From 10/22/2008 to 11/20/2008
- 06:25 PM Bug #3655: create a Workflow Run Manager with ability to export Publication Ready Archives
- Some details on progress on this bug may be found here:
- 04:36 PM Bug #3683 (Resolved): add tokenType to token_flow table in provenance sql schema
- When retrieving a token_flow.data from SQL provenance into Kepler, it will be useful to know its tokenType. A new tok...
- 04:31 PM Bug #3633: New token type: By Reference / By Value
- Refiling under Component core.
- 04:29 PM Bug #3668: Define contents of "Publication Ready Archive"
- Filing under Provenance as requested in last reporting/provenance meeting.
- 04:29 PM Bug #3634: Define the interface between Provenance and Reporting
- Filing under Provenance as requested in last reporting/provenance meeting.
- 12:40 PM Bug #3607: Create model for the Report Object
- Decided to keep this bug open to allow for additions or changes.
- 12:38 PM Bug #3607: Create model for the Report Object
- Created the Report Object class based on the initial Reporting requirements.
- 07:16 AM Bug #3595: Exporting an actor should prompt user to semantically annotate it if it's not already
- I think it could also be possible for the actor and/or workflow to have been annotated with a semantic type, but the ...
- 12:53 PM Bug #3630: Diagram Use Cases for SANPARKS specific actors.
- The use case diagram now shows the sequence of steps for each potential use case for SANPARKS.
- 12:51 PM Bug #3607: Create model for the Report Object
- This should be a JAVA model that knows how to serialize and de-serialize and we also need to define the serialization...
- 12:44 PM Bug #3673 (Resolved): Create model for the Report Instance (RIO)
- Create the model for the Report Instance (RIO). This should be a JAVA model that knows how to serialize and de-seria...
- 05:40 PM Bug #3672: Open/Save Workflow as KAR Archive
- This is very similar to bug #3595, which is the same message but to do with the importing of just an actor kar.
- 04:29 PM Bug #3672 (Resolved): Open/Save Workflow as KAR Archive
- Workflow fails to be imported from a kar file
I do the following
- 02:54 PM Bug #3669: Tabbed pane interface for holding workflow canvas and additional GUI elements
- I like this as well. We just were talking about UI stuff for the reporting subsytem, and one possible UI layout was ...
- 12:35 PM Bug #3669: Tabbed pane interface for holding workflow canvas and additional GUI elements
- Ptolemy has a somewhat primitive tabbed interface in ptII/thales.
To run it, try
- 10:32 AM Bug #3669: Tabbed pane interface for holding workflow canvas and additional GUI elements
- I like this! Indeed this is a great place for the long-running meme of "Data Central" and "Process Central". For exam...
- 10:20 AM Bug #3669 (Resolved): Tabbed pane interface for holding workflow canvas and additional GUI elements
- A number of new user interface elements are being developed for Kepler. Some of these require considerable screen re...
- 02:40 PM Bug #3667: Mock-up Report Designer UI
- first draft in SVN:
- 09:28 AM Bug #3667 (Resolved): Mock-up Report Designer UI
- The general idea is that there is a "palette" of ReportItems on the left of the screen from which a user can drag int...
- 11:04 AM Bug #3671 (New): Configurable workspace directory for holding workflows, data, and run products
- In bug 3558 I requested that a new directory be created on the user's system for each workflow run, and that outputs ...
- 10:30 AM Bug #3546: Automatically load trace for a completed run into the provenance browser
- I suggest the provenance browser integrated with the Kepler GUI itself, possibly as a tabbed pane in the same space a...
- 10:14 AM Bug #3648: Create Report format converter
- Some key considerations:
-Where are images housed and referenced in the HTML case
-Styling (CSS) for HTML needs to be...
- 10:06 AM Bug #3647: Create Report Assembler
- Dynamic ReportItems (i.e. an actor's port) are referenced in the ROML and used to lookup the value[s] in Provenance.
- 09:58 AM Bug #3668: Define contents of "Publication Ready Archive"
- Yes the reap usecase isn't specific, it requests "an archive that contains the Kepler workflow, all required inputs (...
