I see this in my database server logs… SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I see this in my database server logs…
SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897'
looks like a simple bug to me.
But I don’t know an easy way to track it down.
Any ideas?
Brad
-- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
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I tried to do some time correlation between galaxy logs and postgres logs… postgres 2014-08-01 17:15:15.643 EDT handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error: Exit code 1 (Interval subtraction error) galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for <galaxy.model.Job object at 0x7fcbacccbb50> galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for <galaxy.model.Job object at 0x7f15fc281850> galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da ta/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages web0.log 172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:09 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262/contents/datasets/49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:20 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:29 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:37 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:46 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages tool_shed.tool_shed_registry DEBUG 2014-08-01 17:16:41,474 Loading references to tool sheds from tool_sheds_conf.xml web1.log 172.17.130.113 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:29 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:34 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:36 -0400] "GET /datasets/7423d3ce9d139cc4/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:37 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:42 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:46 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:47 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:50 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:51 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:54 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:59 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:02 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:10 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] "GET /dataset/errors?id=49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 5:18 PM, Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> wrote: Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com<mailto:Langhorst@neb.com>> wrote: I see this in my database server logs… SELECT history_dataset_association.id<http://history_dataset_association.id/> AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name<http://history_dataset_association.name/> AS history_dataset_association_name, history_dataset_association.info<http://history_dataset_association.info/> AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id<http://dataset_1.id/> AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id<http://dataset_1.id/> = history_dataset_association.dataset_id WHERE history_dataset_association.id<http://history_dataset_association.id/> = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hey Brad, So I've dug around and replicated all the requests in the web log you sent (central#default tip -- what revision are you running?), but I'm not seeing any unencoded id queries my sql logs (expected this more or less, w/ all of the requests in your web log being 200 OK's). The next guess is that it has to do with job metrics or metadata. The job itself failed, do you know why that is? What job metrics do you have enabled? And has this been a consistent issue, or you just happened to notice the error this one time? -Dannon On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I tried to do some time correlation between galaxy logs and postgres logs…
postgres 2014-08-01 17:15:15.643 EDT
handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error: Exit code 1 (Interval subtraction error) galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for <galaxy.model.Job object at 0x7fcbacccbb50> galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally
handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for <galaxy.model.Job object at 0x7f15fc281850> galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da
ta/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages
web0.log 172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:09 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262/contents/datasets/49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:20 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:29 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:37 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:46 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages tool_shed.tool_shed_registry DEBUG 2014-08-01 17:16:41,474 Loading references to tool sheds from tool_sheds_conf.xml
web1.log
172.17.130.113 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:29 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:34 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:36 -0400] "GET /datasets/7423d3ce9d139cc4/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:37 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:42 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:46 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:47 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:50 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:51 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:54 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:59 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:02 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - " http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:10 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262 HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] "GET /dataset/errors?id=49b19822485c7897 HTTP/1.0" 200 - " http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
On Aug 5, 2014, at 5:18 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request?
-Dannon
On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I see this in my database server logs…
SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897'
looks like a simple bug to me.
But I don’t know an easy way to track it down.
Any ideas?
