18 March Status Update
by Máirín Duffy
Hi everybody,
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.
~m
ChRIS Status 18 Mar 2021
=====================
:Date: 18 Mar 2021
Present
-----------
- CJ Yoruk
- Máirín Duffy
- Gideon Pinto
- Rudolph
Status
---------
Gideon
~~~~~~
Demo
^^^^^^
Images:
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
- new file browser in UI
- a lot of refactoring, refactoring work is done
- will be pushing the PR shortly
- added nifty support but only shows the first slice (.nii)
ideas
^^^^^^
- show controls on preview rather than static thumbnail
- don't display slice 0 (1), display slice from middle of set
- gideon is adding tooling so you can scrollwheel thru the preview
slice:drop app... built on xtk, lightweight and good support js library
slicedrop.com
fnndsc.github.io/medview
Long file name issue
^^^^^^^^^^^^^^^^^^^^
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
- long file names.... mo suggested ellipsize in the middle
- first four digits... final few digits... uuid and timestamp
- dcm extension is important too
CJ
~~~
- finished on ChRIS docs
- in codeready containers / local openshift... when we create the jobs
in openshiftmanager.py, we have json files... the json parser wasnt
working in that env, so it didnt understand the number of workers we
had... when we run script, cpu limit, number of workers, etc. config. in
openshiftmanager.py have schedule job function... theres a json file
there to configure the job with those variables. there's variables like
parallelism, number of workers... in that, when it was reading the JSON,
the things we wrote in the script - it couldn't parse it and was giving
a bad request.
- pman's openshiftmanager.py.... that was supposed to parse json and
it didn't work...
- string/integer issue, MOC parser can understand strings local
codeready/openshift cannot
- schedule() function
- push files to openshift from plugins... local openshift, will create
pull request on legacy pman
- also deployed pman flask to MOC and local openshift and has been
playing with it, using Sandip's image
- Rudolph happy to have a meeting with CJ & Sandip to brainstorm the
flask issue
Sandip is getting the new flask-based pman working on MOC. he is stuck
at the moment, can get it working on MOC if he uses pfurl commands from
command line. when he tries to do thru pfcon, it breaks. Sicne it works
with pfurl we know it can work, so have to figure out the mismatch.
Rudolph
~~~~~~
- still working on the dicom service... total rewrite. shifted to using
python fastapi.... a total regearing of thinking on how to work with
more proper python restapi frameworks instead of previous iteration
(Which was a hackjob) taking a while to get over the first hump, now
over it, so hoping to get going quickly
- fastapi similar to flask, has some good features
- darwin AI, updated their images... Jennings will deploy them to the
public server, so we can see what the new UI looks like.
- questions: does have the multiuser fix, and fixed dicoms?
Mo
~~
- Outreachy community application approved, so we are now an Outreachy
community
- We have funding for one slot, with potential for another
- We have a front end project posted on the site now, Mo will add ChRIS
store front end work as well as two backend projects jbernal suggested.
--
Máirín Duffy, RHCSA
she / her / hers
Sr. Principal Interaction Designer
Red Hat <https://www.redhat.com>
300 A Street
Boston, MA USA
duffy(a)redhat.com <mailto:duffy@redhat.com>
<https://www.redhat.com>
2 years, 8 months
4 Mar Status Update
by Máirín Duffy
Hi everybody,
I forgot to send this out after the last meeting before this one. We
didn't have a meeting last week. Will follow up with minutes from
today's meeting after this email :)
We had our weekly upstream ChRIS status meeting on 4 March - 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.
~m
ChRIS Status 04 Mar 2021
=====================
:Date: 04 Mar 2021
Present
-----------
- CJ Yoruk
- Máirín Duffy
- Gideon Pinto
- Rudolph
Status
---------
CJ
~~
New pman issues
^^^^^^^^^^^^^^^^^^
- Haven't started working on new version of pman yet, have been talking
to Sandip on it. new student group has started trying to run and ran
into some issues, so CJ is now looking into getting legacy pman running
without any problems for them
- Tried a couple of versions on MOC. looks like none of the versions are
working. thought it was bc of MOC nodes not working
CJ couldnt run it, Sandip couldnt, students couldnt run it. jobs were
getting terminated after a specific time. CJ will create a ticket today
- When he runs locally, also gets errors. When we run a job, have an
entry in schedule/manager JSON file, but local cluster cannot parse the
JSON file, so getting cannot read JSON errors
- This doesnt appear in MOC on openshift. Is running same version of
openshift locally.
- Could be an issue with json or yaml file, but can run it on openshift
so doesnt make sense. Not working on MOC or local openshift.
- the variables we have in the yaml/json... number of workers, cpu, etc.
tried to hardcode to see if ti works. one of the errors is gone, but got
another error in its place.
- creating containers on local openshift works fine, its just pman not
working
- Rudolph's suggestion: coordinate with sandip, see if you can get it
working locally. could potentially get something instantiated on our
network to get you something to work on.
ChRIS docs
^^^^^^^^^^^^^^
- ChRIS docs are finished except for pman. got info on openshift
cluster, how to build it
Rudolph
~~~~~~
- Not too many updates...
- Rudolph focusing on PACS integration in the backend
- redesign / rewrite of one of the services
- hardening the system, rewirting services using flask in python
- redid pman to use flask so its a lot simpler, but the code that
connected it to openshift has to be redone from scratch now. Sandip is
working on that
- Arushi working on chrisproject.org
Gideon
~~~~~~
Images:
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
UI update demos
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UI updates include:
- fully resizable panels for node details and file browser
- nav menu - hamburger collapses left side
- will have close panel for bottom right
Spacing between nodes in graph
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- with a common parent, siblings get a wide spacing...
- spacing is not a function of the view port
- it seems that theres wide spacing up until a certain number of
siblings, then it gets scrunched down after it hits a certain number of
siblings
- uses d3 under the hood, not sure how d3 is adding the spacing
- blocked on perf issues with the tree - 40 nodes ok, 100 nodes is slow
Mo
~~
Suggestions for buttons in graph viewer in updated UI
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
https://raw.githubusercontent.com/FNNDSC/cube-design/master/CHRIS-UI/scre...
Buttons to look at:
- first one - vertical/horizontal toggle
- collapsible - collapse certain levels of the tree
- hide labels
Other suggestions for gideon
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- when collapse side panel, fill space with graph automatically
- idea to have faded dotted line when collapsing tree
COVD-Net UI testing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- Rudolph have scripts that generate fake-o data - patient names and
MRNs for creating dicoms - python library called "faker"
Outreachy intern
^^^^^^^^^^^^^^^^
- Started paperwork to see if we could get an Outreachy intern this summer
--
Máirín Duffy, RHCSA
she / her / hers
Sr. Principal Interaction Designer
Red Hat <https://www.redhat.com>
300 A Street
Boston, MA USA
duffy(a)redhat.com <mailto:duffy@redhat.com>
<https://www.redhat.com>
2 years, 8 months