- 09:41 AM Bug #3668 (New): Define contents of "Publication Ready Archive"
- It's still unclear exactly what will be included (user specified?) and how it will be structured.
From past discussi...
- 09:22 AM Bug #3666 (Resolved): Create RIO schema
- The ROML describes a report layout and items to be included - but BEFORE a workflow execution.
The RIO contains simi...
- 10:01 PM Bug #3655: create a Workflow Run Manager with ability to export Publication Ready Archives
- I agree with Tim -- this would be more aptly called a 'Workflow Run Browser' to differentiate it from the Provenance ...
- 07:38 PM Bug #3655: create a Workflow Run Manager with ability to export Publication Ready Archives
- We have a terminology issue here. The term 'Provenance Browser' has been applied to the graphical user interface con...
- 05:28 PM Bug #3655 (New): create a Workflow Run Manager with ability to export Publication Ready Archives
- Users would like to be able to create 'publication ready archives' as described here:
- 05:43 PM Bug #3656 (Resolved): create a Provenance Client
- Create a (non-gui) Provenance Client that can interact with Provenance stores.
Among other things, this interface...
- 04:41 PM Bug #3652 (New): Ensure all Provenance Recording Types record the same things
- Recording Type SQL-SPA-v8 records files referenced by string tokens and the workflow moml. This is not done by the ot...
- 03:28 PM Bug #3649 (Resolved): determine if Provenance has everything needed by Reporting
- Make sure provenance is capturing all data needed by Reporting and check that getting things back out in a form reaso...
- 12:34 PM Bug #3648 (Resolved): Create Report format converter
- Create a report format converter that generates the .pdf and/or .html files from the Report Instance (RIO) XML.
- 12:32 PM Bug #3647 (Resolved): Create Report Assembler
- Create a report assembler that uses the data from Provenance to assemble a specific report instance (RIO) for a given...
- 12:19 PM Bug #3646 (Resolved): Create ROML Schema
- Create ROML Schema, which is the report layout specification for the Report Object Model in XML.
- 12:16 PM Bug #3644: Create report layout controller
- The report layout controller also generates the Report Object model
- 12:12 PM Bug #3644 (Resolved): Create report layout controller
- Create report layout controller that uses the ItemOfInterest model and the ReportItem model to determine the views in...
- 12:13 PM Bug #3645 (Resolved): Create report layout designer
- Create report layout designer which is the GUI for the user to design a report.
- 12:04 PM Bug #3607: Create model for the Report Object
- ReportObjectModel is referred to as ROML
ReportInstanceModel is referred to as RIO
- 12:03 PM Bug #3642 (Resolved): Create model for ReportItem
- Create model for ReportItem (also see bug for ReportItem hierarchy).
A ReportItem is contained in an ItemOfInterest.
- 11:50 AM Bug #3641 (Resolved): Create model for ItemOfInterest
- Create diagram and model classes required for ItemOfInterest, and ItemsOfInterest List. This is a reporting-specific...
- 11:47 AM Bug #3640 (Resolved): Identify items of interest in workflow.
- Create a way for the user to flag items of interest for reporting in the workflow.
Likely to be a right click contex...
- 11:45 AM Bug #3639 (Resolved): Report design features, Stage 3
- Report design features to be implemented for Stage 3.
User specified sizing of report items [contents].
- 11:42 AM Bug #3638 (Resolved): Report design features, Stage 2
- The following report design features should be included in stage 2.
Pagination and page numbers
- 11:30 AM Bug #3637 (Resolved): Report Design Features, Stage 1
- The following report design features should be included in stage 1.
- 11:24 AM Bug #3636 (Resolved): Support multiple Report formats
- Create support for multiple report formats including specifically the ability to display reports for print purposes a...
- 11:21 AM Bug #3635: Create ReportItem Type Hierarchy
- Each report item implementation should be responsible for rendering it's values.
- 11:11 AM Bug #3635 (Resolved): Create ReportItem Type Hierarchy
- Create a type hierarchy for Report Items. It may look something like this:
- 11:05 AM Bug #3634 (Resolved): Define the interface between Provenance and Reporting
- Create a diagram and classes for the interface between Provenance and Reporting.
- Get token data for given workfl...
