Morpho: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362004-04-18T03:55:54ZEcoinformatics Redmine
Redmine Bug #1510 (Resolved): Custom unit problemshttps://projects.ecoinformatics.org/ecoinfo/issues/15102004-04-18T03:55:54ZDan Higginshiggins@nceas.ucsb.edu
<p>There are several problems with the custom unit handler for an attribute. When a<br />custom unit is created, it does now immediately appear in the unit list for use<br />in other columns of a table. Appropriate 'additionalMetadata' tags are created<br />for the new custom unit, BUT THE UNIT IS INSERTED IN THE ATTRIBUTE WITH A<br />'standardUnit' TAG RATHER THAN WITH A 'customUnit' TAG.</p>
<p>When the custom unit is reused with another column, it is also entered with a<br />'standardUnit' tag, rather than 'customUnit' tag.</p>
<p>Also, the attribute editor window position is moved behind the datapackage<br />window when the custom unit dialog is brought up, putting it in the wrong window<br />order when the dialog is closed (This got fixed once, but is not back!)</p> Bug #1488 (Resolved): Taxon page citations list surrogates not updated to reflect remote referenc...https://projects.ecoinformatics.org/ecoinfo/issues/14882004-04-15T17:39:43ZMatthew Brookebrooke@nceas.ucsb.edu
<p>0) Open the datapkg wizard. enter a creator and a contact. Advance to the<br />taxonomic coverage page, then:</p>
<p>1) on the Taxon page, and click add to add a citation in the list at the bottom</p>
<p>2) on the citation page, click "add" to add a creator, and in the party dialog,<br />select a reference from the dropdown list (for example, the contact you entered<br />earlier). click OK to close the party dialog</p>
<p>3) click OK to close the citation dialog</p>
<p>4) look at the surrogate entry for the party in the citations list at the bottom<br />of the taxon page - remember its value.</p>
<p>5) use the back button to go back to the contact page, and edit the contact that<br />you referenced above. Hit OK</p>
<p>6) use the next button to get to the taxon page again. look at the surrogate<br />entry for the party in the citations list at the bottom of the taxon page -</p>
<ul>
<li>NOTE that it hasn't changed to reflect the values you just edited. This is<br />the bug - basically, need to refresh this list in the onLoad() method for this<br />page. **</li>
</ul>
<p>7) if you select the citation and hit edit, the parties list on the citation<br />page <strong>does</strong> have the updated values - so this part is fine</p> Bug #1487 (Resolved): Citation Page: Authors List move up/down button problems on machttps://projects.ecoinformatics.org/ecoinfo/issues/14872004-04-15T04:41:11ZMatthew Brookebrooke@nceas.ucsb.edu
<p>In Mac OS X, on the Citation Page, the Authors List move up button has text truncated to read "Mov..." <br />and because buttons are generally taller than on windows, move down button is pushed downwards so <br />far that only its top border is visible</p> Bug #1484 (Resolved): Taxonomic Coverage Page not being populated properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/14842004-04-14T00:43:59ZMatthew Brookebrooke@nceas.ucsb.edu
<p>if you have a dataset that already has Taxon coverage data, and open the taxon<br />editor from the documentation menu, the citation detailsl are not properly<br />retrieved and displayed. Haven't yet tested this for going back/forwards in the<br />wizard. Suspect a problem with getPageData() method, or the root xpath that is<br />passed to this method. Continuing investigation...</p> Bug #1474 (Resolved): taxon citation screen ok button does nothinghttps://projects.ecoinformatics.org/ecoinfo/issues/14742004-04-12T17:56:29ZMatt Jonesjones@nceas.ucsb.edu
<p>1) The "Citation" screen that is accessible from the taxonomic coverage screen<br />does not work. After entering information and pressing "Ok", nothing happens. <br />Cancel results in going back to the taxon screen with no changes.</p>
<p>2) When adding a Party on the citation screen, if a reference is chosen to a<br />previously entered party then click ok, the name field in the party list does<br />not show the name, and when "Edit" is clicked it is no longer set as a<br />reference, insead displaying it as a regular party with editable fields and no name.</p> Bug #1473 (Resolved): taxon cov info not saved in treehttps://projects.ecoinformatics.org/ecoinfo/issues/14732004-04-12T17:43:34ZMatt Jonesjones@nceas.ucsb.edu
<p>Creating a new package in the DPW with taxonomic information for 3 species does<br />not actually save the taxonomic coverage node in the tree. When<br />"Documentation|Taxonomic Coverage" is opened, the taxa entered previosuly are<br />not displayed, and when the package is opened in the editor the coverage node is<br />not present.</p> Bug #1463 (Resolved): citation dialog box needs repeating authorshttps://projects.ecoinformatics.org/ecoinfo/issues/14632004-04-09T00:04:37ZMatt Jonesjones@nceas.ucsb.edu
