Blog

Work Completed

• KISTI
  • Prepared document that isolated the PTPFlow RMI Client calls in the desktop client that will need to be provided by the REST API, Jong then drew up a draft REST API and I added some comments.
  • Worked on the tupelo bean views for the KISTI Desktop client and resolved bugs for a brief demonstration of new capabilities
• Cyberintegrator
  • Worked through issues getting the Context Server to build with Buckminster (with Rob's help). The next step should be getting this part of the Jenkins automated build process.
  • Resolved CBI-366, data ingest problems. I added error dialogs to better inform users when operations could not be performed (e.g. no context is connected to) and updated dataset import pages to do the same.
  • Worked on CBI-365, add context listener support to the Workflow singleton. ContextBeanUtil was passing events to views and this now should be handled by the Workflow class so views get updated when context events get fired. I still need to check to make sure all views that were listening to events from ContextBeanUtil are updated.
  • Worked on CBI-363 and issues related to connecting and disconnecting from contexts and updating the application status line. This should be nearly finished.
• Medici
  • Attended staff meeting and assigned remaining 1.2 desktop issues to myself
  • Resolved MMDB-845/MMDB-869, removing views that were no longer required or useful. The last remaining view was the ContextDebugView which I used view filters to remove without modifying any code.
  • Resolved MMDB-1139, new tags no longer displayed in tag view. I updated the tagging code to use the TagEventBeanUtil to add tags.
  • Resolved MMDB-1140, duplicate comments in comment view until a refresh. This is fixed and had to do with async update calls.
  • Resolved MMDB-1141, multiple error popups when disconnecting from a server. This is fixed.

Work Planned

• KISTI
  • Document PTPFlow RMI Client APIs that will need to be part of the REST API so Jong can start working on a draft of the REST API.
  • Prepare desktop client demonstration for KISTI visit that demonstrates the progress to date replacing framework pieces with tupelo beans.
• Cyberintegrator/Medici
  • 10am Staff meeting on April 4th
  • Work on assigned Medici issues for the 1.2 release
  • Work on building the ContextServer with Buckminster
  • Work on issues related to Cyberintegrator using the ContextServer instead of ContextBeanUtil to provide the tupelo context.

Comments

This week went as planned. 1 Medici bug remains and should be fixed on April 11th.

Work Completed

• MAEviz
  • Answered questions about MAEviz analysis plug-ins that the University of West Indies people had
  • Tested MAEviz client with the maeviz.ncsa.uiuc.edu server after it was moved by Rob to make sure clients could still obtain HAZUS data and the region of interest, all tests passed.
• KISTI
  • Requested VM to support KISTI tupelo server, it now just needs to be configured with Tupelo.
  • Updated KISTI wiki documentation and spec'd out some beans to fit our needs. Joe reviewed it and we need to do some more work before we can work on the ontology.
• CyberIntegrator
  • Met with Terry et al to discuss my CI activities via skype, based on this discussion I will test ContextServer with Medici and finalize the ContextServer work so we can push out a new build of Cyberintegrator that uses the ContextServer.
  • Worked on building the ContextServer. I found a problem with the Tupelo Jena plug-in build properties that caused a runtime problem for the Context Server. Rob checked in my fix and the ContextServer product files (Headless & GUI) now properly export and run. I also removed some unnecessary UI contributions by Eclipse to clean up the UI. The next step is to get Buckminster to build the ContextServer so we can add this to the Jenkins build server and get this built for use with Cyberintegrator. I have started this process and intend to finish it the week of April 8th. I still need to continue testing Cyberintegrator to complete the transition away from ContextBeanUtil. There is at least 1 or 2 minor issues where information that ContextBeanUtil provided need to be provided by the Workflow singleton.
• Medici
  • Tested Medici with the ContextServer and found a few bugs with Medici. I worked on and resolved MMDB-1144, connection refused connecting to the context server. I also noticed that when changing context servers, there was the potential to throw error messages that a bean could not be found. This is because we save state with Medici. We should probably include additional information with the error messages to let users know that the problem is not really an issue if they are switching contexts. This might even show up if something gets deleted by another desktop client or in the web client between another users desktop sessions. I have filed the issue as MMDB-1145 as something we should look at.
  • Worked on and Resolved MMDB-1080, after clicking on hyperlinked tag in desktop client the gallery view may not update properly. This is fixed.
  • Added an improvement idea, MMDB-1146, login screen should remember multiple servers using a combo box. This would be useful when switching between contexts and not always having to re-enter server URLs.

