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No thumbnails in html report #2052

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tarhil opened this issue Sep 18, 2019 · 26 comments
Open

No thumbnails in html report #2052

tarhil opened this issue Sep 18, 2019 · 26 comments

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@tarhil
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tarhil commented Sep 18, 2019

Hi,
I just installed the latest scipion version from git on a debian stretch system.
To evaluate microscope performance I started a standard workflow of import movies, motioncor2, gctf and monitor summary.
Everything runs like a charm, however I have no thumbnails in the index.html
All thumbnail folders are empty.

Any ideas?
@azazellochg
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azazellochg commented Sep 18, 2019 •
edited

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

@tarhil
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tarhil commented Sep 18, 2019

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

Thanks for the reply, sadly eman2.3 was installed via the plugin manager.

@pconesa
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pconesa commented Sep 18, 2019

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

@tarhil
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tarhil commented Sep 18, 2019

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

Oh, that was misleading. Just wanted to make clear that eman is installed and the problem must be something else...

@pconesa
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pconesa commented Sep 19, 2019

I see....Do you see any hint in the logs of the monitor summary?

@tarhil
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tarhil commented Sep 19, 2019

no errors, seems everything ok.

@pconesa
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pconesa commented Sep 20, 2019

Do you see any log lines like:

"Generating images for mic xxxxx" ?

@tarhil
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tarhil commented Sep 20, 2019

Do you see any log lines like:

"Generating images for mic xxxxx" ?

no

@azazellochg
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azazellochg commented Sep 20, 2019 via email

@tarhil
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tarhil commented Sep 26, 2019

ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 17644
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Restart
MPI: 1
threads: 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:37:32.239072
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 20732
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Continue
MPI: 1
threads: 1
len(steps) 1 len(prevSteps) 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:40:47.504419
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
(END)

@pconesa
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pconesa commented Sep 26, 2019

Which protocols did you select in the summary monitor?

@tarhil
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tarhil commented Sep 26, 2019

I included results from import, motioncor, gctf.

@pconesa
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pconesa commented Sep 27, 2019 via email

@azazellochg
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azazellochg commented Sep 27, 2019 •
edited

@tarhil above is run.log, could you paste run.stdout which is more detailed?
Also, by no thumbnails you mean Micrographs table has no images or the whole report page has no images/plots? Maybe a screenshot? :)

@azazellochg
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azazellochg commented Sep 27, 2019 •
edited

@pconesa if I use a default browser (Konqueror) on a remote host then I have no plots/images at all - I guess JS is not enabled/working there. But in Firefox/Chrome all is ok. However, I think @tarhil has a different issue here..

@delarosatrevin
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delarosatrevin commented Sep 27, 2019 via email

@tarhil
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tarhil commented Sep 28, 2019 •
edited

@tarhil above is run.log, could you paste run.stdout which is more detailed?
Also, by no thumbnails you mean Micrographs table has no images or the whole report page has no images/plots? Maybe a screenshot? :)

scipion

@delarosatrevin
thumbnails are calculated by the original jobs (motioncor, gctf) but not copied into the monitor subfolders. Currently I am trying things on a local machine, therefore no rsync needed.

@pconesa
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pconesa commented Sep 29, 2019

Thanks @tarhil , can you confirm that the /Runs/XXXXProtMonitorSummary/extra/<PROJECT_NAME>imgXXXThumbs

Are all 3 empty?

If not the issue is around the html....otherwise we should focus on the generation of it.

@pconesa
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pconesa commented Sep 29, 2019

May be this will work:
ls /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/img*

@tarhil
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tarhil commented Sep 29, 2019

Thanks @tarhil , can you confirm that the /Runs/XXXXProtMonitorSummary/extra/<PROJECT_NAME>imgXXXThumbs

Are all 3 empty?

If not the issue is around the html....otherwise we should focus on the generation of it.

All are empty, I checked this already.

@pconesa
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pconesa commented Sep 29, 2019

Thanks again, @tarhil .....let's try to test the thumbnail generation. In a terminal type (adapt the path, please):

scipion python -c "from pyworkflow.em.convert import ImageHandler; ih = ImageHandler(); ih.computeThumbnail('/extra/data/tests/relion13_tutorial/betagal/Micrographs/Falcon_2012_06_12-16_59_12_0.mrc','/tmp/thumb2.png')"

@pconesa
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pconesa commented Sep 29, 2019

This should generate a thumbnail in a similar way as the summary protocol does. It should be at /tmp/thumb2.png

Please, replace /extra/data/tests/relion13_tutorial/betagal/Micrographs/Falcon_2012_06_12-16_59_12_0.mrc with a valid path to a micrograph. If you can use one of the mics used in the project that fails is will be better.

@tarhil
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tarhil commented Oct 17, 2019

That works

@pconesa
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pconesa commented Oct 18, 2019

thanks @tarhg I must admit this bug is hard to catch.

Is there any chance we can access your machine to debug in-situ your case? (ssh, teamviewer, VNC)

@tarhil
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tarhil commented Nov 12, 2019

sorry for the late response. At the moment unfortunately not, no remote access due to new firewall policies... I am still trying to get it.

@pconesa
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pconesa commented Jan 9, 2020

I guess this is not fixed yet, right. @tarhil
Are you able to edit some code files? to try to understand why this is failing?

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@pconesa @azazellochg @delarosatrevin @tarhil