search

sivarajankumar / cbio-cancer-genomics-portal

Automatically exported from code.google.com/p/cbio-cancer-genomics-portal
0 stars 0 forks source link

Data too long for column 'FUNCTIONAL_IMPACT_SCORE' #473

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
when importing 
$PORTAL_DATA_HOME/staging/public-portal/ucec/tcga/data_mutations_extended.txt

----------------------
Percentage Complete:  6%
Mem Allocated:  4,869 MB, Mem used:  4,239.102 MB, Mem free:  629.898 MB
org.mskcc.cbio.cgds.dao.DaoException: Data truncation: Data too long for column 
'FUNCTIONAL_IMPACT_SCORE' at row 1
    at org.mskcc.cbio.cgds.dao.DaoMutationEvent.addMutationEvent(DaoMutationEvent.java:92)
    at org.mskcc.cbio.cgds.dao.DaoMutationEvent.addMutation(DaoMutationEvent.java:31)
    at org.mskcc.cbio.cgds.scripts.ImportExtendedMutationData.importData(ImportExtendedMutationData.java:364)
    at org.mskcc.cbio.cgds.scripts.ImportProfileData.main(ImportProfileData.java:177)
    at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.mskcc.cbio.importer.internal.ImporterImpl.loadStagingFiles(ImporterImpl.java:283)
    at org.mskcc.cbio.importer.internal.ImporterImpl.importData(ImporterImpl.java:161)
    at org.mskcc.cbio.importer.Admin.importData(Admin.java:612)
    at org.mskcc.cbio.importer.Admin.run(Admin.java:289)
    at org.mskcc.cbio.importer.Admin.main(Admin.java:730)
Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long 
for column 'FUNCTIONAL_IMPACT_SCORE' at row 1
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3595)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3529)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1990)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2151)
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2625)
    at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2415)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2333)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2318)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:102)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:102)
    at org.mskcc.cbio.cgds.dao.DaoMutationEvent.addMutationEvent(DaoMutationEvent.java:80)
    ... 11 more
..........

Original issue reported on code.google.com by Jianjion...@gmail.com on 9 Feb 2013 at 9:12

GoogleCodeExporter commented 8 years ago 
This is probably because still we have [sent] values (issue 434) in the 
mutation assessor cache and in the MAF files.

One solution is to replace [sent] values with "NA" or empty string within the 
importer. Another solution is to update the MA cache with a newer version of 
the Mutation Assessor files. But the latest MA files still have [sent] values.

Original comment by s.onur.s...@gmail.com on 11 Feb 2013 at 7:22

GoogleCodeExporter commented 8 years ago 
Also, I realized that the FUNCTIONAL_IMPACT_SCORE field in the mutation table 
is defined as longtext, but it is defined as varchar(5) in the mutation_event 
table.

Original comment by s.onur.s...@gmail.com on 11 Feb 2013 at 8:04

GoogleCodeExporter commented 8 years ago 
ah.. right... could you fix that?

Original comment by Jianjion...@gmail.com on 11 Feb 2013 at 8:06

GoogleCodeExporter commented 8 years ago 
This issue was closed by revision 1c8eca402fe9.

Original comment by s.onur.s...@gmail.com on 11 Feb 2013 at 8:45