28 Jan Status Update
by Máirín Duffy
Hi everyone!
We had our weekly upstream ChRIS status meeting this morning - it is
Thursdays @ 0900 EST (1400 UTC) on Google Meet (let me know if you'd
like to be added to the invite!) You are always welcome to join this
public, upstream meeting, it is a great way to check in with other
contributors, let us know how things are going if you have anything to
report, and also a great way to get any questions you might have answered.
The asciidoc meeting minutes are below; the screenshots are here (I
still dont have the website blog rendering asciidoc yet so I wasnt able
to get that working yet :-p):
https://github.com/FNNDSC/cube-design/tree/master/CHRIS-UI/screenshots/UI...
~m
ChRIS Status 28 Jan 2021
====================
:Date: 28 Jan 2021
Present
-----------
- Mo
- Gideon
- Rudolph
Action Items
-----------------
- Moto send Rudolph Artem's email addy so he could be invited to the
talk tomorrow
- Mo to send Gideon quick mockup for changing the slim banner at top of
feed to bump feedname a bit higher in the visual hierarchy of the screen
- Mo wants to do a little more thinking/sketching around the panel
layout to play with it, e.g. mock it up showing how it'd look palette UI
style, mock it up showing how it'd look if we nuked the navy blue node
details panel
Status
---------
Gideon Demo
~~~~~~~~~~~
UI Tweaks
^^^^^^^^^^
- Current version is now in top nav bar
- Banner at top for Feed... has been slimmed down from PatternFly
styling... to maximize feed graph view
- Feed name is now smaller than node name, Mo will mockup idea to adjust
- New feed graph view that is more featureful, can bounce between
horizontal and vertical viewing
- Sidebar for the file viewer - has been modified so the hierarchy of
the file structure mirrors the hierarchy of the nodes, node folders are
nested now
- Changed the bright white of bottom area to a less jarring light grey
UI tweaks have happened slowly over time but many in response to the new
ability to run client-side scripts to build dense trees. For example: 25
subjects... process in parallel... text labels unreadable... changing
orientation makes it easier to make these readable. These changes are
meant to enable the feed view to be better scalable for these
larger/more complex feeds.
UI Suggestions from Mo
^^^^^^^^^^^^^^^^^^^^^^
For the node tree view:
- Stealing ideas from Ancestry's family tree view:
- no labels when viewing full tree, maybe show labels on demand
(hover or select node)
- if a portion of the tree is collapsed/hidden, provide visual hint
that something is underneath (a little icon or smtg)
- Integrating 3D force directed graph view
- Suggestion for the viewer to have two buttons to switch between 3d
graph to flat 2d graph, keep the 2d graph around to understand portions
of the full thing at a more granular level maybe?
- When the original layout for feeds was mocked up, the idea was that
the navy blue panel could be resized/collapsed just like a design
software palette. Adding that functionality could provide a lot more
real estate to graph view.
For the general layout of panels on the screen:
- idea for design software style docked palettes (showed inkscape's
collapsible / dockable palettes, but this is standard across a lot of
design software. Panels tend to be vertical.... example of a horizontal
one is Firefox Web Developer panel but only one tab visible at a time.
Here we want multiples visible at a time so a vertical model would be
better. Example of palette model:
https://guides.lib.umich.edu/c.php?g=283204&p=1886605
<https://guides.lib.umich.edu/c.php?g=283204&p=1886605%A0>) (Blender is
probably a really excellent example too since it has a node viewer)
- like the idea for thinking about UI as three panels (graph viewer,
navy blue node details viewer, bottom file browser/output viewer)
- suggestion to attach terminal output/log viewer to the node details
panel instead of to file tree)
- lighter grey color for the bottom bar so the color is less jarring
Rudolph
~~~~~~
- Busyish with other stuff next week, week after that a lot freer.
- Gideon working on ChRIS UI tweaks for getting ready for Rudolph's
Friday talk
COVIDNet
~~~~~~~~
- COVIDNet intern has the orthanc working on
- Audrey & Mick moving towards user testing
- BCH can host on public-facing site an instance, but haven't done it
yet. Good to go from BCH, just need to coordinate.
- Mo is in user testing status meeting tomorrow, will relay info about
BCH ability to host test instance and waiting for coordination
2 years, 10 months
14 Jan 2021 Status Update
by Máirín Duffy
Hi everyone!
We had our weekly upstream ChRIS status meeting this morning - it is
Thursdays @ 0900 EST (1400 UTC) on Google Meet (let me know if you'd
like to be added to the invite!) You are always welcome to join this
public, upstream meeting, it is a great way to check in with other
contributors, let us know how things are going if you have anything to
report, and also a great way to get any questions you might have answered.
