KBaseExpression is now ready to be deployed and tested. I'll be watching the services spreadsheet to see if there is anything I need to do. I'm expecting the last of Pavel's modules to be checked into git by 8am Pacific time. We should be ready to deploy/test and move to prod after that. I'll try to get out a status report in about an hour. Miriam From: Jason Baumohl <[email protected]<mailto:[email protected]>> Date: Tuesday, February 4, 2014 1:26 AM To: Pavel Novichkov <[email protected]<mailto:[email protected]>>, Miriam Land <[email protected]<mailto:[email protected]>> Cc: Shinjae Yoo <[email protected]<mailto:[email protected]>>, "Thomas S. Brettin" <[email protected]<mailto:[email protected]>> Subject: Re: GIT PUSHED Hi Miriam, KBaseExpression is now ready to be tested. It is currently pointing to the dev database. So later we will need to change the deploy.cfg over. However in the meantime it can be tested vs the dev DB. Thanks, Jason On Mon, Feb 3, 2014 at 10:26 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: Jason, Please send a note to Miriam. Thanks, P. On Feb 3, 2014, at 10:21 PM, Jason Baumohl <[email protected]<mailto:[email protected]>> wrote: OK changes made, tested and committed. -Jason On Mon, Feb 3, 2014 at 9:45 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: host = db4.chicago.kbase.us<http://db4.chicago.kbase.us/> dbname = kbase_sapling_v3_dev user = kbase_sapselect pass = oiwn22&dmwWEe Please try and be sure that you can see expression data, thanks. P. On Feb 3, 2014, at 9:39 PM, Jason Baumohl <[email protected]<mailto:[email protected]>> wrote: Hi Pavel, Please clarify. Is there a read only account? If so what is the user name and pwd? I can put it into the deploy.cfg -Jason On Mon, Feb 3, 2014 at 9:25 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: Shinjae, We can put MySQL credentials into deploy.cfg files… it can be pointed to kbase_sapling_v3_dev on db4.chicago.kbase.us<http://db4.chicago.kbase.us/> for testing… and then deployment team will modify it and point to production CS…. What do you think? Can you do it? Jason, I think you can do the same… (actually please do it..). Let us use kbase_sapling_v3_dev on db4.chicago.kbase.us<http://db4.chicago.kbase.us/> and "read-only" user name and pwd by default... P. On Feb 3, 2014, at 7:33 PM, "Yoo, Shinjae" <[email protected]<mailto:[email protected]>> wrote: Pavel, I’m playing with dataset and one thing is odd: we lost strength
From original dataset you loaded:
{"name":"<->","dataset_id":"kb|g.3899.nds.12","properties":{},"strength":1.04554164409637,"node_id2":"kb|netnode.7691","directed":"false","user_annotations":{},"id":"kb|g.3899.nds.12.edge.12","confidence":0,"node_id1":"kb|netnode.10084”}
From networks api output:
{"id":"kb|netedge.2474","name":"is interact with","node_id1":"kb|netnode.1","node_id2":"kb|netnode.1238","directed":"false","strength":0.0,"confidence":0.0,"dataset_id":"kb|g.3899.nds.12","properties":{},"user_annotations":{}}
From database table:
mysql> select * from AssociationFeature where to_link = 'kb|g.3899.CDS.68927' limit 10; +------------------------------+---------------------+------+---------------+----------+ | from_link | to_link | rank | stoichiometry | strength | +------------------------------+---------------------+------+---------------+----------+ | kb|g.3899.nds.12.edge.93313 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.99086 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.100667 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.115777 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.121994 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.126242 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.127387 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.149415 | kb|g.3899.CDS.68927 | 2 | 0 | 0 | | kb|g.3899.nds.12.edge.163204 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | | kb|g.3899.nds.12.edge.164735 | kb|g.3899.CDS.68927 | 1 | 0 | 0 | +------------------------------+---------------------+------+---------------+----------+ 10 rows in set (0.00 sec) mysql> select * from Association where id = 'kb|g.3899.nds.12.edge.93313'; +-----------------------------+------------+-------------+-------------+------+-----+ | id | confidence | directional | description | name | url | +-----------------------------+------------+-------------+-------------+------+-----+ | kb|g.3899.nds.12.edge.93313 | 0 | 0 | | <-> | | +-----------------------------+------------+-------------+-------------+------+-----+ 1 row in set (0.00 sec) It seems we