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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 41 forks source link

cbUpgrade errors (0.5.49 -> current develop branch) #153

Closed ljpearlman closed 2 years ago

ljpearlman commented 4 years ago

I'd previously installed 0.5.49, and when trying to upgrade, I got this:

cbUpgrade --code -o /var/www/html/demo/cellbrowser
INFO:root:dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported.
INFO:root:Not using dataset hierarchies: no need to rebuild dataset list
INFO:root:Copying js, css and img files to /var/www/html/demo/cellbrowser
Traceback (most recent call last):
  File "/home/laura/.conda/envs/cellbrowser/bin/cbUpgrade", line 11, in <module>
    load_entry_point('cellbrowser==0.7.1.post0.dev22', 'console_scripts', 'cbUpgrade')()
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4789, in cbUpgradeCli
    cbUpgrade(outDir, doCode=options.addCode, devMode=options.devMode, port=options.port)
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4773, in cbUpgrade
    makeIndexHtml(webDir, outDir, devMode=devMode)
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4718, in makeIndexHtml
    md5 = md5WithPython(join(outDir, "dataset.json"))
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 3324, in md5WithPython
    with open(fname, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/var/www/html/demo/cellbrowser/dataset.json'

Also, there's a typo in the help output for cbUpgrade:

Usage: cbUpgrade [options] outDir - update the list of datasets in the output directory, optionally updating the javascript code

but the output directory is specified with the -o option (which is documented later in the help), not as a positional argument.

maximilianh commented 4 years ago

Thanks for the typo!

But are you sure that you have run cbBuild before to convert this dataset ? cbUpgrade does not convert, it only updates the dataset.json files...

On Mon 16 Dec 2019 at 23:02, ljpearlman notifications@github.com wrote:

I'd previously installed 0.5.49, and when trying to upgrade, I got this:

cbUpgrade --code -o /var/www/html/demo/cellbrowser INFO:root:dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported. INFO:root:Not using dataset hierarchies: no need to rebuild dataset list INFO:root:Copying js, css and img files to /var/www/html/demo/cellbrowser Traceback (most recent call last): File "/home/laura/.conda/envs/cellbrowser/bin/cbUpgrade", line 11, in load_entry_point('cellbrowser==0.7.1.post0.dev22', 'console_scripts', 'cbUpgrade')() File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4789, in cbUpgradeCli cbUpgrade(outDir, doCode=options.addCode, devMode=options.devMode, port=options.port) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4773, in cbUpgrade makeIndexHtml(webDir, outDir, devMode=devMode) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4718, in makeIndexHtml md5 = md5WithPython(join(outDir, "dataset.json")) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 3324, in md5WithPython with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/var/www/html/demo/cellbrowser/dataset.json'

Also, there's a typo in the help output for cbUpgrade:

Usage: cbUpgrade [options] outDir - update the list of datasets in the output directory, optionally updating the javascript code

but the output directory is specified with the -o option (which is documented later in the help), not as a positional argument.

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maximilianh commented 4 years ago

Hi @ljpearlman, just wondering if I've misunderstood something. But it looks to me like the dataset.json is not there, which suggests that the dataset was never built.

It may be confusing, but right now we have two different commands: cbBuild, to build the dataset to the output directory and which is documented quite a bit. And cbUpgrade, which we have documented only in the context of dataset hierarchies. chUpgrade recreates the dataset structure, the dataset.json files, but they have to exist already. There is also cbUpgrade --code which we haven't documented at all and only tell people who need to upgrade their code.

(cbUpgrade was changed recently to not automatically upgrade the code anymore, to avoid that someone accidentally overwrites their own code that they need. Now the tool name makes a little bit less sense and we could rename the tool to something that better reflects the fact that it links datasets together by default....)

On Wed, Dec 18, 2019 at 12:41 AM Maximilian Haeussler maximilianh@gmail.com wrote:

Thanks for the typo!

But are you sure that you have run cbBuild before to convert this dataset ? cbUpgrade does not convert, it only updates the dataset.json files...

On Mon 16 Dec 2019 at 23:02, ljpearlman notifications@github.com wrote:

I'd previously installed 0.5.49, and when trying to upgrade, I got this:

cbUpgrade --code -o /var/www/html/demo/cellbrowser INFO:root:dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported. INFO:root:Not using dataset hierarchies: no need to rebuild dataset list INFO:root:Copying js, css and img files to /var/www/html/demo/cellbrowser Traceback (most recent call last): File "/home/laura/.conda/envs/cellbrowser/bin/cbUpgrade", line 11, in load_entry_point('cellbrowser==0.7.1.post0.dev22', 'console_scripts', 'cbUpgrade')() File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4789, in cbUpgradeCli cbUpgrade(outDir, doCode=options.addCode, devMode=options.devMode, port=options.port) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4773, in cbUpgrade makeIndexHtml(webDir, outDir, devMode=devMode) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4718, in makeIndexHtml md5 = md5WithPython(join(outDir, "dataset.json")) File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 3324, in md5WithPython with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/var/www/html/demo/cellbrowser/dataset.json'

Also, there's a typo in the help output for cbUpgrade:

Usage: cbUpgrade [options] outDir - update the list of datasets in the output directory, optionally updating the javascript code

but the output directory is specified with the -o option (which is documented later in the help), not as a positional argument.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

ljpearlman commented 4 years ago

There are dataset.json files for the individual datasets, but it seems to be looking for a top-level dataset.json file.

rbk-staging::laura[~] ls /var/www/html/demo/cellbrowser/
16-2D54  16-2D5A  css  ext  img  index.html  index.html.tmp  js
rbk-staging::laura[~] ls /var/www/html/demo/cellbrowser/16-2D5A
16-2D5A.thumb.png     desc.json        exprMatrix.json    meta.index
cellbrowser.json.bak  discretMat.bin   exprMatrix.tsv.gz  meta.tsv
coords                discretMat.json  markers            Seurat_pca.coords.tsv.gz
dataset.json          exprMatrix.bin   metaFields         Seurat_tsne.coords.tsv.gz

cbupgrade -code gives me a similar error:

(cellbrowser) rbk-staging::laura[~] cbUpgrade --code -o /var/www/html/demo/cellbrowser
INFO:root:dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported.
INFO:root:Not using dataset hierarchies: no need to rebuild dataset list
INFO:root:Copying js, css and img files to /var/www/html/demo/cellbrowser
Traceback (most recent call last):
  File "/home/laura/.conda/envs/cellbrowser/bin/cbUpgrade", line 11, in <module>
    load_entry_point('cellbrowser==0.7.1.post0.dev22', 'console_scripts', 'cbUpgrade')()
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4789, in cbUpgradeCli
    cbUpgrade(outDir, doCode=options.addCode, devMode=options.devMode, port=options.port)
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4773, in cbUpgrade
    makeIndexHtml(webDir, outDir, devMode=devMode)
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 4718, in makeIndexHtml
    md5 = md5WithPython(join(outDir, "dataset.json"))
  File "/home/laura/.conda/envs/cellbrowser/lib/python3.8/site-packages/cellbrowser-0.7.1.post0.dev22-py3.8.egg/cellbrowser/cellbrowser.py", line 3324, in md5WithPython
    with open(fname, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/var/www/html/demo/cellbrowser/dataset.json'
matthewspeir commented 3 years ago

Hi, @ljpearlman! Just going through some old issues. I apologize for not getting back to you. Is this still a problem?