Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-07-26T00:01:50ZEcoinformatics Redmine
Redmine Task #6040 (New): Metacat-index does not handle <references>https://projects.ecoinformatics.org/ecoinfo/issues/60402013-07-26T00:01:50Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I indexed a document from EVOS that uses a reference for a creator rather than the details of the person:<br /><pre>
<creator><references>1359152217358</references></creator>
</pre><br />But in the index it shows up as "||" instead of following the reference back the the id where it was declared:<br /><pre>
<associatedParty id="1359152217358">...
</pre></p>
<p><a class="external" href="http://evos.nceas.ucsb.edu/evos/metacat/df35c.9.14/default">http://evos.nceas.ucsb.edu/evos/metacat/df35c.9.14/default</a></p> Bug #2849 (New): Bounding box problems when spanning the meridianhttps://projects.ecoinformatics.org/ecoinfo/issues/28492007-05-22T16:35:33ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>Bounding box problems when large areas span the meridian. Please see this reference <a class="external" href="http://purl.oclc.org/coordinates/a2.htm">http://purl.oclc.org/coordinates/a2.htm</a></p>
<p>"While there is no beginning or end on a globe, digital spatial data sets have an artificially defined beginning and end. Longitude extends from 180 degrees west (-180) to 180 degrees east (+180) of Greenwich, United Kingdom, and latitude extends from 90 degrees south (-90) to 90 degrees north (+90) of the Equator. This artificial segmentation of geographic coordinates results in a 'Global Gotcha' for bounding boxes of features spanning the 180-degree meridian." .. Consider the imaginary country of Boxtopia, which has a southwest corner at (170, 40) and a northeast corner at (-170, 50). The width of this box is 20 degrees. In a spatial database, Boxtopia would be represented by two rectangles, one which has a southwest corner at (170, 40) and a northeast corner at (180, 50) and a second that has a southwest corner at (-180, 40) and a northeast corner at (-170, 50). This split is required because the longitude must be between -180 and 180 degrees.. "unfortunately, no simple and elegant solution exists to solving the Global Gotchas. Multipart bounding boxes are a possible alternative, but they add complexity to the database and search process, defeating the simplicity of the bounding box." (Unlocking the Mysteries of the Bounding Box <a class="external" href="http://purl.oclc.org/coordinates/a2.htm">http://purl.oclc.org/coordinates/a2.htm</a>)</p>
<p>Rick Reeves recommends having the option to enter more than one bounding box with the KNB online registries. Currently people can enter in more than one keyword and more than one taxonomic entry through an Add button.</p>
<p>This has the potential of helping with searches when users make a large bounding box because they do not have the option of entering in a number of smaller bounding boxes. Bug 2732 mentions the problem of bring up all of the global data sets when doing a search using the KNB Data Catalog Map.</p> Bug #2734 (New): Duplicates between organizations and more than one organization listed as a ownerhttps://projects.ecoinformatics.org/ecoinfo/issues/27342007-01-18T22:46:22ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>There are a number of organizations who participate in projects at NCEAS whos data is currently (or potentially) registered in the KNB data repoitory. This can be done either directly or through replication from their metacat servers. ESA, UCNRS, OBFS, PISCO and LTER are examples of this. If NCEAS projects register data that is connected to the other organizations there is room for duplication. There is also a concern that some of the organization will miss getting credit for the data or be unable to display the data for their own websites and/or skins or have the data package show up for their reports. ESA has the LSID included with the citation that adds to problems with the data package being registered that is "owned" by more than one organization.</p>
<p>ESA is starting to register data sets with their own metacat server and replicate it to the KNB metacat. Here is an example of a duplicate that has been created.</p>
<p>Smith F. . Macroecological database of mammalian body mass. nceas.196.3 (registered earlier)</p>
<p>Smith F. 2006. Macroecological database of mammalian body mass. ESA Data Registry: urn:lsid:esa.org:esa:19:3</p>
<p>(<a class="external" href="http://data.esa.org">http://data.esa.org</a>).</p>
<p>same citation listing in the KNB (view has no lisid information) <br />Smith F. 2006. Macroecological database of mammalian body mass. esa.19.3</p>
<p>NCEAS and ESA data registration for the same Online Distribution Info location and in this case the same title come up when doing a search on the title. I know of three groups (2 are with the SB LTER) that are going to try to submit data papers to the ESA archives who already have data packages in the KNB. This poses the problem of having more duplicates.</p>
<p>Currently the organization field contains a specific name such as: Ecological Society of America, Organization of Biological Field Stations, University of California Natural Reserve System, and National Center for Ecological Analysis and Synthesis. We have views or web skins that will display those specific organizations data sets. This field is automatically generated if people use the skins to register data sets for those specific organizations.</p>
<p>The question is can we avoid duplication and have the different skins and organizations be able to generate views and reports specific to them. Will there be any problems with having more than one organization, who uses metacat, associated with the data package. For instance if UCNRS has a NCEAS postdoc doing research at their reserve can data sets created by this researcher be owned by both organizations.</p>
<p>Here is an example of what the contact section of the eml code might look like for a document that could be associated with more than one organization. If we encourage data packages owned by more than one organization to be listed in the eml file, will that help to prevent duplicates? Will it encourage data sharing.</p>
<p>One consideration, and complication, is that only the ESA site creates and displays a lsid (Life Science ID) along with having only one way replication. ESA registrations have been peer reviewed which can also potentially add more value to them and make them more easily cited. How does this factor in with data sets that are registered on KNB but are scheduled to be added to the ESA Archives data papers?</p>
