17 Dec 2020 project status update
by Jun Aruga
Hi everyone!
We had our weekly upstream ChRIS status meeting just now. - It is
Thursday @ 0900 EST (1400 UTC) on Google Meet. You are always welcome
to join this meeting.
= ChRIS Status Meeting 17th Dec 2020
== Gideon Pinto
* Showed a UI demo about the new feature using pl-med2img plugin to
convert DICON image file to jpg file, and pl-pdfgeneator to convert to
PDF file.
* We discussed how to improve the tree node (tree with circles) UI to
show both the current running status and selecting status in a better
way.
Rudolph suggested using yellow color to the circle node to show the
running status. Jun said it is a consistent color, as it is used in
Travis: running: yellow, success: green, failure: red.
Jun suggested using 2 circles for one node, that is the inner and
outer circle. The inner circle shows the color showing the running
status. The outer circle shows the selected status.
Gideon will send a pull-request about the new feature.
Slack #dev is the channel for all the development in ChRIS.
== Rudolph Pienaar
* Shared a new feature that is a script to enable us to register one
pipeline from the script.
* Rudolph told Jun how to run the ChRIS UI on a machine.
That is to use Dockerfile in https://github.com/FNNDSC/ChRIS_ui
== Jun Aruga
* Has no update.
If there are any other things to append, please tell me as a reply to
this email.
Cheers,
Jun
--
Jun | He - His - Him
2 years, 11 months
10 Dec 2020 project status update
by Máirín Duffy
Hi everyone!
We had our weekly upstream ChRIS status meeting just now - 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 10 Dec 2020
Myself, Jun Aruga, Max Murakami, Astrid Sharpe, and Jennings Zhang were
in this morning's status meeting. Here is a quick rundown of what we
discussed:
== Astrid
* Has an initial draft of the prospective hospital participant FAQ put
together
* Had been waiting on test protocol document, received it, will be
reviewing and integrating information about data privacy / ethics / etc.
into the FAQ
* Has a colleague whose husband is a radiologist and has offered to help
with recruitment
* Mo filled Astrid in on the testing protocol discussed at yesterday's
COVID-Net user testing meeting, and suggested Astrid could be one of the
"user test testers" so she'd be more familiar with how the tests run to
be able to answer any questions prospective participants have about it
== Max
* Continuing to work on pfcon PR: https://github.com/FNNDSC/pfcon/pull/76
* He and Jennings resolved a PR / requested changes issue in GitHub.
* Jorge is currently working on removing pfcon's access to swift... so
making the swift service name configurable in the PR doesn't need to
happen since that work is going on.
== Mo
=== COVID-Net User Testing
* Alana and myself had a meeting with Audrey, Mick, and Sonia on the
DarwinAI side. We discussed the current state of UX testing for the
COVID-Net UI.
* We'll be testing both the user experience of the UI itself as well as
the effectiveness of the model, ideally.
* Alana has a full draft plan for testing the PACS Query UI design Mo
and Rudolph put together a few weeks ago. We are looking at adapting
parts of it to create a COVID-Net UI test plan.
* The test is targeted for screen sharing over a video chat that will be
recorded for data collection.
* We are looking to have participants' own submitted data loaded into a
COVID-Net UI for them to test. Audrey and Mick are looking at figuring
out the logistics of having a system they can log into to do this available.
* Looking at starting testing in Jan or Feb with maybe ~20 participants
(ballpark)
* We are looking to recruit Red Hat Team-19 volunteers to run the tests,
and once the test script is drafted, Mick and Audrey have volunteered to
be test testers to run through the tests so we can work out any kinks
ahead of time.
