Question/Issue: Index not showing about cellbrowser HOT 28 OPEN

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I hadn't done that and just gave it a try, it doesn't seem to have solved the issue (or I did it incorrectly). Unfortunately, our instance is currently not public, so I will try to briefly summarize the situation:

• We have one folder (User1) that contains two datasets (Dataset1 & Dataset2)
• The ~/.cellbrowser.conf file does not seem to be present the home folder so I ran export CBDATAROOT='/home/cellbrowser/User1/'
• I copied cellbrowser.conf and desc.conf from Dataset1 to the User1 folder and edited as described in the link
• I run cbBuild -r /home/cellbrowser/html -p 8999 within the User1 folder, this runs but does not start a CellBrowser server
• I tried running the same command within the Dataset1 folder, which runs and creates a CellBrowser server but no index/title page

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Thanks! My home directory doesn't have a .cellbrowser.conf file though. Is it located somewhere else when using a conda environment by any chance?

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Done, but to no avail. Also the command cbBuild -r -o /home/cellbrowser/html -p 8999 runs but does not yields a message like: Serving /home/cellbrowser/html/ on port 8999
Point your internet browser to http://127.0.0.1:8999 (or the IP address of this server)

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I ran the code as you described. The webserver it launches is empty, I cannot access any datasets even by their url. Going to the html folder and opening the index html gives the following error: Could not find a dataset at dataset.json?86f083f58d. Would it make sense to do a video call so I show you?

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So our ~/.cellbrowser.conf file contains a single line: dataRoot = "/home/cellbrowser/OutputData/Bob/"
Within the html folder there are indeed the desc.json, the inded.html and dataset.json file

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Yes, sorry that was just for privacy reasons. I indeed have the following two folders:
/home/cellbrowser/OutputData/Bob/Dataset1
/home/cellbrowser/OutputData/Bob/Dataset2
These contain the objects created with cbImportScanpy

The folder Bob contains the cellbrowser.conf and desc.conf files as per the documentations instructions.

The newly created .cellbrowser.conf file is in /home/cellbrowser/

I can run cbBuild -r within the folder /home/cellbrowser/OutputData/Bob/ and this will generate the html and json files within /home/cellbrowser/html. However, clicking on the html file I get the error previously mentioned. I can also run cbBuild within the dataset folders themselves but that gives a similar outcome.

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Hi. I'm running into same proplem. In my case a computer restart worked and data hierarchy was created, at least inside the html folder I could see 'inDir' and the path to my root data directory in html/dataset.json file. However, when I open the browser by typing python -m http.server 8080 inside the html directory, the UI shows nothing. Under the developer tools, I see the following error message. Even opening the link http://cells.ucsc.edu/ does not show anything anymore.

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Hi @tkakar and @Bhersbach, sorry that it took me so long to understand what's going on. It had nothing to do with the hierarchy, but was a typo in the new diseases filter, I had fixed that in the develop branch, it slipped into the last release. Here is a new pre-release https://pypi.org/project/cellbrowser/1.2.1a1/ (I must release soon) You can install it with
"pip install --pre cellbrowser --upgrade"

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@maximilianh thanks for fixing the issue. I did as suggested. The disease related error is gone.
The individual datasets can be accessed via ?ds=datasetName on the url, but the data hierarchy still does not work. Under developer tools, I see errors. Posting screen shot of both scenarios (individual dataset and hiararchy).

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@maximilianh. I'm emailing the whole file, but the code around line 1138 is below

for (var category of categories) {
                var filtList = filtVals[category];
                var domList = domVals[category];

                let found = false;
                if (filtList.length===0)
                    found = true;
                for (var filtVal of filtList)
                    if (domList.indexOf(filtVal)!=-1)
                        found = true;

                if (!found) {
                    isShown = false;
                    break;
                }
            }

Unfortunately, due to data confidentiality, I cannot share the website.

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It's this line. if (filtList.length===0)

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@maximilianh thanks for troubleshooting this with me. My .conf files were based on some previous version from repo where other categories were not defined (except the body_parts). I just updated it and it's working now. Thanks for all your help.

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