Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-05-22T21:50:39ZEcoinformatics Redmine
Redmine Kepler - Bug #5611 (New): LinearModel actor doesn't handle input variables properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/56112012-05-22T21:50:39ZJim Regetzregetz@nceas.ucsb.edu
<p>The R code in the RExpression-based LinearModel actor has several problems:<br />1. In a linear model, it's the <em>independent</em> (predictor) variables that can be either numeric or factor (categorical). The dependent (response) variable must be numeric. The actor code gets this reversed, and fails with an error depending on the inputs.<br />2. The conditional is.character() in the final 'if' statement always evaluates to FALSE because of the conversion-to-factor in the first 'if' statement.<br />3. The intercept and slope aren't reported out in any useful way, and the intercept isn't even printed to the console output (if displayed).</p>
<p>I'd suggest the following replacement, which doesn't conform exactly to the intended behavior of the original actor, but I think provides a nice starter template for doing a univariate linear model fit. I also changed it to emit the fitted model object itself, which could be passed to another actor for summarizing, generating an ANOVA table, extracting coefficient estimates, etc.</p>
<p>Note that I wouldn't usually explicitly store the model formula as an object, but here I think it's useful to indicate the mapping of input ports to model variables right at the top.</p>
<p>#--------------------------------------------------<br />model <- Dependent ~ Independent</p>
<p>if (is.character(Independent)) {<br /> Independent <- factor(Independent)<br />}</p>
<ol>
<li>fit model; fitted lm object is available on output port<br />results <- lm(model)<br />print(summary(results))</li>
</ol>
<ol>
<li>plot data, adding regression line if appropriate<br />plot(model)<br />if (is.numeric(Independent)) {<br /> abline(results, col="red")<br />}<br />#--------------------------------------------------</li>
</ol> Metacat - Bug #5114 (Resolved): ESA registry: Bad link in 'register dataset' instructionshttps://projects.ecoinformatics.org/ecoinfo/issues/51142010-07-29T18:23:31ZJim Regetzregetz@nceas.ucsb.edu
<p>If you click the Register Data menu link without being logged in, it returns a page of registration instructions. Under Step 4 is a hyperlink to "ESA Data Registry Form". Clicking it produces a blank page, I imagine because the application context 'esa' is missing from the URL:<br /><a class="external" href="http://data.esa.org/cgi-bin/register-dataset.cgi?cfg=esa">http://data.esa.org/cgi-bin/register-dataset.cgi?cfg=esa</a></p>
<p>It's not a particularly useful or important link in any case (just returning the same page), but it at least shouldn't return a blank page.</p> Morpho - Bug #5058 (Resolved): Access wizard mishandles certain combinations of allow/deny elementshttps://projects.ecoinformatics.org/ecoinfo/issues/50582010-06-25T00:40:08ZJim Regetzregetz@nceas.ucsb.edu
<p>Morpho substrings XPaths improperly in certain cases when extracting data for the Access wizard, ultimately causing it to unnecessarily punt to the tree editor.</p>
<p>Here are some reproducible cases:</p>
<ul>
<li>If there is an 'allow' element for principal 'public', along with 10 or more 'allow' elements for (non-public) principals, Morpho incorrectly parses the 10th one.</li>
<li>If there is an 'allow' element for principal 'public', Morpho incorrectly parses any 'deny' elements for (non-public) principals.</li>
<li>If there is a 'deny' element for principal 'public', along with at least one 'allow' element and at least one 'deny' element for (non-public) principals, Morpho incorrectly parses those 'deny' elements.</li>
</ul>
<p>For a live example of the first case, try to open the Documentation->Access Information interface for this data package:<br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat/krobinson.12.6/nceas">http://knb.ecoinformatics.org/knb/metacat/krobinson.12.6/nceas</a></p>
