Blog

Work Completed

• KISTI
  • Worked on KNSG-107. The majority of my time was spent investigating and building/testing the feasibility of running PTPFlow tools as Java tools. After some work, I believe this is feasible and will eliminate the need to create our own executor. I still have a few more tests to run to make sure I have overcome all issues that I ran into. The biggest issue I had was getting the CoGProperties class in globus to initialize without throwing an ErrorInInitializationException. The CoGProperties class is required as part of obtaining a grid certificate using PTPFlow utility methods. There are a few workarounds for this if we want to run our workflow in Cyberintegrator (e.g. have another standalone eclipse tool that asks for username/password and pass the certficate to the next tool) or in our case, we'll be storing certificates in Tupelo and won't actually need to instantiate CoGProperties inside the PTPFlow tool, the tool will just obtain the cert from Tupelo.
• Cyberintegrator
• Medici

Work Planned

• KISTI
  • KNSG-107- Investigate feasibility of making PTPFlow tool as a Java tool in Cyberintegrator instead of a special executor
• Cyberintegrator
  • None
• Medici
  • None

Comments

This week went as planned. I was out half of Monday and most of Friday. I ran into more issues than I thought I would trying to build PTPFlow as a Java tool, but the effort seems to have paid off and will minimize the effort to setup Cyberintegrator servers to run ptpflow tools.

Work Completed

• KISTI
  • Tested KISTI rmi endpoing. We determined it was a problem with the configuration files on the rmi endpoint. The ember host file did not contain my user-home on host. Once this was completed, I ran a test run of my eAIRS workflow using Cyberintegrator and storing results in the KISTI tupelo machine successfully. More work needs to be done to determine if we move to a command line tool for running the ptpflow workflows.
  • Worked on KNSG-108, design parameter creation tool. This tool will take parameters and write them to a file for input to the eAIRS workflow. A first cut is finished and some work remains to finish this tool.
  • Worked on KNSG-109, design and create a tupelo bean to store X509 certificates. I have finished some preliminary work and am waiting for feedback on the bean design before finishing this implementation.
• Medici
  • Worked on and resolved MMDB-1193. I created a sample splashscreen and after presenting it to others and including Terry's and Rob's suggestions, I finished a new splashscreen for the Medici desktop app.
• Cyberintegrator
  • None

Work Planned

• KISTI
  • Work on storing X509 certificates with Tupelo
  • Test running basic test ptpflow workflow with KISTI rmi since previous runs of more complex workflows were not succeeding. Also test using KISTI Tupelo repository with more complex workflows once the test workflows are working.
  • Create standalone parameter creation tool (input parameter file for eAIRS)
• Medici
  • MMDB-1193 - add NCSA logo and pics of desktop to desktop splash screen
• Cyberintegrator
  • None

Comments

This week went as planned. I took a personal day on Friday July 15th.

Work Completed

• KISTI
  • Met with Jong using google chat to discuss KISTI project and received some tasks to accomplish
  • Looked over Dr. Nam's test code and provided instructions on how to get the PTPFlow RMI Test client working as a runnable jar
  • Added isse KNSG-108, design parameter generation tool. I started looking into designing the parameter generation tool that will be required for the workflow
  • Tested launching jobs using kist.ncsa tupelo server and the kisti.ncsa rmi service. The tupelo repository works fine for me, but I could not get a job to run on the RMI service. I will try more testing this week to determine the cause.

• Cyberintegrator
  • None
• Medici
  • Attended Medici Testing meeting. Several issues/improvements were identified and below is a list of those that were resolved for 1.2
  • Resolved MMDB-1194, bigger default size for desktop application so welcome screen shows without scroll bars
  • Resolved MMDB-1195, move server pulldown to the top of the login screen
  • Resolved MMDB-1196, make Data Browse perspective the default
  • Resolved MMDB-1197, allow users to move views in perspectives
  • Resolved MMDB-1198, align metadata fields in Info view
  • Resolved MMDB-1199, center preview in Info view
  • Resolved MMDB-1200, change "contributor" for collection Info view to "Collection creator" to make it more clear
  • Resolved MMDB-1204, add on enter listener to search text field to avoid pressing search button
  • Resolved MMDB-1208, add Info view to Import perspective
  • I will be closing MMDB-1206 because I think this was a permissions issue making add tag/comment not work/show as anonymous.