Work Planned

• KISTI
  • Update KISTI architecture documentation for version 2.0 so that we can get it reviewed and start working on the ontology
  • Request VM to support KISTI tupelo server
• CyberIntegrator/Medici
  • Meet with Terry, Joe & Rob to discuss my CI activities on March 23, 2011 at 2pm.
  • Work on desktop issues for the 1.2 release.
  • Work on the ContextServer and any issues Cyberintegrator has with it. Add the pieces to get Buckminster building these products.

Comments

This status report covers the week of March 25th and April 1st. I was on vacation March 28, 29 and 30th so I did not do a report for the week of the 25th as usual. These weeks went as planned. Some of this work that is unfinished will continue the week of April 8th.

Work Completed

• Medici
  • Attended staff meeting
  • Started working on remaining 1.2 issues, found a bug in the web client that didn't allow users to log in.
  • Worked on and resolved MMDB-1142, Tag view has no refresh action associated with it. Users can now push the refresh icon to pull updates from the context that may have been added via the web client.
• Cyberintegrator
  • Continued working on CBI-363. Workflow singleton now manages the context instead of ContextBean/ContextBeanUtil. I'm still working on making sure we can disconnect/connect cleanly.
  • Added issue CBI-364, Context Server does not provide enough support for context authorization. The context needs some way of knowing who the users are and there currently is no support in the Context Server app for adding new people authorized to use it. Currently only shared u/p is supported.
  • Added issue CBI-365. The Workflow singleton will need to have context listener support since it is managing the Context now. Views will need to get events when a context is changed and take the appropriate actions. Previously this was done by the ContextBeanUtil.
• KISTI
  • Attended NARA meeting via google chat.
  • Continued the work to adapt KNSG classes to tupelo beans and added the ability to login to a tupelo context provided by Context Server. This is still a work in progress, but I have so far been able to import datasets to dataset beans and create a new scenario backed by a tupelo bean. Views will need to be added that work with beans as we move away from the old repository.
  • Asked Rob to setup a tupelo repository for the KISTI project
• General
  • Updated my position profile for Terry
  • Updated desktop to ubuntu 10.10 from 10.04

Work Planned

• Medici
  • Attend staff meeting, 10 am March 14
  • Work on remaining desktop issues for version 1.2 with Joel
• Cyberintegrator
  • Continue working on CBI-363, moving login with cyberintegrator and using the Context Server to provide contexts. Update views effected by this change.
• KISTI
  • Attend March 18 NARA meeting via google chat (9am - 11am)
  • Continue working on adapting KNSG core classes to tupelo beans backed by a context.

Comments

This week went as planned.

Work Completed

• KISTI
  • Drove to Champaign on Monday and attended the KISTI meeting from 3 - 4:30pm.
  • Reviewed KNSG framework data model to determine adapting it to a tupelo bean model
  • Started writing the equivalent tupelo beans, but will need a context to write against. This lead to some common work between KISTI and Cyberintegrator, both needing what the Context Server application can provide
• Cyberintegrator
  • Started working on the Context Server and CBI-363, moving the login inside Cyberintegrator and removing the interactive splash screen. This is a work in progress to remove the reliance of Cyberintegrator on a context.xml file that it should no longer need.

Work Planned

• KISTI
  • Attended March 7th KISTI meeting
  • Work on adapting KNSG core classes to tupelo beans.
• Cyberintegrator
  • Work on Context Server, a small rcp application to make it easier to setup new contexts and remove the dependency on context.xml. This is part of task CBI-363, users should be able to login from within Cyberintegrator instead of from the interactive splash screen.
  • Continue reviewing UI to suggest improvements.

Comments

This week went as planned. Next week I will continue to work on the Context Server since both projects need it and I will continue working on adapting KNSG classes to the bean model.