- 11:01 AM Bug #3633 (In Progress): New token type: By Reference / By Value
- Create a new token type to handle references to files that can act as a pointer to a file (or other large data object...
- 10:56 AM Bug #3632 (Resolved): TPC exceedence notification feature
- Email alert and notification feature is required as part of the remote workflow execution. Specifically, it will be ...
- 10:53 AM Bug #3631 (Resolved): Create diagram for Scheduler / Reporting interaction.
- Create a diagram of the interactions between the workflow execution Scheduler and the Reporting engine.
- 10:46 AM Bug #3630 (Resolved): Diagram Use Cases for SANPARKS specific actors.
- Modify general use cases for reporting feature to specify SANPARKS actors.
- 12:18 PM Bug #3608: Create initial class diagrams for the reporting feature.
- Specifically for the following classes:
- 12:11 PM Bug #3608 (Resolved): Create initial class diagrams for the reporting feature.
- Create class diagrams for the reporting feature.
- 11:56 AM Bug #3607 (Resolved): Create model for the Report Object
- Create object models for the Report Object (ROML), and Report Instance (RIML).
- 05:59 PM Bug #3606 (Resolved): ProvenanceRecorder config actor menus
- The DB Type menu item needs to be added to the v8 menu.
Also I think the menu ordering should change to be more user...
- 05:54 PM Bug #3605: problem with ProvenanceRecorder
- You'll want to first change the days wf portParam to be 2 instead of 145, so it finishes more quickly.
- 05:51 PM Bug #3605 (Resolved): problem with ProvenanceRecorder
- Seeing a new issue with ProvenanceRecorder. It seems to be occurring with both schemas v7 and v8. I've not narrowed i...
- 02:38 PM Bug #3595 (New): Exporting an actor should prompt user to semantically annotate it if it's not already
- When exporting an actor without a semantic annotation, the user is not prompted to do so. When someone then tries to ...
- 04:27 PM Bug #3593 (Resolved): exporting an actor to kar does not save portparameters that have been defined
- If you configure an actor's portparameter by right clicking on it, and filling in the portparam's dialog, and then Ex...
- 04:11 PM Bug #3576: support for accessing cascading metadata from within CompositeCoactor
- I just committed an alternative version of CompositeCoactor that supports binding to cascading metadata (or annotatio...
- 01:41 PM Bug #3586 (Resolved): COMAD traces should be reproducible when there is limited concurrency
- The ComadTest actor is roughly the COMAD equivalent of Ptolemy's NonStrictTest. It records the stream of data it rec...
- 11:47 AM Bug #3585 (New): Provide API for creating output files during a workflow run
- I suggested in bug 3558 that Kepler should create a directory on the user's system for each workflow run and store th...
- 11:58 AM Bug #3578 (New): optimize timing of data download by EML and other data source actors
- The EML actor and some other data source actors download data when the drag and drop on the workflow canvas occurs, o...
- 05:49 PM Bug #2023: remove redundant labeling in tree
- I randomly looked at this old bug and decided to close it out.
- 05:31 PM Bug #3542: Tree View menu is too wide when opened
- A solution for this is to hard wire the width and height in the show() method of the TreeTableau Class.
- 05:08 PM Bug #3242: dlls should not go in c:/Windows/System32
- I think the right solution is to add the proper directory to the user's path
upon startup. Ptolemy does this in $PTI...
- 04:12 PM Bug #3242: dlls should not go in c:/Windows/System32
- I agree that its a problem putting dll's in system32, but we've had extremely poor success trying to keep them contai...
- 03:07 PM Bug #3242: dlls should not go in c:/Windows/System32
- The ant build failed for me under Windows:
c:\tmp\cxh\src\kepler\build.xml:210: Failed to copy c:\tmp\c...
- 11:36 AM Bug #3577 (New): FilterUI actor has problems
- User reports Browser actors not working on Mac. I note Browser Display and BrowserUI seem to work (BrowserUI could us...
- 03:04 PM Bug #3576 (New): support for accessing cascading metadata from within CompositeCoactor
- The CompositeCoactor class extends TypedCompositeActor (and implements Coactor) to provide a mechanism for implementi...
