Ecoinformatics Redmine: gastil gastilhttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-08-24T19:06:07ZEcoinformatics Redmine
Redmine Metacat - Bug #5696 (Resolved): pathQuery returns eml docs which have no public access grantedhttps://projects.ecoinformatics.org/ecoinfo/issues/56962012-08-24T19:06:07Zgastil gastilmarygastil@yahoo.com
<p>As far as I remember, non-public eml docs did not used to be returned in pathQuery result sets in earlier versions of metacat.<br />This is with<br /><a class="external" href="http://metacat.lternet.edu/knb/metacat?action=getversion">http://metacat.lternet.edu/knb/metacat?action=getversion</a><br /><version>2.0.3</version></p>
<p>A pathQuery returns an eml doc which does not have public read access.<br />Example: knb-lter-sev.389.3</p>
<p>with<br /><access authSystem="knb" order="denyFirst" scope="document"><br /> <allow><br /> <principal>uid=SEV, o=lter, dc=ecoinformatics, dc=org</principal><br /> <permission>all</permission><br /> </allow><br /></access></p>
<p>A pathQuery returned this in its result set:<br /><document><br /><docid>knb-lter-sev.389.3</docid><br /><docname>eml</docname><br /><doctype>eml://ecoinformatics.org/eml-2.0.1</doctype><br /><createdate>2005-07-29</createdate><br /><updatedate>2012-08-22</updatedate><br /><param name="@packageId">sev.00389.1</param><br /><param name="dataset/title">Lightning Strike Data for New Mexico, 1989</param><br /></document></p>
<p>This may be related in part to bug <a class="issue tracker-1 status-1 priority-2 priority-default" title="Bug: setaccess action may have deleting access rule functionality (New)" href="https://projects.ecoinformatics.org/ecoinfo/issues/5553">#5553</a> (not sure).<br />The denyFirst may be part of the problem. The older revisions also had denyFirst.</p> EML - Bug #5617: date time format strings need a systemhttps://projects.ecoinformatics.org/ecoinfo/issues/5617#change-194802012-07-05T15:14:43Zgastil gastilmarygastil@yahoo.com
<p>Hi Matt, Well stated. I would assign higher than normal importance to this one because the temporal dimension of ecological data is so important and this limatation in translating dateTime formatStrings has held back some important features in pasta. - Gastil</p> EML - Bug #5615: Examine HTML skins for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/5615#change-194722012-06-14T01:16:08Zgastil gastilmarygastil@yahoo.com
<p>Actually, in the intel rights of that example<br /><a class="external" href="https://demo2.test.dataone.org/knb/metacat/knb-test-mcm.58.4/default">https://demo2.test.dataone.org/knb/metacat/knb-test-mcm.58.4/default</a></p>
<p>the text gets repeated THREE times: twice as para and then a third time all concatenated together as if there were no listitem nor para tags.</p> EML - Bug #5615: Examine HTML skins for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/5615#change-194712012-06-14T01:12:39Zgastil gastilmarygastil@yahoo.com
<p>Category (B) Layout or Labeling ... though a rather embarrassing one.</p>
<ul>
<li>A <literalLayout> inside a <section> is causing text to appear twice in the html.</li>
</ul>
<p>See for example <a class="external" href="https://demo2.test.dataone.org/knb/metacat/knb-test-mcm.58.4/default">https://demo2.test.dataone.org/knb/metacat/knb-test-mcm.58.4/default</a><br />I looked in the EML doc and there is nothing repeated there.</p>
<p>The abstract/section/para/literalLayout is repeated in the html.<br />The intellectualRights/section/para/itemizedlist/listitem/para/literalLayout are all repeated<br />But the methodStep/description/para/literalLayout are NOT repeated</p>
<p>It only gets repeated when the literalLayout is under a section.</p>
<ul>
<li>literalLayout is not getting rendered as pre</li>
</ul>
<p>A good reason for stalling on fixing that one is that a lot of existing EML in the LTER catalog still uses literalLayout when pre is NOT intended, due to not understanding its purpose. That is gradually getting fixed. So, just as well that the skins not fix this just yet. Unfortunately, there is also some EML which is using literalLayout as intended, and that isnt getting rendered properly yet.</p> EML - Bug #5615: Examine HTML skins for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/5615#change-194702012-06-10T01:16:16Zgastil gastilmarygastil@yahoo.com