Brad
-- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
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Hi Dannon: I just happened to notice this when looking for another problem. There are a few notices in the logs (pasted below). So I don’t know why the job failed… we have lots of job failures though (people learning what they’re doing) This could be related to job metrics… I do have that turned on. Interesting that it seems to be for certain datasets multiple times… not sure what that means. I’m running the most recent stable distribution. Brad grep "invalid input syntax for integer" * postgresql-Fri.log:< 2014-08-08 14:28:59.707 EDT >ERROR: invalid input syntax for integer: "49972967cbdd31bf" at character 2721 postgresql-Fri.log:< 2014-08-08 14:31:16.226 EDT >ERROR: invalid input syntax for integer: "b77d1ea36a7250f7" at character 2721 postgresql-Mon.log:< 2014-08-04 10:07:37.126 EDT >ERROR: invalid input syntax for integer: "270da62aa76049d0" at character 2721 postgresql-Mon.log:< 2014-08-04 10:47:14.995 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 10:51:51.417 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 12:37:34.711 EDT >ERROR: invalid input syntax for integer: "bd58eac042bdbc07" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:22.972 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:59.205 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:53:42.061 EDT >ERROR: invalid input syntax for integer: "83474adb31f2c058" at character 2721 postgresql-Mon.log:< 2014-08-04 17:11:35.156 EDT >ERROR: invalid input syntax for integer: "a41888ad995eb533" at character 2721 postgresql-Mon.log:< 2014-08-04 17:31:36.930 EDT >ERROR: invalid input syntax for integer: "b11c79a044405a2a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:22:03.623 EDT >ERROR: invalid input syntax for integer: "24a943e6f4a29f4a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:28:49.471 EDT >ERROR: invalid input syntax for integer: "86dfc6e4c9cce855" at character 2721 postgresql-Sat.log:< 2014-08-09 14:18:23.045 EDT >ERROR: invalid input syntax for integer: "7d3bfe1e356e7080" at character 2721 postgresql-Tue.log:< 2014-08-05 11:35:48.801 EDT >ERROR: invalid input syntax for integer: "6db657495fed0283" at character 2721 postgresql-Tue.log:< 2014-08-05 11:42:49.568 EDT >ERROR: invalid input syntax for integer: "ed396693b50513d4" at character 2721 postgresql-Tue.log:< 2014-08-05 11:59:00.467 EDT >ERROR: invalid input syntax for integer: "2a70b08a2fcb0a55" at character 2721 postgresql-Tue.log:< 2014-08-05 12:05:18.614 EDT >ERROR: invalid input syntax for integer: "76563aa4638621ff" at character 2721 postgresql-Tue.log:< 2014-08-05 13:07:40.330 EDT >ERROR: invalid input syntax for integer: "0ee316c13ff7f765" at character 2721 postgresql-Tue.log:< 2014-08-05 14:26:15.277 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 14:48:32.188 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:49:19.149 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:58:52.634 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 16:08:43.447 EDT >ERROR: invalid input syntax for integer: "fbea15ad7b6a3c1c" at character 2721 postgresql-Wed.log:< 2014-08-06 14:57:47.711 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:01:59.911 EDT >ERROR: invalid input syntax for integer: "669c887f39dcb67f" at character 2721 postgresql-Wed.log:< 2014-08-06 15:04:26.964 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:20:06.512 EDT >ERROR: invalid input syntax for integer: "dcdc4c79298533e4" at character 2721 postgresql-Wed.log:< 2014-08-06 15:22:41.220 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:25:22.955 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:16.015 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:26.196 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721 postgresql-Wed.log:< 2014-08-06 15:45:03.724 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721 -- Brad Langhorst, Ph.D. Applications and Product Development Scientist On Aug 8, 2014, at 10:40 AM, Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> wrote: Hey Brad, So I've dug around and replicated all the requests in the web log you sent (central#default tip -- what revision are you running?), but I'm not seeing any unencoded id queries my sql logs (expected this more or less, w/ all of the requests in your web log being 200 OK's). The next guess is that it has to do with job metrics or metadata. The job itself failed, do you know why that is? What job metrics do you have enabled? And has this been a consistent issue, or you just happened to notice the error this one time? -Dannon On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad <Langhorst@neb.com<mailto:Langhorst@neb.com>> wrote: I tried to do some time correlation between galaxy logs and postgres logs… postgres 2014-08-01 17:15:15.643 EDT handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error: Exit code 1 (Interval subtraction error) galaxy.jobs<http://galaxy.jobs/> DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs<http://galaxy.jobs/> INFO 2014-08-01 17:15:09,196 Collecting job metrics for <galaxy.model.Job object at 0x7fcbacccbb50> galaxy.jobs<http://galaxy.jobs/> DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs<http://galaxy.jobs/> INFO 2014-08-01 17:14:40,804 Collecting job metrics for <galaxy.model.Job object at 0x7f15fc281850> galaxy.jobs<http://galaxy.jobs/> DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da