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 #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 #6042 (New): Cannot save/synchronize Morpho data package to the networkhttps://projects.ecoinformatics.org/ecoinfo/issues/60422013-08-01T01:55:54Zunset unsetkmwolf@ucdavis.edu
<p>Hi everyone,</p>
<p>I have saved a data package and completed all fields. I have tried saving it to the network (while logged in), and synchronizing, and both give me multiple errors, starting with this one:</p>
<p>Some problem with saving data files has occurred! <?xml version = "1.0"?> <error> Permission denied for upload </error></p>
<p>I am sure this is some simple thing that I am not understanding as a new user, but I would certainly appreciate some guidance. Thanks!</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 #4542 (New): Feature Request: Import / update metadata from MySQL databasehttps://projects.ecoinformatics.org/ecoinfo/issues/45422009-11-11T22:05:02ZDavid LeBauerdlebauer@gmail.com
<p>I am writing to request a feature for Morpho that would facilitate creating and updating metadata from an existing database. I am using MySQL, but I imagine that the feature could be more general.</p>
<p>I would like for it to:</p>
<p>a) query a database to generate relevant metadata <br />or <br />b) generate metadata from an SQL CREATE script</p>
<p>For each table<br /> give table name to entityName<br /> Add comments to Description<br /> Make list of attributeNames from column headers<br />For each attributeName<br /> entityName: is column name<br /> attributeDefinition: state if it is a primary key or foreign key, if foreign key, write foreign key and the name of referenced table<br /> storageType derived from datatype<br /> managementScale/unit/numericDomain/range etc. should be derived from datatype (and data if connected to database)</p>
<p>Thanks!</p>
<p>-David</p> Bug #2980 (New): pubDate is not created for citation use when a Morpho Dataset is submittedhttps://projects.ecoinformatics.org/ecoinfo/issues/29802007-10-10T17:22:49ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>Citations for datasets uploaded by Morpho do not have a pubDate so the date part of the citation is missing for these dataset submissions. I think we need to have a submission date included. The online forms for knb, obfs, nceas, esa and I believe sanparks all automatically create a pubDate when the form is submitted.</p>
<p>Currently only esa has a complete citation with the lsid information and name of the server included. I have an update for the other skins but I am uncertain about what needs to happen regarding the lsid (Life science id"authority").</p>
<p>Examples</p>
<p>submitted through the online form<br />on production server:<br />Harmon M. 2007. Analysis of long-term litter decomposition experiments. nceas.328.26</p>
<p>inserted by Morpho<br />on production server:<br />Harmon M. . Mass loss datafile and Nitrogen concentration data. bowdish.154.6</p>
<p>With citation changes on test server, inserted from Morpho:<br />Lafferty K. . Symmetrical web of Carpinteria Salt Marsh TEST. KNB Data Registry: urn:lsid:knb.ecoinformatics.org:bowdish:292:7 (<a class="external" href="http://knb.ecoinformatics.org">http://knb.ecoinformatics.org</a>).</p>
<p>Note that the default skin will not incorporate the citation information because it can be used by organizations or individuals working with their own version of Metacat and their server information is unknown. Also they most likely do not have a lsid.</p> Bug #2473 (In Progress): Morpho uses too much memoryhttps://projects.ecoinformatics.org/ecoinfo/issues/24732006-06-27T18:12:08ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>Currently, Morpho needs 512M of RAM to run successfully. If it is set to a lower value, Morpho will freeze in the Data Table Wizard when importing a table with many columns.</p> Bug #2213 (New): "Show all" Morpho editor handles coverage incorrectly depending on orderhttps://projects.ecoinformatics.org/ecoinfo/issues/22132005-09-30T19:37:39ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>If coverage elements in an EML document are listed in an order other than the<br />order used by the DPW (geographicCoverage, temporalCoverage, then<br />taxonomicCoverage), the "Show all" function in the Morpho editor works<br />incorrectly. Extra empty geographic, temporal, and/or taxonomic coverage nodes<br />are added. Some of these extra nodes are inserted checked, others not. I<br />believe this may be the same as bug 1668.</p> Bug #2042 (In Progress): Failure when using dataTable, spatialRaster, and spatialVector in tree e...https://projects.ecoinformatics.org/ecoinfo/issues/20422005-03-11T22:53:59ZVeronique Connollyconnolly@nceas.ucsb.edu
<p>Creating metadata using the dataTable, spatialRaster, and spatialVector modules<br />in the Morpho Editor results in an error message and a lost of the information<br />entered in the editor:</p>
<p>I created a simple data package in Morpho using the DPWizard (I only filled in<br />the required fields). Then I opened the tree editor. I clicked on “Show All”<br />and then expanded the dataTable module and entered info for the required fields.<br />I made sure only one SEQUENCE radio button was selected whenever there was a<br />CHOICE (see bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: Radio buttons for choice are "all" set as default in Tree Editor (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1712">#1712</a>). I clicked on “Trim” and then made sure the<br />spatialRaster and spatialVector boxes were not checked. I clicked OK on the<br />Morpho editor. I got the following message:</p>
<p>"The saved document is not valid EML2 for some reason. You can save it <br />locally and fix the problem later, but you will be unable to submit it <br />to the network storage system. Do you want to Continue Exiting the Editor?"</p>
