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Fix incorrect R syntax #861

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Merged
bbimber merged 2 commits into from
Nov 20, 2024
Merged

Fix incorrect R syntax #861

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4936018
Fix incorrect R syntax
bbimber Nov 15, 2024
a559935
Add format to line number logging
bbimber Nov 15, 2024
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2 changes: 1 addition & 1 deletion ehr/resources/pipeline/install.r
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@
##

#installs required packages for populateKinship.r
install.packages("kinship2", "Rlabkey", "getopt", "Matrix", "pedigree", dependencies=TRUE);
install.packages(c("kinship2", "Rlabkey", "getopt", "Matrix", "pedigree"), dependencies=TRUE);
6 changes: 3 additions & 3 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java
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Expand Up @@ -306,13 +306,13 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())

if (lineNum % 250000 == 0)
{
log.info("imported " + lineNum + " rows");
log.info("imported " + String.format("%,d", lineNum) + " rows");
}
}

stmt.executeBatch();
transaction.commit();
log.info("Inserted " + lineNum + " rows into ehr.kinship");
log.info("Inserted " + String.format("%,d", lineNum) + " rows into ehr.kinship");
}
}
catch (RuntimeSQLException | SQLException | IOException e)
Expand Down Expand Up @@ -705,7 +705,7 @@ private static void processInbreeding(Container c, User u, File pipelineDir, Log

transaction.commit();
}
log.info("Inserted " + lineNum + " rows into inbreeding coefficients table");
log.info("Inserted " + String.format("%,d", lineNum) + " rows into inbreeding coefficients table");

}
catch (DuplicateKeyException | SQLException | IOException | QueryUpdateServiceException e)
Expand Down