Indeed, following error occurs:
157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] "GET /visualization/trackster HTTP/1.1" 200 - "http://galaxy.bits.vib.be/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+" galaxy.webapps.galaxy.api.datasets ERROR 2013-03-19 08:30:13,722 Error in dataset API at listing contents: : Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 41, in show is_true( kwd.get( 'retry', False ) ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 814, in has_data st = summary_tree_from_file( self.converted_dataset.file_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py", line 114, in summary_tree_from_file st = cPickle.load( st_file ) EOFError
I have found the root cause I believe:
when I visualize datasets from a data library, the data is not
displayed.
Getting them from the source history gets displayed is OK Importing them from a data library in a history, and displaying in
trackster works
Thanks, Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 03/18/2013 07:14 PM, Jeremy Goecks wrote:
It's likely that the job creating the summary tree failed for some reason. Can you please look through your database for summary tree jobs and see if they have any standard out/err that could provide insight into the problem?
Thanks, J.
On Mar 15, 2013, at 9:47 AM, Joachim Jacob | VIB | wrote:
Hi all,
Since the last updata of Galaxy, I was not able anymore to view newly added tracks to existing or newly created visualisations.
In the webhandler, I have traced down this error:
193.191.128.2 - - [14/Mar/2013:11:02:13 +0200] "GET /api/datasets/407a09c0b5976b4e?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr4 HTTP/1.1" 500 - "http://galaxy.bits.vib.be/visualization/trackster?id=1ec2297821c7f2cb" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+" galaxy.webapps.galaxy.api.datasets ERROR 2013-03-14 11:03:02,409 Error in dataset API at listing contents: : Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 41, in show is_true( kwd.get( 'retry', False ) ) ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 814, in has_data st = summary_tree_from_file( self.converted_dataset.file_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py", line 114, in summary_tree_from_file st = cPickle.load( st_file ) EOFError
Thanks for any assistance,
Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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