ta/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages web0.log 172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:09 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262/contents/datasets/49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:20 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:29 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:37 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:46 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages tool_shed.tool_shed_registry DEBUG 2014-08-01 17:16:41,474 Loading references to tool sheds from tool_sheds_conf.xml web1.log 172.17.130.113 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:29 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:34 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:36 -0400] "GET /datasets/7423d3ce9d139cc4/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:37 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:42 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:46 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:47 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:50 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:51 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:54 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:59 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:02 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:10 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] "GET /dataset/errors?id=49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 5:18 PM, Dannon Baker <dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>> wrote: Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com<mailto:Langhorst@neb.com>> wrote: I see this in my database server logs… SELECT history_dataset_association.id<http://history_dataset_association.id/> AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name<http://history_dataset_association.name/> AS history_dataset_association_name, history_dataset_association.info<http://history_dataset_association.info/> AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id<http://dataset_1.id/> AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id<http://dataset_1.id/> = history_dataset_association.dataset_id WHERE history_dataset_association.id<http://history_dataset_association.id/> = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Doubt this is job metrics related - fairly certain the problematic line is: https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/g... It tried to determine if a dataset id is encoded or not by hitting the database. It could possible just check the ID without hitting the database like this: https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/g... But then there is the one-in-a-billion datasets that happen to fail this second check even though they are encoded - which I think happened to Lance one time: https://trello.com/c/AzWW0dDd (in comments) So I wouldn't worry about this - it is not a bug it is not a bug per se. Hopefully both these checks for unencoded ids can just go away - everything should be encoded now? I'll create a Trello card. -John On Sat, Aug 9, 2014 at 9:50 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Hi Dannon:
I just happened to notice this when looking for another problem. There are a few notices in the logs (pasted below).
So I don’t know why the job failed… we have lots of job failures though (people learning what they’re doing)
This could be related to job metrics… I do have that turned on.
Interesting that it seems to be for certain datasets multiple times… not sure what that means.
I’m running the most recent stable distribution.
Brad grep "invalid input syntax for integer" * postgresql-Fri.log:< 2014-08-08 14:28:59.707 EDT >ERROR: invalid input syntax for integer: "49972967cbdd31bf" at character 2721 postgresql-Fri.log:< 2014-08-08 14:31:16.226 EDT >ERROR: invalid input syntax for integer: "b77d1ea36a7250f7" at character 2721 postgresql-Mon.log:< 2014-08-04 10:07:37.126 EDT >ERROR: invalid input syntax for integer: "270da62aa76049d0" at character 2721 postgresql-Mon.log:< 2014-08-04 10:47:14.995 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 10:51:51.417 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 12:37:34.711 EDT >ERROR: invalid input syntax for integer: "bd58eac042bdbc07" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:22.972 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:59.205 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:53:42.061 EDT >ERROR: invalid input syntax for integer: "83474adb31f2c058" at character 2721 postgresql-Mon.log:< 2014-08-04 17:11:35.156 EDT >ERROR: invalid input syntax for integer: "a41888ad995eb533" at character 2721 postgresql-Mon.log:< 2014-08-04 17:31:36.930 EDT >ERROR: invalid input syntax for integer: "b11c79a044405a2a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:22:03.623 EDT >ERROR: invalid input syntax for integer: "24a943e6f4a29f4a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:28:49.471 EDT >ERROR: invalid input syntax for integer: "86dfc6e4c9cce855" at character 2721 postgresql-Sat.log:< 2014-08-09 14:18:23.045 EDT >ERROR: invalid input syntax for integer: "7d3bfe1e356e7080" at character 2721 postgresql-Tue.log:< 2014-08-05 11:35:48.801 EDT >ERROR: invalid input syntax for integer: "6db657495fed0283" at character 2721 postgresql-Tue.log:< 2014-08-05 11:42:49.568 EDT >ERROR: invalid input syntax for integer: "ed396693b50513d4" at character 2721 postgresql-Tue.log:< 2014-08-05 11:59:00.467 EDT >ERROR: invalid input syntax for integer: "2a70b08a2fcb0a55" at character 2721 postgresql-Tue.log:< 2014-08-05 12:05:18.614 EDT >ERROR: invalid input syntax for integer: "76563aa4638621ff" at character 2721 postgresql-Tue.log:< 2014-08-05 13:07:40.330 EDT >ERROR: invalid input syntax for integer: "0ee316c13ff7f765" at character 2721 postgresql-Tue.log:< 2014-08-05 14:26:15.277 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 14:48:32.188 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:49:19.149 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:58:52.634 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 16:08:43.447 EDT >ERROR: invalid input syntax for integer: "fbea15ad7b6a3c1c" at character 2721 postgresql-Wed.log:< 2014-08-06 14:57:47.711 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:01:59.911 EDT >ERROR: invalid input syntax for integer: "669c887f39dcb67f" at character 2721 postgresql-Wed.log:< 2014-08-06 15:04:26.964 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:20:06.512 EDT >ERROR: invalid input syntax for integer: "dcdc4c79298533e4" at character 2721 postgresql-Wed.log:< 2014-08-06 15:22:41.220 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:25:22.955 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:16.015 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:26.196 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721 postgresql-Wed.log:< 2014-08-06 15:45:03.724 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721
-- Brad Langhorst, Ph.D. Applications and Product Development Scientist
On Aug 8, 2014, at 10:40 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Brad,
So I've dug around and replicated all the requests in the web log you sent (central#default tip -- what revision are you running?), but I'm not seeing any unencoded id queries my sql logs (expected this more or less, w/ all of the requests in your web log being 200 OK's). The next guess is that it has to do with job metrics or metadata. The job itself failed, do you know why that is? What job metrics do you have enabled? And has this been a consistent issue, or you just happened to notice the error this one time?
-Dannon
On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I tried to do some time correlation between galaxy logs and postgres logs…
postgres 2014-08-01 17:15:15.643 EDT
handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error: Exit code 1 (Interval subtraction error) galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for <galaxy.model.Job object at 0x7fcbacccbb50> galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally
handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for <galaxy.model.Job object at 0x7f15fc281850> galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da
ta/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages
web0.log 172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:09 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262/contents/datasets/49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:20 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:29 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:37 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:46 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages tool_shed.tool_shed_registry DEBUG 2014-08-01 17:16:41,474 Loading references to tool sheds from tool_sheds_conf.xml
web1.log
172.17.130.113 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:29 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:34 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:36 -0400] "GET /datasets/7423d3ce9d139cc4/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:37 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:42 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:46 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:47 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:50 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:51 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:54 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:59 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:02 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:10 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] "GET /dataset/errors?id=49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
On Aug 5, 2014, at 5:18 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request?
-Dannon
On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I see this in my database server logs…
SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897'
looks like a simple bug to me.
But I don’t know an easy way to track it down.
Any ideas?
Brad
-- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
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Hey Brad, Pretty sure John is right here; I didn't realize we even had any of those unencoded id checks still around. John, I agree they should go away at this point. -Dannon On Sun, Aug 10, 2014 at 5:13 AM, John Chilton <jmchilton@gmail.com> wrote:
Doubt this is job metrics related - fairly certain the problematic line is:
https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/g...
It tried to determine if a dataset id is encoded or not by hitting the database. It could possible just check the ID without hitting the database like this:
https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/g...
