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Question/Issue: Index not showing #251

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Bhersbach opened this issue Sep 12, 2022 · 28 comments
Open

Question/Issue: Index not showing #251

Bhersbach opened this issue Sep 12, 2022 · 28 comments

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@Bhersbach
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Bhersbach commented Sep 12, 2022 •
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We are setting up Cell Browser in our lab and have successfully prepared two Cell Browser folders as a test. However, when we use cbBuild to host the data, we can access the individual datasets only by using the dataset name, i.e., server address:/?ds=dataset_name. The index/title page, does not load and, instead, we get an empty Cell Browser page. cbBuild was ran with the same output folder and indeed confirms it found two datasets within that folder. When attempting to open a dataset through file > open dataset, no options are given either. Is there something we are forgetting to specify?

System specs:
OS: Linux (Ubuntu 18.04)
Cell Browser v1.2.1
@maximilianh
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maximilianh commented Sep 12, 2022 via email

@Bhersbach
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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

@maximilianh
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maximilianh commented Sep 12, 2022 via email

@Bhersbach
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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?

@maximilianh
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maximilianh commented Sep 12, 2022 via email

@Bhersbach
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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)

@maximilianh
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maximilianh commented Sep 12, 2022 via email

@Bhersbach
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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?

@maximilianh
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maximilianh commented Sep 13, 2022 via email

@Bhersbach
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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

@maximilianh
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maximilianh commented Sep 13, 2022 via email

@Bhersbach
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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.

@maximilianh
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maximilianh commented Sep 13, 2022 via email

@maximilianh
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maximilianh commented Sep 13, 2022 via email

@tkakar
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tkakar commented Sep 15, 2022 •
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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.

Screen Shot 2022-09-15 at 2 39 40 PM

@maximilianh
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maximilianh commented Sep 15, 2022 via email

@tkakar
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tkakar commented Sep 15, 2022 via email

@maximilianh
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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"

@tkakar
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tkakar commented Sep 16, 2022 •
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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).
Screen Shot 2022-09-16 at 10 49 42 AM
Screen Shot 2022-09-16 at 10 49 10 AM

@maximilianh
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maximilianh commented Sep 19, 2022 via email

@tkakar
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tkakar commented Sep 19, 2022 •
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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.

@maximilianh
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maximilianh commented Sep 19, 2022 via email

@tkakar
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tkakar commented Sep 19, 2022

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

maximilianh added a commit to ucscGenomeBrowser/cellBrowser that referenced this issue Sep 20, 2022
@maximilianh
small UI changes after feedback from Matt, adding a missing function …
8a9075f 
…from cbData, more debugging output for the hierarchies, no redmine, github issue maximilianh#251
@maximilianh
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maximilianh commented Sep 20, 2022 via email

@tkakar
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tkakar commented Sep 20, 2022

@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.

@maximilianh
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maximilianh commented Sep 20, 2022 via email

@maximilianh
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maximilianh commented Oct 11, 2022 via email

@maximilianh
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maximilianh commented Oct 11, 2022 via email

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@maximilianh @tkakar @Bhersbach