Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-08-10T16:07:14ZEcoinformatics Redmine
Redmine Bug #7205 (New): IDs mishandled when an update is made to a package with a DOIhttps://projects.ecoinformatics.org/ecoinfo/issues/72052017-08-10T16:07:14ZJeanette Clark
<p>From a user:</p>
<p>"Hi Julien, sorry to bother you again but I have one more question. I’m<br />trying to update my data sets to include the DOI for the accompanying<br />article (it’s not out yet but I just got the DOI). For one of my data sets<br />I mistakenly hit “publish with DOI” and now I can’t edit / update the<br />record at all either online or via morpho:</p>
<p><a class="external" href="https://knb.ecoinformatics.org/#view/doi:10.5063/F12Z13MD">https://knb.ecoinformatics.org/#view/doi:10.5063/F12Z13MD</a></p>
<p>Online it says I don’t have access, in morpho I get this error:</p>
<p>"Problem with saving to metacat in EML200DataPackage! <?xmlversion = "1.0"><error>Could not write file: /var/metacat/documents/doi:10.5063/F12Z13MD.2: /var/metacat/documents/doi:10.5063/F12Z13MD.2 (No such file or directory)</error></p>
<p>Any tips on how I can fix this and update the record to include the DOI?"</p>
<p>It seems like the user accidentally applied a DOI and then tried to go back to Morpho to edit the package, where it tried to write the new identifier as the DOI.2</p>
<p>The user's problem has been remedied but it seems like this behavior should be fixed</p> 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 #6846 (New): Morpho hangs when exporting data packagehttps://projects.ecoinformatics.org/ecoinfo/issues/68462015-09-25T17:33:14ZBryce Mecummecum@nceas.ucsb.edu
<p>I was able to hang Morpho sometimes when exporting a newly-created data package.</p>
<p>Summary of my environment:<br />- OS: Mac OS X 10.10.5<br />- JRE: 1.8.0_51-b16<br />- Morpho: 1.11.0</p>
<p>Steps to reproduce:<br />- Open Morpho (Mac application form of it, launched via the Finder)<br />- Click File > Create new data package<br />- Enter information for 'Title', 'Owner', 'Contact', hitting next and accepting defaults for all other fields.<br />- Click Finish in the new data package wizard<br />- Save the data package using File > Save, and leave 'Save Locally" checked and click "Save" <br />- Attempt to export the package using File > Export, leave 'Export to a Directory' selected and click 'Export'<br />- Observe that the program is now hung.</p>
<p>The last step sometimes works and sometimes doesn't. I haven't determined what I'm doing that makes it hang sometimes and not other times.</p> Bug #6745 (New): Morpho main window doesn't look good in windows 8https://projects.ecoinformatics.org/ecoinfo/issues/67452015-05-04T17:15:30ZJing Taotao@nceas.ucsb.edu
<p>Margaret reported the morpho main window doesn't look good in windows 8. However, Jing didn't see the issue when he ran windows 8-1 in VirtualBox.</p> Bug #6702 (New): Import metadata indexing optionhttps://projects.ecoinformatics.org/ecoinfo/issues/67022015-03-27T21:59:28ZJessica Couturecouture@nceas.ucsb.edu
<p>When metadata is added to a package from an external file, Morpho creates a new identifier for it rather than incrementing the existing identifier. It would be great to have the option to either add the metadata to the existing series or create a new identifier when the file is brought in.</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 #6618 (New): Make production morpho work on Java 7https://projects.ecoinformatics.org/ecoinfo/issues/66182014-11-12T19:49:03ZJing Taotao@nceas.ucsb.edu
<p>Currently, the production Morpho only works on java 6. We should modify the izpack configuration to make it work in java 7.</p> Bug #6589 (New): common name in taxonomic coveragehttps://projects.ecoinformatics.org/ecoinfo/issues/65892014-08-28T20:02:32ZJessica Couturecouture@nceas.ucsb.edu
<p>When inputting taxonomic coverage manually there is an option to put common name but when assigning columns of names from a table, only the scientific classes are available. It would be helpful to be able to add common names from a table too.</p> Bug #6584 (New): bug in validity of personnel elementhttps://projects.ecoinformatics.org/ecoinfo/issues/65842014-08-12T17:51:28ZMatt Jonesjones@nceas.ucsb.edu
<p>I got a report from Zach Hoyt about having trouble uploading a document from Morpho to the KNB. In looking at the document, it appears to have `references` keys in the personnel section that are not present as `id` fields in any creator or contacts in the document. So, it appears Morpho is creating invalid documents somehow. He says he is using Morpho 1.10.2. Excerpts from the conversation are below, and the file produced by Morpho is be attached.</p>