Work Completed

• Cyberintegrator
  • Began reviewing Cyberintegrator UI and placing comments on an internal page
  • Opened bug CBI-362, Info and Workflow views do not check for null values when creating UI controls. This leads to some blocking on the UI thread that can hang the application. This might be the source of some strange unhandled event loop exceptions because my sessions seem to go smoother now that these checks are in place. I will continue searching for any cases that null isn't checked while evaluating the UI.
  • Checked in more changes to remove unwanted eclipse UI contributions, CBI-118
• KISTI
  • Created a list of design questions for the KISTI project to help frame the discussion on March 7th.
• General
  • Transferred data from an old laptop to my new laptop so I can return my old laptop.

Work Planned

• Work on Cyberintegrator
  • Begin reviewing UI to gain a better understanding of the software and offer suggested improvements
  • Scope work for Context Server to manage setting up & deploying tupelo contexts for Cyberintegrator
• KISTI
  • Work on list of design questions for the project that will help frame the discussion for the March 7th meeting.
• General
  • Transfer data from old laptop to new laptop

Comments

I had some doctor visits and was sick for part of this week. I took a half day on Monday, Thursday and Friday so I did not get to as much as I had planned.

Work Completed

• MAEviz
  • On Monday we solved the issue of the Synergy special iteration case and then between the rest of Monday and Tuesday I tested the solution, added an example of using a style to color an analysis output, and documented parts of the code that would help the Synergy developers complete their tasks for the Hungarian exercise.
  • Resolved an issue with MAEviz launching under 64 bit windows. The Eclipse 64 bit launcher was not included in the product file.
• KISTI
  • Discussed briefly with Jong about getting started on the KISTI project and what lies ahead. We will setup a meeting to discuss design strategies for the upcoming project.
• Cyberintegrator
  • Started cleaning up undesirable UI contributions from Eclipse plugins. I provided some screenshots to Rob to ensure that I was on the right track for what he wanted cleaned up as part of CBI-118. I haven't checked in the code yet since I didn't have write privileges to SVN.

Work Planned

• KISTI
  • If contract is completed, begin project to create a Web application version of eAIRs.
• MAEviz
  • Assist Synergy visitors with issue running a special iteration case
  • Document new analyses created for Synergy visitors
• Cyberintegrator
  • Work on cleaning up undesireable UI contributions from Eclipse plugins

Comments

This week went as planned. Next week I will continue working on Cyberintegrator and KISTI.

Work Completed

• MAEviz Workshop
  • Travelled to Champaign on Wednesday morning
  • Met with SYNERGY visitors from Wednesday afternoon through Friday. I gave a short introduction to Eclipse RCP development and MAEviz extension points. The visitors had a list of MAEviz/Eclipse questions that we went through. We discussed their MAEviz exercise and strategies to implement their new analyses. We also went through creating a new analysis that could be the basis for their exercise.
• Medici
  • Attended Monday staff meeting using Skype.
  • Fixed MMDB-1128, removing a dataset from a collection doesn't check for null collection beans, which is possible if a dataset was part of a collection that was deleted.
  • Fixed MMDB-1129, MyDatasetsView does not provide a popup menu. Since a context menu was not attached to this view, none of the right click actions such as add tag, add annotation, etc were available in this view. A Dataset had to be part of a collection so it was viewable in the Gallery in order to add a tag.
  • Fixed MMDB-1112, added a remove collection option to the Collection view.
  • Resolved [MMDB-726|https://opensource.ncsa.illinois.edu/jira/browse/MMDB-726, delete tag in desktop client. This issue had been fixed, but not closed.
  • Resolved MMDB-1081, desktop client should login from within application. All that remains is the main issue of anonymous login that is mostly a server side issue. Once an anonymous role is created, the desktop client anonymous button can be enabled and tested. The anonymous issue, MMDB-1072 remains open.
  • Resolved MMDB-1110, improve recent additions view. This view displays both the latest uploads by session or the last 10 based on the toolbar menu.
• Cyberintegrator
  • Rob gave me a short introduction to Cyberintegrator, which I will be doing some work on in the next few months. We walked through some examples and some of the core classes/interfaces in Friday afternoon.