lost strength… Thanks, -SJ On Feb 3, 2014, at 9:56 PM, Shinjae Yoo <[email protected]<mailto:[email protected]>> wrote: Yup, mysql> use kbase_sapling_v3_dev; Reading table information for completion of table and column names You can turn off this feature to get a quicker startup with -A Database changed mysql> select count(*) from AssociationDataset; +----------+ | count(*) | +----------+ | 265 | +----------+ 1 row in set (0.01 sec) I could see that now… I was using v3_empty instead of v3_dev… I’m generating test cases… Thanks, -SJ On Feb 3, 2014, at 9:57 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: I just reconnected to db4.chicago.kbase.us<http://db4.chicago.kbase.us/> and kbase_sapling_v3_dev from your instance and see everything: mysql> select count(*) from AssociationDataset; +----------+ | count(*) | +----------+ | 265 | +----------+ 1 row in set (0.00 sec) Can you reproduce it? Unfortunately I thought that the data was not loaded correctly and loaded one JM's PPI dataset: kbase_sapling_v3_dev.AssociationDataset: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 kbase_sapling_v3_dev.IsDatasetFor: Records: 1 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.IsGroupingOf: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 kbase_sapling_v3_dev.Association: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 kbase_sapling_v3_dev.AssociationFeature: Records: 220 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.AssociationDetectionType: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 kbase_sapling_v3_dev.DetectedWithMethod: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 kbase_sapling_v3_dev.Publication: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 kbase_sapling_v3_dev.PublishedAssociation: Records: 110 Deleted: 0 Skipped: 110 Warnings: 110 kbase_sapling_v3_dev.Source: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 kbase_sapling_v3_dev.IsSourceForAssociationDataset: Records: 1 Deleted: 0 Skipped: 1 Warnings: 1 Most records were fortunately skipped, but for tables they are now duplicated…. So, we might have wrong data for: kb|ppid.0 P. On Feb 3, 2014, at 6:43 PM, "Yoo, Shinjae" <[email protected]<mailto:[email protected]>> wrote: Ah you directly touched base_sapling_v3_dev… I’ll change db from v3_empty to v3_dev… Thanks, -SJ On Feb 3, 2014, at 9:36 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: I do not undertand that…. Yes, I see that there are only 4 datasets… but here is the statistics of loading: Mon Feb 3 22:26:32 UTC 2014 kbase_sapling_v3_dev.AssociationDetectionType: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.DetectedWithMethod: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.Association: Records: 51099805 Deleted: 0 Skipped: 3619 Warnings: 3619 kbase_sapling_v3_dev.AssociationFeature: Records: 102313637 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.IsGroupingOf: Records: 51099805 Deleted: 0 Skipped: 3619 Warnings: 3619 kbase_sapling_v3_dev.PublishedAssociation: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.Publication: Records: 0 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.AssociationDataset: Records: 256 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.IsDatasetFor: Records: 258 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.IsSourceForAssociationDataset: Records: 256 Deleted: 0 Skipped: 0 Warnings: 0 kbase_sapling_v3_dev.Source: Records: 256 Deleted: 0 Skipped: 256 Warnings: 256 Tue Feb 4 00:41:34 UTC 2014 256 records should be loaded… not warnings, no skipping…. P. On Feb 3, 2014, at 6:21 PM, "Yoo, Shinjae" <[email protected]<mailto:[email protected]>> wrote: Pavel, mysql> select count(*) from AssociationDataset; +----------+ | count(*) | +----------+ | 4 | +----------+ 1 row in set (0.00 sec) mysql> select * from AssociationDataset limit 10; ERROR 2006 (HY000): MySQL server has gone away No connection. Trying to reconnect... Connection id: 2697 Current database: kbase_sapling_v3_empty Am I using the same database with you? Thanks, -SJ On Feb 3, 2014, at 9:11 PM, Shinjae Yoo <[email protected]<mailto:[email protected]>> wrote: Great… Thanks… I’ll test it… -SJ On Feb 3, 2014, at 9:00 PM, Pavel Novichkov <[email protected]<mailto:[email protected]>> wrote: Shinjae, All data is loaded to kbase_sapling_v3_dev. P. On Feb 3, 2014, at 1:04 PM, "Yoo, Shinjae" <[email protected]<mailto:[email protected]>> wrote: Pavel, I just pushed… Now I’m leaving for home… if you have burning questions, just call me `412-467-6860<tel:412-467-6860>’… I should be able to answer your call… Thanks, -SJ