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 #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> 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 #5864 (Resolved): ECP login causes new DN so user's can't see their datahttps://projects.ecoinformatics.org/ecoinfo/issues/58642013-02-13T02:25:06ZMatt Jonesjones@nceas.ucsb.edu
<p>Logging into the new version of Morpho using ECP has two negative side effects that need to be resolved.</p>
<p>1) The ECP login uses the ou=Account subtree, so my password changed and most users will not realize this, and thus will not be able to find their previously saved data packages</p>
<p>2) the DN for logged in users changes to the CILogon DN, which also causes their previously created data to not show up. Even once the user's old knb id is mapped to their new CILogon DN, its not clear if their data will be accessible in Morpho.</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>