<p>I believe the problem lies at least partly in lines 1304-1305 of AccessPage.java (as of rev 4925). For the cases above, this.xPathRoot.length() isn't actually the right value to pass to the substring statement. Depending on the case, the trimmed XPath ends up either having an extra character at the start, or having its first character truncated.</p>
<p>From stderr.log, here's an example of the first case above (note the extra ']' as the first character of the trimmed nextXPaths):</p>
<p>...<br />Access: nextXPath = /access/allow<sup><a href="#fn10">10</a></sup>/principal<sup><a href="#fn1">1</a></sup><br /> nextVal = user10<br />Access: TRIMMED nextXPath = ]/principal<sup><a href="#fn1">1</a></sup><br />Access: nextXPath = /access/allow<sup><a href="#fn10">10</a></sup>/permission<sup><a href="#fn1">1</a></sup><br /> nextVal = read<br />Access: TRIMMED nextXPath = ]/permission<sup><a href="#fn1">1</a></sup><br />...</p>
<p>And here's an example of the second case (note the missing first letter in the trimmed nextXPaths -- actually, maybe they're missing a leading '/' too?):</p>
<p>...<br />Access: nextXPath = /access/deny<sup><a href="#fn1">1</a></sup>/principal<sup><a href="#fn1">1</a></sup><br /> nextVal = user09<br />Access: TRIMMED nextXPath = rincipal<sup><a href="#fn1">1</a></sup><br />Access: nextXPath = /access/deny<sup><a href="#fn1">1</a></sup>/permission<sup><a href="#fn1">1</a></sup><br /> nextVal = read<br />Access: TRIMMED nextXPath = ermission<sup><a href="#fn1">1</a></sup><br />...</p> Morpho - Bug #5046 (Resolved): wrong text label for attributeOrientation in xslhttps://projects.ecoinformatics.org/ecoinfo/issues/50462010-06-10T16:47:33ZJim Regetzregetz@nceas.ucsb.edu
<p>Open jscientist.7.2 in Morpho and look at the entity metadata panel on the right. Under Physical Structure Description, it says that the Maximum Record Length is 'column', but column is actually the attributeOrientation.</p>
<p>Looks like this was a copy-and-paste error in the eml-physical-*.xsl files (all versions back to EML 2.0.0). The HTML text is "Maximum Record Length" inside two different xls:templates: one that matches maxRecordLength, and one that matches attributeOrientation. In the second case, the text should probably read "Attribute Orientation" instead.</p> Metacat - Bug #5007 (New): ESA registry: Logout link appears even when not logged inhttps://projects.ecoinformatics.org/ecoinfo/issues/50072010-05-12T20:29:35ZJim Regetzregetz@nceas.ucsb.edu
<p>Even when I'm not logged in, I see the Logout link rather than the expected Login link in the top menu at <a class="external" href="http://data.esa.org">http://data.esa.org</a>. Clicking Logout just redirects back to the front page, where I still see the Logout link rather than the Login link. And clicking "My Submissions" reports "0 data set(s) found", whereas I think the expected behavior when logged out is to present the login screen.</p>
<p>This is an issue Daigle and I experienced on esa-dev during Metacat 1.9.1 testing, and it seems to have propagated to the production ESA site after the upgrade. AFAIR, on esa-dev it would go away after a restart, but return eventually. No idea what triggers it. For what it's worth, Mike suggested at some point that it involved some convoluted javascript. When I reload the page (or click Logout), I do see Login for a split second before it gets replaced by Logout.</p>
<p>For the record, in order to log in, you can still scroll down to find the "Login to the ESA Registry" link on the front page.</p> Morpho - Bug #4975 (Resolved): Morpho can't handle docid prefix containing a periodhttps://projects.ecoinformatics.org/ecoinfo/issues/49752010-05-04T16:53:07ZJim Regetzregetz@nceas.ucsb.edu
<p>A user just reported mysterious problems attempting to save and reopen documents in Morpho. It appears the problem is that her prefix contains a period, impairing Morpho's ability to parse the document id.</p>
Steps to reproduce:
<ul>
<li>Create a new profile, choosing a prefix that contains a period (foo.bar)</li>
<li>Create a new data package, and save locally</li>
<li>Restart Morpho</li>
</ul>
<p>The saved package doesn't appear in the Open Data Package window.</p>
