Re: [galaxy-dev] Issue with viz of mapped data in Trackster
OK (I see now I have posted twice the same error from the log - silly of me, sorry). First this: yes, the permissions in the data library are set so that only I and one other person can access the data library (set by one sharing role for both of us) The entries in the job table related to the summary tree converter: -- select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc; -- id |create_time |update_time | history_id | tool_id| tool_version | state | info | command_line | param_filename | runner_name | stdout | stderr | traceback | s ession_id | job_runner_name | job_runner_external_id | library_folder_id | user_id | imported | object_store_id | params | handler | exit_code --++++--+--+---+--- +-- --- ---++-+ +---+---+-- --+-++---+-+--+-++--+--- 8186 | 2013-03-19 09:22:29.165135 | 2013-03-19 09:27:44.335526 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10477.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1481.dat /m nt/galaxydb/files/013/dataset_13752.dat || | | | | 6188 | local:/// | 25218 | | 1 | f| || handler3 | 0 8185 | 2013-03-19 09:22:19.463602 | 2013-03-19 09:22:23.644461 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | new | | || | | | | 6188 | local:/// | | | 1 | f | || handler2 | 8184 | 2013-03-19 09:20:45.225881 | 2013-03-19 09:26:54.337624 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1478.dat /m nt/galaxydb/files/013/dataset_13749.dat || | | | | 6188 | local:/// | 25112 | | 1 | f| || handler1 | 0 8183 | 2013-03-19 09:20:44.865602 | 2013-03-19 09:27:19.370773 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1477.dat /m nt/galaxydb/files/013/dataset_13750.dat || | | | | 6188 | local:/// | 25113 | | 1 | f| || handler1 | 0 8163 | 2013-03-19 08:29:59.965262 | 2013-03-19 08:34:30.257029 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10457.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1475.dat /m nt/galaxydb/files/013/dataset_13719.dat Thanks, Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/19/2013 10:54 PM, Jeremy Goecks wrote: 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
Re: [galaxy-dev] Issue with viz of mapped data in Trackster
> 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 This is the error that occurs when trying to read a dataset's index. What you want to look for is the error that occurs when creating this index; you'll need to look in the database to find this error. Here's a SQL command that will look for the most recent summary tree converter jobs: -- select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc; -- Is there anything in standard out/error that would explain why the summary tree is not created? > 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 I cannot reproduce this on a clean version of galaxy-dist. One guess is library permissions may be causing a problem. Are the datasets that you want to visualize in a library (or they themselves) under restricted access? Thanks, J. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Issue with viz of mapped data in Trackster
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Issue with viz of mapped data in Trackster
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 > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Issue with viz of mapped data in Trackster
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
