ncihtan / htan-portal Goto Github PK

When I go to:

https://htan-portal-nextjs.now.sh/atlas/hta12

I get an error:

No synapse data corresponding to ID "centerA"

Small thing, but can we align the bread crumbs to match the other elements on the page?

• write in google docs https://docs.google.com/document/d/1xsjZSW4t2wqOj0a2Xo1pNWUcc0zQ-vxDzudDHoLB8c8/edit?usp=sharing
• add to wordpress

If I go to: https://htan-portal-nextjs.now.sh/atlas/hta2

and click the tab "Clinical Biospecimen"

and then click Biospecimen Tier 1

I see a table with Demographics data.

This is just a question. In the My Atlas page, I see something like:

What/where does the content of that first text box go?

We currently have two kinds of IDs in HTAN.

HTAN IDs look something like "HTA1", etc. These are public. And, also used to create patient IDs, sample IDs, etc.

Synapse IDs look something like: syn21261141.

Each Atlas will have one HTAN ID and one Synapse ID.

In the My HTAN Atlas feature:

• Can we add a field for HTAN ID?
• Can we make the links use the HTAN ID (instead of Synapse ID)? So, for example, when we have a link like: https://htan-portal-nextjs.now.sh/atlas/centerA, this should be the public HTAN ID, e.g. https://htan-portal-nextjs.now.sh/atlas/hta1

Can we make the Data Release Table sortable by each of the columns.

And, by default, can we sort by Atlas Name?

No idea is this can even be fixed.

But, whenever I go to: https://htan-portal-nextjs.now.sh/standards

Chrome always thinks this is Norwegian, and asks me if I want to translate! Is this fixable?

See proposal here: https://docs.google.com/presentation/d/1VGJ7yYNzemMNnOvYaS9mrH0EAm5raOQn9xfNdk7PwQk/edit#slide=id.g97a635f497_0_142

The current homepage shows very little numbers. Show some overview numbers (e.g. number of samples cancer types etc)

• Re-design homepage, include
  • number of atlases, institutions, donors, single cell datasets, imaging datasets etc
  • some of theses numbers could be links to some filtering state of the data release table
  • it might be nice to include some projection of what the numbers will look like in the future vs where we are now (can use image from https://humantumoratlas.org/dashboard/)

If I go here: https://htan-portal-nextjs.now.sh/atlas/hta2

then, click the derived tab and then the new button, I see the UCSC Browser.

But, when I click the back button, I can't seem to go back to the list of files. I actually have to click back three times.

JSON Data should use actual HTAN IDs, e.g. HTA1, etc, and not HTAN_CENTER_A, etc.

Within wordpress, I have some content like:

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

But, when I go to the data portal, the new lines are ignored and everything is merged into one long paragraph. See for example: https://htan-portal-nextjs.now.sh/atlas/hta2

Let's make the current Lorem ipsum text on the home page come from Word Press.

When done, let me know the slug name, and I can add some content.

• Need to figure a DNS name. Maybe https://ucsc-single-cell.humantumoratlas.org/?
• Where do we store the static files? Could be some bucket or maybe github?

Backend should only generate JSON data for public data sets

When I go to various pages on the site, e.g. the home page: https://htan-portal-nextjs.now.sh/

There is always a little bit of a lag, because we are retrieving content from WP and WP is sometimes a little sluggish.

Can we only get the content from WP only once an hour and cache the results? Perhaps, that would speed it up?

Discussed with @ethansiegl, but he suggested I ask @alisman to think on it further. Not urgent, just want to keep this on our radar.

in data.json derived data section, we have a bunch of IDs, e.g. CenterA_1_1 that do not follow the HTAN ID Spec. These should be prefixed with HTA2_, etc.

On the main nav bar, please add a link flush right that says:

"HTAN Main Site" and link it to https://humantumoratlas.org/

Placeholder to integrate UCSC Cell Browser via iFrame.

on https://data.humantumoratlas.org/explore

• Add loading indicator (Done in #78)

• Add nicer loading indicator (ADAM) (Done in #93)

• Add route/parameter for tabs (default listing can be /explore?tab=atlas then when you go to files tab it is /explore?tab=files (ADAM) (Done in #92)

• Add file type filter button and tooltip: (ADAM) (Done in #106)

  

- [ ] Add assay type: (ADAM) (Putting off more for now)

• Assay Type First Iteration Improvements (#89)

• Add Files as separate column aligned in tooltip as in above images (instead of showing it in parentheses with e.g. Cancer Type (xxx))

• Add filtering string to URL to allow for URL sharing (#96)

• The download button should give explanation of how to download the selected files using the synapse command line client (#87)

• Add BioSpecimen Tab (?)

• Add Cases Tab (?)

• Default should be atlas Tab (not files) (#111)

  • Atlas Tab should list Atlas ID (#111)

• Search filter should cover some more use cases:

  • search for single case id on case id
  • search for fields on atlas page
  • search by biospecimen id on files tab

• Add reset filters button (delete all filters) (Done in #110)
  cancelled - [x] purple download button remains blue after clicking on it (Done in #112)

Bugs:

• All filter search bug (#94)
• Removing filters by clicking on the group name doesn't work (try e.g. removing stage):
  (Done in #110)

If I go to: https://htan-portal-nextjs.now.sh/atlas/hta2

and click on derived data, I see lots of columns when I scroll left.