<p>Jing has already been interacting with this group on related issues in Morpho.</p>
<blockquote>
<p>Also I am having a hard time saving this version to the network and don't know why.<br />I get an error; "Problems with saving to metacat in EML200DataPackage! The content of element 'personnel' is not complete." Any suggestions here?</p>
<p>I then tried to save a duplicate and it too failed. Maybe a KNB server issue so I will try again later.<br />I have tried to attach the current wraymond8.6 to this email as I can save it to my machine. Can you open this? The current version of this file should be wraymond8.6. You might have to add this to your \.morpho\profiles\ \data file. Let me know if this works? If it does could you load it onto the KNB server?</p>
</blockquote>
<blockquote>
<p>From: Zac Hoyt <<a class="email" href="mailto:znhoyt@alaska.edu">znhoyt@alaska.edu</a>><br />Date: August 11, 2014, 7:34:50 PM PDT<br />To: Ginny Eckert <<a class="email" href="mailto:gleckert@alaska.edu">gleckert@alaska.edu</a>><br />Subject: Re: Forage metadata</p>
<p>I downloaded the file wraymond8.6 from the KNB server. I then used Morpho to do all the editing. I then went to save and selected both Locally and Network. It appears to have saved locally to my machine just fine but I get the error when it attempts to save to the Network. Thanks for the help, Zac</p>
<p>On 8/11/2014 5:42 PM, Ginny Eckert wrote:<br />Talked with Matt and he's wondering how you generated that file. He says you deleted some parts but not others, so that's why you have a personnel error. Did you edit it outside of Morpho in a text editor? The fix is different depending on how you got there, so let me know and I'll get guidance.</p>
<p>Ginny</p>
</blockquote> Bug #6544 (New): Check the validity of the URL before letting someone save it.https://projects.ecoinformatics.org/ecoinfo/issues/65442014-04-30T00:14:43ZJing Taotao@nceas.ucsb.edu
<p>Corinna found that the morpho hangs if the metacat url is set incorrectly. But I can't reproduce it. If the url missed a "metacat" ( see using <a class="external" href="https://poseidon.limnology.wisc.edu/metacat">https://poseidon.limnology.wisc.edu/metacat</a> rather than <a class="external" href="https://poseidon.limnology.wisc.edu/metacat/metacat">https://poseidon.limnology.wisc.edu/metacat/metacat</a>), morpho is still responsive. But the login takes for ever.</p>
<p>No matter what behavior it is, we need to check the the validity of the URL.</p> Bug #6500 (New): Give users ability to import certifates into Morpho easilyhttps://projects.ecoinformatics.org/ecoinfo/issues/65002014-04-05T00:52:36ZJing Taotao@nceas.ucsb.edu
<p>We may create a ~/.morpho/certs directory and have a simple UI for users to drop certificates to the directory.</p>
<p>On startup, morpho looks in that dir and adds any CA certs it finds to the keystore, and keeps track of them, so if the user removes one then it removes it from the truststore on next restart.</p>
<p>The d1_libclient already has some features. The d1_libclient does this all dynamically at runtime - it does not actually write entries to the trustore, just merges them for runtime use</p> Bug #6410 (New): The box selection of Geographic Coverage screen doesn't work https://projects.ecoinformatics.org/ecoinfo/issues/64102014-02-06T18:36:48ZJing Taotao@nceas.ucsb.edu
<p>Hi Ben,</p>
<p>OK, got it!</p>
<p>One other issue that you may or may not be aware of: in the Geographic<br />Coverage section you can choose box or point methods. Regardless of whether<br />I choose box or point, it only allows me to put in points. So even if I put<br />in four coordinates for bounding a location, it automatically fills in the<br />other boxes (e.g. I put in 38.32 N and the box below is filled in with the<br />same coordinates; when I try to alter it to be the southern boundary, it<br />then changes the northern boundary in the box above; however, in the<br />metadata, it identifies the coordinates of the box as N, S, E, and W, even<br />though it only lets me enter N and W coordinates in the box).</p>
<p>Thank you for your help!</p>
<p><strong>~ Kristina</strong></p>
<p>Kristina Wolf<br />Restoration Ecology Lab<br />Ph.D. Student, Graduate Group in Ecology<br />Department of Plant Sciences<br />B.S. Animal Science, M.S. Soil Science<br />(530) 750-9771</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> Story #6084 (New): Use SOLR query instead of pathqueryhttps://projects.ecoinformatics.org/ecoinfo/issues/60842013-09-06T20:23:20Zben leinfelderleinfelder@nceas.ucsb.edu