Firefox/Mozilla bug with Google Colab about jbrowse-jupyter HOT 11 CLOSED

@arpanda Where are these commands being ran import subprocess subprocess.Popen(["python3", "server.py"])? Could you share what command was used to add the track or additional steps that were taken to configure the track?

The server provided by JBrowse has range request enabled. It is possible to view bw files with the server provided by JBrowse. Here is a screenshot of a bw file that i have in my local directory and have served using the JBrowse dev server and rendered in colab

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@arpanda Is there a specific reason why you are using that to run the python script vs just $ python serve.py?

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@arpanda I just replicated your steps with your script and your command, and I was able to get it to work with subprocess.

Any chance you have cookies blocked? If so you may need to enable cookies like this https://stackoverflow.com/questions/53581023/google-colab-file-download-failed-to-fetch-error/53582239#53582239

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That's great. But I am still getting similar errors.
Here is the code that I used to create tracks.

assembly_data = "https://jbrowse.org/genomes/CHM13/fasta/chm13v2.0.fa.gz"

ref_name_aliases = {
    "adapter": {
        "type": "RefNameAliasAdapter",
        "location": {"uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt"},
    },
}
chm13 = create('LGV')

chm13.set_assembly(assembly_data, aliases=["chm13v2"], refname_aliases=ref_name_aliases)
chm13.set_location("chr10:100..350")

# add a track
track_data = "https://jbrowse.org/genomes/CHM13/gff/chm13v2.0.gff.gz"
chm13.add_track(track_data, name="test-demo", track_id="test-track")

track_data="http://127.0.0.1:8082/his_rd_p_10000.bw"


chm13.add_track(track_data, track_id="bw1")
chm13.set_default_session(['bw'], False)
new_conf = chm13.get_config()
launch(new_conf, port=3013, height=400)

Here is the link of my colab . https://colab.research.google.com/drive/15swbptXiCOoOAxZGnfb0Ve_urQbZ71RO?usp=sharing

I am using Mozilla and don't think there is any cookie block enabled.

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@arpanda is your his_rd_p_10000.bw in the same place where your serve.py gets created? Your fourth cell should output serve.py and his_rd_p_10000.bw under the directory listing. I ran your notebook and the only thing that I changed was the bw file since I do not have access to yours, and I uploaded it to the same directory where the serve.py exists. It ran fine for me. There is also a typo in your code chm13.add_track(track_data, track_id="bw1") chm13.set_default_session(['bw'], False) where bw1 and bw should be the same but I am assuming it was fixed since it does not exist in your shared colab notebook. Another thing that you can do to get additional info, is to change launch(new_conf, port=3013, height=400, mode="external") then you will able to click the link and inspect or look at the console for more error messages.

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The path for his_rd_p_10000.bw is in the same place where server.py gets created and I also fixed the track_id. The only difference is with the bigwig file. I m not sure what's going on and still facing the issue.

Maybe sharing the bigwig file helps. but GitHub don't support bw file sharing directly. So I zipped it.
his_rd_p_10000.bw.zip

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@arpanda Have you tried running this on Chrome out of curiosity? I am attempting to debug, and it seems like it could be an issue with mixed content on Mozilla firefox. Before jumping into that conclusion, I wanted to make sure it also did not run in Chrome.

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@arpanda Just added your file and it is running on Chrome.

https://colab.research.google.com/drive/1pylspdKFvTQsuNu8dEip7XCRvO4Hc887?usp=sharing

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I tried with Chrome too but still facing the same issue. The error message is slightly different.

Chrome output

Firefox Mozila output

Note I enabled the third party cookies for chrome too.
It's probably something with system setting as you'r able to run the same google colab file with same input data.

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@arpanda
Do you have any blocking extensions on chrome? This is how my chrome is set up

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maybe close for now.... let me know if there are any updates @arpanda

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