Ecoinformatics Redmine

05/05/2009

10:45 AM Kepler Bug #4010: RExpression2 - tracking for backwards compatibility

ReadTable.xml
there's a issue with how I'm setting up the graphics device. it's purely my R code, since the followin... ben leinfelder

05/04/2009

03:09 PM Kepler Bug #4010: RExpression2 - tracking for backwards compatibility

FIXED:
RExpression_Matrix_IO_Test.xml
-matrices now handled like R wants them to be (column-major) ben leinfelder

01:20 PM Kepler Bug #4051 (Resolved): R - include R distribution in separate module

Instead of including the R dist in the core Kepler module, we want to have it in a separate module so that upgrades t... ben leinfelder

11:10 AM Kepler Bug #3999: WRP - create event-driven states for Kepler

TODO: design document. ben leinfelder

10:52 AM Kepler Bug #3999: WRP - create event-driven states for Kepler

Added Morpho-based "event-state" module to be use for communicating between tabs/views.
Likely need modifications to ... ben leinfelder

10:56 AM Kepler Bug #3931: Get the R actor working with JNI

The more I/We work with the RNI implementation of this actor, I believe we'll need to seriously consider using some o... ben leinfelder

05/01/2009

01:41 PM FIRST Bug #4045: Incorrect use of <item> elements in QTI

It's not really the code that is generating the XML - I think it's just that the classes (Question.java) that end up ... ben leinfelder

12:42 PM FIRST Bug #4045 (Resolved): Incorrect use of <item> elements in QTI

While researching a different bug, it came to my attention that there are cases in which the parser is generating QTI... ben leinfelder

12:40 PM FIRST Bug #3974: Saved parsed items do not show up in the Assessment Importer (in DataPackage wizard)

While researching this bug, it came to my attention that there are cases in which the parser is generating QTI docume... ben leinfelder

12:31 PM FIRST Bug #3971: The original PDF document does not open when you reopen parsed items under Data Package interface

This is expected - we are not saving a reference to the PDF file and therefore are not displaying it when you come ba... ben leinfelder

04/29/2009

06:24 PM Kepler Bug #4034: "Invalid memory access" when running workflow from the command line

re-assigning to David - maybe he can shed some light on what might be happening.
(Unfortunately it seems like it migh... ben leinfelder

06:08 PM Kepler Bug #4034: "Invalid memory access" when running workflow from the command line

This same error occurs when we use the "run-workflow" ant target:
$> ant run-workflow -Dworkflow=../common/demos/gett... ben leinfelder

06:00 PM Kepler Bug #4034: "Invalid memory access" when running workflow from the command line

removing the call to the EcogridService does not fix the invalid memory error. This doesn't have to do with that serv... ben leinfelder

04:04 PM Kepler Bug #4034: "Invalid memory access" when running workflow from the command line

reverting to an older org.ecoinformatics.ecogrid.RegistryService-stub.jar version did not work (still had the same er... ben leinfelder

03:18 PM Kepler Bug #4037 (Resolved): WRM - connect to Kepler-wide configurable provenance store

This is Phase 2 for the WRM interface:
-Add a Kepler-wide provenance configuration. The intent is that the WRM inter... ben leinfelder

03:11 PM Kepler Bug #4036 (Resolved): WRM - connect to configurable provenance store

Currently the WRM viewer connects to the default provenance store specified in a .properties bundle in the WRM module... ben leinfelder

02:58 PM Kepler Bug #3634: Define the interface between Provenance and Reporting

we have this look up implemented now - closing ben leinfelder

02:53 PM Kepler Bug #3990: Include "workflow-run-manager" module in "wrp" suite

closing this - now running with the real WRM in the "wrp" module ben leinfelder

01:58 PM Kepler Bug #3990: Include "workflow-run-manager" module in "wrp" suite

I've removed the [placeholder] WRM screen from reporting's config and module.
I've added the WRM module to the wrp su... ben leinfelder

04/28/2009

12:51 PM Kepler Bug #3998: Report Viewer - render Report Instance on???Event

I've got the "event-state" module in Kepler now. It's based on the Morpho event management classes.
The "test" button... ben leinfelder

12:01 PM Kepler Bug #3986: RExpression confounding R working directory and .kepler folder

we might consider removing this parameter since it's not really useful and will loose any utility it provides once we... ben leinfelder

09:14 AM Morpho Bug #1782: Seperate access rules for data and metadata portions of dps

double checked that this was, indeed, complete. it is! ben leinfelder

04/27/2009

04:04 PM Kepler Bug #3332: RExpression_Matrix_IO_Test workflow gives an error

Derik - are you still seeing this bug?
I do not encounter the parsing error ("4L" etc...)
I believe we changed some t... ben leinfelder

