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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
104 stars 40 forks source link

Could not find a dataset when opening index.html file #207

Closed frankligy closed 3 years ago

frankligy commented 3 years ago

Hi,

Thanks a lot for developing this awesome tool. Here's my inquiry:

I use scanpy and I have a h5ad file, I use cbImportScanpy and cbBuild to build necessary files for the webpages. I can successfully display the cell browser on my local machine, meaning localhost:8888 if I specified -p 8888. But I was wondering if I want to share the output folder with other people, how should they open it? I tried to click the index.html file, but I got the following error:

Could not find a dataset at dataset.json?654183357a. If you are sure that the link is correct, please contact the administrator of this server, or cells@ucsc.edu if this is running at UCSC.

Would you mind giving some hints on that? Much appreciated!

Best, Frank

maximilianh commented 3 years ago

Hi Frank,

thanks for your feedback. You cannot open index.html file in your file browser (e.g. OSX Finder or Microsoft Explorer). Our tool is a website with a lot of Javascript in it and the internet browsers don't allow opening such a file anymore, they prevent javascript from opening all the other files it needs. It needs to be served via a webserver. Did you see the documentation about this topic? https://cellbrowser.readthedocs.io/en/master/internet.html If you didn't see this documentation, do you have a suggestion how we could best point people to it?

Note that we can host the files for you at cells.ucsc.edu. Just send us the output of cbImportScanpy (not the cbBuild output directory) and the desc.conf file filled out with your paper information (title, abstract, etc) and we can add it to cells.ucsc.edu. Please tell us a short label for your dataset, like "mouse-cortex" or "breast-cancer", you will then be able to use .cells.ucsc.edu into your manuscript. We can hide the data until the paper is accepted. You can send a (dropbox?) link to a zip of your data to @.***

If you have other questions or feedback, please don't hesitate to let us know.

best Max

On Tue, Mar 9, 2021 at 10:31 PM Guangyuan(Frank) Li < @.***> wrote:

Hi,

Thanks a lot for developing this awesome tool. Here's my inquiry:

I use scanpy and I have a h5ad file, I use cbImportScanpy and cbBuild to build necessary files for the webpages. I can successfully display the cell browser on my local machine, meaning localhost:8888 if I specified -p 8888. But I was wondering if I want to share the output folder with other people, how should they open it? I tried to click the index.html file, but I got the following error:

Could not find a dataset at dataset.json?654183357a. If you are sure that the link is correct, please contact the administrator of this server, or **@.* if this is running at UCSC.

Would you mind giving some hints on that? Much appreciated!

Best, Frank

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frankligy commented 3 years ago

Hi Max,

Thanks very much for your prompt reply. Yes, I actually saw the documentation pages and it was very well-documented. I think the reason why I am asking is that compared to another interactive tool cellxgene, the advantages of UCSC cell browser as far as I can tell is that it is a static webpage, which means it is easy to migrate and send out to my collaborators who may don't have any knowledge about pip install or web deployment. That's why I am trying to figure out if there's a way I can simply copy and paste the cbBuild output directory and send it to others. From my conversations with my colleagues, this is a functionality that highly demanded and hasn't been solved. But I certainly understand you have other more important considerations during development and I appreciate the technical challenges here.

Thanks a lot for being willing to host our dataset, currently we don't have the demand but I will keep that at the back of my head when this kind of need comes along.

Much thanks, Frank

maximilianh commented 3 years ago

I think it is possible but it requires that you make a change to your chrome or Firefox configuration. For security reasons, data requests from a webpage opened as a file are blocked. This is why there is no single cell software anymore that works this way.

Don’t you prefer to simply copy the files onto some webserver? I imagine you have one via your institute ?

On Thu 11 Mar 2021 at 17:22, Guangyuan(Frank) Li @.***> wrote:

Hi Max,

Thanks very much for your prompt reply. Yes, I actually saw the documentation pages and it was very well-documented. I think the reason why I am asking is that compared to another interactive tool cellxgene, the advantages of UCSC cell browser as far as I can tell is that it is a static webpage, which means it is easy to migrate and send out to my collaborators who may don't have any knowledge about pip install or web deployment. That's why I am trying to figure out if there's a way I can simply copy and paste the cbBuild output directory and send it to others. From my conversations with my colleagues, this is a functionality that highly demanded and hasn't been solved. But I certainly understand you have other more important considerations during development and I appreciate the technical challenges here.

Thanks a lot for being willing to host our dataset, currently we don't have the demand but I will keep that at the back of my head when this kind of need comes along.

Much thanks, Frakn

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frankligy commented 3 years ago

Thank you Max, yes I will consult the IT team in the institute!

Best, Frank

maximilianh commented 3 years ago

Hi @frankligy , did it work? Can we close this ticket?

frankligy commented 3 years ago

Hi @frankligy , did it work? Can we close this ticket?

Yes it works, you can close it. Thanks again

maximilianh commented 3 years ago

I'm curious what it looks like. Do you want to send me the URL to it? Or is it internal?

On Tue, Apr 20, 2021 at 3:05 AM Guangyuan(Frank) Li < @.***> wrote:

Hi @frankligy https://github.com/frankligy , did it work? Can we close this ticket?

Yes it works, you can close it. Thanks again

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