expfactory/lobby

Vanessasaurus

@vsoch

So here is what happens - you need to generate the recipe again

yes there are two containers

show me the command you use to generate the dockerfile first

something like $ docker run -v $PWD:/data vanessa/expfactory-builder build test-task

you'll need to run that first

earcanal

@earcanal

docker run -v $HOME/study7:/data \
              vanessa/expfactory-builder \
              build test-task \
              --input build/docker/Dockerfile.https

Vanessasaurus

@vsoch

yep exactly right!

earcanal

@earcanal

That's how I did it originally, but I've been copy/pasting that recipe around for a while and manually editing the experiment section.

Vanessasaurus

@vsoch

Now check out the Dockerfile - it's different by one line

RUN python3 -m pip install pyaml pymysql psycopg2==2.7.5

earcanal

@earcanal

ah, ok

Vanessasaurus

@vsoch

You can't use the Dockerfile you posted above

earcanal

@earcanal

ideal

Which line should I paste it after in the above Dockerfile?

Vanessasaurus

@vsoch

You can't just run the command to generate it agian?

Just replace RUN python3 -m pip install pyaml pymysql psycopg2 with RUN python3 -m pip install pyaml pymysql psycopg2==2.7.5

earcanal

@earcanal

My laptop is off at the moment and is seriously running on fumes.

When I switch it on I need to tweak the Dockerfile and try to build as quickly as possible!

^^ OK

Vanessasaurus

@vsoch

lol ok

earcanal

@earcanal

cracks knuckles

Vanessasaurus

@vsoch

rofl

have you published any papers yet?

Don't forget to cite expfactory, so I can show it's helping people and justify the work

earcanal

@earcanal

about to start writing one

will do!

build got past postgres this time :)

remaining issues are mine

Vanessasaurus

@vsoch

good to hear

earcanal

@earcanal

resolved

shiny new container built :)

thanks again for rapid response. I should be able to do final testing tomorrow morning after refuelling my laptop!

Vanessasaurus

@vsoch

you're welcome

Vanessasaurus

@vsoch

@yarikoptic it might be your lucky day, no promises about timing, but I'm looking into if Google Cloud Build is comparative (cost wise) to handle running the builds, which means more ability to select singularity versions and also fewer issues with larger repos.

Yaroslav Halchenko

@yarikoptic

Hi Vanessa! Is there a programmatic way to obtain a list of images for a collection on singularity hub? I see https://github.com/tanhnhn/singularityhub-sregistry/blob/1b8737e66e9205b9c5031f9144a1e76c0807e8dc/shub/apps/api/templates/routes/api.html#L15 which mentions /sitemap.xml but there is no https://singularity-hub.org/sitemap.xml

Vanessasaurus

@vsoch

Not anymore.

All non essential API endpoints were removed.

Yaroslav Halchenko

@yarikoptic

oh... so to see if an image was built I have to scrape collections page?

Vanessasaurus

@vsoch

You can use the GitHub webhooks API, or go to the page, sure.

Yaroslav Halchenko

@yarikoptic

webhooks on github get notified when an image finished building?

Vanessasaurus

@vsoch

No it would just alert that it received

Yaroslav Halchenko

@yarikoptic

so there is no way to discover that image finally finished building then... even with scraping not trivial since collection status webpage is populated by JS

Yaroslav Halchenko

@yarikoptic

eh, even phantomjs hacky way to obtain the page (https://askubuntu.com/a/547126) didn't work for me. So it seems there is no longer any way to see if image was built (or errorred) besides looping the trying to fetch the image for a while.

Yaroslav Halchenko

@yarikoptic

on https://singularity-hub.org/collections/2761 I am trying to remove ReproNim/containers:bids-afni-proc--v0.0.2 (should be the last one if you sort by date as of the moment) but nothing happens. When I try to remove next one - dialog appears asking to confirm that and I can remove (but not that first one).

Also after removing sorting resets, so I have to reorder again manually

Yaroslav Halchenko

@yarikoptic

hm... later was able to remove that and other images

Yaroslav Halchenko

@yarikoptic

what have I done to deserve a multi-hour throttling? https://github.com/datalad/datalad-container/issues/103#issuecomment-532250564

earcanal

@earcanal

@vsoch this is nice https://github.com/satchmorun/writ

I have a vision of markdown in experimental tasks that can go directly into a Methods section.

earcanal

@earcanal

e.g. https://github.com/satchmorun/writ/blob/master/writ.js.md

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