The asciidoc meeting minutes are below; the screenshots are here (I dont
have the website blog rendering asciidoc yet so I wasnt able to get that
working yet):
https://github.com/FNNDSC/cube-design/tree/master/CHRIS-UI/screenshots/Ku...
= ChRIS Status Meeting 7th Jan 2021
== Max
=== Demo of Kubernetes support
* Max will not be able to contribute much going forward, have
overcommitted / the new year is too busy.
* Finishing up his ChRIS Kubernetes project. Demo'ed current state. Open
pull request for pfcon. Once that's resolved, it should all work. Should
be done soon - fixing the last integration test.
* Pull request for documentation of this there as well
image:img_0.png[]
==== Repos where the work lives:
* Pull request #76 under pfcon (to make pfcon kubernetes compliant)
* pull request for pull request in CHRIS_docs. docs uses minikube for
local deployment.
==== Demo Narrative
* Need to tunnel to access individual pods locally
* use IP addresS
* minikube apply…
* cube_script => smoke test (e.g pfcon_test.py)
==== Next Steps
* Rudolph going to have someone from his team to go over Max’s
Kubernetes work and replicate it.
** There are newer backend changes with pfcube, changed internals to
hopefully be cleaner, will use flask instead of httpserver... hoping
what Max has done here can be rebased to the new cuve without issue.
** Will have Jorge or Jennings look at it
* (Max) Documentation is pretty thorough so should be useful there
* (Max) Added three more tasks to the "pending to do" list on the
kanban for Team-19 as suggestions for further development
** frontend resources are not in kubernetes yet
** pods are started at the same time, may need to enforce deployment
ordering for the order of the container startups. there are diff ways to
handle this in kubernetes, wrote up some options in the ticket (CUBE #279)
** storage resources - not currently included in K8s deployment,
needs to be focused on CUBE #280
==== Questions / Requirements to Run
* Could be set up on RHEL, Fedora, Ubuntu. Set up with Kubernetes upstream
* Not sure about Travis. Max suggests a dedicated test cluster somewhere
- this is one of the things OpenShift takes care of, makes this a little
bit easier. Could also use the GitHub CI/CD.
* Weakness is integration testing is on docker swarm, no openshift
testing. Would be nice to have everything fully tested.
* There is a new OpenShift deployment anyone can use for free,
developers.redhat.com/ (devcentbox?) Max will look up the link and post
it. Free to use for development.
== Rudolph
* A lot of backend work
* Commandline clients that pull full workflows to backend instance
image:img_1.png[]
=== Demo
* covidnet feed script - 12 branches
* scripts describe workflows in JSON, gives to a parser, and builds the
workflow for you
Sample JSON for COVID-Net sample feed:
image:img_2.png[]
Screenshot showing the sample feed getting built (terminal where script
was run):image:img_3.png[]
ChRIS UI: shows progress per node
image:img_4.png[]
ChRIS UI: shows view-only terminal output for node as it gets setup in a
new panel
image:img_5.png[]
image:img_6.png[]
image:img_7.png[]
JSON to set up new feed using covidnet.sh client:
image:img_8.png[]
=== UI Issues
*Graph labels:* graph labels overflow, hard to read w 12-branch/parallel
covidnet feed
*4 Panels issues:*
* CSS issue, panels shift width...
* 4 quadrants are not fixed width, might be better
* a lot of white space in the file viewer quadrant
* Some ideas:
* floating terminal (similar to youtube video preview) that could be
full-screened
*Super-long vertical scroll-list of folders on the left*
Some ideas:
* filter folders to only show folders for the currently-selected node
* filter folders to only show folder for currently-selected node and its
descendants
* gray out / visually minimize any folders that dont apply to the
current selected node
* offer maybe via tab a categorized view of folders (collapse folders of
the same plugin type into one category, leaf nodes into its own category)
*Patternfly left vertical nav wastes horizontal space*
* should be able to collapse ala hamburger menu, functionality built
into patternfly, Mo to look up docs for Gideon on this
=== Misc
+
*GPU resource management issues*
- some nodes use GPU, some don't (highlight on graph?)
- if another node wants GPU, itll die somehow if another node is
taking it up
- resource mgmt of GPUs is wonky, with the scripts you can ... in
script -W (if multibranch structure, makes it wait at the end of the
branch until starting next one)
- openshift autoscaling can handle this GPU waiting issue
+
+
*Test environment for COVID-Net UI testing*
- can use this scripting setup to set up test environment for COVID-Net test
+
+
*Orthanc help for DarwinAI*
- aravind could work with darwinai on orthanc
== Mo
* Have a lot going on with Red Hat work the next 2-3 weeks so
temporarily a little less available
* Looking at COVIDNet testing in the next 2-3 weeks with internal
stakeholders to test the test first
* Testing environment will use publicly available images that will be
preloaded into UI
* Will use publicly-available BCH-hosted ChRIS environment to run tests
2 years, 10 months
7 Jan 2020 ChRIS project status update
by Máirín Duffy
Hi everyone!