<p>1) The current Citation dialog box that can be reached from the taxonomic<br />coverage screen does not allow for all of the needed authors for the citation. <br />Authors should be a list. Probably can reuse the party dialog and make this a<br />table showing the currently entered authors.</p>
<p>2) Also, the author fields currently require all of lastname,<br />organizationName,and positionName, which is wrong. What should be required is<br />one of those three fields. The organizationName and positionName will be so<br />infrequently needed that its a shame to include them at all, but I'm not sure we<br />are justified in removing them altogether.</p>
<p>3) Its not clear that "Title" is the title of the publication, rather than title<br />of the author (e.g., Sir). Need to use some whitespace there. It will help if<br />(1) above is implmented.</p>
<p>4) Its not clear what "Publishing Orgn" is (and I know eml inside and out). Is<br />it origin? location? origination? Need to be more decriptive.</p>
<p>5) Under "article", one should be able to enter the "Issue" along with the<br />volume. Issue is very commonly used for articles.</p> Bug #1345 (Resolved): cannot edit Interval/Ratio attributeshttps://projects.ecoinformatics.org/ecoinfo/issues/13452004-02-12T16:37:45ZDan Higginshiggins@nceas.ucsb.edu
<p>If user selects a column in a data table and tries to edit it using the 'Edit<br />Column Metadata' menu item, a NullPointer exception is thrown if the attribute<br />is Interval/Ratio. (error is in IntervalRatioPanel.setPanelData method (line<br />583). The editing dialog never appears. <br />The editing dialog appears properly if column is Nominal/Ordinal data.</p> Bug #1255 (Resolved): Java Version dependency problemhttps://projects.ecoinformatics.org/ecoinfo/issues/12552004-01-07T23:26:04ZDan Higginshiggins@nceas.ucsb.edu
<p>Morpho 1.5.0alpha2 will not run under Java 1.3. Needed to update to Java 1.4.2<br />to get it to run correctly (class not found error). We need to track down this<br />problem.</p> Bug #1251 (Resolved): Wizard: Taxonomic Coverage Pagehttps://projects.ecoinformatics.org/ecoinfo/issues/12512004-01-07T01:35:46ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Create new datapackage wizard page for Taxonomic Coverage.</p>
<p>Should create a photoshop mockup of the page/widgets before writing the code,<br />since the UI problem is quite complex...</p>
<p>We are basically filling out the eml subtree under:</p>
<p>/eml:eml/dataset/coverage/taxonomicCoverage/</p>
<p>Eric & Christy's notes say they'd like to see the following completed:</p>
<p>Taxonomic Authority <br />(Dataset/coverage/taxonomicCoverage/taxonomicSystem/classificationSystem)</p>
<p>Taxonomic Level<br />(Dataset/coverage/taxonomicCoverage/taxonomicClassification/taxonRankName)</p>
<p>Taxonomic Value<br />(Dataset/coverage/taxonomicCoverage/taxonomicClassification/taxonRankValue)</p>
<p>(Eric & Christy's notes also say:<br />should be optional... this is tricky... this could be worked into the text<br />import wizard. In the data table upload section give them an opportunity to<br />identify species codes by importing another table and could ask for the EML tags<br />above. Taxonomic Authority is part of taxonomicSystem which requires<br />identifierName... this may be problematic. Potentially lots of options to get<br />at this but maybe should begin by seeing what information can be created with a<br />species name/code lookup table upload function)<br />*<strong>My note - this is partly covered by bug 1250 *</strong></p>
<p>so, in summary, we need to complete the following EML fields as a minimum:</p>
<p>(Once only):<br />----------------------------<br />dataset/coverage/taxonomicCoverage/taxonomicSystem/classificationSystem<br />dataset/coverage/taxonomicCoverage/taxonomicSystem/identifierName<br />----------------------------</p>
(min One, unlimited repeats):<br />----------------------------<br />dataset/coverage/taxonomicCoverage/taxonomicClassification/taxonRankName<br />dataset/coverage/taxonomicCoverage/taxonomicClassification/taxonRankValue
<ul>
<li>optional:<br />dataset/coverage/taxonomicCoverage/taxonomicClassification/taxonomicClassification/...<br />----------------------------</li>
<li>NOTE that taxonomicClassification can contain nested taxonomicClassification<br />types, leading to recursion; view recursion as a way of being more specific, eg:</li>
</ul>
<p>taxonRankName (eg "genus")<br />taxonRankValue (eg "psycotria")
|
|- taxonRankName = species
|- taxonRankValue = whatever
|
|- taxonRankName = species
|- taxonRankValue = whatever
|
|- taxonRankName = species
|- taxonRankValue = whatever
|
|- etc...
