Idr front page #2

will-moore · 2022-03-14T16:51:22Z

Rename the module to idr_gallery and remove non IDR pages.
Also ports new IDR front page work from ome#91

Deployed at https://merge-ci.openmicroscopy.org/web/idr_gallery/

NB: that doesn't require much config as this is now the default behaviour (although the same config exists and can be overridden).
Deployment above is now:

pip install git+https://github.com/will-moore/omero-gallery.git@idr_front_page#egg=idr_gallery
omero config append omero.web.apps '"idr_gallery"'
omero config set omero.web.gallery.base_url "https://idr-testing.openmicroscopy.org/"
omero config set omero.web.gallery.gallery_index "https://idr-testing.openmicroscopy.org/"

See ome#91

Try to make idr-gallery show the IDR front page 'out of the box' without needing config

These aren't set on idr or idr-testing, so we don't want the default to be idr-testing

pwalczysko · 2022-03-15T13:05:52Z

deployed locally successfully. Also checked the deployment on merge-ci.
Works fine, just a minor point

There used to be a scrollbar on the twitter feed column ? That seems to be gone now. Is it intentional ?

sbesson · 2022-03-15T13:12:42Z

idr_gallery/gallery_settings.py

+        ],
+    "omero.web.gallery.idr_studies_url":
+        ["IDR_STUDIES_URL",
+         'https://raw.githubusercontent.com/IDR/idr.openmicroscopy.org/master/_data/studies.tsv',


There are two concerns to be reviewed before moving to production here:

first, although the impact is probably low, I fear we are introducing unnecessary friction and coupling between this app and the master branch of the other repository. For instance, a PR adding the statistics for a study loaded into idr-next but not released yet would need to be put on hold

second, as mentioned on Monday, we will want to tests what happens when this UI gets deployed and accessed externally. Is there a risk we will get a Rate Limit error?

Cross-linking to the discussion on ome#91 (comment) where a couple of options were proposed.

sbesson · 2022-03-15T13:13:32Z

idr_gallery/gallery_settings.py

+        ["INDEX_JSON_URL",
+         'https://raw.githubusercontent.com/will-moore/idr.openmicroscopy.org/idr_index_data/_data/idr_index.json',
+         str,
+         "URL to load JSON, with a 'tabs' list of {'title':'', 'text':'', 'videos':[]}"


Similarly to #2 (comment), I am concerned about this coupling and how it works in practice. Now the app is effectively forked, is there still an incentive to loading this content from a third-party location?

The reason not to simply include this as HTML in the app was because updating the content would need a re-release of the app, and re-deploy etc. instead of a config change.
If that's no-longer a concern, then I can add this JSON back into the idr-gallery repo?

Yes, I brought up this issue in the former omero-gallery repository because of the number of steps (app release, configuration change) involved to upgrade a production deployment e.g. when fixing a typo.

Looking at this proposal, my concern we are shifting this burden from to the review process. For instance, a change to the content of this tab (e.g. a video update or a description update) would require a PR against idr.openmicroscopy.org, a temporary IDR/deployment PR pointing at a personal branch and a deployment of the playbook with this temporary PR to be evaluated?

@sbesson That commit (4ed9441) moves the tabs JSON into the idr_gallery app, instead of loading from github.

jburel · 2022-03-17T14:28:27Z

From CELL-IDR or Tissue-IDR

Select group by type
Click on the icon to view the image
It does not launch the viewer but redirect to cell/tissue idr

jburel · 2022-03-17T17:01:52Z

#2 (comment) has been fixed

It will look neater if the height of the twitter feed and the height of videos box match

MANIFEST.in

jburel · 2022-03-17T17:13:43Z

idr_gallery/static/idr_gallery/autocomplete.js

+        return $("<li>")
+            .append("<a>" + item.label + "</a>")
+            .appendTo(ul);
+    } 


idr_gallery/static/idr_gallery/categories.js

jburel · 2022-03-17T17:15:39Z

idr_gallery/static/idr_gallery/categories.js

+  // Load stats and show spinning counters...
+
+  // In case studies.tsv loading from github fails, show older values
+  let totalImages = 12840301;


Values will need to be updated at regular interval.
Could a note be added in the instructions otherwise we won't be able to find it

jburel · 2022-03-18T09:59:56Z

The "Eye" icon on the background image does not open on idr-testing but on idr like the rest. So that should probably be configured correctly. Also I think it will be better to open that image in iviewer than the standard web view to match the other "eye" icons behaviour.

will-moore · 2022-03-18T11:30:40Z

I think that the link from the background image should show the image in webclient because it provides context: If you're interested in what study etc. the Image is from and what it shows then it is more useful to see it in the webclient. And it's very easy to go from there to the full viewer if you want. It's much harder to go from iviewer back to webclient.
We discussed this in one of the meetings a while back and I think people were OK with that approach, but we could bring it up again to check?
For me, the usage of the "eye" icon really means "this is a link to show that image" and doesn't necessarily mean it has to go to iviewer. We could try a different icon, but it might be less clear that it's referring to the image? If we were going for 2 links, then we could have (i) info link and "eye" link to viewer, but I think that adds clutter without providing much benefit (since it's easy to open the viewer from webclient).

For some links to idr, I have used absolute URLs for convenience, since they will be the same once this is deployed on IDR.
But I could look at changing that...

jburel · 2022-03-18T11:46:35Z

The context is no different for the thumbnails and the background image. We have the idr accession number/name when mousing over the "circle"
Having the same icon for 2 different outcome is confusing in my view.
I do not remember that discussion (I might not have been there!)

jburel · 2022-03-18T13:13:15Z

For some links to idr, I have used absolute URLs for convenience, since they will be the same once this is deployed on IDR.