Work Planned

• KISTI
  • Meet with Jong to discuss KISTI project
  • Start testing kist.ncsa.illinois.edu Tupelo repository and RMI endpoint
  • Work on Parameter generation tool for eAIRS
  • Work on issue Dr. Nam is having with exporting Jars for testing his PTPFlow Client
• Cyberintegrator
• Medici
  • Attend Medici Testing meeting at 10am on July 5
  • Fix bugs/issues found during Medici Testing

Comments

This was a short week, but it went as planned. Monday July 4th was a holiday and I took personal days on Thursday July 7 and Friday July 8.

Work Completed

• KISTI
  • Helped answer questions that Dr. Nam had using ptpflow. I edited his test script and tested running it on Ember.
  • Worked on KNSG-107, design ptpflow tool. I am currently testing using JAX-B to package information for a workflow tool (similar to how Rob uses JAX-B for matlab and external tools) so I can store as xml the ptpflow script and information needed to launch it (e.g. which RMI endpoint). I need to discuss with Rob and Jong my implementation to see if I should proceed down this path or if there is a way to make ptpflow a generic Java tool to avoid having a ptpflow executor.
• Cyberintegrator
• Medici
  • Tested the Medici desktop client. I found and fixed MMDB-1191. I also noted an improvement for the login portion of the client, MMDB-1192. A client that is not authorized to use the desktop client fails in the same way that a bad u/p fails, this is bad. A user could keep trying endless passwords not realizing their account type does not have access to the desktop client. There needs to be a way to tell the user they aren't authorized to use the desktop client.
  • Resolved MMDB-1176, welcome page is not displayed. All that remains is to add links to the user guide when it's.
  • Tested Medici web client and reported MMDB-1180, upload hands after a few datasets. Desktop client does not display same issues so it must be with the web portion of the upload.
  • Attended June 27th Medici Staff Meeting and June 29th Medici Testing meeting.

Work Planned

• KISTI
  • Continue working on PTPFlow tool design
  • Help Dr. Nam and Yong Wook Kim as needed
• Cyberintegrator
• Medici
  • Test Medici Desktop client
  • Test Medici Web client
  • Attend Medici staff meeting on Monday June 27, 2011.

Comments

This week went as planned. I did not get to cyberintegrator this week due to the short week and the Medici release testing. I took a personal day on Friday July 1, 2011.

Work Completed

• KISTI
  • Talked with Rob to get ideas on how to proceed with getting Trebuchet to run as a command line tool in Cyberintegrator and outputing what the next step in the workflow needs
  • Finished first version of Trebuchet as a command line tool to stage files to HPC. There is still work remaining to get each users certificate to the machine that runs the Trebuchet tool. The next step is to discuss whether ptpflow should be a Java tool or a special Cyberintegrator tool. I will need to discuss this with Rob and Jong.
  • The KISTI RMI service is up and needs to be tested. I did not get to this.
• Cyberintegrator
  • Added issue CBI-378. We need more preview types to cover more dataset types. I also made it so that if no preview was found, it would default to the "Default Preview" which displays a "no preview found" image and the basic dataset information (date, author, etc).
  • Added issue CBI-377. It would be helpful if the popup dialogs for the command line options page could indicate what is required and what is optional, if possible. Certain fields seem to be required since without them, the OK button will not enable.
  • Looked into issue CBI-159. I could not reproduce the bug where adding/removing inputs/outputs/parameters caused a UI glitch. I commented on the issue looking for more information, possibly steps to reproduce.
  • Worked on CBI-28. I added a busy indicator to the import process.
  • Tested ContextServer GUI application, no issues setting up a new context, connecting and uploading data.
• Medici
  • Attended Monday staff meeting via skype
  • Updated user guides with information about each perspective and links to pages that discuss each view. I need to add screenshots and the information about each view (currently just empty placeholder pages).
  • Found and fixed MMDB-1178. Desktop search view did not handle being disconnected properly, it still made an attempt to search.
  • Found and fixed MMDB-1179. MyDatasets view displayed a popup menu even when nothing is or can be selected. The declarative code for when to display the menus was not correct.