<p>Also, .morpho/profiles/foo.bar/data looks like this:<br />`-- foo<br /> `-- bar.3.1</p>
<p>Rather than this:<br />`-- foo.bar<br /> `-- 3.1</p>
<p>Either Morpho needs to be smarter about parsing IDs, or if such a prefix is illegal, it shouldn't allow users to create one containing periods in the first place (and this should be documented).</p> Metacat - Bug #4904 (Resolved): NCEAS Projects list is missing from registry form dropdownhttps://projects.ecoinformatics.org/ecoinfo/issues/49042010-03-27T05:46:16ZJim Regetzregetz@nceas.ucsb.edu
<p>On the NCEAS data registry form, the dropdown menu for "NCEAS Project(s)" only has a small number of what appear to be placeholder entries, rather than the complete set of NCEAS projects.</p>
<p><a class="external" href="http://knb.ecoinformatics.org/knb/cgi-bin/register-dataset.cgi?cfg=nceas">http://knb.ecoinformatics.org/knb/cgi-bin/register-dataset.cgi?cfg=nceas</a></p>
<p>I have a vague memory (which could be wrong) of this happening after a previous Metacat upgrade.</p> Metacat - Bug #4892 (New): ESA registry shouldn't allow accepted docs to be modifiedhttps://projects.ecoinformatics.org/ecoinfo/issues/48922010-03-18T18:33:02ZJim Regetzregetz@nceas.ucsb.edu
<p>As submitter of an ESA document, I was able to modify the doc <strong>after</strong> it was accepted by the moderator, which I believe shouldn't happen. There is no GUI element to do it, so it's not as though this is likely to happen, but as either the submitter or the moderator, I can edit an accepted doc by entering a URL like the following:</p>
<p><a class="external" href="http://data.esa.org/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.70">http://data.esa.org/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.70</a></p>
<p>To reiterate, this doc (esa.70) was already accepted when I did this, but I was nevertheless able to edit it and submit a modification. This triggered a 'doc has been revised' email to the ESA moderator list, and threw the doc back into the moderation queue.</p> Metacat - Bug #4862 (Closed): NCEAS registry form now creates access rules for extra partieshttps://projects.ecoinformatics.org/ecoinfo/issues/48622010-03-02T22:11:28ZJim Regetzregetz@nceas.ucsb.edu
<p>In the past, EML documents created using the NCEAS registry form were written with the following automatic access rules:</p>
<p>ALLOW: [all] uid=nceasadmin,o=NCEAS,dc=ecoinformatics,dc=org<br />ALLOW: [read][write] [...dn of document submitter...]<br />ALLOW: [read] public</p>
<p>However, as of approx March 2009, it looks like the following extra access rules are also being added:</p>
<p>ALLOW: [all] cn=knb-prod,o=NCEAS,dc=ecoinformatics,dc=org<br />ALLOW: [all] cn=esa-moderators,dc=ecoinformatics,dc=org</p>
<p>This doesn't seem right. My guess is that the NCEAS registry has been polluted by rules that are supposed to apply to other registries?</p>
<p>AFAICT, the most recent package created with the original access rules is nceas.955.1, submitted on 26-Feb-2009. The first package created with the extra rules is nceas.956.1, submitted on 31-Mar-2009. Presumably a change was made sometime in between those dates.</p> Metacat - Bug #4843 (New): ESA registry: Remove 'station' default value from Organization Namehttps://projects.ecoinformatics.org/ecoinfo/issues/48432010-02-25T00:53:13ZJim Regetzregetz@nceas.ucsb.edu
<p>In the ESA registration form, the Organization Name field under Basic Information is prepopulated with the value 'station'. This shouldn't be in there.</p> Metacat - Bug #4842 (Resolved): ESA moderators should receive email notification of document revi...https://projects.ecoinformatics.org/ecoinfo/issues/48422010-02-25T00:46:56ZJim Regetzregetz@nceas.ucsb.edu
<p>A notification should be sent to the ESA moderators list (but probably not to the document owner? no point...) whenever a document is revised during the review process. This isn't currently happening.</p>
<p>The message text can be very similar to the initial document submission notice to the moderators, although preferably with the rev number included along with the docid. E.g.,</p>