But then there is the one-in-a-billion datasets that happen to fail this second check even though they are encoded - which I think happened to Lance one time:
https://trello.com/c/AzWW0dDd (in comments)
So I wouldn't worry about this - it is not a bug it is not a bug per se. Hopefully both these checks for unencoded ids can just go away - everything should be encoded now? I'll create a Trello card.
-John
On Sat, Aug 9, 2014 at 9:50 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
Hi Dannon:
I just happened to notice this when looking for another problem. There are a few notices in the logs (pasted below).
So I don’t know why the job failed… we have lots of job failures though (people learning what they’re doing)
This could be related to job metrics… I do have that turned on.
Interesting that it seems to be for certain datasets multiple times… not sure what that means.
I’m running the most recent stable distribution.
Brad grep "invalid input syntax for integer" * postgresql-Fri.log:< 2014-08-08 14:28:59.707 EDT >ERROR: invalid input syntax for integer: "49972967cbdd31bf" at character 2721 postgresql-Fri.log:< 2014-08-08 14:31:16.226 EDT >ERROR: invalid input syntax for integer: "b77d1ea36a7250f7" at character 2721 postgresql-Mon.log:< 2014-08-04 10:07:37.126 EDT >ERROR: invalid input syntax for integer: "270da62aa76049d0" at character 2721 postgresql-Mon.log:< 2014-08-04 10:47:14.995 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 10:51:51.417 EDT >ERROR: invalid input syntax for integer: "72ad64a92e81c05e" at character 2721 postgresql-Mon.log:< 2014-08-04 12:37:34.711 EDT >ERROR: invalid input syntax for integer: "bd58eac042bdbc07" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:22.972 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:32:59.205 EDT >ERROR: invalid input syntax for integer: "196f590f5ff39e1a" at character 2721 postgresql-Mon.log:< 2014-08-04 16:53:42.061 EDT >ERROR: invalid input syntax for integer: "83474adb31f2c058" at character 2721 postgresql-Mon.log:< 2014-08-04 17:11:35.156 EDT >ERROR: invalid input syntax for integer: "a41888ad995eb533" at character 2721 postgresql-Mon.log:< 2014-08-04 17:31:36.930 EDT >ERROR: invalid input syntax for integer: "b11c79a044405a2a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:22:03.623 EDT >ERROR: invalid input syntax for integer: "24a943e6f4a29f4a" at character 2721 postgresql-Mon.log:< 2014-08-04 18:28:49.471 EDT >ERROR: invalid input syntax for integer: "86dfc6e4c9cce855" at character 2721 postgresql-Sat.log:< 2014-08-09 14:18:23.045 EDT >ERROR: invalid input syntax for integer: "7d3bfe1e356e7080" at character 2721 postgresql-Tue.log:< 2014-08-05 11:35:48.801 EDT >ERROR: invalid input syntax for integer: "6db657495fed0283" at character 2721 postgresql-Tue.log:< 2014-08-05 11:42:49.568 EDT >ERROR: invalid input syntax for integer: "ed396693b50513d4" at character 2721 postgresql-Tue.log:< 2014-08-05 11:59:00.467 EDT >ERROR: invalid input syntax for integer: "2a70b08a2fcb0a55" at character 2721 postgresql-Tue.log:< 2014-08-05 12:05:18.614 EDT >ERROR: invalid input syntax for integer: "76563aa4638621ff" at character 2721 postgresql-Tue.log:< 2014-08-05 13:07:40.330 EDT >ERROR: invalid input syntax for integer: "0ee316c13ff7f765" at character 2721 postgresql-Tue.log:< 2014-08-05 14:26:15.277 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 14:48:32.188 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:49:19.149 EDT >ERROR: invalid input syntax for integer: "86b9abc3d918bc58" at character 2721 postgresql-Tue.log:< 2014-08-05 14:58:52.634 EDT >ERROR: invalid input syntax for integer: "0bf6863f6ac1fe4c" at character 2721 postgresql-Tue.log:< 2014-08-05 16:08:43.447 EDT >ERROR: invalid input syntax for integer: "fbea15ad7b6a3c1c" at character 2721 postgresql-Wed.log:< 2014-08-06 14:57:47.711 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:01:59.911 EDT >ERROR: invalid input syntax for integer: "669c887f39dcb67f" at character 2721 postgresql-Wed.log:< 2014-08-06 15:04:26.964 EDT >ERROR: invalid input syntax for integer: "a328cf0b6432c591" at character 2721 postgresql-Wed.log:< 2014-08-06 15:20:06.512 EDT >ERROR: invalid input syntax for integer: "dcdc4c79298533e4" at character 2721 postgresql-Wed.log:< 2014-08-06 15:22:41.220 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:25:22.955 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:16.015 EDT >ERROR: invalid input syntax for integer: "054cf6e4a4f90798" at character 2721 postgresql-Wed.log:< 2014-08-06 15:44:26.196 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721 postgresql-Wed.log:< 2014-08-06 15:45:03.724 EDT >ERROR: invalid input syntax for integer: "d9e57b7bae035246" at character 2721
-- Brad Langhorst, Ph.D. Applications and Product Development Scientist
On Aug 8, 2014, at 10:40 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Brad,
