Ecoinformatics Redmine

02/04/2010

04:48 PM Semtools Bug #4739 (Resolved): Re-Reorder after editing Annotation

Whenever the annotation is edited, the annotation table gets updated and returned to it's original column order.
If ... ben leinfelder

04:40 PM Semtools Bug #4738 (Resolved): Discard Annotation changes when datapackage window is closed

Because the SMS library keeps it's annotations in memory, you can actually close the data package after editing the a... ben leinfelder

04:37 PM Semtools Bug #4737 (Resolved): Provide menu option for removing Observations and Measurements

If you add an observation annotation there is no way to remove it - you can only edit it and remove all of the classe... ben leinfelder

03:41 PM Semtools Bug #4732: Directly select/edit the Annotation classes from the table

Now if you don't select a class in the ontology browser (actually it's not that easy to do since you have to cntrl+cl... ben leinfelder

03:02 PM Semtools Bug #4732: Directly select/edit the Annotation classes from the table

Double click on the cell you want to edit:
-if there's an existing value, the ontology browser opens to that selected... ben leinfelder

08:21 AM Semtools Bug #4732 (Resolved): Directly select/edit the Annotation classes from the table

Instead of going through the motion of selecting a column, bringing up the annotation page, then bringing up the onto... ben leinfelder

02:05 PM Morpho Bug #4733: Checking the permission of the user before he/she saves a data package to metacat

from regetz:
Jing phrased the bug report in terms of verifying that a user has write permission before saving anythin... ben leinfelder

12:49 PM Kepler Bug #4161: Develop kepler workflow execution engine

Need to move the authentication credentials from the old config system (ptolemy-based) to the new configuration.xml s... ben leinfelder

10:47 AM Kepler Bug #4734 (Resolved): ant run-workflow-no-gui cannot read configuration

Trying to run a workflow (xml or kar) from the ant task or the kepler.sh script results in an exception reading the s... ben leinfelder

10:39 AM Kepler Bug #4730: Kepler cannot run workflows stored in KAR files from the command-line.

This is not just files with spaces in the path - I'm getting an error as well:
Unsupported file type or connection n... ben leinfelder

02/03/2010

05:20 PM Semtools Bug #4718: Include help text on the Annotation wizard page

i've added a snippet of Shawn's explanation to the main UI page for annotations, and then put more text on a Help pop... ben leinfelder

08:21 AM Semtools Bug #4718: Include help text on the Annotation wizard page

Added help for the class selection items (Entity, Char, Standard, Protocol).
I'd like some guidance on the Observati... ben leinfelder

11:56 AM Semtools Bug #4717: Grey-out Annotation menu options when not-applicable

Here are the current scenarios:
1. When you first open Morpho (no data package is open)
-Only Search Annotations... i... ben leinfelder

02/02/2010

01:32 PM Semtools Bug #4724 (New): Mark data package as changed when Annotation is edited

Currently you can make as many changes as you want to an Annotation without ever changing the EML data package that i... ben leinfelder

12:33 PM Semtools Bug #4720: Automatically generate Measurement and Observation labels

disabling the text field for the labels - now observations and measurements will be auto labeled ben leinfelder

11:27 AM Semtools Bug #4719: Filter the Ontology Browser by superclass

Now only the subclasses of the Annotation class being collected are shown in the tree.
Note: this involves regenerati... ben leinfelder

02/01/2010

01:52 PM Semtools Bug #4720 (Resolved): Automatically generate Measurement and Observation labels

It's more of a burden than a feature to have to type in a custom label for your observation or measurement at this po... ben leinfelder

01:49 PM Semtools Bug #4719 (Resolved): Filter the Ontology Browser by superclass

The Ontology Browser is reused for many fields (Entity, Characteristic, Standard, Protocol, Relationship). Rather tha... ben leinfelder

01:46 PM Semtools Bug #4718 (Resolved): Include help text on the Annotation wizard page

Each field/checkbox/class selection widget should have a brief explanation about what is expected input (similar to t... ben leinfelder

01:44 PM Semtools Bug #4717 (Resolved): Grey-out Annotation menu options when not-applicable

If a column is currently selected that is not part of an Observation, it makes no sense to add or remove a Context fr... ben leinfelder

01/29/2010

04:35 PM Kepler Bug #4462: Component search in remote repositories not working

looks like each and every search result is being fully parsed, which then kicks off the data download for EML actors ... ben leinfelder

01/28/2010

10:19 AM Kepler Bug #4682: losing reports from KARs

needed to ensure we were listening to all revisions of the named object.
reopen if the problem persists ben leinfelder

