idp's People
idp's Issues
"Scene" Schema RFC
Support for setting the story publishing tool from Jeremy's team
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.
Create census wrt to imaging
From the IDP call 2/5, DCC will census centers on plans with respect to imaging
Check Minerva story files and other artifacts can be made public via bucket links
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
Bucket URLs for Minerva iframe in portal
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
Host and integrate a Minerva instance with the data portal
Ensure HMS/TNP SARDANA imaging data is stored on public S3 bucket
Grant access to OHSU S3 bucket to HMS IAM role user
The ARN of our role user is as follows:
arn:aws:iam::292075781285:user/idp-import
Add http-to-https redirect to nginx config
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.
Minerva SOPs & resources for centers
Use this space to link/upload info for centers
Add Synapse team numeric ID sync to onboarding checklist for new centers/TNPs
Process published Minerva story artifacts made available as public links
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.
Consider modifying lambda to trigger after metadata submission
IDP work for first public data release
Curate list of all Synapse group IDs that should have access to OMERO
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?
Inventory of what we expect to be available in Minerva for April
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
Check we can publish a minerva story
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
Production EC2 instance for DSA
Prod server requirements:
- Should be the same as the dev server; provision the same resource
- This is going to be
thea 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
BF Convert compression change issue
From 2/5 meeting: Sheila to send specifics of issue to Jeremy to investigate
OME-TIFF Intro and Conversion Wiki
https://www.synapse.org/#!Synapse:syn24322768
- 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
- Add link to RFC and reasoning that it was going to be the standard!
- Add other conversion tools, or explain why bftools is preferred
- Add FAQs (maybe the imageJ stuff could be turned into a question here?)
You can edit under "Folder Tools" and "Edit Folder Wiki"
Testing of larger Minerva story
Jeremy to provide larger Minerva story for further DCC testing
HMS/TNP SARDANA timeline for submitting imaging data
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
Check that imaging data can be made public
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)
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