Cleanup PC2 access log db

[GoogleCodeExporter]

Due to having logs also from older PC2 releases, when provider names were 
different, one can find that, e.g., there are two 'PANTHER' and also two 'NCI' 
data source items on the http://www.pathwaycommons.org/pc2/log/PROVIDER/stats 
page, in the drop-down combo-list. There is also "Musmusculus PROVIDER" entry 
in that list (probably was a bug at some point, not cleared).

Therefore, we have to manually (or write a script) merge those before next 
release and thereafter. 

PS:
In fact I did clean up before the v6 release, but apparently missed several db 
records.
Same problem - if we look at the test PC v7 instance at 
http://pathwaycommons.baderlab.org/log/PROVIDER/stats, but  this (log db) is no 
surprise much more messy due to it's a test one and I exported/imported/merged 
there quite a few times with less care.

Original issue reported on code.google.com by rod...@gmail.com on 22 Jan 2015 at 7:01

[GoogleCodeExporter]

Cleaned, but forgot to remove 'musmusculus' (will do on the next server 
restart)...

Original comment by rod...@gmail.com on 4 Mar 2015 at 6:23

• Changed state: Started

[IgorRodchenkov]

Well, we have to manually delete weird rows (from the LogEntity H2 table), where:

• name in ('','Pathway','Pathway Commons ','Musmusculus','formats','index.html','Pathway Commons.4.Al','Pathway Commons 2 Panther Pathway.BIOPAX.owl.gz','Pathway Commons.4.Panther Pathway.BIOPAX.owl.gz','Pathway Commons.4.musmusculus.BIOPAX.owl.gz','Pathway Commons all.BIOPAX.owl.gz','Pathway Commons homo sapiens.EXTENDED_BINARY_SIF.tsv.gz','Pathway Commons mus musculus.EXTENDED_BINARY_SIF.tsv.gz');
• name like '%*%' OR name like '%null%'
• type='FILE' and name like 'Pathway Commons.4.Musmusculus%'
• type='FILE' and name like 'Pathway Commons.4.9606%'
• type='FILE' and name like 'Pathway Commons.4.10090%'
• type='FILE' and name like 'Pathway Commons.4.homo%'
• name='OTHER' (type='FORMAT') - won't log such events anymore
• type='FILE' and name like '%homo%' (about 44 rows with count=1 or2)
• type='FILE' and name like '%all%' (just 22 rows with count=1; it's from the first PC2 release)
• type='FILE' and name like '%ambiguous%'
• type='FILE' and name like 'PathwayCommons%' (a user guessed filenames, and these were logged due to a bug...)

And do:

• update LOGENTITY set count=1 where city='Nanjing' and (date between '2014-04-10' and '2014-04-12');
• update LOGENTITY set count=2 where city='Nanjing' and type='TOTAL' and date='2014-04-10';
• update LOGENTITY set count=3 where city='Nanjing' and type='TOTAL' and date='2014-04-11'

[IgorRodchenkov]

Applied to and restarted the production server.