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Many warnings from InMemoryDAO while reading DIP data #8

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
When parsing DIP db (human only, PSI-MI 2.5, 
ftp://dip.doe-mbi.ucla.edu/2014/mif25/Hsapi20140117.mif25.gz) 
I am getting hundreds of warnings from 
psidev.psi.mi.xml.dao.inMemory.InMemoryDAO class
(mostly about ExperimentDescription or Participant, and id - either 0, 1, or 
2....):

2014-03-24 12:53:06,308 WARN  p.p.m.x.d.i.InMemoryDAO - Attempt to overwrite an 
existing ExperimentDescription with id: 0
2014-03-24 12:53:06,308 WARN  p.p.m.x.d.i.InMemoryDAO - The new 
ExperimentDescription was different
2014-03-24 12:53:06,308 WARN  p.p.m.x.d.i.InMemoryDAO - Original : 
ExperimentDescription{id=0, names=null, 
bibref=Bibref{xref=Xref{primaryRef=DbReference{attributes=null, db='pubmed', 
dbAc='MI:0446', id='7739537', refType='identity', refTypeAc='MI:0356', 
secondary='null', version='null'}, secondaryRef=null}, attributes=null}, 
xref=Xref{primaryRef=DbReference{attributes=null, db='dip', dbAc='MI:0465', 
id='DIP-698X', refType='identity', refTypeAc='MI:0356', secondary='null', 
version='null'}, secondaryRef=null}, hostOrganisms=null, 
interactionDetectionMethod=CvType{names=Names{shortLabel='null', 
fullName='coimmunoprecipitation', aliases=null}, 
xref=Xref{primaryRef=DbReference{attributes=null, db='psi-mi', dbAc='MI:0488', 
id='MI:0019', refType='identity', refTypeAc='MI:0356', secondary='null', 
version='null'}, secondaryRef=null}}, participantIdentificationMethod=null, 
featureDetectionMethod=null, confidences=null, 
attributes=[Attribute{value='MI:0218', name='dip:evidence-for-ac', 
nameAc='null'}, Attribute{value='physical interaction', 
name='dip:evidence-for-name', nameAc='null'}, Attribute{value='dip:0002', 
name='dip:evidence-scale-ac', nameAc='null'}, Attribute{value='small scale', 
name='dip:evidence-scale-name', nameAc='null'}, Attribute{value='', 
name='dip:evidence-processing-status-ac', nameAc='null'}, Attribute{value='', 
name='dip:evidence-processing-status-name', nameAc='null'}]}

Are these norm, i.e., the parser successfully recovers from those errors; can 
we depend on the data/model after it's read or something to be fixed?

Original issue reported on code.google.com by rod...@gmail.com on 24 Mar 2014 at 9:55

GoogleCodeExporter commented 9 years ago 
Forgot to tell that I used psidev.psi.mi:psi25-xml:1.8.4 s/w library on

Linux ubuntu 3.2.0-60-generic #91-Ubuntu SMP Wed Feb 19 03:54:44 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)

Original comment by rod...@gmail.com on 24 Mar 2014 at 10:00