Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362003-12-24T01:26:55ZEcoinformatics Redmine
Redmine Morpho - Bug #1239 (Resolved): morpho fails when lastId gets out of synchttps://projects.ecoinformatics.org/ecoinfo/issues/12392003-12-24T01:26:55ZDavid Kaplandmkaplan@ucdavis.edu
<p>I recently had to delete all the profile information that was contained in<br />.morpho. A new .morpho was created when I restarted morpho, but when I went to<br />"Add documentation" to a package it failed stating that id "dmk.1" was in use<br />already. The only way to fix this was to modify by hand the lastid in dmk.xml</p> Metacat - Bug #1238 (Resolved): postgresql JDBC config problem in metacathttps://projects.ecoinformatics.org/ecoinfo/issues/12382003-12-12T00:10:27ZDavid Kaplandmkaplan@ucdavis.edu
<p>I was looking at the configuration information for using postgresql in metacat<br />and I think that the current JDBC setup in build.properties and build.xml needs<br />modification for newer versions of postgresql. For newer versions, the JDBC<br />driver (that comes in a standard package) looks like:</p>
<p>/usr/share/pgsql/pg73jdbc3.jar</p>
<p>where 73 refers to the version and the 3 relates to the java version<br />(unfortunately, the 3 does not imply jre-1.3). The driver that comes with<br />metacat will not work with these versions of postgresql. I recommend dropping<br />this driver from the distribution as it could create more problems than solutions.</p>
<p>The easiest fix for this is to change (in build.xml):</p>
<pre><code>&lt;property name="jdbc" value="lib/jdbc7.1-1.2.jar" /&gt;</code></pre>
<p>to</p>
<pre><code>&lt;property name="jdbc" value="${jdbc-base}"/&gt;</code></pre>
<p>and put in build.properties:</p>
<ol>
<li>Location of postgresql JDBC driver<br />#jdbc-base=/usr/share/pgsql/pg73jdbc3.jar</li>
</ol>
<p>This has the disadvantage of having jdbc-base mean slightly different things for<br />the different backends.</p>
<p>I also noticed that in build.xml you have jdbc-base in some places and jdbc_base<br />in others.</p> Morpho - Bug #1237 (Resolved): After edit in morpho, package title and info disappears in package...https://projects.ecoinformatics.org/ecoinfo/issues/12372003-12-11T01:22:25ZDavid Kaplandmkaplan@ucdavis.edu
<p>I am using metacat-1.3.1 and morpho-1.4.0 and have found that editing the<br />overall description of a dataset (i.e. the part with the title, description,<br />originator, etc.) causes metacat and morpho to not display the title and other<br />info in the package display even though that information is still in the<br />document. The only solution I have found is to edit the information and add<br />something that was not in the document previously. For example, editing the<br />document and adding temporalCov if that was not previously in the document<br />appears to fix the problem, although I haven't repeated it enough to be sure.</p>
<p>As an example, if you look at:</p>
<p><a class="external" href="http://erizo.ucdavis.edu/metacat/">http://erizo.ucdavis.edu/metacat/</a></p>
<p>Document ID: dmk.16.21 appears blank, but if you do</p>
<p><a class="external" href="http://erizo.ucdavis.edu/metacat/servlet/metacat?action=read&qformat=xml&docid=dmk.16.21">http://erizo.ucdavis.edu/metacat/servlet/metacat?action=read&qformat=xml&docid=dmk.16.21</a></p>
<p>all of the information is there.</p>
<p>I haven't been able to find any significant EML differences that might explain<br />this. (And at the moment I can't fix dmk.16.21 despite several efforts).</p> Metacat - Bug #1236 (Resolved): enhancement to metacat: overall access controlshttps://projects.ecoinformatics.org/ecoinfo/issues/12362003-12-11T00:54:26ZDavid Kaplandmkaplan@ucdavis.edu
<p>I am submitting this bug to archive discussions we have been having regarding<br />access priviledges to the entire metacat system. Basically, I would like to (1)<br />allow write access and the ability to create new EML documents to only a subset<br />of the authenticated users, i.e. to an LDAP group/user and (2) provide the name<br />of a LDAP user or group that always has full priviledges on all documents, i.e.<br />a sysadmin type priviledge.</p>
<p>I envision a special access list that would be stored in the database that<br />contained access priviledges for the entire metacat system. This document could<br />set all the same type of priviledges that you can set in a normal ACL document<br />associated with a package, but they would apply to all documents before applying<br />the documents own ACL list. The owner of this special ACL list would be a<br />user/group specified in the config file and this would essentially create an<br />admin user/group.</p>
<p>I haven't looked at the code, but this might not be that difficult to implement<br />considering that you already have to do the same sort of access control on<br />updates with the package ACL document. You could just consider it a<br />concatenation of priviledges, although you might have to take care that the user<br />can never overide overall access controls in his document's ACL list. If not,<br />it could just be another level of checking before taking any action.</p> Morpho - Bug #1231 (Resolved): morpho skips columns during metadata entry of data file.https://projects.ecoinformatics.org/ecoinfo/issues/12312003-12-06T01:22:38ZDavid Kaplandmkaplan@ucdavis.edu
<p>I just tried enterring some metadata for a file and found that morpho would not<br />let me enter metadata for certain columns. It would skip over those columns and<br />refuse to display information about them. I was able to later go back and edit<br />the column information, but was not able to do so in the wizard.</p>
<p>The columns in question were Grapsid, Pagurid and Pinnotherid I believe. A<br />piece of the file is below:</p>
<p>date_in date_out buoy replicate sample_id Cancrid Crabs Grapsid Majid<br />Non-cancrid crabs Pagurid Pinnotherid Porcellanid Urchins<br />1992-03-20 1992-04-02 alpha 1 4859 1 1 0 0 0 0 0 0 0<br />1992-03-20 1992-04-02 alpha 2 4860 1 1 0 0 0 0 0 0 1<br />1992-03-20 1992-04-02 alpha 3 4863 6 6 0 0 0 0 0 0 1<br />1992-03-20 1992-04-02 moms 1 4861 5 5 0 0 0 0 0 0 0</p>