<p>I clicked Yes to that message and then got a message saying "physicalList null" <br />message. I then clicked OK (it takes 4 clicks) to that message and got another<br />error message: “Exception in converting edited XML to DOM!null.”</p>
<p>After I clicked OK for this last message, the dp window was grey (empty) and the<br />butterfly continuously beat its wings, and I had to close the dp. The info I<br />entered in the tree editor was lost. I had saved the dp before I went into the<br />tree editor, but if you don't, you also loose what you had entered in the DPW.</p>
<p>Laura Downey discovered this bug using the spatialRaster module. I tried<br />replicating what I described above using the spatialRaster module and got the<br />same result (I made sure the dataTable and spatialVector boxes were not<br />selected): error messages and lost of info.</p>
<p>I also tried this with the spatialVector, got the first message mentioned above,<br />and then got a message saying “Unable to display this data. However, an empty<br />table with the column header information will be shown.” The info I entered in<br />the editor was then displayed in the data package (data table and table<br />documentation panels). However, this only happened once. After that time, I<br />repeated this process several times in the spatialVector (trying to repeat what<br />I did the first time) and got the same error messages and lost of info described<br />above for the dataTable and spatialRaster modules.</p> Bug #1702 (New): spatial search is not savedhttps://projects.ecoinformatics.org/ecoinfo/issues/17022004-09-28T23:47:07ZChad Berkleyberkley@nceas.ucsb.edu
<p>when you revise a search that you have just performed, the spatial bounding box<br />is reset to the default instead of being left in the state that you left it. <br />When opening a saved search or revising an existing search, the bounding box<br />should retain its position.</p> Bug #1651 (New): Scale requestshttps://projects.ecoinformatics.org/ecoinfo/issues/16512004-08-01T22:29:04ZRobert Washington-Allenwashingtonra@mac.com
<p>In the beginning of Mopho data entries for study scales you have requests for <br />geographic extent and temporal extent. The Temporal extent request does not <br />account for studies that occurr on hour, minute or second scales which will be <br />the case for sudies of high temporal frequency, genomic and microbiological <br />studies. Further you are requesting scale information and scale is both grain <br />(the smallest spatial unit of measure or time step) or extent(the bounds, what <br />you required).</p> Bug #1426 (In Progress): closing unsaved package does not close packagehttps://projects.ecoinformatics.org/ecoinfo/issues/14262004-03-30T22:19:51ZChad Berkleyberkley@nceas.ucsb.edu
<p>if you have an unsaved package open and you close the window, morpho asks you <br />if you'd like to save the package. if you click yes, it saves the package but <br />forgets that your original request was to close the window and leaves it open.</p> Bug #1381 (In Progress): keyword set editor efficiency problemshttps://projects.ecoinformatics.org/ecoinfo/issues/13812004-03-24T18:42:39ZChad Berkleyberkley@nceas.ucsb.edu
<p>In the "Define Keyword Set" screen of the new package wizard, I click the add <br />button and yet another dialog pops up with an add button (this, in-and-of-<br />itself, is confusing but not the point of this bug). When I click the add <br />button in the new dialog a highlighted entry is added to the keyword list box <br />but it is not evident at all that I'm supposed to click this to add a keyword. <br />it should put a new entry in the list and immediately open that entry for <br />editing. Also, I can click add multiple times without entering any text in the <br />box leaving me with n empty keywords. If you click the add button and a blank <br />line exists, it should be opened for editing instead of adding a new line.</p>
<p>When you do click the added highlighted section, the text box that finally <br />appears is too small vertically so the bottom of the letters you are typing <br />gets cut off.</p>
<p>When there are blank lines in the list box and you click somewhere else, they <br />seem to disappear, but if you click around they are still there, even though <br />they are empty.</p>
<p>If there are items in the list already and you hit the add button, a text box <br />actually is displayed but it is not focused so you have to click in it to edit <br />text. it should be focusses upon creation.</p>
<p>This dialog is a bit clumsy for data entry because you have to click so much. <br />You should just be able to type a keyword, hit enter, then type the next. You <br />should only have to click to say move up, remove or ok. When at all possible, <br />the number of clicks should be minimized.</p>
<p>The next thing I noticed is when I click ok on the popped up dialog and return <br />to the actual wizard screen, if I want to edit one of the keyword sets, I can't <br />double click on it to reopen the editor, which is how it should work. The fire <br />action of the edit button just needs to be linked into the list box <br />onDoubleClick.</p> Bug #548 (In Progress): consolidate metadata editing systems in morphohttps://projects.ecoinformatics.org/ecoinfo/issues/5482002-07-09T15:18:24ZMatt Jonesjones@nceas.ucsb.edu
<p>The data package wizard contains a series of screens that represent modules in<br />EML. These screens can be used to edit an initial set of metadata, but then we<br />switch to the editor package to make other modifications. We need to be able to<br />use one editing environment in Morpho both in wizards and for other eidting<br />tasks. This environment needs to have the capability for a flexible layout<br />system so that it can be used in multiple contexts. We will be using work from<br />the Jalama project to accomplish this.</p>