Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-10-01T23:31:22ZEcoinformatics Redmine
Redmine Bug #6111 (Closed): No resource map (ORE) document was created if morpho create an eml metadata d...https://projects.ecoinformatics.org/ecoinfo/issues/61112013-10-01T23:31:22ZJing Taotao@nceas.ucsb.edu
<p>Currently morpho will not create a resource map document for a eml document without data files. In the future, we may switch morpho from eml-oriented to datapackage-oriented. So it is good every eml document will have a data package document.</p> Feature #6083 (Closed): Morpho should use MN.query() to look for existing resourceMaps (OREs) whe...https://projects.ecoinformatics.org/ecoinfo/issues/60832013-09-06T20:18:13Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Instead of relying on the naming pattern ("resourceMap_" + metadataId) for ORE objects, we should query the MN for OREs that package the metadata we are updating.</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 #5900 (Rejected): There is no a menu item for editing the Access information in the Document ...https://projects.ecoinformatics.org/ecoinfo/issues/59002013-04-08T18:40:55ZJing Taotao@nceas.ucsb.edu
<p>There was a menu item for editing the access information in the Document menu. But now I can't find it. So how can i edit the access rules for the data package right now?</p> Bug #5899 (Closed): Morpho can't save a existed UUID package by DOI format without changing anythinghttps://projects.ecoinformatics.org/ecoinfo/issues/58992013-04-04T23:04:18ZJing Taotao@nceas.ucsb.edu
<p>matt: so let's say I have a package saved locally and on the net with a UUID<br />[3:58pm] matt: I want to give it a DOI<br />[3:59pm] matt: how do I do that without changing it? the Save dialog has the options disabled....<br />[4:00pm] Jing: good question.<br />[4:01pm] Jing: before, you could select DOI from the combo box, then the save dialog would be enabled.<br />[4:02pm] Jing: but we changed to the check box, we didn't consider this. it is a bug.</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 #5897 (Closed): Improve UI for saving using a DOIhttps://projects.ecoinformatics.org/ecoinfo/issues/58972013-03-26T21:03:05ZJing Taotao@nceas.ucsb.edu
<p>1. In the Save Dialog, replace the selection list by a check box with the following text:</p>
<p>Publish with a DOI and make all metadata and data publicly readable</p>
<p>2. Add the following tooltip for the DOI:</p>
<p>A DOI (Digital Object Identifier) is a unique, permanent identifier that can be assigned to journal articles and data sets and is widely recognized as a means of citing these published products. An example DOI is doi:10….</p>
<p>3. If there are any data objects or metadata object is not public readable in this data package, the access policy will be changed to be public readable.</p> Bug #5896 (Closed): Get an error when user save a data package to net and local by using DOIhttps://projects.ecoinformatics.org/ecoinfo/issues/58962013-03-26T20:58:25ZJing Taotao@nceas.ucsb.edu
<p>matt: However, I just changed the data package, and tried to save to net and local again with a DOI, and I got this error:<br />[10:56am] matt: "Morpho couldn't find the source data file doi:10.5072/FK22F7WKT in any location (the temp, incomplete, data directories and the network) for copying" <br />[10:57am] benMac: that's no good. Jing - have you had problems with this before?<br />[10:57am] matt: and then the data isn't showing up in the morpho window any longer<br />[10:58am] matt: also, the newly saved data package didn't replace the original, so now the same data package is listed twice in my open dialog.</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 #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 #5885 (Resolved): Upgrading EML version causes access policy to be losthttps://projects.ecoinformatics.org/ecoinfo/issues/58852013-02-27T06:21:44Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Matt saved a DataONE package to the MN using R, but the EML was 2.0.1 and had no access rules in it. The SystemMetadata specified public access. When he opened it in Morpho it had him upgrade it to 2.1.1, but the access rules were lost.</p> Bug #5881 (Resolved): How can we change the access policy for the resource map documenthttps://projects.ecoinformatics.org/ecoinfo/issues/58812013-02-23T00:56:47ZJing Taotao@nceas.ucsb.edu
<p>When we create a data package with a data object by the new data package wizard and entity wizard, a resource map document will be generated as well.</p>
<p>Morpho has explicit ways to change the the access policy for the metadata and data objects. There is no explicit ways to modify the access policy for the resource map document. I guess we has implicit way for the resource map - it will be modified when you modify the access rules for the metadata object (eml document). However, this doesn't work. After i successfully modified the metadata's access policy, the resource map doesn't change.</p> Bug #5860 (Resolved): When morpho saves a network data package to local, the system metadata may ...https://projects.ecoinformatics.org/ecoinfo/issues/58602013-02-12T07:17:52ZJing Taotao@nceas.ucsb.edu
<p>Here are the steps to produce the bug:<br />1. Create a data package with data object and save it to the network. It contains:<br />resourceMap_foo.1, foo.1 and data.1</p>
<p>2. Update data.1 and save it to both network and local. It contains resourceMap-foo.2, foo.2 and data.2.</p>
<p>When we check the metadata for the resourceMap_foo.2, we found it has the <obsoletes>resourceMap_foo.1</obsoletes>. Actually the local doesn't have resourceMap_foo.1.</p>
<p>Same thing to the foo.2 and data.2.</p> Bug #5854 (Resolved): Include Replication Policy screen in the NDP wizard sequencehttps://projects.ecoinformatics.org/ecoinfo/issues/58542013-02-06T06:46:28Zben leinfelderleinfelder@nceas.ucsb.edu
<p>When I was updating the user guide, I added the Replication Policy instructions to the new datapackage wizard section even though it is not currently part of that 15 (!) step workflow. I think it should be considered for inclusion in the wizard since it is one of the main selling points of DataONE and having it in the wizard would highlight the importance of a solid replication strategy.</p>
<p>If we do not include it in the wizard sequence, then we might consider using a reasonable default (allow replication at 2 copies?) but this could be considered heavy handed and not appreciated by sensitive users.</p>