01/27/2010

09:41 PM Kepler Bug #4682: losing reports from KARs

when I reopen the saved KAR I see that the model (TypedCompositeActor) NamedObj that issues the updateRevision() is a... ben leinfelder

07:49 PM Kepler Bug #4682: losing reports from KARs

i'm testing a Map-based ObjectManager implementation so that we don't end up with different namedObjs with the same L... ben leinfelder

12:32 PM Kepler Bug #4682: losing reports from KARs

I'm not seeing it called for any workflow that i open via a KAR.
It is called when I open a MOML xml file.
Something... ben leinfelder

01/25/2010

02:38 PM Kepler Bug #4010: RExpression2 - tracking for backwards compatibility

Stupid Responses (SRs):
SR1 - you can change the "environment.txt" file in the r module to reflect the correct R_HOME... ben leinfelder

01/22/2010

05:10 PM Morpho Bug #2502: Should be able to enter missingValueCode elements to dp

The fields are in the current wizard page - but they are not made visible.
We need more room on the page.
Make the fr... ben leinfelder

02:04 PM Morpho Bug #3314: Morpho abstract search comes up with 0

just using <para> to match would free us from concerns of how deeply nested they might be...but it also wouldn't rest... ben leinfelder

01:57 PM Morpho Bug #2379: Table metadata lost when trying to import codes from second file

as part of the save-for-later enhancements recently made, this is no longer a problem.
After the message indicating t... ben leinfelder

01:17 PM Morpho Bug #3171: Morpho install in Vista does not create a viewable sterr.log file

is this possibly a permission issue - the log is usually written to the install directory.
if we can't write to that ... ben leinfelder

01:03 PM Morpho Bug #4106: Add Cancel button to dialog for closing unsaved package

actually you can cancel it from the "save locally/network?" dialog after you say "yes" - but I added another cancel t... ben leinfelder

12:34 PM Morpho Bug #2308: No metadata shown if schemaLocation attribute set improperly

while this example of a "bad" schemaLocation isn't really a valid use of the schemaLocation attribute, I do think we ... ben leinfelder

11:45 AM Morpho Bug #1771: Deleting row of taxonomic info in DPW prevents selection of other rows,

now checking for out of range ben leinfelder

11:09 AM Morpho Bug #1771: Deleting row of taxonomic info in DPW prevents selection of other rows,

i'll take a look at this ben leinfelder

11:07 AM Morpho Bug #3897: Controlled vocabulary for Taxonomic Coverage

not part of 1.8 release. ben leinfelder

10:58 AM Morpho Bug #3482: Morpho options hang up on Ubunto 8.04 platform

was a symptom of a different bug ben leinfelder

10:58 AM Morpho Bug #4692: Morpho cannot open EML docs with <?xml-stylesheet> directive

recursively going through the XML to find the correct line - not assuming it is on the second. ben leinfelder

10:22 AM Morpho Bug #4692 (Resolved): Morpho cannot open EML docs with <?xml-stylesheet> directive

SBC and MCR LTER sites are including <?xml-stylesheet> directives in their EML docs. This is valid XML, but Morpho wa... ben leinfelder

01/21/2010

05:10 PM Kepler Bug #4671: cannot export workflow runs when workflow has actors with <> in the names

retargeting to wrp - though perhaps it's a larger kepler issue? ben leinfelder

02:06 PM Morpho Bug #4688: miss-labeled Measurement Scale example

this has been fixed.
it is a duplicate of:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2508 ben leinfelder

02:04 PM Morpho Bug #4687: Morpho logs password in plaintext

the value is not printed for passwords now. ben leinfelder

12:50 PM Morpho Bug #4687 (Resolved): Morpho logs password in plaintext

from Gastil:
Morpho logs my password in plain text in the stderr.log file when there is a login error.
Call me para... ben leinfelder

11:15 AM Morpho Bug #3482: Morpho options hang up on Ubunto 8.04 platform

will try harder to break it - work with gastil to verify ben leinfelder

01/20/2010

05:10 PM Kepler Bug #4682 (Resolved): losing reports from KARs

I'm losing reports (still? again? I don't even know anymore). I'm
running r22544, with the modification to RExpre... ben leinfelder

05:03 PM Morpho Bug #4096: Must click tab twice to display metadata for table without read access

this is so odd - must have something to do with differences in the AWT events between the OSes. Looked into it a bit ... ben leinfelder

03:15 PM Morpho Bug #3482: Morpho options hang up on Ubunto 8.04 platform

On my Ubuntu 8.04/JRE 1.5.0_15:
-downloaded 1.7.0 installer: no freezing
-ran from current SVN source: no freezing
W... ben leinfelder