* There is a UI bug in the COVID-Net UI that we've been aware of for a
while that will block testing. Howard is stuck on it, so I ping him with
Arushi's advice as she wasn't able to reproduce the bug and had a
suggestion for him to try
=== asciidoc effort
* Mo was able to stand up a jekyll-asciidoc-quickstart on github pages
using github actions: https://github.com/mairin/jekyll-asciidoc-quickstart
* Mo is working on converting the existing jekyll/markdown
chrisproject.org over to jekyll-asciidoc, with an eye towards then
integrating asciidoc format docs into the main chrisproject.org website
so they appear native to the website (and they will be :) )
* Looking at having a substantial enough chunk of the work done before
holidays but prolly won't be finished until Jan
Cheers,
~m
2 years, 11 months
3 Dec 2020 project status update
by Máirín Duffy
Hi everyone!
We had our weekly upstream ChRIS status meeting just now - 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.
Myself, Jun Aruga, Max Murakami, and Jennings Zhang were in this
morning's status meeting. Here is a quick rundown of what we discussed:
## Mo:
Mo has been talking with Serratus project (https://serratus.io) [1] for
a possible COVID-related collab with ChRIS. Serratus in a nutshell
discovers viral RNA from a multi petabyte public db of vertebrate
genetic info, then assembles full viral genomes to open databases for
vaccine researchers to consume. The general idea is preventing the next
pandemic by proactively discovering viruses and crafting vaccines for
them before they spread. The collab potential here is to run the genome
assembly process on ChRIS; the software that does it is python based [2]
so I'm hoping there's a possibility of containerizing it as a ChRIS plugin.
More info at [3, 4].
## Jennings:
Jennings has been investigating converting the ChRIS store from
Patternfly 3 to Patternfly 4:
https://github.com/FNNDSC/ChRIS_store_ui/issues/101
He is taking a two-phased approach, first to convert the PF3 and custom
widgets to native PF4 widgets, then to evaluate where PF4 native widgets
should be overridden for our own branding purposes.
We also talked about having a visual distinction between the ChRIS web
app and the ChRIS Store website - Mo suggested overriding the PF black
navbar with a white navbar so that the ChRIS store would be more in
harmony with chrisproject.org than the actual app website so there's a
distinction between them.
## Jun:
Jun is busy with Ruby release tasks since Ruby has new releases each
December and he is a RHEL Ruby maintainer. He has been working on a
journey map / funnel for ChRIS project website visitors => contributors,
which is accessible here for Red Hat accounts (if you would like to take
a look with a non-Red Hat acct please contact Jun for an invite):
https://docs.google.com/drawings/d/16AixE2vqMv_u_EfJHE6uGEnc8mw13mPWsCkS4...
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fdocs.g...>
He is looking at the Open Source Way book for inspiration on how to
better attract and retain contributors to the project:
https://www.theopensourceway.org/preview-1.99-book.html
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fwww.th...>
&
https://chaoss.community/
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fchaoss...>
## Max
Max is working on a pfcon PR and having some issues smoketesting. He is
running locally on kubernetes and gets this error:
"Table 'chris_store.django_celery_beat_periodictask' doesn't exist"
Jennings and Max discussed how a new celery beat service was added and
how to get it set up on Max's end to remove the error, looking at the
order of how docker-compose brings stuff up and I think emulating that
in the kubernetes-based set up. See [4,5].
Cheers,
~m
[1] This is a preprint paper describing Serratus
https://www.biorxiv.org/content/10.1101/2020.08.07.241729v1
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fwww.bi...>
[2] Serratus' corona assembler software
http://cab.spbu.ru/software/coronaspades/
<https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fcab.spb...><https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fcab.spb...>
<https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fcab.spb...>
<https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fcab.spb...>http://cab.spbu.ru/files/release3.14.1/
<https://meet.google.com/linkredirect?authuser=0&dest=http%3A%2F%2Fcab.spb...>
[3] This is the main github repo for Serratus
https://github.com/ababaian/serratus
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fgithub...>
[4]
https://github.com/FNNDSC/ChRIS_ultron_backEnd/blob/master/docker-compose...
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fgithub...>
[5]
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fgithub...>https://github.com/FNNDSC/cube-integration-action/blob/master/make.sh#L32
<https://meet.google.com/linkredirect?authuser=0&dest=https%3A%2F%2Fgithub...>
2 years, 12 months