Work Planned

• MAEviz Workshop
  • Travel to Champaign on Wednesday morning to meet with SYNERGY visitors interested in MAEviz from Wednesday afternoon through Friday
  • Prepare introductory Eclipse/MAEviz slides
• Medici
  • Attend Medici Staff meeting on Monday at 10am
  • Wrap up UI improvement work
• Other
  • Meet with Terry/Rob to discuss TRECC funding work

Comments

Work Completed

• Medici
  • Attended Wednesday staff meeting
  • Resolved MMDB-1073, I put the finishing touches on the login dialog by adding Anonymous button for logging in anonymously. When the backend supports this, we just need to enable this button (current it is disabled) and anonymous login should work.
  • Resolved MMDB-1074, all welcome screen code is checked in and working as expected.
  • Resolved MMDB-1099, I put the finishing touches on the 3 defined perspectives (Import, Data Browsing, Execution). I also made static references to the view's ID from the class itself so if the package changes, perspectives will still work (all views were originally hard coded).
  • Resolved MMDB-1104, I renamed Image Dropbox to just Dropbox.
  • Resolved MMDB-1106, the desktop search query for the gallery displayed the wrong dataset count. Zero was not an expected dataset count so when a search query tried to display the results in the Gallery, instead of saying 1 Dataset, it would say 1 of 0 datasets. This is fixed.
  • Resolved MMDB-1107, I reorganized the top level menus a little, I removed unwanted commands contributed from Eclipse core plugins (such as show key assist, which has no relevance for us). I also added a few more options such to show titles and dates in both ascending and descending order, previously only ascending was allowed, but even this was no obvious from the menu label (Sort -> Date).
  • Worked on MMDB-1110, the Recent Additions view only displayed what was uploaded in the current session. With two defined commands and some minor modifications, we could toggle between showing the datasets uploaded in the current session and the last 10 datasets uploaded (similar to the web client). This will be resolved shortly once all testing is complete.
  • Worked on MMDB-1112, add remove collection command to desktop client. A bug remains that I am tracking down. Where if you select a collection, remove it, select another collection and then click "add collection" and add a collection, the currently selected collection is unselected. It should remain selected.

Work Planned

• Medici, main focus is working on UI Improvements
  • Staff meeting at 2pm on Wednesday
  • MMDB-1073 - Create login dialog box for desktop client
  • MMDB-1074 - Add welcome screen to desktop client with short introduction
  • MMDB-1099 - Add perspectives to organize views by primary task focus
  • MMDB-1104 - Image dropbox should have a more general name
  • MMDB-1106 - Desktop query returns incorrect dataset count
  • MMDB-1107 - Cleanup top-level menus to make them more intuitive
  • MMDB-1109 - Desktop client doesn't fire subject added event when a dataset is added
  • MMDB-1110 - Improve recent additions view
  • MMDB-1112 - Add remove collection command to desktop client

Comments

This week went as planned. Next week I will be in Champaign on Wed/Thurs/Fri to discuss MAEviz with some researchers interested in the project.

Work Completed

• Medici
  • Attended Monday January 31, 2011 staff meeting via skype
  • Worked on MMDB-1074, add a welcome screen to the desktop client. I ran into an Eclipse fixed-layout bug and ran a solution by Rob/Luigi/Joel to change from a single perspective to multiple perspectives as had been discussed before as part of the UI redesign. I will continue working on the welcome screen content this week.
  • Worked on MMDB-1099, add perspectives to organize views. This is still a work in progress to come up with the view combination for each perspective. I have a first cut checked in and will continue to refine it.
  • Worked on MMDB-1081, desktop client login from within application. This included bug fixes caused by the login process change. I also changed the current splash to show a progress bar.

Work Planned

• Medici
  • Attend Monday staff meeting
  • MMDB-1074, Add welcome screen to desktop client
  • MMDB-1081, Desktop client users should login from within application
  • MMDB-1099, Add perspectives to organize Medici views

Comments

This week went as planned. I took a personal day on Wednesday February 2nd.