02:57 PM Morpho Bug #2280: methodStep creation error

I used the wizard to create a methods element. This creates a description/section/para element. THen using the tree e... ben leinfelder

01:28 PM Morpho Bug #2988: Custom unit does not allways create the needed <additionalMetadata> tags

now Morpho inserts the appropriate additionalMetadata for any custom units that are used in the datapackage.
Note: cu... ben leinfelder

11:06 AM Morpho Bug #2988: Custom unit does not allways create the needed <additionalMetadata> tags

figured out how to recreate this error:
-define a custom unit in one EML file
-save and close that file
-open another... ben leinfelder

01/19/2010

03:33 PM Morpho Bug #2206: Tree editor does not properly process additionalMetadata items when "trimming"

it seems that the "Show all" button can get us into dicey territory with the tree editor (adding all sorts of element... ben leinfelder

03:12 PM Morpho Bug #2206: Tree editor does not properly process additionalMetadata items when "trimming"

does not seem to be a problem with current Morpho codebase (circa 1.8 release)
additionalMetadata has changed for EM... ben leinfelder

03:02 PM Morpho Bug #2957: Other entity does not display other entity Description

added 'entitytype' parameter for the XSL. now the other entity meta data is rendering when appropriate ben leinfelder

01:28 PM Morpho Bug #2957: Other entity does not display other entity Description

the stylesheet that is checked in does not render other entity (for some unknown reason). Code is in the XSL to rende... ben leinfelder

12:25 PM Morpho Bug #2957: Other entity does not display other entity Description

we'll do this as part of being able to view/convert otherEntity elements to datatable entities. ben leinfelder

11:52 AM Morpho Bug #2988: Custom unit does not allways create the needed <additionalMetadata> tags

a few notes:
-this was an EML 2.0.1 document
-the latest codebase creates EML 2.1.0 that has a slightly different add... ben leinfelder

01/15/2010

12:17 PM Kepler Bug #4671: cannot export workflow runs when workflow has actors with <> in the names

can you just not use those characters in your names in this [heavily-XML-based] application?
I'm mostly being serious. ben leinfelder

12:13 PM Morpho Bug #4677 (Resolved): Windows 7 installer/testing

Make sure Morpho installs and runs on Windows 7 ben leinfelder

12:07 PM Morpho Bug #3473: allow user to attach, replace, or delete data table on existing entity description

reassign/target for semtools ben leinfelder

12:07 PM Morpho Bug #4364: Convert otherEntity from registry to dataTable

reassign/target (semtools) ben leinfelder

11:54 AM Morpho Bug #1830: add KU to the org list in morpho

you can refresh the list now - driven by the LDAP that the Metacat points to... ben leinfelder

11:51 AM Morpho Bug #4623: docid conflict box needs a button or something

should be addressed for the 1.8 release. ben leinfelder

09:58 AM Semtools Bug #4675 (New): EML:DataTable:Annotation cardinality

Currently we have the following relationships:
(1) EML Datapackage
(1...n) DataTables in the Datapackage
(1) Annot... ben leinfelder

01/14/2010

10:59 PM Kepler Bug #4671: cannot export workflow runs when workflow has actors with <> in the names

this was for kruger tpc09?
Where was the actor with the ">" in the name?
This might be a larger ptolemy restriction a... ben leinfelder

05:00 PM Kepler Bug #4669: report layout changes, but text field displays previous content

This sounds like a problem with the text field value not properly being stored in the underlying ReportLayout model.
... ben leinfelder

11:20 AM FIRST Bug #4643: Images missing from a re-opened assessment when the images are the choices of a multiple-choice question

code is committed to SVN - would appreciate it if you (Sandeep) tried it on the test case you have. ben leinfelder

11:13 AM FIRST Bug #4643: Images missing from a re-opened assessment when the images are the choices of a multiple-choice question

i'm almost done putting in the code changes.
But I'd appreciate someone testing/making sure it works! ben leinfelder

10:59 AM FIRST Bug #4643: Images missing from a re-opened assessment when the images are the choices of a multiple-choice question

during the save, only images returned in by ResponseItem.getImageList() are being saved with ecogrid URIs. It sounds ... ben leinfelder

10:08 AM Kepler Bug #4549: String Replace actor "remembers" previous execution values

[i know you think i didn't test it, but i did...that's confusing since now it is erring for me, too]
How should this ... ben leinfelder

09:39 AM Kepler Bug #4549: String Replace actor "remembers" previous execution values

added a check for the channel width.
ran the tests - passed.
committed r56911
Now the actor will not fire if there i... ben leinfelder