Work Planned

• KISTI
  • Continue working on eAIRS workflow, including Trebuchet as a command line tool to stage files.
  • Open Jira entries to track design and implementation work that needs to be done for each tool.
• Cyberintegrator
  • Continue working on Cyberintegrator Jira issues
• Medici
  • Attend 10am Staff meeting June 20th
  • Continue working on User guides and debugging Desktop application

Comments

This week went as planned. I took a personal day on Friday June 24, 2011

Work Completed

• General
  • Drove to Champaign on June 13th and attended Medici, KISTI, Tupelo meetings and a proposal discussion.
• MAEviz
  • Reviewed requirements document for MAEviz that was received from Syner-G. I provided comments on existing modules that met their requirements and those that would need to be new features.
• KISTI
  • Tested Kisti RMI server. Jong and I are currently (mostly Jong) debugging our connection to it.
  • Continued looking at using Trebuchet as a command line tool. I talked with Rob and believe I can make more progress on this after discussing some design issues.
  • Started opening Jira issues to track work for the project now that we have an architecture plan to move forward with.
• Medici
  • Worked on welcome page bug, MMDB-1176. Welcome page would not display using Ubuntu 11.04. Mac and Windows were fine. I changed the welcome page from xhtml files to xml files using the Eclipse universal welcome page. This is a cleaner implementation (with a Go to Workbench button that our original page did not have), and it will allow use to link to individual wiki pages for additional help. If this is satisfactory, then I will add links to additional help on the wiki (user guides) and close this issue.
  • Continued working on the Desktop User guide on the wiki. Some of these pages or at least the main wiki page will be linked to in the new Welcome Screen.
• Cyberintegrator
  • Started looking at CBI-159, a bug with the external executor GUI page not updating correctly. I am trying to reproduce this bug so I can fix the issue.
  • ContextServer GUI is now ready for testing. I will test it this week so users can start using it to setup new Contexts.

Work Planned

• General
  • Visit Champaign on Monday June 13 to meet and discuss projects
• KISTI
• Medici
• Cyberintegrator
  • Continue working on CI issues and recommending UI improvements on the wiki page

Comments

This week went as planned. The all day meeting in Champaign and MAEviz work took away some time from my other projects. I took half a personal day on Tuesday afternoon to deal with some house issues that came up.

Work Completed

• KISTI
  • Worked on reviewing interfaces for Cyberintegrator tools and trying to convert Trebuchet to a CI tool. I'm partway through this process (I took an unintended personal day Friday the 10th to deal with house stuff). We will need a mechanism to get a valid certificate to the location running the tool and refresh the certificate if it is required (e.g. long queued job).
• Cyberintegrator
  • none
• Medici
  • Attended Monday 10am staff meeting via skype
  • Created a VM and went through the installation process of a Medici 1.1 Repository, added images/tags/comments/users/etc and upgraded to 1.2 to document what breaks. While the anonymous role and user get added, they are inactive. When activated, the server still does not use the role until you reset all roles to default which clears out all defined roles for users and sets all users inactive.
  • Created a wiki page outlining the upgrade process steps including where to put your google key since there is a server.properties file that gets read for the key (previously this was inserted into the html file). I also noted that the upgrade process is still being debugged so it is a use at your own risk. It will need to be updated with the links to the 1.2 release files (currently pointing at latest build) once the build is finalized.

    Work Planned

• KISTI
  • Review how to implement a Cyberintegrator tool so it can recognize the tool in the jar file. We need to run Trebuchet as a gridftp tool that can stage files to an HPC.
• Cyberintegrator
• Medici
  • Attend Monday staff meeting
  • Go through the Medici server upgrade process from 1.1 to 1.2 to determine upgrade issues that need to be resolved
  • Start documenting desktop and repository guides.