<p>another permutation on missing methods text...<br />(A) Missing content or functionality</p>
<ul>
<li>When there is no section/para, just methodStep/description, then the just-text in the description does not appear in the html. <br />ie docId knb-lter-mcr.99910109.6 in demo2<br /> <methodStep><br /> <description>A method step for this dataset</description><br /> </methodStep></li>
</ul> EML - Bug #5615: Examine HTML skins for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/5615#change-194692012-06-07T22:31:25Zgastil gastilmarygastil@yahoo.com
<p>Adding to the list, in category (A) Missing content or functionality</p>
<ul>
<li>"Sampling Unit Location" is blank when eml does contain spatialSamplingUnits/coverage/boundingCoordinates. The sibling geographicDescription is displayed with the label "Sampling Area and Frequency".<br />Example: knb-lter-fce.515.1 which is eml 2.0.1</li>
</ul> EML - Bug #5615: Examine HTML skins for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/5615#change-194682012-06-07T20:15:31Zgastil gastilmarygastil@yahoo.com
<p>List of xsl issues to fix or improve:</p>
<p>Categorized into (A) Missing content or functionality vs (B) Layout or labeling.</p>
<p>(A) Missing content or functionality</p>
<ul>
<li><ulink url=""> not made into an <a href="">. The old skins missed this also. See Margaret's text template.</li>
</ul>
(B) Layout or labeling
<ul>
<li>de-couple the width of the physical description and other table-level eml display from the width of the table displaying attribute metadata. Often there are so many columns as to render the above <tr> too wide. See for example how showDataset table width for attributeList pushes outside its parent table's width. That is not a bug. That's a feature. Some attributeLists have > 100 attributes.</li>
</ul>
<ul>
<li>consider moving the table-level coverage and constraints to below the attribute information.</li>
</ul>
<ul>
<li>Table layout in methods sampling description: See for example knb-lter-gce.1.19 (inserted into demo2 as knb-test-gce.1.19). The text of the description gets smushed way over to the right column while the label "Description" takes up most of the page width.</li>
</ul>
<ul>
<li>"Number of Foot lines" to "Number of Footer lines".</li>
</ul>
<ul>
<li>entityName appears in html as if it were the entityLabel. Good to display both, but large/bold labeling one should be label. (in a <th> perhaps) Understood that entityLabel is not a required element.</li>
</ul>
<ul>
<li>link to "Domain Info" change to "Allowed values and codes defined". This is per feedback from our data users who did not know what Domain Info was.</li>
</ul>
<ul>
<li>hide the xml download of the EML file at the bottom of the page. If someone knows to want it, they'll know to look for it. Too often, our data users think they're going to get a formatted-for-humans file.</li>
</ul>
<ul>
<li>hide <access>. Unless there is really a desire to see this info, perhaps it should not even be displayed. And it is not good to advertise usernames.</li>
</ul> Metacat - Bug #5516: continue updating user documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/5516#change-190972012-06-07T03:40:05Zgastil gastilmarygastil@yahoo.com
<p>one important edit is the description of the "delete" behavior.</p>
<p>The other edits are just references to Figures and an updated pathQuery example.</p>
<p>I have not finished revising this section 7 but wanted to be sure the "delete" edit gets in.</p>
<p>thank you.</p> EML - Bug #5618: odd characters cause html display of eml to failhttps://projects.ecoinformatics.org/ecoinfo/issues/5618#change-194862012-06-07T02:50:32Zgastil gastilmarygastil@yahoo.com
<p>Another example of this is the difference between<br /><a class="external" href="https://demo2.test.dataone.org/knb/metacat/knb-test-nrs.569.3/default">https://demo2.test.dataone.org/knb/metacat/knb-test-nrs.569.3/default</a><br />which does display <br />versus<br /><a class="external" href="https://demo2.test.dataone.org/knb/metacat/knb-test-nrs.569.2/default">https://demo2.test.dataone.org/knb/metacat/knb-test-nrs.569.2/default</a><br />which does not display, but instead fails with a "white-page".</p>
<p>The ONLY diff between revisions 2 and 3 is the pacakgeId and <br />Bancroft's office<br />vs<br />Bancroft ’s office</p>
<p>in the abstract.</p>
