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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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Can't get description for a quick gene to display #97

Closed matthewspeir closed 5 years ago

matthewspeir commented 5 years ago

I have a quickGenes.csv file. In the first column, I've placed the gene name and in the second column, I've placed the description. After running cbBuild, the genes show up in the 'Dataset genes' section, but when I mouse over the genes, the little popup just says 'undefined'.

Maybe I'm just doing this wrong?

Files here: /hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/cbScanpyOut_quakeGlio Cell Browser here: https://hgwdev.gi.ucsc.edu/~mspeir/cb_demo/?ds=Quake_Glioblastoma_GSE84465

matthewspeir commented 5 years ago

So, I think I fixed this by removing the trailing comma in my quickGenes.csv file. After removing the trailing slash, everything is displaying just fine: https://hgwdev.gi.ucsc.edu/~mspeir/cb_demo/?ds=quake-gbm

Maybe the step that loads the quickGenes.csv can ignore these extra commas?

maximilianh commented 5 years ago

This line makes this file an invalid CSV file, as this line has more fields than the other lines:

GPR17,High expression characteristic of OPCs; Expressed highly in tumor periphery cells versus tumor core,,

How did you create this file?

On Thu, Apr 11, 2019 at 5:20 PM Matt Speir notifications@github.com wrote:

I have a quickGenes.csv file. In the first column, I've placed the gene name and in the second column, I've placed the description. After running cbBuild, the genes show up in the 'Dataset genes' section, but when I mouse over the genes, the little popup just says 'undefined'.

Maybe I'm just doing this wrong?

Files here: /hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/cbScanpyOut_quakeGlio Cell Browser here: https://hgwdev.gi.ucsc.edu/~mspeir/cb_demo/?ds=Quake_Glioblastoma_GSE84465

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matthewspeir commented 5 years ago

I created it by hand. Copied gene symbols in and then typed out the descriptions.

matthewspeir commented 5 years ago

The quickGenes.csv file in /hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/quakeGlioblastomaGSE84465 doesn't have that issue with that line.

maximilianh commented 5 years ago

OK, what I can do in this case is to make the error message better? I can't reproduce the error anymore, can you?

On Mon, May 20, 2019 at 5:52 PM Matt Speir notifications@github.com wrote:

I created it by hand. Copied gene symbols in and then typed out the descriptions.

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matthewspeir commented 5 years ago

I think a better error message or some warning during the cbBuild process would be good. During the cbBuild process right now, there are no complaints about the quickGenes file.

I mean if I go back to the quickGenes file with that broken line in it, I can still see the issue: https://hgwdev.gi.ucsc.edu/~mspeir/cb_GSE84465_v3/?ds=Quake_Glioblastoma_GSE84465

Data:
/hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/cbScanpyTests/cbScanpyOut_quakeGlio

maximilianh commented 5 years ago

Oh! Now I understand - you didn't even get an error message! I didn't understand that. I read over the code, apparently I on purpose wrote this code to be more error tolerant than the standard csv parser I use. You're right, this was a bug or very close to one. I hope it's fixed now. 0.5.26

On Mon, May 20, 2019 at 8:17 PM Matt Speir notifications@github.com wrote:

I think a better error message or some warning during the cbBuild process would be good. During the cbBuild process right now, there are no complaints about the quickGenes file.

I mean if I go back to the quickGenes file with that broken line in it, I can still see the issue: https://hgwdev.gi.ucsc.edu/~mspeir/cb_GSE84465_v3/?ds=Quake_Glioblastoma_GSE84465

Data:

/hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/cbScanpyTests/cbScanpyOut_quakeGlio

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maximilianh commented 5 years ago

So with the new version it should show the descriptions in the final browser and not output an error in cbBuild (even though the .csv file is not fully correct, but that commas shouldn't do any harm.

On Tue, May 21, 2019 at 2:36 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Oh! Now I understand - you didn't even get an error message! I didn't understand that. I read over the code, apparently I on purpose wrote this code to be more error tolerant than the standard csv parser I use. You're right, this was a bug or very close to one. I hope it's fixed now. 0.5.26

On Mon, May 20, 2019 at 8:17 PM Matt Speir notifications@github.com wrote:

I think a better error message or some warning during the cbBuild process would be good. During the cbBuild process right now, there are no complaints about the quickGenes file.

I mean if I go back to the quickGenes file with that broken line in it, I can still see the issue: https://hgwdev.gi.ucsc.edu/~mspeir/cb_GSE84465_v3/?ds=Quake_Glioblastoma_GSE84465

Data:

/hive/users/mspeir/cellbrowserTest/quakeGlio_GSE84465/cbScanpyTests/cbScanpyOut_quakeGlio

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matthewspeir commented 5 years ago

Have you pushed this new version yet? I'm still seeing the old 'undefined' behavior on 0.5.26. No rush if you haven't pushed it out yet, just trying to make sure I keep up with closing issues that should be closed.

maximilianh commented 5 years ago

I somehow must have lost this change, no idea what happened. I've added it again and the descriptions show up. Many thanks for checking!

https://cells.ucsc.edu/dev/?ds=quake-gbm&gene=EGFR

On Wed, May 22, 2019 at 11:44 PM Matt Speir notifications@github.com wrote:

Have you pushed this new version yet? I'm still seeing the old 'undefined' behavior on 0.5.26. No rush if you haven't pushed it out yet, just trying to make sure I keep up with closing issues that should be closed.

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matthewspeir commented 5 years ago

Looking good. I was able to build a cell browser using the weird files and the gene descriptions still displayed.

Thanks!