Comments

I took a personal day on Friday June 10th. I will be visiting Champaign on June 13th to attend several meetings on my various projects.

Work Completed

• KISTI
  • Continued working on getting PTPFlow to run in Cyberintegrator and pulling results back to a local tupelo instance. Running everything locally works so the next steps will be to run on a cyberintegrator server that stores results back to a specified context instead of locally run context.
  • Met with Jong Wednesday evening to briefly discuss KISTI project
  • Worked on creating GridFTP as a tool for Cyberintegrator. This is still in progress. I was looking on the globus website learning how to create GridFTP as a tool=
• Cyberintegrator
  • Worked on and resolved CBI-326, preview screen should show something. If a dataset did not have a supported preview, nothing would show up in the info view, not even the metadata for the object. I added a DefaultView for unknown type that displays a generic preview (tooltip says preview not found). The basic metadata (date, creator, etc) gets displayed.
  • Worked on and resolved CBI-376, Login dialog should indicate that it is loggin in. There is a small delay (sometimes longer depending on internet connection) when connecting to a context and the UI would hang with no indication about what is going on. I've added a busy indicator to show that something is happening after pressing the login button.
  • Started looking at CBI-289, adding a KML viewer to Cyberintegrator to determine if it's feasible in the time remaining on the project and adds enough value over other bugs/features. One possibility is to use Nasa Worldwind to provide a KML viewer.
• Medici
  • MMDB-1174, Login dialog should indicate that it is loggin in. There is a small delay (sometimes longer depending on internet connection) when connecting to a context and the UI would hang with no indication about what is going on. I've added a busy indicator to show that something is happening after pressing the login button. The same fix that was applied to cyberintegrator was applied to Medici since they share similar login code for the desktop.
  • My remaining issues for 1.2 are user guides and any bugs that come up when the desktop client is tested.

Work Planned

• KISTI
  • Meet with Jong Wednesday to discuss KISTI project progress
  • Continue working on breaking out eAIRS PTPFlow workflow into tools that can be run with cyberintegrator
• Cyberintegrator
  • Continue working on Cyberintegrator Jira issues & documenting UI suggestions
• Medici
  • Work on remaining 1.2 issues

Comments

This week went as planned. Monday May 30, 2011 was a holiday so this was a short week.

Work Completed

• KISTI
  • Investigated how to retrieve results from a finished PTPFlow workflow within cyberintegrator's execution process. I am working through how cyberintegrator works and how we can get cyberintegrator to launch ptpflow workflows and retrieve results that will be ingested into a tupelo backed repository.
  • Waiting on response from Luigi about how to get access to DSE repository so I can browse the code.
• Cyberintegrator
  • Rob added ContextServer headless to the build and I tested the build. The build worked as expected. We still need to add the ContextServer GUI version to the build and test it.
  • Opened and Resolved CBI-374, login dialog should remember multiple servers. Added a combo box that remembers up to 15 servers, each new server will be saved using the Eclipse infrastructure for saving dialog settings. In the future we may want to expose how many servers get saved and a way of clearing the cache.
  • Resolved CBI-118, create our own import/export/new wizard menu to prevent from getting eclipse additions to these menus. I added a few final changes to this and now the issue is finished. I created import/export categories appropriate for our import/export wizards to provide a slightly cleaner/more organized view of the wizards in the Import/Export menu.
  • Opened CBI-375, delete tool/workflow/data should not be done in the UI thread. There is some lag between deleting an item and the response of the UI and I suspect there is some work being done on the UI thread that should be an Eclipse job to improve UI reponse.
• Medici
  • Resolved MMDB-1065, changed add tag to use wizard instead of dialog.
  • Resolved MMDB-1145, desktop client throws exception if bean is not available in the context. I changed the log level to warn since there was a comment in the code that the error should not be displayed to the user. A warning seemed sufficient since the most likely cause was not really a major concern (e.g. connected to a different repository).
  • Resolved MMDB-1146, login dialog should remember multiple servers. Added a combo box that remembers up to 15 servers, each new server will be saved using the Eclipse infrastructure for saving dialog settings. In the future we may want to expose how many servers get saved and a way of clearing the cache
  • Reopened and fixed MMDB-839. We changed the GroupedView view name to "Users" with a user icon believing that it only showed user accounts. This was incorrect. This view grouped data by categories specified (by user, by tag) so you could see all the data uploaded by User Foo or with tag Foo1. I changed the name to Grouping and gave it a different icon. We can change this in the future (maybe Data Grouping) since it's old name "Groups" didn't identify clearly what the view was intended for. The grouping is controlled through the views menu with the ability to add additional groupings in the future.
  • Opened issue MMDB-1173 with fix version 1.3. The GroupedView menu should use radio buttons to identify what the current grouping mechanism is. The menu is currently push buttons so it's unclear what the grouping is. Also, the state does not get saved between closing and reopening the application. This can be resolved using radio buttons that save their state.