03:42 PM Kepler Bug #3986: RExpression confounding R working directory and .kepler folder

i see that it fails until you game the type lattice, but afterward I believe this functions as designed.
The "R worki... ben leinfelder

10:34 AM Kepler Bug #3649: determine if Provenance has everything needed by Reporting

Derik and I were talking about how the schema could accommodate more than just the MOML file. Currently there is a co... ben leinfelder

10:19 AM Kepler Bug #2315: Unable to run multiple Kepler instances simultaneously

set the error writer for the DB server to null unless debug log level is enabled.
this prevents the stacktrace from s... ben leinfelder

04/24/2009

12:43 PM FIRST Bug #3514: Import assessments with no assessment-level score detail

there's no place in the EdML (metadata) for the aggregate scores (data).
I think we though it could be accommodated i... ben leinfelder

12:32 PM Kepler Bug #4014: Remove "include class" checkbox in export kar dialog

commented out the dialog. ben leinfelder

12:28 PM Kepler Bug #4014: Remove "include class" checkbox in export kar dialog

This is not a checkbox - it is a JOptionPane dialog with the prompt:
"Would you like to save the actor's class file w... ben leinfelder

09:52 AM FIRST Bug #3863: Parser could not launch.

Just tried:
New Data Package
Entered metadata
Saved
Launched parser
Parsed
Saved and closed
Saved
Exited morpho
Start... ben leinfelder

04/23/2009

04:53 PM Kepler Bug #3934: Report Designer - editable Report Title field

The text I enter in the Text Field does not seem to be present in the ReportLayout object that I get from the Workflo... ben leinfelder

11:09 AM FIRST Bug #3829: Support UTF8 encoded XML in Metacat

Metacat 1.9.1 does not include this feature.
We are using 1.9.1 for the prototype.
Will likely continue to see some o... ben leinfelder

11:04 AM FIRST Bug #3875: seraching for items does not return individual item

determined it was out of scope to switch to items-based interface for searching ben leinfelder

10:51 AM FIRST Bug #3914: Trying to add a category/keyword from Bloom thesarus results in error

This was a bug that we encountered in Morpho, as well.
Jing fixed it. Apparently it only shows up in Windows systems ... ben leinfelder

10:39 AM Kepler Bug #3986: RExpression confounding R working directory and .kepler folder

retarget and reassign to myself
(hunch is that working directory hasn't been "working" in a while since it subverts t... ben leinfelder

09:35 AM Kepler Bug #4021 (Resolved): KAREntry Handler

This is a somewhat amorphous topic for me (ben) - but I wanted to make a place holder for it. Hopefully we can flesh ... ben leinfelder

08:45 AM Kepler Bug #4020 (Resolved): WRP - create WorkflowRun object to encapsulate provenance/report instances

We've got a "Workflow" object that allows us to keep track of Workflow models (MOML) and Report Layouts (ROML). We ne... ben leinfelder

04/22/2009

02:03 PM Kepler Bug #4001: WRP - Save/Open KARs containing MOMLs and ROMLs

retarget to 2.0 ben leinfelder

10:57 AM Kepler Bug #3999: WRP - create event-driven states for Kepler

Looking at taking work done in the Morpho project that deals with tracking application events and state changes and b... ben leinfelder

04/21/2009

06:19 PM Kepler Bug #4010: RExpression2 - tracking for backwards compatibility

I've gone through the existing R demos (now in modules/r/demos/R) and tested them with the RExpression2 actor in plac... ben leinfelder

04:59 PM Kepler Bug #4010: RExpression2 - tracking for backwards compatibility

1. Numbers are converted to ArrayTokens of numbers when going from JRI -> Ptolemy. This is a JRI quirk/feature in tha... ben leinfelder

04:47 PM Kepler Bug #4010 (New): RExpression2 - tracking for backwards compatibility

This bug is meant to help identify and track differences between the script-based (original) RExpression actor and th... ben leinfelder

04:00 PM Kepler Bug #3809: jni actors do not work

now that the R actors (and the JRI implementations) have been moved to another module, I'm using a colon-separated li... ben leinfelder

03:06 PM Kepler Bug #3931: Get the R actor working with JNI

We've moved RExpression actors (both the script-based and the JRI-based implementations) to a new and separate module... ben leinfelder

02:48 PM Kepler Bug #4006: Move R actor to separate module

-moved code and demos and dlls and jars to the "r" module
-added "r" module to "kepler-trunk" modules.txt (might need... ben leinfelder

11:30 AM Kepler Bug #4006 (Resolved): Move R actor to separate module

We want better facilitate modularization (and allow different release schedules for this very important actor).
I'll... ben leinfelder

02:24 PM Kepler Bug #4008: EML 2 Dataset throws errors when accessing public data from mixed public/private datasets