09:57 AM Kepler Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time

save for later as open... ben leinfelder

09:47 AM Kepler Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time

This would be part of an entire Kepler UI redesign. ben leinfelder

08:59 AM Kepler Bug #1750: Allow KAR files to include jar/class files

did i miss something yesterday? - we are dropping a feature that was in 1.0.
(In reply to comment #15)
> This can be... ben leinfelder

01/13/2010

10:12 PM Kepler Bug #4668: Documentation for event-state module

created wiki page with explanation and example code:
https://kepler-project.org/developers/reference/using-event-stat... ben leinfelder

03:24 PM Kepler Bug #4668 (Resolved): Documentation for event-state module

Need developer-level documentation for how to use the even-state module in other modules. ben leinfelder

03:46 PM Kepler Bug #4439: reporting displays output for a different actor

oh, neat! ben leinfelder

01/12/2010

11:11 PM Kepler Bug #4549: String Replace actor "remembers" previous execution values

changed in the ptolemy code to not fire the old token if a new one did not exist ben leinfelder

10:32 AM Morpho Bug #4657: morpho creates <keyword> elements out of keywordType attribute content

the keywordType attribute will now be preserved behind the scenes when editing with the wizard interface. ben leinfelder

01/11/2010

01:58 PM EML Bug #2756: Single quote characters from data are not escaped when performing inserts

We should be escaping the special characters in any value using backslash.
Not sure this is currently going through t... ben leinfelder

12:10 PM EML Bug #2844: Need adding a javadoc target in build file

There is a target in the build.xml ("javadoc-datamanager-lib")
Docs should probably be included in the release distri... ben leinfelder

11:53 AM EML Bug #3096: Date data type (domain) need be handled correctly

as a bug this is resolved - just a final note that format strings are crucial for datetime parsing to be accurate. ben leinfelder

11:50 AM EML Bug #2507: Data Manager Library: Create a EML parser lib to digest eml document

this has been completed. Moreover, it has been extended to support any XML schema that makes use of the EML dataSet m... ben leinfelder

11:41 AM EML Bug #2573: Data manager library need to handle binary data file format

Excel:
-would this be limited to a single sheet workbook?
-would we use apache's POI library for extracting the data?... ben leinfelder

11:38 AM EML Bug #2575: Data Manager Library: Support for query object API

There are Java and XML query specifications at this point.
The Java API abstracts the SQL-specifics quite well (save ... ben leinfelder

11:19 AM EML Bug #2576: Data Manager Library: Database Connection Pooling

We might also want to exploit third party connection pooling resources - web app containers and application context p... ben leinfelder

11:09 AM EML Bug #2979: create Union query to concatenate results from multiple entities

this has long been resolved and is in use extensively in the FIRST project ben leinfelder

11:06 AM EML Bug #2578: Data Manager Library: Release and Distribution

We should also provide all the supporting/runtime jar files needed to use the DML. In the past (possibly when this bu... ben leinfelder

10:56 AM EML Bug #2737: Exception when attributeName contains SQL keywords

We should be able to wrap the attribute names in quotes to escape the reserved words. Not sure if it's standard acros... ben leinfelder

09:54 AM Metacat Bug #4641: must support java 1.6

I don't think we should yet _require_ 1.6. It's great that it runs under it, however. ben leinfelder

08:39 AM Kepler Bug #4439: reporting displays output for a different actor

I'm thinking you'd still want the report to render if al but one reference were valid, right? Maybe just a warning th... ben leinfelder

01/10/2010

10:24 PM Kepler Bug #4439: reporting displays output for a different actor

i suppose we could be listening for the MOML change request that deletes actors/ports/parameters that are referenced ... ben leinfelder

10:21 PM Kepler Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer

what was the difference for linux? ben leinfelder

01/08/2010

04:00 PM Morpho Bug #4657: morpho creates <keyword> elements out of keywordType attribute content

simple solutions:
-pop up the tree editor when we encounter keywordType attributes
-remove them and carry one with th... ben leinfelder

02:39 PM Morpho Bug #4657: morpho creates <keyword> elements out of keywordType attribute content

is there a docid that hasn't yet been corrected? ben leinfelder

01:46 PM Kepler Bug #4653: error message says "data cloumn"

search. replace. done. ben leinfelder

01:37 PM Kepler Bug #4655: data packages are suddenly unusable

dan fixed it ben leinfelder

12:39 PM Kepler Bug #4655: data packages are suddenly unusable

the cached data files are set as a data source for HSQL tables (SET TEXT....SOURCE) - but the path to the hsqldb was ... ben leinfelder

01/06/2010

11:36 AM Kepler Bug #4161: Develop kepler workflow execution engine

installed on my local system - did a roundtrip:
-upload workflow+report
-schedule
-wait
-view PDF report when complet... ben leinfelder