Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-12-14T20:56:10ZEcoinformatics Redmine
Redmine Morpho - Bug #4628 (New): Testing version 1.7.1 beta: Morpho Tree Editor produces invalid documentshttps://projects.ecoinformatics.org/ecoinfo/issues/46282009-12-14T20:56:10ZRick Reevesreeves@nceas.ucsb.edu
<p>Condition: I am using the Morpho Tree Editor to edit the columns in an attribute table. The table was, incidentally, imported into an existing Data Package (originally, nceas.906.5) using the 'Import MS Access Database' utility.</p>
<p>Here are the steps that I took:<br />Click Green Edit button, wait about 45 seconds for the Morpho Editor to <br />appear. I am editing column attributes by clicking each attribute in the 'tree', changing the value, and then clicking on the next attribute. This is a very efficient way to edit multiple table columns/attributes. Once I have modified all of the attributes, and am ready to save them, I click the OK button. Sometimes, the editor window closes and the modifications appear in the attribute table display (on the right side of the screen).</p>
<p>But several times, when I click OK, the Morpho editor screen freezes<br />and the first of the attached messages displays. Trying to recover from the error, I click the 'X' box in the upper right corner of the screen.When I click<br />to close the window (URC), the screen goes away and the second message<br />appears. My changes to the table metadata do not appear, and have been lost.</p>
<p>Note: the alternative method of editing column metadata, the Edit Column Documentation option, requires more mouse clicks and about 25 % more time <br />to use for a given group of attribute edits. this is because of the delay (of several seconds) between the time that the user clicks the mouse on an attribute column and the time that the selection 'registers' on the screen so that the user<br />can edit the field.) And I have some evidence that even using this method to edit columns, sometimes the attribute edits are not saved to the table.</p>
<p>Because of these defects, it takes a very long time to edit large groups of column attributes on stored tables in Morpho. The defects make it difficult to do error-free edition of column attributes. I think that many would-be Morpho users will become frustrated with this performance and resist using the software.</p> Morpho - Bug #3476 (New): Search Result Selection list elements change when selectedhttps://projects.ecoinformatics.org/ecoinfo/issues/34762008-08-26T22:33:40ZRick Reevesreeves@nceas.ucsb.edu
<p>Intermittent software 'lockup' (approx 50 % of attempts results in the condition):</p>
<p>Occurs on Ubuntu 7.10 platform, JRE 1.5.0.13, Morpho 1.6.1 -</p>
<p>To re-create:</p>
<p>1) Start Morpho (from command line) and log in<br />2) Search Network and Local, All, search string: 'NCEAS 2017'<br />3) From search results, select (double click) DocumentID chadden.48.2 <br /> for viewing.<br />4) Here is what happens: When I select the item, it immediately changes<br /> to another item in the list (e.g., to the entry for DocID nceas.149.17)<br />5) When this happens, the list 'locks up', and selections can not be made.</p>
<p>Again, this only happens about 50 % of the time, and only on Ubuntu (so far).</p> Metacat - Bug #2229 (New): Allowing web registry pull-down menu for "Station Name" to select mul...https://projects.ecoinformatics.org/ecoinfo/issues/22292005-10-11T23:07:08ZWill Tyburczytyburczy@nceas.ucsb.eduMorpho - 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> Metacat - Bug #2176 (New): Moderator UI and functionality for ESAhttps://projects.ecoinformatics.org/ecoinfo/issues/21762005-09-06T00:06:30ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Implement the moderator UI and functionality..(MODERATE) -- Sid
* replication issues - e.g. when a user tries to update a document on <br /> knb.ecoinformatics which was replicated from esa.ecoinformatics<br /> (replication locks are denied if the replication is asynchronous - <br /> with proper error sent back to user explaining replication is only one <br />way)<br />(This is from the ESA tasklist)</p>
<p>Detailed Notes describing this functionality</p>
<p>-> The first step in the life cycle of a registry entry is document insertion <br />by the author. For this the author should have a ldap account. <br />Issue: Should links to the ldap account creation be provided from the ESA home <br />page?</p>
<p>-> When the document is created it does not have public read access. <br />ToDo: Modify the register-dataset.cgi to not give public read access for the <br />documents created. <br />ToDo: The document has to viewed/deleted by the moderators. Hence all the <br />moderators should have all permission on the document. <br />Issue: Should email alert be sent to the moderator? To the author also with <br />instructions for viewing and editing the document?</p>
<p>-> Once the document is created, it has to be queued up for moderation. Hence <br />when the moderator logs into the system, he/she should be directly taken to a <br />search page which displays <br />ToDo: Create a new login page for the moderator<br />ToDo: Check that login/logout functionality for the moderator is working in the <br />skins.<br />ToDo: A new action should be created for moderator login? action=login can not <br />be used here because Metacat has to be told to check if the user is a moderator <br />or not. Hence either a new action has to be created. Or a new arguement to the <br />login action has to be creater. Metacat has to read the moderator list from <br />metacat.properties and it should check if the specified user is part of it.</p>
