Add `Human Reference Atlas` section to organ specific view pages #1150

maxsibilla · 2024-01-09T00:43:06Z

See https://portal.hubmapconsortium.org/organ/kidney#Human%20Reference%20Atlas

This section loads an iFrame: https://portal.hubmapconsortium.org/iframe/organ?iri=http://purl.obolibrary.org/obo/UBERON_0002113

Utilizes the hra-api endpoint (SenNet's is https://apps.humanatlas.io/sennet-hra-api/v1):
https://github.com/hubmapconsortium/portal-ui/blob/309ae9688283fb25b8f9442abe5bb515913bb7e9/context/app/static/js/pages/Iframe/Iframe.jsx#L20

The text was updated successfully, but these errors were encountered:

tjmadonna · 2024-01-10T21:15:47Z

It looks like there are some hardcoded urls in the library.
https://github.com/hubmapconsortium/ccf-ui/blob/332cbcf7cca411cfdf1b7a2bce141d112a517c67/projects/ccf-organ-info/src/app/modules/link-cards/link-cards.component.ts#L20

maxsibilla · 2024-01-10T21:18:31Z

@tjmadonna We can probably ignore the section Register Tissue. For Explore Tissue we can point to https://data.sennetconsortium.org/ccf-eui

maxsibilla · 2024-01-10T21:20:28Z

Or you can use this https://sennetconsortium.github.io/ccf-preview/ccf-rui.html as a placeholder

tjmadonna · 2024-01-10T21:22:32Z

I get a Unknown IRI: http://purl.obolibrary.org/obo/UBERON... for numerous Organs. I have to look into this a little more.

Adipose Tissue
Blood
Bone
Bone Marrow
Breast
Lung (Left)
Lung (Right)
Muscle
Ovary (Left)
Ovary (Right)

maxsibilla · 2024-01-10T21:24:24Z

Hmm the Uberon codes provided by UBKG should resolve
Adipose Tissue maps to UBERON:0001013:
https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0001013

tjmadonna · 2024-01-11T16:06:45Z

All the UBERON codes resolve at the purl.obolibrary.org pages but not with ccf-organ-info. For example:
https://portal.hubmapconsortium.org/iframe/organ?iri=http://purl.obolibrary.org/obo/UBERON_0001013

bherr2 · 2024-01-11T16:20:13Z

The only IRIs supported by the ccf-organ-info component are those that have a 3D Reference Organ. Adipose does not have an associated reference organ and thus does not show any 3d organ / info.

bherr2 · 2024-01-11T16:21:08Z

You should probably check if the organ/IRI is supported by the HRA / RUI and then conditionally include the web component or not.

tjmadonna · 2024-01-11T19:09:10Z

@bherr2 Is there anyway to override the button URLs? For instance, the "Register Tissue" button currently takes you to https://hubmapconsortium.github.io/ccf-ui/rui/.

bherr2 · 2024-01-11T19:22:35Z

No, but it should be possible to add those as web component inputs. What would you set the URLs to?

tjmadonna · 2024-01-11T19:54:29Z

I wanted to set the URLs to their SenNet equivalents.

bherr2 · 2024-01-11T21:20:39Z

Ok, please submit an issue to ccf-ui and we'll get it scheduled.

tjmadonna · 2024-01-16T15:18:40Z

Submitted issue #1220 in ccf-ui.

maxsibilla · 2024-06-26T17:31:54Z

https://apps.humanatlas.io/us6/
EUI > Organ Information

<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8" />
    <title>EUI Organ Info Web Component</title>
    <meta name="viewport" content="width=device-width, initial-scale=1" />
    <link href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500&amp;display=swap" rel="stylesheet" />
    <link href="https://fonts.googleapis.com/icon?family=Material+Icons|Material+Icons+Outlined" rel="stylesheet" />
    <link href="https://cdn.humanatlas.io/ui/ccf-organ-info/styles.css" rel="stylesheet" />
    <script src="https://cdn.humanatlas.io/ui/ccf-organ-info/wc.js" defer></script>
  </head>
  <body style="margin: 0">
    <ccf-organ-info
      base-href="https://cdn.humanatlas.io/ui/ccf-organ-info/"
      use-remote-api="true"
      remote-api-endpoint="https://apps.humanatlas.io/api/v1"
      organ-iri="http://purl.obolibrary.org/obo/UBERON_0002107"
    >
    </ccf-organ-info>
  </body>
</html>

bherr2 · 2024-06-26T17:50:55Z

For sennet-only data, switch the remote-api-endpoint to "https://apps.humanatlas.io/sennet-hra-api/v1"

bherr2 · 2024-07-01T16:03:55Z

PS we did resolve #1220 but not quite in production yet. Will update when it's available!

bherr2 · 2024-08-09T19:32:47Z

PS it's in production now! See https://apps.humanatlas.io/us6/

maxsibilla · 2024-08-09T20:56:21Z

Thanks @bherr2 I have tried to specify every configuration parameter but I can't seem to get any numerical results for tissue data providers, sources, etc...