<p>Here is an example of the eml section that could allow for more than one organization that could be searched on.</p>
<p>....<br /><creator id="1169157059583"><organizationName>NCEAS 5600: Vazquez: Null models for specialization and asymmetry in plant-pollinator systems</organizationName><br /></creator><br /><creator id="1169157150489"><organizationName>National Center for Ecological Analysis and Synthesis</organizationName><br /></creator><br /><creator id="1169157197942"><individualName><givenName>Kevin D.</givenName><br /><surName>Lafferty</surName><br /></individualName><br /><organizationName>USGS Channel Islands Field Station Marine Science Institute</organizationName><br /><positionName>Research Ecologist</positionName><br /><address><deliveryPoint>University of California</deliveryPoint><br /><city>Santa Barbara</city><br /><administrativeArea>CA</administrativeArea><br /><postalCode>93106</postalCode><br /><country>USA</country><br /></address><br /><phone phonetype="voice">(805) 893-8778</phone><br /><electronicMailAddress><a class="email" href="mailto:klafferty@usgs.gov">klafferty@usgs.gov</a></electronicMailAddress><br /></creator><br /><creator id="1169157176598"><organizationName>University of California Natural Reserve System</organizationName><br /></creator><br />...</p> Bug #2501 (New): Add links to FGDC-tranformed version of EML documentshttps://projects.ecoinformatics.org/ecoinfo/issues/25012006-07-27T16:51:32ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>When viewing EML documents, the user should be provided with a link (under "Metadata Downloads") that gives the EML-to-FGDC transformed version of the metadata.</p> Bug #2313 (New): Metacat Skins: Skins should not be installed by defaulthttps://projects.ecoinformatics.org/ecoinfo/issues/23132005-12-08T18:50:45ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Not all skins should be installed when metacat is installed. Hence it should be <br />configurable in build.properties which skins should be installed. And bu <br />default, only default skin should be installed.</p>
<p>Also skins like esa should not be part of the shipped release.</p> Bug #2229 (New): Allowing web registry pull-down menu for "Station Name" to select multiple stat...https://projects.ecoinformatics.org/ecoinfo/issues/22292005-10-11T23:07:08ZWill Tyburczytyburczy@nceas.ucsb.eduBug #2228 (New): Use method other than metadata string filters for determining the organizations ...https://projects.ecoinformatics.org/ecoinfo/issues/22282005-10-11T23:04:46ZWill Tyburczytyburczy@nceas.ucsb.edu
<p>Right now when data is registered through an organization's skin, the metadata<br />for the entry is made to include a specific string, such as "UC Natural Reserve<br />System". When listing all the data packages from that organization, the current<br />method is to use that string as a filter. Unfortunately, if a data package<br />affiliated with an organization (such as the NRS) is submitted via a different<br />registry (such as ESA), the data package won't show up in the list of that<br />organization's data. Thus, a different approach is needed.</p>
<p>From Matt's email:</p>
<p>"The right way to do this would be to decouple the metadata entry from <br />the filter that controls whether a given entry shows up in the registry. <br /> We've been experimenting with some ways to do this through 'semantic <br />annotations' that are maintained separately from the rest of the <br />metadata. This would allow us to retroactively label data packages with <br />annotations that could control which skin they show up in. It still <br />doesn't solve the maintenance problem (for each new registry skin that <br />we create, we need to annotate all past data packages that we want to <br />show up in the skin). I'm still not sure how to deal with that issue."</p> Bug #2187 (New): Option to view map or metadata.https://projects.ecoinformatics.org/ecoinfo/issues/21872005-09-06T17:08:08ZJohn Harrisharris@nceas.ucsb.edu
<p>When the users issues a Metacat query, the user should be given the option of<br />seeing the results of the query within the Metacat spatial viewer.</p> 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> Bug #2159 (New): Metacat Performance: Divide xml_nodes based on the doctypehttps://projects.ecoinformatics.org/ecoinfo/issues/21592005-07-14T01:34:01ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Matt suggested that xml_nodes table can probably be divided into multiple <br />tables based on the doctype. For example, xml_nodes can be divided into the <br />following: <br />1. xml_nodes_eml_2_0_0<br />2. xml_nodes_eml_2_0_1<br />3. xml_nodes_default</p>
<p>Hence any query for searching for a given text will be divided into 3 sub <br />queries, results of which can be unioned. While we are still going through the <br />same number of records (assuming the query is for all doctypes), this might <br />result in performance enhancement in a db like Oracle on a multi-proc machine. <br />From experience, Postgres will still run it on one proc... unless we run a <br />seperate query on each of the tables and union the results in the servlet</p>
<p>Though it is not clear how much performance would be achieved by this...</p> Bug #2130 (New): Not able to delete DPs from KNBhttps://projects.ecoinformatics.org/ecoinfo/issues/21302005-06-17T17:57:04ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Not able to delete rwilliams.4.1 and rwilliams.10.1 from KNB. The message sent <br />back by Metacat is <br />Docid rwillliams.4.1 does not exsist. Please check that you have specified the <br />revision number of the document also</p>
<p>This error is generated in DocumentImpl after running followign query:<br />"SELECT * FROM xml_documents WHERE docid = ?" (The logs indicate that ? was <br />replaced by rwilliams.4)</p>
<p>If no record is found, then the above error is generated. Otherwise the <br />document is deleted. Hence it means no document was found.</p>
<p>However, running the same query via sqlplus returns one record. Weird.</p> 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> 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> 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> Bug #1297 (New): Registry: Changes in the Basic Informationhttps://projects.ecoinformatics.org/ecoinfo/issues/12972004-02-02T22:46:11ZSaurabh Gargsgarg@nceas.ucsb.edu
<p><del>> Add middle name to first name and last name fields<br /></del>> Rearrange names into one line</p>
<p>-> Dataset title should go before projects.</p>