Work Completed

• Medici
  • Attended Monday staff meeting via skype on January 24
  • Worked on MMDB-1083, adding support for SSL certificates and handling them properly. I created a dialog that displays if the user attempts to log into a server with HTTPS if the server is untrusted. We obtain the servers certificate, display it to the user and ask them if they trust it. If they do, we store the certificate so the next time they will be able to log in without seeing the certificate. I discussed briefly on Friday with Rob the implementation of the https to clarify some expectations.
  • After getting the https working, I continued working on MMDB-1081 and fixing bugs with views and menus caused by a context/user not being logged in when the application starts and handling this scenario. In most cases, the user is informed that they must log in to use that operation.
  • Joe was not able to get to the backend support for anonymous login last week so that issue is still on hold. I will start working on adding a "log in anonymously" button this week that should log the user in anonymously once the backend supports it.

Work Planned

• Medici
  • Work on MMDB-1081 - Desktop client users should login from within application
  • Work on MMDB-1083 - Desktop client should handle ssl certificates properly
  • Work on MMDB-1072 - Desktop client should provide anonymous login option.
  • Attend staff meeting via skype on January 24

Comments

This week went as planned.

Work Completed

• Medici
  • Checked in changes to MMDB-726, tag display and deletion now handled in tag view and the Info view no longer displays the tags. I left the issue open if we wish to address the issue I had with TagEventBeanUtil returning the incorrect information (possibly a bean out of date) versus another method that returned the right information. I changed the code to use the method returning correctly. I will talk to Joel to see if we should close this issue open a bug.
  • Started working on MMDB-1081, a sub-task of MMDB-1072, anonymous login. I moved the login code to a new dialog that is accessible from the File > Login As... menu. I started looking at which views and actions would break if a Context and PersonBean are null from removing the interactive splash screen login and fixing them. This is a work in progress and nearly finished.
  • I opened an issue, MMDB-1083, to document the issue that came up when Rob switched to https. The desktop client fails to login because of an unrecognized ssl certificate. Rob has sent some examples on handling the cert issue and I will work on it the week of January 24th.

Work Planned

• Medici
  • Finish work on delete tag from within tag view, move tag display from info view to tag view, MMDB-726
  • Start working on Anonymous login, MMDB-1072, move login to within application

Comments

This week went mostly as planned. I ran into some issues when Rob upgraded to https and logging in from the desktop. I found a workaround and will work on a more permanent solution this week. Monday was a holiday so there was no staff meeting.

Work Completed

• MAEviz
  • I was on IRC and Skype ready to answer questions during Jong's presentation of MAEviz at the Univ of West Indies.
• KISTI
  • Met with Jong on google chat to discuss KISTI project
  • Finished statement of work and returned final edits/comments to Jong to finalize.
• Medici
  • Attended Medici staff meeting on Monday January 10, 2011
  • Worked on MMDB-726, add delete tag capabilities to desktop client and move tag view/delete to the TagView. This issue involved several changes to be made including adding a TagView to the desktop UI plugin so I could reuse code from the Info view for dealing with tags. The intent was to make the TagView more useful by displaying tags and adding the ability to delete them. This required adding some listeners and a callback to listen for delete events. When I removed displaying tags from the Info view this required me to update some of the UI layout. I also uncovered some odd behavior in deleting tags that Joel and I are looking into. It seemed that TagEventBeanUtil.getTags(subject) returned correctly, but TagEventBeanUtil.getAssociationsFor(subject) returned incorrectly (it still returned the deleted tag) so something appears to be out of date. When the app restarts, the getAssociationsFor returns correctly. This issue is still open while we track down what is happening. I will test my changes this week and check in my updates shortly.
  • Started working on different perspectives that can be used with Medici to provide users with views associated with their primary interest (e.g. uploading data, browsing data/images, executing tools, etc). I am updating the wiki with perspective mockups and will continue this week.

Work Planned

• KISTI
  • Add final comments and tweaks to KISTI Statement of Work, it needs to be finished by the end of the week
• MAEviz
  • On Jan 11/12th, MAEviz meeting at Univ of West Indies, I plan to be on IRC and have skype ready if needed to answer MAEviz questions
• Medici
  • Attend staff meeting
  • Work on improving Medici UI based on feedback from UI review

Comments

This week went as planned.