            <ccf-organ-info
                organ-iri={uberonUrl}
                hubmap-data-service='search-api'
                hubmap-portal-url='https://data.sennetconsortium.org/search'
                hubmap-data-url='https://search.api.sennetconsortium.org/entities/search'
                hubmap-asset-url={getAssetsEndpoint()}
                use-remote-api='true'
                donor-label='Sources'
                token={getCookie('groups_token')}
                remote-api-endpoint="https://apps.humanatlas.io/api"
                eui-url='https://data.sennetconsortium.org/ccf-eui'
                rui-url='https://apps.humanatlas.io/rui'
                asctb-url='https://hubmapconsortium.github.io/ccf-asct-reporter/'
                hra-portal-url='https://humanatlas.io/'
                online-course-url='https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc'
                paper-url='https://www.nature.com/articles/s41556-021-00788-6'
            />

maxsibilla · 2024-08-09T21:51:58Z

@bherr2 It looks like the token parameter is not overwriting the default value of 9070a30087cc3562131d1069c8497f6b. Its making the following request: https://apps.humanatlas.io/api/v1/aggregate-results?ontology-terms=http://purl.obolibrary.org/obo/UBERON_0000955&sex=male&token=9070a30087cc3562131d1069c8497f6b

This link does work when I pass it a token generated by Globus on the SenNet side

bherr2 · 2024-08-09T22:03:17Z

Ok, I'll look into it on Monday! We've made some changes to the API so we may need to update the example.

bherr2 · 2024-08-12T13:26:45Z

Hi Max, here is how I got it to work:

<!doctype html>
<html lang="en">
  <head>
    <meta charset="utf-8" />
    <title>EUI Organ Info Web Component</title>
    <meta name="viewport" content="width=device-width, initial-scale=1" />
    <link href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500&amp;display=swap" rel="stylesheet" />
    <link href="https://fonts.googleapis.com/icon?family=Material+Icons|Material+Icons+Outlined" rel="stylesheet" />
    <link href="https://cdn.humanatlas.io/ui/ccf-organ-info/styles.css" rel="stylesheet" />
    <script src="https://cdn.humanatlas.io/ui/ccf-organ-info/wc.js" defer></script>
  </head>
  <body style="margin: 0">
    <ccf-organ-info
      organ-iri="{uberonUrl}"
      data-sources='["https://apps.humanatlas.io/api/ds-graph/sennet?token={getCookie('groups_token')}"]'
      eui-url="https://data.sennetconsortium.org/ccf-eui"
      rui-url="https://apps.humanatlas.io/rui/"
      asctb-url="https://hubmapconsortium.github.io/ccf-asct-reporter/"
      hra-portal-url="https://humanatlas.io/"
      online-course-url="https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc"
      paper-url="https://www.nature.com/articles/s41556-021-00788-6"
    ></ccf-organ-info>
  </body>
</html>

Note that with this version we've made some updates to how you specify the sennet token (see the data-sources line). The API generates a "session-token" which is what you see as the other token passed around.

Also, I'm not seeing female heart blocks, but seeing male heart blocks. I'll look into it, but this code should get things up and running.

Thanks,
Bruce

bherr2 · 2024-08-12T13:34:14Z

Also, EUI is specified similarly here:

<!doctype html>
<html lang="en">
  <head>
    <meta charset="utf-8" />
    <title>SenNet - HRA Exploration User Interface</title>
    <meta name="viewport" content="width=device-width, initial-scale=1" />
    <link href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500&amp;display=swap" rel="stylesheet" />
    <link href="https://fonts.googleapis.com/icon?family=Material+Icons|Material+Icons+Outlined" rel="stylesheet" />
    <link href="https://cdn.humanatlas.io/ui/ccf-eui/styles.css" rel="stylesheet" />
    <script src="https://cdn.humanatlas.io/ui/ccf-eui/wc.js" defer></script>
  </head>
  <body>
    <ccf-eui
      base-href="https://cdn.humanatlas.io/ui/ccf-eui/"
      logo-tooltip="SenNet Data Portal"
      home-url="https://data.sennetconsortium.org/"
      data-sources='["https://apps.humanatlas.io/api/ds-graph/sennet?token={getCookie('groups_token')}"]'
      theme="sennet"
      login-disabled="true"
    ></ccf-eui>
  </body>
</html>

maxsibilla · 2024-08-12T13:48:06Z

@bherr2 awesome thank you for this!

bherr2 · 2024-08-12T13:54:55Z

Also, I remembered why the female heart blocks weren't showing. Its because all the female heart registrations were somehow registered to the male heart! All the registrations look to have been done by "Lorena Rosas". Dan Qaurooni @danqaurooni may already be aware, but if assistance is needed for updating the registrations, he can help!

maxsibilla · 2024-08-12T17:23:52Z

@tjmadonna

Remove laterality from organ page
Queries for Datasets/Samples need to be updated to ignore laterality
2 new properties
- Is hra supported
- Organ URL - determine HRA link AND the link at top of page (uberon or fma)
Only rely on config and not UBKG for what organs
Make the organ link open in a new tab

maxsibilla assigned tjmadonna Jan 9, 2024

tjmadonna added the external issue label Jan 23, 2024

maxsibilla added this to CODCC May 20, 2024

maxsibilla moved this to In Progress in CODCC May 20, 2024

maxsibilla moved this from In Progress to Backlog in CODCC May 23, 2024

maxsibilla linked a pull request Aug 12, 2024 that will close this issue

Tjmadonna/1150 hra #1584

Merged

maxsibilla moved this from Backlog to Review/QA in CODCC Aug 12, 2024

maxsibilla linked a pull request Aug 14, 2024 that will close this issue

Tjmadonna/1150 hra #1597

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maxsibilla closed this as completed in #1597 Aug 16, 2024

github-project-automation bot moved this from Review/QA to Done in CODCC Aug 16, 2024

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Add `Human Reference Atlas` section to organ specific view pages #1150

Add `Human Reference Atlas` section to organ specific view pages #1150

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Add Human Reference Atlas section to organ specific view pages #1150

Add Human Reference Atlas section to organ specific view pages #1150

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Add `Human Reference Atlas` section to organ specific view pages #1150

Add `Human Reference Atlas` section to organ specific view pages #1150

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