What datapackage (id) are you downloading? ben leinfelder

11:13 AM Kepler Bug #3803: Cannot open a workflow through the command prompt, open with, or send to menus

not critical for 2.0 release. it's a nice feature to have, but not blocking the release. ben leinfelder

04/20/2009

05:07 PM Kepler Bug #4002: RExpression2 - handle arbitrary R data structures

Here is an example script that creates different data objects:
x <- 1:10
y <- x + rnorm(10)
f <- y ~ x
l <- lm(f)
s <... ben leinfelder

05:06 PM Kepler Bug #4002 (New): RExpression2 - handle arbitrary R data structures

Not everything in R fits into the Ptolemy types (nor the JRI types, for that matter).
The lm() method, for instance,... ben leinfelder

04:56 PM Kepler Bug #4001 (Resolved): WRP - Save/Open KARs containing MOMLs and ROMLs

In order to support report layouts with momls, we want to shift over to opening and saving not just the moml xml, but... ben leinfelder

04:53 PM Kepler Bug #4000 (Resolved): WRP - upload PRAs to repository

Similar to the KAR upload feature for sharing actors, Publication Ready Archives should be uploadable so that people ... ben leinfelder

04:43 PM Kepler Bug #3999 (Resolved): WRP - create event-driven states for Kepler

This is probably more general than the "reporting" module, but I am putting it here because this has the most immedia... ben leinfelder

04:37 PM Kepler Bug #3998 (Resolved): Report Viewer - render Report Instance on???Event

We need to create an event/state feature that allows us to trigger events in different views. One such action would b... ben leinfelder

01:58 PM Kepler Bug #3996 (Resolved): Report Model - [de]serialize Items of Interest

After selecting items of interest from a workflow model, you will loose those selections if you close Kepler. We need... ben leinfelder

01:53 PM Kepler Bug #3995 (Resolved): Report Model - [de]serialize Report Item properties

Need to make sure we are saving the properties when they are edited, and also setting them when report layouts are op... ben leinfelder

01:49 PM Kepler Bug #3994 (Resolved): Report Designer - use "workflow outline" rather than Items of Interest

Instead of requiring that users manually add ports and parameters to the list of "Items of Interest" - we could use a... ben leinfelder

01:44 PM Kepler Bug #3993 (Resolved): Report Designer - add parameters to the Items of Interest

Actor ports are currently the only "reportable item" - we need to include diretor/actor/workflow parameters as "Items... ben leinfelder

01:42 PM Kepler Bug #3992 (Resolved): Report Designer - finalize Report item properties

We've got the window for editing them - but it's still unclear exactly what properties we'll want/need to support. Ri... ben leinfelder

11:54 AM Kepler Bug #3990 (Resolved): Include "workflow-run-manager" module in "wrp" suite

Rather than running as it's own suite, the WRM module should be included in the WRP suite. WRP includes provenance an... ben leinfelder

04/14/2009

11:17 AM Kepler Bug #3809: jni actors do not work

i'd assume that the installer/launcher version of Kepler will be able to set the java.library.path property on start ... ben leinfelder

09:07 AM Kepler Bug #3963: RExpression2 - support mixed lists output from R

the R expression:
list(1, TRUE, 3)
preserves the numeric/boolean typing in the list:
{{1.0}, {true}, {3.0}}
This is c... ben leinfelder

04/13/2009

05:09 PM Kepler Bug #3910: RExpression multiport input drops record columns

I tried this with the RExpression actor (AKA the original "RExpression1") off of kepler-trunk and it seems to work. E... ben leinfelder

04:29 PM Kepler Bug #3960: RExpression2 - support arrayType(arrayType(....)) tokens

out of my control! ben leinfelder

04:01 PM Kepler Bug #3960: RExpression2 - support arrayType(arrayType(....)) tokens

can now handle arrayType(arrayType(...) so that the given expression ends up looking like:
{"1", "b", "3"}
Notice tha... ben leinfelder

03:13 PM Kepler Bug #3962: RExpression2 - support RecordTokens with length=1

RExpression2 actor now accepts the length=1 RecordToken, but slightly mutates the structure during the conversion.
Pt... ben leinfelder

10:44 AM Kepler Bug #3962: RExpression2 - support RecordTokens with length=1

I can see in the RExpression2 code that I'm assuming RecordTokens contain ArrayTokens. But when there's only one Toke... ben leinfelder

10:53 AM Kepler Bug #3963: RExpression2 - support mixed lists output from R

for mixed-type lists that contain strings, all items will end up as strings in Ptolemy. arrayType(scalar, ...) token... ben leinfelder

10:35 AM Kepler Bug #3961: RExpression2 - support arrayType(scalar, ....) tokens

My only guess with handling heterogenous array items is to use the low-level rniPut(...) methods in JRI and manually ... ben leinfelder