So I've dug around and replicated all the requests in the web log you sent (central#default tip -- what revision are you running?), but I'm not seeing any unencoded id queries my sql logs (expected this more or less, w/ all of the requests in your web log being 200 OK's). The next guess is that it has to do with job metrics or metadata. The job itself failed, do you know why that is? What job metrics do you have enabled? And has this been a consistent issue, or you just happened to notice the error this one time?
-Dannon
On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I tried to do some time correlation between galaxy logs and postgres
logs…
postgres 2014-08-01 17:15:15.643 EDT
handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681:
Fatal
error: Exit code 1 (Interval subtraction error) galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for <galaxy.model.Job object at 0x7fcbacccbb50> galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally
handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for <galaxy.model.Job object at 0x7f15fc281850> galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib,
/mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg,
/mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
/mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da
ta/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages
web0.log 172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:09 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262/contents/datasets/49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:20 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:29 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:37 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.131.223 - - [01/Aug/2014:17:15:46 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg,
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib,
/mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg,
/mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
/mnt/galaxy/data/galaxy/sw/lib/python27.zip, /mnt/galaxy/data/galaxy/sw/lib/python2.7, /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-old, /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages tool_shed.tool_shed_registry DEBUG 2014-08-01 17:16:41,474 Loading references to tool sheds from tool_sheds_conf.xml
web1.log
172.17.130.113 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:25 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:29 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:34 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:36 -0400] "GET /datasets/7423d3ce9d139cc4/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:37 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:42 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:46 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:47 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:14:50 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:51 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:14:54 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:14:59 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0 .4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:02 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Ge cko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] "GET /api/histories/39a249c523d1b262/contents HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr ome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:04 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrom e/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:07 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.131.223 - - [01/Aug/2014:17:15:08 -0400] "GET /api/histories/11ff4619ea0fcba9/contents HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3) AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0.4 Safari/537.76.4" 172.17.130.113 - - [01/Aug/2014:17:15:10 -0400] "GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] "GET /datasets/49b19822485c7897/show_params HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] "GET /api/histories/39a249c523d1b262 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] "GET /dataset/errors?id=49b19822485c7897 HTTP/1.0" 200 - "http://galaxy.neb.com/root/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36" -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
On Aug 5, 2014, at 5:18 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request?
-Dannon
On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
I see this in my database server logs…
SELECT history_dataset_association.id AS
history_dataset_association_id,
history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1,
history_dataset_association.copied_from_library_dataset_dataset_association_id
AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897'
looks like a simple bug to me.
But I don’t know an easy way to track it down.
Any ideas?
Brad
-- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist
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participants (3)
-
Dannon Baker -
John Chilton -
Langhorst, Brad