> [java] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)<br /> [java] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)<br /> [java] at java.awt.Container.dispatchEventImpl(Container.java:2273)<br /> [java] at java.awt.Window.dispatchEventImpl(Window.java:2719)<br /> [java] at java.awt.Component.dispatchEvent(Component.java:4687)<br /> [java] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:729)<br /> [java] at java.awt.EventQueue.access$200(EventQueue.java:103)<br /> [java] at java.awt.EventQueue$3.run(EventQueue.java:688)<br /> [java] at java.awt.EventQueue$3.run(EventQueue.java:686)<br /> [java] at java.security.AccessController.doPrivileged(Native Method)<br /> [java] at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)<br /> [java] at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)<br /> [java] at java.awt.EventQueue$4.run(EventQueue.java:702)<br /> [java] at java.awt.EventQueue$4.run(EventQueue.java:700)<br /> [java] at java.security.AccessController.doPrivileged(Native Method)<br /> [java] at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)<br /> [java] at java.awt.EventQueue.dispatchEvent(EventQueue.java:699)<br /> [java] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)<br /> [java] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)<br /> [java] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)<br /> [java] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)<br /> [java] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)<br /> [java] at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)</p> Bug #5889 (Resolved): Update documentation and installers to require Java 7https://projects.ecoinformatics.org/ecoinfo/issues/58892013-03-09T00:01:43Zben leinfelderleinfelder@nceas.ucsb.edu
<p>ECP is using OpenSAML 3.0 that is now requiring Java 7.</p> Bug #5888 (Resolved): Couldn't log in as a NCEAS account in Morphohttps://projects.ecoinformatics.org/ecoinfo/issues/58882013-03-08T19:13:58ZJing Taotao@nceas.ucsb.edu
<p>When I tried to log in the DataONE network as a NCEAS account, i got this error:<br /> [java] Could not authenticate: org/opensaml/core/config/InitializationException : Unsupported major.minor version 51.0<br /> [java] java.lang.UnsupportedClassVersionError: org/opensaml/core/config/InitializationException : Unsupported major.minor version 51.0<br /> [java] at java.lang.ClassLoader.defineClass1(Native Method)<br /> [java] at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)<br /> [java] at java.lang.ClassLoader.defineClass(ClassLoader.java:615)<br /> [java] at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)<br /> [java] at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)<br /> [java] at java.net.URLClassLoader.access$000(URLClassLoader.java:58)<br /> [java] at java.net.URLClassLoader$1.run(URLClassLoader.java:197)<br /> [java] at java.security.AccessController.doPrivileged(Native Method)<br /> [java] at java.net.URLClassLoader.findClass(URLClassLoader.java:190)<br /> [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:306)<br /> [java] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)<br /> [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:247)<br /> [java] at edu.ucsb.nceas.morpho.dataone.EcpAuthentication.authenticate(EcpAuthentication.java:142)<br /> [java] at edu.ucsb.nceas.morpho.framework.LoginCommand.execute(LoginCommand.java:80)<br /> [java] at edu.ucsb.nceas.morpho.framework.ConnectionFrame$1.doInBackground(ConnectionFrame.java:367)<br /> [java] at javax.swing.SwingWorker$1.call(SwingWorker.java:277)<br /> [java] at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)<br /> [java] at java.util.concurrent.FutureTask.run(FutureTask.java:138)<br /> [java] at javax.swing.SwingWorker.run(SwingWorker.java:316)<br /> [java] at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)<br /> [java] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)<br /> [java] at java.lang.Thread.run(Thread.java:680)<br /> [java] LoginCommand: Login failed.<br /> [java] Login failed.<br /> [java] Please check the Caps Lock key and try again.</p> Bug #5887 (New): Handle the query result set which contains the revision chains of documentshttps://projects.ecoinformatics.org/ecoinfo/issues/58872013-03-07T23:48:28ZJing Taotao@nceas.ucsb.edu
<p>Morpho network query now experiences a performance issue because the merge of the network and local search results.</p>
<p>During the merge, morpho needs to make lots of calls the DataONE MN to get the revision chains.</p>
<p>The proposed solution is to add the revision chain for each eml document to the result set. This can avoid lots of network traffic.</p>
<p>So morpho needs to handle the new result set.</p> Bug #5886 (Resolved): Rework AccessPolicy and ReplicationPolicy editinghttps://projects.ecoinformatics.org/ecoinfo/issues/58862013-03-05T01:04:47Zben leinfelderleinfelder@nceas.ucsb.edu
