ncihtan / idp Goto Github PK

From 2/5 IDP meeting:

TNP SARDANA planning to submit data to DCC - ready, just need to complete metadata; check with Alyce and Madison on timeline for this

• Someone is working on stories for melanoma samples they will be submitting but these are large images
• Madison has document tracking what stories are being developed

An inventory and status indication for:

• which data already has stories authored vs. stories pending
• what’s gone through the DCC ingress process vs. what still needs to do so

From 2/5 meeting data portal expectations: process the published Minerva story artifacts made available as public links (above) to visualize each image, when a user clicks a respective link on the data portal.

Prod server requirements:

• Should be the same as the dev server; provision the same resource
• This is going to be the a public facing image viewer portal available for HTAN -- gateway to access image resources
• Bruno will work with the IT team to get this set up, if there are any additional requirements that come up, send it in the #htan slack channel
• will contain the stable, tested code and QC-ed/de-id-ed data

Timeline: May 17, 2021

Where would this list be maintained? I saw #4 was created and closed but it doesn't mention where to find the list of IDs. Is the SOP to just update the live OMERO OAuth configuration whenever a new group is created?

From IDP 2/5 meeting:

Ensure that imaging data in Harvard, OHSU and SARDANA Synapse projects live on buckets that can be made public (or at least imaging data can be made public)

Jeremy to provide larger Minerva story for further DCC testing

From the 2/5 IDP meeting:

Ensure that we can publish a minerva story (e.g. generating jpeg files, and other Minerva inputs artifacts for each source image and associated Minerva story) via deploying a headless Minerva publishing tool to be provided by Jeremy's team

From the 2/5 IDP meeting:

ensuring that published Minerva stories (dependent on #14 ) for data in Harvard, OHSU and SARDANA Synapse projects can be made accessible via public bucket http links; that's required for the Minerva visualization on the data portal end

From the IDP call 2/5, DCC will census centers on plans with respect to imaging

Users typing in idp.tissue-atlas.org in most browsers will end up at the http:// site which currently just shows the nginx default page. I will add a configuration entry to redirect this to the actual https:// site.

https://www.synapse.org/#!Synapse:syn24322768

1. Add really basic intro on what it is, why its complicated, and why standards are good for everyone if a little more work in the beginning
2. Add link to RFC and reasoning that it was going to be the standard!
3. Add other conversion tools, or explain why bftools is preferred
4. Add FAQs (maybe the imageJ stuff could be turned into a question here?)

You can edit under "Folder Tools" and "Edit Folder Wiki"

An inventory and status indication for:

• which data already has stories authored vs. stories pending
• what’s gone through the DCC ingress process vs. what still needs to do so

The ARN of our role user is as follows:
arn:aws:iam::292075781285:user/idp-import

Use this space to link/upload info for centers

From 2/5 IDP meeting:

ensure that bucket urls (including story file for each image) are included in json generated for portal, for each source image so that Ino can render the minerva iframe

From 2/5 meeting: Sheila to send specifics of issue to Jeremy to investigate

From 2/5 meeting: Ensure that we can publish a minerva story (e.g. generating jpeg files, and other Minerva inputs artifacts for each source image and associated Minerva story) via deploying a headless Minerva publishing tool to be provided by Jeremy's team

ISB work expectations: support for setting the story publishing tool from Jeremy's team, if we decide to deploy as a lambda python function.