- 02:33 PM Bug #3575 (New): A representation of COMAD collections on the file-system
- It would be useful if there were a representation of Collections in the file
system. In particular, I could imagine ...
- 11:49 AM Bug #3574 (New): Support for importing directory contents using CollectionSource
- A common workflow pattern is to take as input all of the files (or those of a particular type) in a directory on a re...
- 11:32 AM Bug #3573 (New): Support for importing file contents automatically using CollectionSource
- The CollectionComposer and CollectionReader actors extend CollectionSource to read XML representations of the input t...
- 04:48 PM Bug #3568 (New): support for writing COMAD-style trace files from the Provenance Recorder
- I have heard rumors that there are plans to enable the general-purpose Provenance Recorder in Kepler to (optionally) ...
- 02:09 PM Bug #3566: order collection contents displayed in provenance browser?
- We have noticed this and Bertram brought this "feature request" a long time ago. It's nice to have this in this bugzi...
- 01:04 PM Bug #3566 (New): order collection contents displayed in provenance browser?
- When the data elements inside COMAD collections are displayed in the provenance browser they seem to be arbitrarily o...
- 01:18 PM Bug #2369: Scrollbars Disappear After Using Fullscreen Mode--Now crashes
- I am encountering this problem as well (on OSX). The scrollbars disappear when I go to full screen mode. They do not...
- 01:09 PM Bug #3552: Annotation elements in trace file do not appear in details pane of provenance browser
- Cool! It also would be nice somehow to distinguish annotations and metadata applied directly to the element in quest...
- 05:53 PM Bug #3560 (New): Color-code contents of CollectionDisplay
- The CollectionDisplay actor provides a live, XML-formatted view of the data stream arriving at the actor in a COMAD w...
- 05:38 PM Bug #3559 (New): month field in trace file name is off by one
- The name of a new run trace file comprises the name of the workflow, a timestamp, and a number distinguishing the tra...
- 04:46 PM Bug #2252: Need to add actors for aligning mulitiple DNA or protein sequences
- Actors for running ClustalW and Gblocks are included in the ppod-actors module.
- 04:33 PM Bug #3558 (New): Store each workflow run trace in it's own directory
- The ppod-gui module includes enhancements to the Kepler GUI for browsing and viewing the traces of previously run wor...
- 11:51 AM Bug #3557: Provide data dependency graph view in provenance browser
- This is a well accepted data-dependency view, and in our current dependency view, we have included "actors" to make t...
- 11:21 AM Bug #3557 (New): Provide data dependency graph view in provenance browser
- The provenance browser currently provides four views of a workflow run: the raw trace file, the "Collection History"...
- 11:43 AM Bug #3552: Annotation elements in trace file do not appear in details pane of provenance browser
- This feature has been implemented in a local version. Shawn and I are working on revised provenance model, which will...
- 05:25 PM Bug #3555 (New): enhancements to Trace File view in provenance browser
- The provenance browser allows one to view the raw trace file (in XML format) of the run currently loaded in the brows...
- 03:36 PM Bug #3543: org.ecoinformatics.seek.R.RExpression
- Thanks for reporting, I broke this with my last checkin when trying to clean up hardcoded paths. R wants paths to use...
- 07:49 AM Bug #3543 (Resolved): org.ecoinformatics.seek.R.RExpression
- Actor is failing to properly generate directory name for setwd() R command. R is expecting "/" as file separators yet...
- 01:29 PM Bug #3547: CollectionReader actor throws exception when input file contains Metadata or Parameter elements
- The problem was that AnnotationSet was trying to record invocation dependencies implied by the addition of annotation...
- 10:59 AM Bug #3547 (Resolved): CollectionReader actor throws exception when input file contains Metadata or Parameter elements
- The CollectionReader actor reads in an XML representation of the input to a COMAD workflow and translates the Collect...
- 01:07 PM Bug #3552 (In Progress): Annotation elements in trace file do not appear in details pane of provenance browser
- The provenance browser shows the details for the selected data or collection element of a trace in the lower left-han...
- 10:40 AM Bug #3546 (New): Automatically load trace for a completed run into the provenance browser
- At present, viewing the trace of a workflow run via the provenance browser (the one in the provenance-apps module) re...
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