Work Planned

• KISTI
  • Continue to work on running a ptpflow workflow job with cyberintegrator
  • Look at DSE code if I can get access to repository.
• Cyberintegrator
  • Continue working on Cyberintegrator Jira issues.
• Medici
  • Attend Monday staff meeting (May 23rd)
  • Work on remaining assigned Jira issues and designate issues as fix for version 1.2 or 1.3

Comments

This week went as planned.

Work Completed

• KISTI
  • Continued working on getting eAIRS to run on the HPC machine Ember since Abe/Lincoln are retired. I was able to successfully run a job using both eAIRS and a really simple PTPFlow Cyberintegrator executor. I added a plug-in that lets a user specify a PTPFlow workflow and then launch the job using the ptpflow engine, which submits the job to an RMI endpoint. I will continue with this work next week to make this more general.
• Cyberintegrator
  • Opened and resolvedCBI-373, an issue with the command line not properly validating executables if you browse for one. It was not calling validate. This is fixed.
  • Resolved CBI-358, a bug reported that if you create a new workflow and make a tool, the data won't show up properly and the data will disappear. Also, the workflow name was lost. This appears fixed with some updates I've made over the past few weeks. We can reopen if the issue recurs.
  • Resolved CB-36, ability to remove multiple tools/datasets from the tools/data view. I also moved some actions to commands because of a weird UI glitch I was running into mixing commands/actions. It turns out the glitch was caused by the command not having an icon, but the actions are now commands as they should be. This issue does not deal with the implication of what should be done if tools/data are deleted (e.g. should a workflow get updated?) since the data/tool are simply marked deleted. We should open a new issue that defines what the appropriate behavior should be for each view effected.
• Medici
  • Attended staff meeting. Issues to look into: internationalization with 1 properties file per plug-in, unassigned issues and remaining 1.2 issues)
  • Internationalization with 1 properties file per plug-in deviates from Eclipse best practice, but does not present a problem. We now have a way forward if internationalization is required
  • Users view renaming needs to be reverted (MMDB-839) because it is not a Users view, it is a view that groups data based on menu selection with the ability to add more groupings in the future. This view currently has two menu items, it can show the number of datasets per user or show the number of datasets by tag. We need to come up with a better name/icon for this view.
  • Reopened and resolved MMDB-1141, multiple error popups when disconnecting from a context. The "Users" and "ContextDebugView" do not properly handle disconnecting. This is fixed and the issue is again closed

Work Planned

• KISTI
  • Work on getting eAIRS to run on the HPC Machine Ember since Abe/Lincoln are retired.
  • Work on getting eAIRS to run using Cyberintegrator launching a PTPFlow job for the eAIRS specific case and then the general case of running a ptpflow workflow.
• Cyberintegrator
  • Continue working on CI Jira issues, specifically supporting delete for tools/workflows/datasets.
  • Continue working on commenting on the UI and making recommendations for future work.
• Medici
  • Attend Monday Staff meeting
  • Finish up assigned desktop issues for 1.2

Comments

This week went as planned. I took a personal day on Friday May 20th.