The reason I am indicating that is if we want to use a non-release background image, the link will fail if we use the "eye" mentioned above.

will-moore · 2022-03-18T13:13:39Z

In the tooltip you have a link to the Experiment/Screen (which gives you context), but you don't have that for the background images. If both the tooltip thumbnail and the background image have to link to the same place, I'd prefer is if they both link to webclient/?show=image-id.
If I'm interested in the image, e.g. https://idr.openmicroscopy.org/webclient/img_detail/13965767/ tells me the name E14.lif but tells me nothing about the image, whereas https://idr.openmicroscopy.org/webclient/?show=image-13965767 I can see the Organism, and Organism Part from KV pairs and find the study. The iviewer is a dead-end, whereas the webclient encourages more browsing of data.

jburel · 2022-03-18T13:14:21Z

you do have the name and accession number when you mouse over the circle

jburel · 2022-03-18T13:17:30Z

A point discussed with @will-moore that might confuse people (I was!)
104 studies != 70 Cell-idr, 35 Tissue-IDR!

will-moore · 2022-03-18T13:28:20Z

But the accession number isn't the same as a link. You'd have to search for the study, and even then, you wouldn't be able to find that Image in the study.

sbesson · 2022-03-18T13:53:40Z

104 studies != 70 Cell-idr, 35 Tissue-IDR!

I can understand the confusion but that reflects the fact these categories are not mutually exclusive for a submission.
Actually, in a sentence, these numbers should be read "There are 7,401,738 cell images (126 TB) across 70 studies". Does that speak for swapping the order and putting images first ?

jburel · 2022-03-18T13:59:44Z

The fact that we only have one is probably why it can be confusing.
Maybe having X images Y TB across Z studies will be better.
@will-moore what do you think?

will-moore · 2022-03-18T14:19:33Z

I honestly don't think that anyone is going to visit IDR and Cell - IDR and Tissue - IDR, note the numbers, do the maths and find any problem. I also don't think that X images Y TB across Z studies solves the 35 + 70 != 104 problem because it still says that there are 35 Tissue studies and 70 Cell studies, so it doesn't explain that some studies can be both.

Also, I like 104 Studies first, as that's the primary counter of what IDR contains. And Images is nicer in the middle from a design perspective as it's the longest text looks more symmetrical.

This is less nice:

I don't think this is an improvement:

jburel · 2022-03-18T15:52:55Z

@will-moore thanks for the various options.

will-moore · 2022-03-18T16:46:21Z

@jburel background images/links now use the 'current' server. Same for study links in tooltips. Deployed on testing server.

sbesson · 2022-03-22T10:22:54Z

As discussed this morning, the last commit proposes to have two links associated with each image in the top-level carousel:

link to the viewer URL directly via the eye icon
link to the webclient URL via the info icon

pwalczysko · 2022-03-22T10:29:22Z

The icon on the carousel images was discussed with the team this morning and the result of the discussion was implemented - two icons, one leading to webclient, one to iviewer, see below. LGTM

jburel

Tested the icons and it works
I assume the package will be pushed to pypi. cf README instructions

will-moore added 3 commits March 14, 2022 12:44

rename gallery to idr_gallery

6b65843

Port idr front page from omero-gallery PR

2076e0d

See ome#91

Remove code not used by idr-gallery

bb57f23

will-moore mentioned this pull request Mar 14, 2022

rename gallery to idr_gallery #1

Closed

will-moore added 5 commits March 14, 2022 22:49

Update MANIFEST.in to include idr_gallery

8c164ad

Fix static links to idr_gallery css

e108d77

Removing unused config. Hard-coding defaults for others

26849da

Try to make idr-gallery show the IDR front page 'out of the box' without needing config

Fix static links to idr_gallery js

9fbfe64

Don't show filter controls

86c5d77

will-moore mentioned this pull request Mar 15, 2022

Idr gallery config IDR/deployment#364

Merged

will-moore added 2 commits March 15, 2022 11:14

Fix template formatting { { -> {{

548c555

Don't set base_url and gallery_index by default

895d38a

These aren't set on idr or idr-testing, so we don't want the default to be idr-testing

will-moore added 3 commits March 15, 2022 13:08

Update copyright date

5310caa

Use GALLERY_HOME to fix /search URLs

cf031e4

Remove src/ and package.json build etc. IE not supported

028eb1c

sbesson reviewed Mar 15, 2022

View reviewed changes

Don't load tabs json from github

4ed9441

This was referenced Mar 16, 2022

Add _data/idr_index.json IDR/idr.openmicroscopy.org#155

Closed

Add studies.json created from studies.tsv IDR/idr.openmicroscopy.org#156

Closed

will-moore added 6 commits March 17, 2022 14:57

Fix thumbnail viewer links when 'group studies by type'

43f167a

Fix embedded twitter height

07246fb

Remove print()

c6bb5a8

properly hide the filter controls

bdc3be0

Use ?_=VERSION to avoid caching issues with js, css etc

1200eba

setup.py uses from idr_gallery.version import VERSION

f335c47

jburel reviewed Mar 17, 2022

View reviewed changes

Make twitter panel same height as tabs

94dd41b

Fix suggestions from JM

defb406

Don't hard-code idr.openmicroscopy/ for background images and links

0873dfc

Don't hard-code idr.openmicroscopy for study link in tooltip

02acb10

Background image links to webclient and iviewer

a91d13e

sbesson requested review from jburel and pwalczysko March 22, 2022 10:23

pwalczysko approved these changes Mar 22, 2022

View reviewed changes

jburel approved these changes Mar 22, 2022

View reviewed changes

sbesson merged commit 84fdbda into IDR:master Mar 22, 2022

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Idr front page #2

Idr front page #2

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Idr front page #2

Idr front page #2

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