|
|- etc...
|
|- etc...
|
|- etc...</p>
<p>Possible enhancement:<br />if user enters a species, do an ITIS lookup to get all the stuff above it (genus<br />etc.)?</p>
<hr />
<p>FOR INFO:</p>
<p>Taxonomists classify all organisms into a hierarchy, and give them standardized<br />Latin or Latinized names. There are seven main levels of classification in the<br />hierarchy. They are, from most to least inclusive:<br />Kingdom<br />Phylum (or Division for algae, fungi, and plants) <br />Class<br />Order<br />Family<br />Genus<br />Species</p> Bug #1250 (Resolved): Wizard Attribute Page: allow enumerations to be populated from other tables...https://projects.ecoinformatics.org/ecoinfo/issues/12502004-01-07T00:59:31ZMatthew Brookebrooke@nceas.ucsb.edu
<p>This is a copy of part (a) of bug 1201, which is now closed</p>
<p>On the Wizard Attribute Page, allow enumerations to be populated from other<br />tables (eg species lists). These other tables may or may not have already been<br />described in morpho.</p>
NominalOrdinalPanel.java needs to be changed so that the "enumerated" panel has<br />a button or url link saying something like "are definitions for these codes<br />found in another table?". When clicked, a dialog presents the user with<br />radiobuttons:
<ul>
<li>I will import the definitions table into Morpho later</li>
<li>The definitions table has already been included in my datapackage</li>
</ul>
<p>If they choose the first (import definitions later), add the required details to<br /> a java.util.List to keep track, then close dialog and move on. (the "required<br />details" might be an object that records the attribute identifier and maybe a<br />summary description, so the user will recognize the attribute when asked about<br />it at the end)</p>
<p>If the second choice is selected (table is already in datapackage), allow the<br />user to select the correct table (from a dropdown?), and then somehow display<br />that table in the dialog and enable user to choose relevant columns, and then<br /><strong>reference</strong> these in the metadata (don't copy them), using the eml<br />"dataset/dataTable/attributeList/attribute/measurementScale/nominal(or<br />ordinal)/nonNumericDomain/enumeratedDomain/entityCodeList/" subtree (see eml<br />documentation).</p>
<p>Finally, when the user gets to the last page and hits finish, we should check<br />the java.util.List to see if any tables are not yet available (i.e. choice <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need more extensive element documentation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1">#1</a>).<br />Then present the user with the list of incomplete attribs, and for each entry in<br />the list, we should do the following:</p>
<p>1) (not for first item, only for second onwards) - ask the user if the data for<br />this entry is in an existing table. If yes, skip to dialog described above, so<br />they can select it. If no:</p>
<p>2) start data wizard so they can import or describe table (do we want to limit<br />them to describing imported text tables for this step??)</p>
<p>3) After this import is done, skip to dialog described above, with the new table<br />already selected, so they can select the columns.</p>
<p>4) repeat as necessary</p> Bug #1216 (Resolved): Adding a Print menu option in Morphohttps://projects.ecoinformatics.org/ecoinfo/issues/12162003-11-20T19:55:56ZPerumal Sambasivamsambasiv@nceas.ucsb.edu
<p>A 'Print' menu item needs to be added to Morpho, which will allow the user to <br />view the metadata in a java browser and print it. The metadata is to styled <br />using the the stylesheets being developed by Sid</p> Bug #1215 (Resolved): Adding a Print menu option in Morphohttps://projects.ecoinformatics.org/ecoinfo/issues/12152003-11-20T19:55:30ZPerumal Sambasivamsambasiv@nceas.ucsb.edu
<p>A 'Print' menu item needs to be added to Morpho, which will allow the user to <br />view the metadata in a java browser and print it. The metadata is to styled <br />using the the stylesheets being developed by Sid</p> Bug #1188 (Resolved): add 'formatted printed output' for datapackage metadatahttps://projects.ecoinformatics.org/ecoinfo/issues/11882003-10-16T20:24:27ZDan Higginshiggins@nceas.ucsb.edu
<p>Comment from Sandy Andelman -<br />Formatting metadata output for printing. Again, based on our experience, most<br />ecologists want to be able to print out the metadata they have entered in an<br />easily readable format. I don't think it is sufficient to be able to view it on<br />the screen. Right now one can print out metadata, but not in a format that is<br />useful.</p>