We had our weekly upstream ChRIS status meeting this morning - it is
Thursdays @ 0900 EST (1400 UTC) on Google Meet (let me know if you'd
like to be added to the invite!) You are always welcome to join this
public, upstream meeting, it is a great way to check in with other
contributors, let us know how things are going if you have anything to
report, and also a great way to get any questions you might have answered.
= ChRIS Status Meeting 7th Jan 2020
== Máirín Duffy
=== Docs / website updates
Made some good progress on Jekyll / asciidoc setup for chrisproject.org
docs before holidays, basic framework is ready, and just need to
complete markdown=>asciidoc conversion as well as the bigger task of
culling / revising out-of-date docs and organizing / sorting existing docs
Working notes on reorganizing docs structure:
https://scalar.vector.im/etherpad/p/!IKmVVQadmbxyOTXTzk_matrix.org_ChRIS
=== Additional COVID collaboration possibilities
We reviewed two COVID-related potential collaborations with ChRIS, Mo is
going to invite Serratus lead to ChRIS Slack
==== Serratus
*https://serratus.io <https://serratus.io/>
* Serratus.io (viral RNA genome discovery), Red Hat is looking at
onboarding as another Team-19 project this spring
* Would be good to evaluate the python coronaspades client to see how
difficult it would be to package up as a ChRIS plugin
==== Giger Lab Covid Lung Images AI project
* Maryellen Giger's research group working with AI on COVID-19 chest xrays:
* https://c3dti.ai/
*
https://news.uchicago.edu/story/researchers-develop-ai-help-diagnose-unde...
=== COVID-Net User Testing
* For testing purposes the UI as is right now for COVID-Net should be
sufficient.
** Further down the line may want to include a fuller PACS query type
interface, in which case having the to-be-implemented PACS query UI
implemented as a component one-off plugin UIs like COVID-Net could use
would be really nice
* Meeting tomorrow with DarwinAI re: use test plan for COVID-Net.
* User testing should not require PACS or orthanc to be functional
because Jeffer put a script to prepopulate swift with any submitted
anonymized data which will make the UI function as if PACS or orthanc
was connected anyway.
=== New PACS query design for ChRIS UI
* before the holidays we had an initial click-thru prototype put
together using Figma that needs some updates
* Alana put together a fantastic UX testing plan for the click-thru
prototype
* Sanjay @ BCH would be a good candidate to run through the test
* Mo to update the click-thru prototype based on feedback we had on it,
then maybe we can run an initial user test with Sanjay
== Rudolph Pienaar
*
*
=== Project Chat system
Some history from Slack from before the holidays lost. Our Slack is
getting big enough now that the paywall is going to cause issues. We
might want to evaluate a different chat system like RocketChat.
Mo will reach out to OSPO comminfra team to see if they offer any chat
options, follow up with Slack folks to see if we could at least get the
90 day COVID free access, and also see if element.io has a non-profit or
COVID plan.
Update - comminfra may be offering matrix at some point in the future,
currently working on Ansible roles for it. Fedora may be able to give us
some channels / accounts for their upcoming new private Matrix server.
Sent Slack free access application to Rudolph as FNNDSC admin to fill it
out so they can evaluate if we qualify.
=== Ongoing backend work / stress testing
Jorge has been working on some redesign & updating of backend
components. Part of system stress testing using complex feeds that has
exposed some issues. This work will be ongoing for the next few weeks.
=== UI fit & finish
Gideon has been working on a lot of fit & finish work for the core UI,
including implementing the pulsing nodes indicators in the feed UI
=== DarwinAI sync
Had a quick syncup with Mick @ DarwinAI, they are bringing some more new
folks on board
=== Workflows to generate ChRIS feeds
We have a new workflows folder under ChRIS docs that has scripts that
will create multi-node ordered ChRIS feeds, we have one for COVID-Net
and it's working. It creates nodes and hooks them together in order,
uses shell scripting atm
https://github.com/FNNDSC/CHRIS_docs/tree/master/workflows
These are more meant to get full workflows up and running in ChRIS for
dev purposes but could also be built out into a kickstart like interface
for feeds, could be cool at some point to autogenerate scripts for
UI-created feeds as well so you could DL the script for any feed you
could view in the UI
Cheers,
~m
2 years, 10 months