<p>(revision 1 had denyFirst.)</p> EML - Bug #5618: odd characters cause html display of eml to failhttps://projects.ecoinformatics.org/ecoinfo/issues/5618#change-194852012-06-06T18:38:53Zgastil gastilmarygastil@yahoo.com
<p>To clarify this bug, see knb-lter-bug.4103.2 versus knb-lter-bug.4103.3 in demo2.</p>
<p>The only difference is the presence of higher-order ascii characters in the abstract.<br />In revision 3 they are commented-out.</p> Metacat - Bug #5620: access order="denyFirst" now means public deny (except pre-existing docs)https://projects.ecoinformatics.org/ecoinfo/issues/5620#change-194912012-06-06T17:19:04Zgastil gastilmarygastil@yahoo.com
<p>Results of pathQuery:</p>
<p>In the current inventory on the LTER metacat, the only occurance of access order="denyFirst" are 144 SBC docs, 1 MCR doc and 1 SEV doc.</p>
<p>knb-lter-mcr.2003.2<br />knb-lter-sev.402.1</p>
<p>So this is only important for consistent documentation for future eml creators.</p> Metacat - Bug #5620 (Resolved): access order="denyFirst" now means public deny (except pre-existi...https://projects.ecoinformatics.org/ecoinfo/issues/56202012-06-06T17:07:35Zgastil gastilmarygastil@yahoo.com
<p>This is a feature, not a bug:<br />Metacat 2.0.0 no longer implements denyFirst, only allowFirst.</p>
<p>Ben explained to me why the same eml doc already-submitted to the metacat2 installation on lava is public read while the same eml doc submitted to the metacat2 on demo2 makes it not public read.</p>
<p>Observation:<br /><a class="external" href="https://demo2.test.dataone.org/knb/metacat/knb-lter-mcr.2003.2/default">https://demo2.test.dataone.org/knb/metacat/knb-lter-mcr.2003.2/default</a><br />User public does not have permission to read the document with the docid knb-lter-mcr.2003.2<br /><a class="external" href="http://lava.lternet.edu:8080/knb/metacat/knb-lter-mcr.2003.2/default">http://lava.lternet.edu:8080/knb/metacat/knb-lter-mcr.2003.2/default</a><br />displays fine (not restricted)</p>
<p>That same eml doc on the LTER metacat 1.9.5 is public read.</p>
<p>The reason:<br />Metacat 2.0.0 no longer implements denyFirst, only allowFirst. EML docs with order="allowFirst" are not affected by this change. EML docs already in metacat before the upgrade will not be affected. EML docs with order="denyFirst" which are updated or inserted after the upgrade will not be public read. This is to protect any possible deny rules not implemented (even if those eml docs contain no deny rules.)</p>
<p>Since the EML 2.1.0 specification still contains denyFirst and does not warn of this change in Metacat, users may be caught unaware.</p>
<p>Im runing a pathQuery on LTER's metacat 1.9.5 now to see how widely denyFirst is used. I'll post summary results as a comment to this "bug".</p> Metacat - Bug #5619 (Resolved): metacat homepage Login anchor link not connected to idhttps://projects.ecoinformatics.org/ecoinfo/issues/56192012-06-06T01:25:29Zgastil gastilmarygastil@yahoo.com
<p>On the metacat homepage or first-page, knb/style/skins/default/index.jsp, the (Login) link to #loginanchor goes nowhere because there is no id="loginanchor", at least not that I can find.</p>
<p>This may be due to the use of iframe.</p>
<p>Possible fix: change the link to #iframeloginboxclass"</p>
<p>This is trivial... unless a new user does not realize they can scroll down to log in.</p> Metacat - Bug #5516: continue updating user documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/5516#change-190952012-06-06T00:46:49Zgastil gastilmarygastil@yahoo.com
<p>Minor edits to configuration page: two same-page links and one word change.</p> Metacat - Bug #5516: continue updating user documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/5516#change-190942012-06-05T23:41:01Zgastil gastilmarygastil@yahoo.com
<p>Section 4. Downloading and Installing<br />Just a presentation issue. <br />NOT IMPORTANT.<br />In Firefox, Safari, and chrome, <a class="external" href="http://dev-testing.dataone.org:8080/hudson/job/Metacat-unstable/javadoc/install.html">http://dev-testing.dataone.org:8080/hudson/job/Metacat-unstable/javadoc/install.html</a> <br />displays with the light-grey background div.side-bar overlapping the text of the main part of the page when that text is in a <pre>.
This section is hands-down the best ever instructions Ive seen for such complex installation.</p></pre>