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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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URL not working? #188

Closed ltosti closed 2 years ago

ltosti commented 4 years ago

Hi there,

I added to the following lines to my desc.conf file:

biorxiv="link" ega="XXX"

and I cannot see any link appearing in the description of the dataset (but title, abstract and methods are all working fine). Is there something I'm missing?

Thank you for your help!

maximilianh commented 3 years ago

Sorry, I didn't see this!

there variables biorxiv and ega don't exist. Can you tell me where you found them?

As described in the documentation, the names are "ega_study" and "biorxiv_url". https://cellbrowser.readthedocs.io/dataDesc.html

let us know if you have any other questions.

On Mon, Sep 7, 2020 at 5:03 PM ltosti notifications@github.com wrote:

Hi there,

I added to the following lines to my desc.conf file:

biorxiv="link" ega="XXX"

and I cannot see any link appearing in the description of the dataset (but title, abstract and methods are all working fine). Is there something I'm missing?

Thank you for your help!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/188, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TJANSDMBEERBB5WHWLSETY4BANCNFSM4Q6MHXHA .

ltosti commented 3 years ago

Thank you for the clarification!

My fault, I was following another file I downloaded long time ago, like the one here: https://github.com/maximilianh/cellBrowser/blob/93171bfb855396d249a10cb0d0bd89a0dbaf7461/src/cbPyLib/cellbrowser/sampleConfig/desc.conf

I tried now and the biorxiv_url works indeed, but I still don't get the ega_study, as the link does not appear. I also tried to use custom or urls using key-value, but nothing appears below the Biorxiv URL.

ltosti commented 3 years ago

Ok, I looked at the cellBrowser.js file, I think the problem is a missing htmlAddLink(htmls, desc, "ega_study"); here https://github.com/maximilianh/cellBrowser/blob/93171bfb855396d249a10cb0d0bd89a0dbaf7461/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js#L690

Also, I installed the software using pip install but it doesn't seem to install the latest version?

matthewspeir commented 3 years ago

I believe the latest version is 0.7.11. Is that not what was installed for you by pip?

ltosti commented 3 years ago

Yes @matthewspeir @maximilianh ,

I just checked and I do have the version 0.7.11 installed.

The line I suggested above is missing - I added it and the EGA link appears. The urls and custom are not working, not sure where the issue is for those.

matthewspeir commented 3 years ago

Thanks. I believe @maximilianh fixed the issue with the EGA links in the develop branch of Gtihub, we just haven't had a chance to merge them into master and package up a new pip release.

I'm not aware of the issues with urls (I don't even see this in the example desc.conf) and the custom settings. Can you provide a bit more detail? e.g. example lines you are trying to use.

ltosti commented 3 years ago

At the bottom here it says:

The following tags contain key-value information:

  • custom: anything about the dataset that does not have an existing tag, e.g. {'taxon_id':'9606'}
  • urls: any url you want to show, e.g. { 'Raw data on synapse':'https://www.synapse.org/#!Synapse:syn21560407' }.
  • algParams: algorithm parameters, e.g. { 'louvainRes':'0.7' }. This tag is generated by cbScanpy.

So, in my desc.conf file I added:

custom={'technology'='single-nucleus sequencing'}
urls={'Lab website'='https://xxx'}

But these are not added in the Abstract of my dataset. Hope this is a bit clearer :)

maximilianh commented 3 years ago

Yes, I think we have the problem now that the documentation is too far ahead of the released version, because we update the docs immediately instead of just showing the most current version. Also, we haven't released in a long time.

the "urls" feature is only in the current pre-release. "custom" unfortunately went away with the supplFiles change, many thanks for pointing this out! I've added "custom" again. I've pushed a new pre-release 0.7.12a4, you should be able to install it with "pip install cellbrowser --upgrade --pre". Let us know if it works for you. We will make a real release very soon.

On Wed, Sep 9, 2020 at 5:41 PM ltosti notifications@github.com wrote:

At the bottom here https://cellbrowser.readthedocs.io/dataDesc.html it says:

The following tags contain key-value information:

  • custom: anything about the dataset that does not have an existing tag, e.g. {'taxon_id':'9606'}
  • urls: any url you want to show, e.g. { 'Raw data on synapse':' https://www.synapse.org/#!Synapse:syn21560407' }.
  • algParams: algorithm parameters, e.g. { 'louvainRes':'0.7' }. This tag is generated by cbScanpy.

So, in my desc.conf file I added:

custom={'technology'='single-nucleus sequencing'} urls={'Lab website'='https://xxx'}

But these are not added in the Abstract of my dataset. Hope this is a bit clearer :)

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ltosti commented 3 years ago

Just an update: I have now installed the 0.7.14 version and 'custom' and 'biorxiv' links are still not working.

maximilianh commented 3 years ago

Thanks for checking. The tag is actually called "biorxiv_url" did you try that?

As for custom, you would specify it like this:

custom = { "my website" : "https://my.website.com" }

Is this not working either?

On Wed, Nov 4, 2020 at 4:48 PM ltosti notifications@github.com wrote:

Just an update: I have now installed the 0.7.14 version and 'custom' and 'biorxiv' links are still not working.

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ltosti commented 3 years ago

Oh, sorry for my same mistake again: biorxiv_url works indeed, but custom does not.

ltosti commented 3 years ago

Also, @maximilianh @matthewspeir I just tried to add supplFiles=[{'file':'seurat3.rds', 'label':'Seurat3 RDS'}] to my desc.conf but no link appears in the download sections.

maximilianh commented 3 years ago

I just tried custom = {"test":"test"} in desc.conf with the mini.tgz example file we have and test: test showed up on the dataset info page, the first tab. Did you check this first tab? Initially I was looking at the wrong page.

If this browser installation is publicly accessible, I can also have a look directly.

On Thu, Nov 5, 2020 at 9:49 AM ltosti notifications@github.com wrote:

Also, just tried to add supplFiles=[{'file':'seurat3.rds', 'label':'Seurat3 RDS'}] to my desc.conf but no link appears in the download sections.

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matthewspeir commented 2 years ago

Hi @ltosti! It's been over since the last update in this ticket. Going to close this, but feel free to re-open if there's still something unaddressed here.