<p>1. Move "Edit XXX Policy..." from the Documentation menu into File menu.<br />2. Add "Inherit from package" checkbox to the main edit page.<br />2a. Check the box if the data files all share the same access/replication policies as for the EML object<br />2b. If it is unchecked (policies differ) then display info message when it is checked my the user ("Existing Policy for the data object[s] will be overridden by changes made here")<br />3. Make the "Success" pop up message more pleasing (right now it looks like an error/warning box because it reuses the same mechanism for displaying warnings to the user).</p> Bug #5882 (Resolved): Get a system metadata version number error when morpho tried to change the ...https://projects.ecoinformatics.org/ecoinfo/issues/58822013-02-23T01:10:51ZJing Taotao@nceas.ucsb.edu
<p>When I tried to change the access rule of a network document, i got this error:</p>
<p>The requested system metadata version number 0 differs from the current version at 1. Please get the latest copy in order to modify it.</p>
<p>Here is what i did:</p>
<p>1. Used the new data package wizard to create an new eml only document and saved it to the network.</p>
<p>2. Chose Documentation|Access Information to add a new access rule and got an error - the cn doens't have the id and please try again later.</p>
<p>3. A while later, i clicked the Documenation|Access Information again (I didn't close the data package) and I saw the new rules i added in previous step (this is a little bit confusing - users may think the new rule already has been added). Then i clicked the okay button and got this error.</p> Bug #5805 (In Progress): Local and Network revisions show at same time in search resultshttps://projects.ecoinformatics.org/ecoinfo/issues/58052013-01-24T00:31:32Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I can see an older local version of a package in the search results along with the newer network version by doing the following steps:<br />1. Save new package to Local+Network<br />2. Edit title<br />3. Save only to Network<br />4. Launch the open dialog and see the two revisions -- the newer network one and the older local one.</p>
<p>This is somewhat accurate in that it captures exactly what versions are store where, but I do not think we want this behavior. Only the network (newest) revision should show. This may just be a search result merge issue.</p> Bug #5799 (New): publish using DOI featurehttps://projects.ecoinformatics.org/ecoinfo/issues/57992013-01-23T06:48:40ZMatt Jonesjones@nceas.ucsb.edu
<p>Morpho currently uses local identifiers that are not necessarily globally unique for data objects and metadata documents. Users should be able to publish their data packages and associated objects with a digital object identifier that is universally recognized as a citable object. Towards this end, add a feature to morpho that allows a user to choose a particular version of a data set to be 'published' with a DOI. This effectively means that a new version of all associated objects will be created, each with a minted, unique DOI that can be used to cite the object. Morpho will undertake the following steps when a user selects 'Publish using Digital Object Identifiers (DOIs)' as an action:</p>
<p>1) Ensure that all objects in the current package are saved and valid<br />2) For each data object, metadata object, and package ORE in the package<br /> a) Call the MN to reserve a DOI for that object, if it hasn't already been assigned a DOI<br /> -- if DOI minting errors occur, fail with explanation to user<br /> b) Update all metadata and package pointers to use these new DOIs to reference data, etc.<br /> c) save a new version of the object using update() to replace the old version with the DOI-named version</p>
<p>Note that when the receiving MN receives a create() or update() call that uses a DOI as its identifier, it will ensure that the user has the right to mint that DOI (either it is unreserved or reserved by that user), and then it will register that identifier with the EZID DOI registry service with appropriate metadata based on the DataCite standards.</p>
<p>The GUI for publishing with a DOI could either be part of the current Save dialog when users are saving to the network, or might be a separate menu action that is independent of the Save dialog.</p> Bug #5736 (New): Morpho DataONE refactor - trackerhttps://projects.ecoinformatics.org/ecoinfo/issues/57362012-11-19T23:33:24Zben leinfelderleinfelder@nceas.ucsb.eduBug #2852 (In Progress): Unable to delete a table that only includes the data file documentaionhttps://projects.ecoinformatics.org/ecoinfo/issues/28522007-05-24T18:49:32ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>The option to delete the curreent data table is not avaialbe when only the attribues are listed. To test this Import a table , choose DESCRIBE - include only the data file documentation (but not the data file itself) in the package. The data menu has no options for deleting the table when only the attribures are listed. The edit feature does not work on this either I got a trim error.</p>