Work Completed

• General
  • Attended Tupelo code review meeting using google chat.
• KISTI
  • Started looking at creating a Cyberintegrator executor for PTPFlow workflows.
  • Worked through an issue I had trying to run ptpflow workflows using my renewed grid account/cert with the new HPC machines and PTPFlow. I was getting a "cert expired" error. After working with Al, the cert expired issues is resolved and this week I'll continue working on running eAIRs on different HPC machines since Abe/Lincoln are retired. Once this is finished I can finish my first attempt at a CI executor running a ptpflow workflow job.
  • Reviewed security documents and architecture documents that Jong prepared based on our meeting (May 4th) and his meeting with Jim Basney last week.
• Cyberintegrator
  • Looked at internationalization with 1 properties file per plug-in. It is possible, but one problem with this is repeated class names. The recommended best practice for internationalization is to use the class name + key for the static string (e.g. MyClass.KEY1 in the properties file); however if there are two MyClass files, then I must deviate from this best practice and do something different. Essentially deviating from one best practice (1 properties file per package) might force you to violate a second best practice (Class name + Key).
• Medici
  • Attended staff meeting. Tasks include looking over unassigned task list, role enforcement on the desktop and internationalization with 1 properties file per plug-in.
  • Resolved MMDB-1163, remove unnecessary eclipse contributions to the UI. I also created a new category, Debug, for two Bard views (RDF XML and Debug). Those were the last two views listed as questionable in MMDB-845, check that all views are implemented and useful (done by Joel). Those views are useful, but I believe categorizing them as Debug helps the user realize they are more advanced. We can probably close MMDB-845 unless something different should be done with those views.
  • Worked on MMDB-1164, enforce "ViewData" permission. This is mostly done, except that we should decide if the GroupedView should enforce a permission that limits who can view registered user accounts. As an anonymous user, it doesn't seem right that I can see all registered accounts on a server. We probably want to limit this. If not, then this issue is finished.
  • Resolved MMDB-1138, current medici server wasn't displayed. I added this to the status line.
  • Looked over unassigned issues. I updated the assignment/fix versions for issues I knew about or had reported.

Work Planned

• KISTI
  • Work on creating Cyberintegrator executor to run eAIRS as a PTPFlow tool.
  • Test running eAIRS using the renewed teragrid account. With Abe/Lincoln retiring, we'll need to test to make sure everything is running with different HPC machines and with our renewed account.
• Cyberintegrator
  • Look at internationalization for CI/Medici projects to see feasibility of 1 properties file per plug-in
• Medici
  • Attend Monday staff meeting.
  • Work on Medici desktop client tasks. From the staff meeting, there were a few issues I needed to look at (see above).

Comments

This week went as planned. I spent more time this week on Medici to finish off some issues in the desktop client and cleaning up some unwanted UI contributions from Eclipse plug-ins.

Work Completed

• MAEviz
  • Finished documenting step by step the process of creating a new analysis on the MAEviz wiki in the Documentation section under Tutorials.
• KISTI
  • Drove to Champaign on Wednesday May 4th, spent the day discussing Cyberintegrator/DSE with Jong/Luigi/Rob. The meeting was very productive and I believe we have a way forward to use those technologies along with PTPFlow in the KISTI project.
  • Worked on and successfully ran eAIRS executable as a command line tool using Cyberintegrator. This should allow us to quickly put together a demo of eAIRS running as a web application using the DSE project.
• Cyberintegrator
  • Worked on CBI-101, Basic delete is in place for all except step. It's not clear where this should take place and how the various views should respond to delete events. Should workflow with deleted tools be updated? What should they display in the workflow graph view if a tool is marked as deleted? Right now the tools view does not display deleted tools, the data view doesn't display deleted data and the workflows view doesn't display deleted workflows. I have commented about this on the issue for further clarification.
  • Resolved CBI-370. MimeMap was not being initialized properly since a Context was no longer available when Cyberintegrator started. This initialization had to be moved to when a context was set (previously was located inside Activator start method).
  • Resolved CBI-372, a helios bug involving Eclipse p2, exported product files would display an error about the p2 service not being initialized when the application first launched (windows and linux). This can be fixed by specifying start levels for a few plug-ins. The fix is checked in.
  • Added Cyberintegrator text image to login screen to make the login screen more like Medici's and more polished. This was done as part of CBI-363.
  • Resolved CBI-371, updated the about screen with updated links and text.
• Medici
  • Attended staff meeting
  • Resolved MMDB-1072. Worked with Joe after he implemented an anonymous role on backend server. After a few modifications, we successfully got the anonymous role working on the desktop.
  • Put together wiki page on internationalization options for Medici/Cyberintegrator and future CET projects.
  • Made notes about each remaining desktop issue assigned to me. None are high priority.
    • MMDB-1146 is in regards to the login screen potentially saving more than 1 server address to make it easier to switch between servers. Some thought would have to be given about how this works, how users can clear this out (e.g. if it is saving an erroneous login attempt).
    • MMDB-1145 is one I cannot seem to reproduce again. It involved switching between contexts and an error message popping up if the last selected subject could not be found. I will have to dig a little more and see if I can get this issue to show up or close this issue.
    • MMDB-1065 add tag wizard. This is just cosmetic. We could use a wizard instead of an input dialog to do tagging. It would allow us to tap into the eclipse help mechanism if we wanted to.
    • MMDB-1064 is internationalization. We simply need to pick a method (I documented this on Medici's wiki) and start externalizing strings.