<p>-> Once the Metacat has checked that a user is a moderator, the moderator <br />should be forwarded to the search page. The search page should show all the <br />documents which do not have public read access with links/buttons for viewing, <br />accept, decline and revision of the document.<br />ToDo: Modify Resultset.xsl to have the above links/buttons. <br />ToDo: Accept leads to modification of the document to have public read access, <br />the document is updated in the repository and an email is sent to the author<br />ToDo: Decline leads to a page where the moderator can spefiy reason for <br />declining. Then the document is deleted and an email is sent to the author with <br />the reason. <br />ToDo: Revision leads to a page where the moderator can spefiy reason for <br />requesting revision. Then an email is sent to the author with the reason.</p> Morpho - Bug #2042 (In Progress): Failure when using dataTable, spatialRaster, and spatialVector ...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> Morpho - Bug #1985 (New): add morpho support for LSID identifiershttps://projects.ecoinformatics.org/ecoinfo/issues/19852005-02-18T01:54:06ZMatt Jonesjones@nceas.ucsb.edu
<p>Morpho currently uses traditional metacat identifiers when creating EML<br />documents. It needs to support LSIDs as described in Bug# 1984 both for<br />metadata and data references.</p> Morpho - 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> Morpho - 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> Morpho - Bug #1561 (In Progress): EML Attribute Page Editor doesn't handle some XML Schema attrib...https://projects.ecoinformatics.org/ecoinfo/issues/15612004-05-13T02:16:39ZChris Jonescjones@nceas.ucsb.edu
<p>In morpho 1.5.1, the data Package Wizard creates EML2.0.0 packages without<br />inserting the (optional) enforced="yes|no" schema attribute in the nominal and<br />ordinal measurement scale enumeratedDomain elements. If packages are then<br />edited with the Tree Editor, the enforced="yes|no" attribute is inserted<br />(confirmed by Sid).</p>
<p>Subsequent edits of the column metadata with the Data --> "Edit Column<br />Documentation" menu incorrectly brings up the Tree Editor for Nominal and<br />Ordinal columns. AttributePage.java calls setPageData() in order to populate<br />the fields found in the OrderedMap of XPATH strings and values. All of the<br /><strong>elements</strong> in the map are handled NominalOrdinalPanel.java, but the XML<br /><strong>attributes</strong> are not, such as the enforced="yes\no" attribute.</p>
<p>In AttributePage.java, attributes are discarded with:</p>
<p>map.remove(xPathRoot + "/@id");<br />map.remove(xPathRoot + "/@scope");</p>
<p>and so the 'enforced' attribute can be discarded with:<br />map.remove(xPathRoot +<br />"/measurementScale<sup><a href="#fn1">1</a></sup>/nominal<sup><a href="#fn1">1</a></sup>/nonNumericDomain<sup><a href="#fn1">1</a></sup>/enumeratedDomain<sup><a href="#fn1">1</a></sup>/@enforced");</p>
<p>However, this seems like a hack, since at some point down the line the<br />'enforced' field should be presented as a check box or another widget. <br />Likewise, other XML attributes should be handled as to not discard the information.</p> Metacat - Bug #1542 (New): SQL Server support brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/15422004-04-30T15:35:59ZMatt Jonesjones@nceas.ucsb.edu
<p>Support for the MS SQL Server database was maintained in versions prior to 1.3<br />of metacat. Now the xmltables-sqlserver.sql and the associated<br />upgrade*-sqlserver.sql are either not up to date or are missing entirely. Need<br />to port the database changes to SQL Server and test all functions, including<br />upgrades from 1.3 to 1.4 before releasing 1.4.</p> Metacat - Bug #1300 (New): Changes in DataSet Orignatorhttps://projects.ecoinformatics.org/ecoinfo/issues/13002004-02-02T23:03:10ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>1) Eliminate the label "Originator Address Information" <br />2) Change the Originator label to "Principal Data Set Owner" <br />3) Decerease # of roles to: PI, Custodian/Steward, Metadata Provider, Owner. <br />This change will need to be done at other places also where this list is being <br />used.</p> Metacat - Bug #1299 (New): Registry: NCEAS: Changes in project list boxhttps://projects.ecoinformatics.org/ecoinfo/issues/12992004-02-02T22:56:44ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>The project list structure needs to be explained. So a legend is needed for <br />decoding enteries like Alroy: FossilRecord (NCEAS 2088)</p>
<p>Also in project list, the interface needs to be changed. There should be two <br />lists. One with the list of projects and other empty. The user should be able <br />to add and remove project names from the second list.</p> Metacat - Bug #1213 (In Progress): emlbeta6 to eml2 conversion stylesheets should be relocatablehttps://projects.ecoinformatics.org/ecoinfo/issues/12132003-11-20T00:23:55ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>The emlb6 to eml2 conversion stylesheets that are used by webmdentry are <br />presently in a temp directory. This is the directory where all the emlb6 files <br />are downloaded and converted. But the stylesheets should go in a permanent <br />directory. They are presently in the temp directory because they are not able <br />to convert emlb6 files if the emlb6 files are downloaded to any other directory <br />other than the directory in which the stylesheets are stored. This is the bug <br />which needs to fixed so that the stylesheets should be able to transform the <br />emlb6 files irrespective of where they are downloaded.</p> EML - Bug #501 (New): change in documentation structurehttps://projects.ecoinformatics.org/ecoinfo/issues/5012002-05-09T16:11:17ZChad Berkleyberkley@nceas.ucsb.edu
<p>We should change the structure of the documentation xsd so that each of the<br />documentation tags (summary, tooltip and description) are inlined into one bit<br />of text instead of sibling elements. The new documentation should look<br />something like</p>
<p><description><summary>The <tooltip>title field</tooltip> is used to generally<br />describe the resource.</summary> It is typically 15 to 20 words long, and<br />provides a concise yet thorough descrition of the resource.</documentation></p>