Work Completed

• Medici
  • Resolved MMDB-1075 - remove Statistics view and move the statistics to the Collections view. Based on feedback from the UI review, the statistics did not require an entire view and could be moved to the collections view. This is completed and tested. I also removed the statistics view from the Perspective and updated the layout accordingly for those views dependent on the Statistics view location and size.
  • Resolved MMDB-1076 - update the add comment wizard to match the functionality of the web client. The web client did not allow a user to provide a title so that field was removed from the Desktop Add Comment UI. I also changed the comment text field label from "Description" to "Comment" so it was more intuitive and added a title to the Add Comment wizard window.
  • Resolved MMDB-1078 - updated the add collection icon. The old icon matched the collection view icon (a stack of books); however, this didn't match the rest of the UI where adding something had a "plus" icon, also add collection only allowed you to add a single collection and the icon indicated multiple collections could be added with the stack of books. This is fixed. I located a suitable icon inside ncsa.icons plugin which is where most (possibly all) of the Medici icons come from.
  • Working on MMDB-1079 - Update gallery to display collection and dataset information at the bottom of the view. Currently, the collection being displayed is added to the view title and the number of datasets displayed is at the top of the view. I have moved this information to the bottom of the view as "Collection: collection-name" and below that "Showing: X datasets". This should be finished Monday January 10th after it is tested.
• KISTI
  • Helped Jong put together the statement of work for the 2nd year of the KISTI project. This is nearly finished.
• MAEviz
  • Answered some questions that Machel from the University of West Indies had about MAEviz and extending/using parts of it and provided references to publisehd fragility papers.

Work Planned

• Medici
  • Identify and work on improvements from the UI review that don't require additional group input
• KISTI
  • Work on KISTI statement of work, it is due January 15th.

Comments

This week went as planned. I spent a brief amount of time digging through some MAEviz documentation to provide Jong with information for his and Danny Powell's meeting this week with the University of West Indies.

Work Completed

• Medici
  • Attended Monday staff meeting and it was determined I should apply the desktop fix for dropping files to collections to the 1.1 branch for a 1.1.1 release. This work was tracked by MMDB-1067. I implemented the fix and tested the desktop client. I also helped test the web client when Joe applied his fix for the drop applet.
  • Continued refining my desktop UI review by adding more possible views/perspectives to capture comments Joel made about the desktop client. I added text refining my comments and replying to others comments. I also tweaked some of the views and text describing each view on the implementation wiki page so we have good visuals to start discussion.
  • Attended the Friday December 17th design review and described my thoughts on how the desktop client can be improved. We also discussed the anonymous login options and I will need to tweak the design page based on feedback (e.g. slow connections will not want to forced to login to a server even anonymously).
• MAEviz
  • Helped Jong redirect maeviz.ncsa.uiuc.edu to the MAEviz wiki page

Work Planned

• Medici
  • Check out 1.1 branch and add desktop fix for dropping files to collections. Test both desktop and web client which is applying a fix for the upload applet.
  • Work on UI design review implementation by proposing sketches for each view, add more possible views/perspectives and tweak the UI 's as necessary before Friday's review
  • Attend staff meeting on December 13th at 10am
  • Attend meeting on Friday December 17th from 2 - 3pm to discuss UI Design review

Comments

This week went as planned. I took 1/2 of a sick day for a doctor's appointment on December 17th.

Work Completed

• Medici
  • Attended December 6th staff meeting via Skype
  • Created a wiki page outlining possible options for anonymous login and sent the link to Joel for review and to add his input. One question we will need to answer is do we create a single anonymous account or is every unauthenticated user anonymous and how do we support this?
  • Worked on and Resolved MMDB-1063, Import Datasets file browser is replaced by an import dataset wizard from the File menu under File -> Import > Datasets. The new UI also allows users to add the files to an existing collection. Comments are added to the code where we could improve/add functionality. I found and fixed a bug in our code introduced during our change to Post for uploading files. Dropping files on a collection no longer added them to the collection, it only imported them.
  • Updated the Desktop UI design wiki, added another UI sketch for the proposed add tag wizard

Work Planned

• Medici
  • Attend December 6th Staff Meeting at 10am
  • Work with Joel and propose anonymous login strategies
  • Work on implementing wizard for importing datasets and in general, change dialog boxes to use wizards.

Comments

This week went as planned. Next week I plan to continue working on UI improvements for Medici and working on the anonymous login design with Joel.