Work Planned

• MAEviz
  • Finish documenting process of creating a new MAEviz analysis
• KISTI
  • Meet with Jong/Rob/Luigi on Wednesday May 4th to discuss Cyberintegrator and DSE technologies and how they might be used in the KISTI project
• Cyberintegrator
  • Continue working on Cyberintegrator issues. Primary focus will be working on delete for tools/datasets/steps/workflows, CBI-101 and getting all views to be synchronized after this occurs and making sure no bugs are introduced. This can be checked in shortly with the understanding that what should happen to certain views is still a work in progress (e.g. does a workflow graph remove deleted tools?).
• Medici
  • Attend Monday 10am staff meeting
  • Finish Anonymous login for desktop once backend provides role support

Comments

This week went as planned.

Work Completed

• MAEviz
  • Started on wiki page documenting the step by step creation of a new analysis. This is about 50% done. MAE-1124
• KISTI
  • Met with Rob, Luigi & Jong via google video chat to discuss eAIRS/KISTI workflow structure and how we can capture this with either the current bean structure or new beans to track provenance. There will be a follow-up meeting this week since it looks like Cyberintegrator/DSE could be a good fit for our problem.
  • Looked a BlobBean, a suggested bean type that could allow us to associate more than 1 blob with a bean.
  • Started working on wiki page that lays out the eAIRS problem in more detail for the Wednesday meeting to make sure everyone understands our needs so we can determine if DSE/Cyberintegrator will be a good technology fit for our project. I will continue to work on this for the coming meeting so the problem scope is clear.
  • Briefly went through KISTI's eAIRS UI Mockup. I will continue this before Wednesday's meeting so we can discuss the UI and required tasks.
• Cyberintegrator
  • Added more comments to Cyberintegrator UI review
  • Added a comment to CBI-111 (improve Info view) about including more workflow information. It wasn't clear what Luigi was information he was referring to so I asked for clarification. I have added more info for datasets and tools (e.g. created by, date, etc), but I don't see what else can be displayed for workflows.
  • Worked on CBI-101, I added delete handlers for datasets, workflows and tools. I am still testing everything to make sure all views are in sync after a tool/dataset/workflow gets deleted.
  • Resolved/Closed CBI-126, password in context login is visible. This does not appear to be relevant. The login screen does not display the password field.
• Medici
  • Added a comment to Medici UI review. If an image preview is not created (e.g. an image was ingested using a different tool), there is no way to view the image information inside Medici (e.g. InfoView) because it expects there to be a preview available.

Work Planned

• MAEviz - add wiki page that documents how to create a new MAEviz analysis step by step
• KISTI - Meet with Rob and Luigi to discuss using/creating Tupelo beans to capture provenance for KISTI workflows
• Cyberintegrator/Medici
  • Work on Cyberintegrator issues, including CBI-111 (improve info view) and CBI-101 (allow to delete tool/data/step/workflow).
  • Continue working on CBI UI review

Comments

This week went as planned. Next week (week of May 2nd) I will be visiting Champaign all day Wednesday.