<p>----------------------------------------------------------------------<br />Ecological Society of America moderator notice:</p>
<p>The following document has been modified and is awaiting review:</p>
<p>Title: Foo<br />Creator: Foo Bar<br />Document: foo.1.4</p>
<p>Log in to review this document at <a class="external" href="http://data.esa.org">http://data.esa.org</a>.<br />----------------------------------------------------------------------</p> Metacat - Bug #4841 (Resolved): Review page for new data registration omits spatial/temporal infohttps://projects.ecoinformatics.org/ecoinfo/issues/48412010-02-24T23:57:55ZJim Regetzregetz@nceas.ucsb.edu
<p>Both for the ESA and NCEAS data registries, information entered in the temporal coverage and spatial coverage sections does <strong>not</strong> appear on the review page that appears after submitting the initial registration form. This seems like an oversight, as all other fields on the form are presented for review.</p> Metacat - Bug #4840 (New): When registering, U.S. State/Territory of owner is also applied to con...https://projects.ecoinformatics.org/ecoinfo/issues/48402010-02-24T23:50:25ZJim Regetzregetz@nceas.ucsb.edu
<p>When registering a new data set, dropdown menus for "U.S. State or Territory" appear both in the Principal Data Set Owner section and in the Data Set Contact section. However, whatever value is submitted under Owner is evidently getting applied to Contact as well, and the value (if any) selected under Contact is ignored. This is true even if no state was selected under Owner, in which case no state is recorded for Contact.</p>
<p>This was observed both for the ESA and NCEAS registries.</p> Metacat - Bug #4839 (Resolved): Fix URL in "revision notification" email sent to ESA moderatorshttps://projects.ecoinformatics.org/ecoinfo/issues/48392010-02-24T22:33:40ZJim Regetzregetz@nceas.ucsb.edu
<p>The "revise document" notification that gets sent to ESA moderators after requesting a revision contains a URL like this:</p>
<p><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65">http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65</a></p>
<p>It probably shouldn't specify stage=modify, because the moderator is unlikely to want to modify the document at this point. A simple view action for the document would be more appropriate.</p>
<p>Alternatively, it would probably be sufficient to omit the URL altogether, and instead just indicate the docid and include a link to the ESA registry home page as a convenience.</p> Metacat - Bug #4838 (Resolved): Permissions error for link contained in Data Set Citation sectionhttps://projects.ecoinformatics.org/ecoinfo/issues/48382010-02-24T22:24:33ZJim Regetzregetz@nceas.ucsb.edu
<p>It's easiest to describe this by documenting the steps to reproduce. This involves ESA, but I haven't checked whether it happens with non-public documents viewed using other registries.</p>
<p>After logging into ESA, click My Submissions (or View Submissions if logged in as a moderator), then click to view any one of the listed documents. Note that these are all documents that are <strong>not</strong> publicly readable, but should be readable by the logged-in user. The Data Set Citation section near the top of the document contains a link that refers to the document itself, e.g.: <a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/metacat/esa.65.3/esa">http://esa-dev.nceas.ucsb.edu/esa/metacat/esa.65.3/esa</a></p>
<p>Clicking on the link produces an error:</p>
<p>--------------------------------<br />This XML file does not appear to have any style information associated with it. The document tree is shown below.</p>
<p><error><br />User public does not have permission to read the document with the docid esa.65.3<br /></error><br />--------------------------------</p>
<p>The underlying URL for the example above is:<br /><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/metacat?action=read&qformat=esa&sessionid=&docid=esa.65.3">http://esa-dev.nceas.ucsb.edu/esa/metacat?action=read&qformat=esa&sessionid=&docid=esa.65.3</a></p>
<p>Perhaps the issue is the missing session variable?</p>