Are there options for making this more readable? For example, we only show the first x columns, and then have an option to expand? or put the table in it's own scroll pane?

Probably due to some flexbox situation

Let's add a footer to the portal site.

For now, let's just put:

Human Tumor Atlas Network (HTAN) @ National Cancer Institute

If I got to: https://htan-portal-nextjs.now.sh/standards/biospecimens

I see the content for clinical data blurb.

Maybe a small bug?

Two small changes on the home page:

1. Can we make the "hero blurb" wider? right now, it seems too narrow.
2. Please remove the Learn More button.

When I go to various pages on the site, e.g. the home page: https://htan-portal-nextjs.now.sh/

There is always a little bit of a lag, because we are retrieving content from WP.

Can we only get the content from WP only once an hour and cache the results? Perhaps, that would speed it up?

Some of the tool tips are very long over one line.

Example:

Can we add line breaks to these, so that they appear on multiple lines and are easier to read?

At the top of the https://htan-portal-nextjs.now.sh/data page, we have some latin text.

Can you make that served from WP, and ping back with the slug?

In the data.json file https://github.com/ncihtan/htan-portal/blob/master/data/data.json, we currently have:

"description": "HTAN Biospecimen Identifier from which these files were derived [https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing]",

Can you please remote the google doc link?

In the current portal, we have a Data Standards Landing Page:

https://htan-portal-nextjs.now.sh/standards

This links to pages, such as: https://htan-portal-nextjs.now.sh/standard/cds

This is not as elaborate yet as e.g. https://portal.hubmapconsortium.org/docs/metadata or https://data.humancellatlas.org/metadata

We would like each data standards page to consist of two parts. Something like this:

Tasks:

• Set up JSON-LD page like https://discovery.biothings.io/schema-playground (@milen-sage )
• Add links to JSON-LD page from the data standards page, iframe it in or generate it with next somehow (whatever works easiest) (@inodb)
• Add intro documentation for all data types we want to describe (managed by @elysekozlowski )
• Make sure language/grammar is consistent across all pages (@elysekozlowski)

When I go to the data release pages, eg. https://htan-portal-nextjs.now.sh/data/hta3

The bread crumb is hard-coded to something like this:

Home > Data Release > Boston University

Instead of hard-coded, can you use the blurbs instead, e.g.

Home > Data Release > [content from hta12-short-blurb]

Currently the DSA, Luna and UCSC single cell browser are kind of hidden. Let's have a single section with all of them combined as well

• Add section Analysis Tools with easy access to demos
• Add new analysis tools, such as spatial transcriptomics viewers

Placeholder to integrate DSA via iFrames.

For some reason...

On this page: https://htan-portal-nextjs.now.sh/data

the footer does not appear. but, it appears on the other pages.

When I go here: https://htan-portal-nextjs.now.sh/atlas/centerA

I see Category 1 in the pull-down menu.

But, this tab should actually contain both clinical data and biospecimen data, e.g. if we use the fake file that Milen created, we should see both Category 1 and Category 2 in the pull-down menu.

Let's make the cards on the Home Page derived from Word Press content.

Let me know when set-up and I can try to make some sample cards.

Create google doc with all render types.

If I go to: https://htan-portal-nextjs.now.sh/data_releases, I only see 3 atlases.

We should show all the atlases.

Right now, the synapse tables show the JSON "description" field as the column name.

For example:

Instead, I suggest we show the JSON "name" field as the column name, and make the "description" file available as a tooltip.

In adding the short blurbs, I realized that we will need to make a few changes to the Data release page.

1. We will need four columns:

• Atlas Name
• Atlas Type
• Lead Institution(s)
• Data Release

2. Can we make the columns sortable?

Let's add four pages for HTAN data standards, each with content served by WordPress.

The four are:

• Biospecimens
• Clinical
• Single Cell RNASeq
• Imaging

We should remove Single Cell from the Main Nav Bar.

• Footer
• Figure out where news/twitter feed etc can go
• Improve navigation between main humantumatlas.org site and this site

Send some sample single cell links to Milen

If you go here: https://htan-portal-nextjs.now.sh/atlas/hta2

and, then click on clinical data, you see two rows of data.

If you scroll all the way to the right, you see download links for Synapse, e.g.

I believe this is due to a "downloadLink" in the JSON.

But... I don't think individual rows of data should not have a download link. You should only be able to download all the clinical data in one go, e.g. by clicking the download button on the clinical data tab.

The Primary NGS Tab will actually be just a blurb of text, and not based on anything from Synapse.

Can we modify, so that it's a field in the "My HTAN Atlas" feature?

It's possible/likely that some atlases will not have data for the release.

So...

if at atlas has no Synapse ID, can we hide the "Data Release" link on this page? https://htan-portal-nextjs.now.sh/data_releases

In WordPress, we have 12 atlases.

But, on the Data Release Page: https://htan-portal-nextjs.now.sh/data_releases currently only shows 10 atlases.

On the Home Page, please link "Explore the Data" to the Data Release page, e.g. https://htan-portal-nextjs.now.sh/data