Work Completed

• MAEviz
  • Went through my MAEviz archives and sent Jong some presentation material on MAEviz temporary housing that he requested.
• KISTI
  • Met with Jong to discuss KISTI project
  • Created a wiki page outlining the eAIRS workflow and a possible bean structure to capture the workflow information with Tupelo. We intend to meet with Rob/Luigi to discuss this and get their insight into capturing a PTPFlow workflow with a set of beans and see if my bean structure is reasonable.
  • Continued working with RESTlet. I have a semi-functioning RESTlet version of Medici's upload blob servlet. I am using that servlet to restlet conversion to gain a better understanding of how RESTlet works.
• Cyberintegrator
  • Resolved CBI-369, adding missing icons for views and actions
  • Resolved CBI-368, add refresh commands for views
  • Resolved CBI-363, CBI-365. CBI-363 involved users logging in from within the cyberintegrator and CBI-365 was a sub-task where context listener support needed to be added to the Workflow class and used everywhere ContextBeanUtil was used to listen for context updates. All views should now be getting context update events from the Workflow class.
  • Worked on CBI-362, checking for null values when a Context isn't connected (ToolGraphView was not expecting null values).
  • Worked on CBI-111, improving Info view workflow description. I updated this view to show more information similar to the Medici Info view. There is still some tweaking to be done.
  • Resolved CBI-109, moved the annotations view to the bottom tabbed pane so as not to confuse it with the Annotation tab located in the Info view.
• Medici
  • Resolved MMDB-1156, collection info page had a few gray-background labels on a white background (toolkit.createLabel was not being used).

Work Planned

• KISTI
  • Meet with Jong to discuss project
  • Create wiki page describing eAIRS workflow and possible tupelo bean structure for review
  • Continue working with RESTlet to understand designing RESTlets.
• Cyberintegrator/Medici
  • Work on Cyberintegrator UI Review
  • Work on Jira issues for Cyberintegrator, specifically improving the Info view (CBI-111), adding icons for views/commands and adding refresh options for views that might need to pull updates.
  • Work on last remaining issues for Medici and test to find bugs.

Comments

This week went as planned.

Work Completed

• MAEviz
  • Answered questions from the Synergy project about the MAEviz attenuations
• KISTI
  • Reviewed RESTlet wiki pages (http://wiki.restlet.org/docs_2.1/2-restlet.html) and worked through short tutorials. I also started reading a book I have on RESTful Web Services to get a better understanding of REST.
  • Met with Jong using google chat to discuss the KISTI project.
• Cyberintegrator
  • Opened and Resolved CBI-367 - Remove unnecessary wizard contributions that allowed users to create contexts in Cyberintegrator, this should all happen through the Context Server or elsewhere.
  • Opened CBI-368 - it could be useful to add a refresh action to the Context View in Cyberintegrator so users can pull updates.
  • Created a cquery for the ContextServer so they can be added to Jenkins for continuous build.
  • Continued testing Cyberintegrator using the new ContextServer provided context and updating areas that were still listening for ContextBeanUtil to send update events.
• Medici
  • Fixed MMDB-1041 - Gallery Widget display code. I could not exactly reproduce the issue described (out of bounds), but there was an issue with refreshing the view properly after disconnecting from a context and the paged list relied on object equals to remove items. There were cases where object equals failed on two equal objects. I changed this to check URIs for equality.
  • General testing of Medici Desktop.

Work Planned

• KISTI
  • Review architecture of RESTlet and work through some short tutorials
  • Meet with Jong to discuss KISTI project
• Cyberintegrator/Medici
  • Create cquery files for ContextServer GUI/Headless so they can be added to the continuous build
  • Continue working on Cyberintegrator issues in Jira and testing the new ContextServer provided context.
  • Finish any remaining Medici desktop bugs
  • Test Medici Desktop for release.

Comments

This week went as planned. I took half a personal day on Friday April 15th.