Skip to content

Commit

Permalink
Merge branch 'master-ohdsi'
Browse files Browse the repository at this point in the history
  • Loading branch information
Maxim Moinat committed Feb 22, 2019
2 parents 93f4fea + a2c727c commit 3cebf14
Show file tree
Hide file tree
Showing 5 changed files with 3 additions and 59 deletions.
1 change: 1 addition & 0 deletions .classpath
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,5 +22,6 @@
<classpathentry kind="lib" path="lib/commons-lang-2.0.jar"/>
<classpathentry kind="lib" path="lib/RedshiftJDBC4-1.1.10.1010.jar"/>
<classpathentry kind="lib" path="lib/ojdbc7.jar"/>
<classpathentry kind="lib" path="lib/ojdbc14.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
4 changes: 2 additions & 2 deletions build.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
<jar destfile="${build.dir}/WhiteRabbit.jar">
<manifest>
<attribute name="Main-Class" value="org.ohdsi.utilities.WhiteRabbitLauncher"/>
<attribute name="Class-Path" value=". WhiteRabbit_lib/terajdbc4.jar WhiteRabbit_lib/tdgssconfig.jar WhiteRabbit_lib/ojdbc7.jar WhiteRabbit_lib/sqljdbc4.jar WhiteRabbit_lib/mysql-connector-java-5.1.37-bin.jar WhiteRabbit_lib/dom4j-1.6.1.jar WhiteRabbit_lib/poi-3.9-20121203.jar WhiteRabbit_lib/poi-excelant-3.9-20121203.jar WhiteRabbit_lib/poi-ooxml-3.9-20121203.jar WhiteRabbit_lib/poi-ooxml-schemas-3.9-20121203.jar WhiteRabbit_lib/stax-api-1.0.1.jar WhiteRabbit_lib/xmlbeans-2.3.0.jar WhiteRabbit_lib/postgresql-9.4-1201.jdbc4.jar WhiteRabbit_lib/postgresql-9.4-1201.jdbc41.jar WhiteRabbit_lib/json-io-3.0.1.jar WhiteRabbit_lib/commons-csv-1.1.jar WhiteRabbit_lib/commons-lang-2.0.jar WhiteRabbit_lib/commons-logging-1.2.jar WhiteRabbit_lib/hsqldb-2.2.5.jar WhiteRabbit_lib/jackcess-2.1.3.jar WhiteRabbit_lib/ucanaccess-3.0.3.1.jar WhiteRabbit_lib/RedshiftJDBC4-1.1.10.1010.jar"/>
<attribute name="Class-Path" value=". WhiteRabbit_lib/terajdbc4.jar WhiteRabbit_lib/tdgssconfig.jar WhiteRabbit_lib/ojdbc14.jar WhiteRabbit_lib/sqljdbc4.jar WhiteRabbit_lib/mysql-connector-java-5.1.37-bin.jar WhiteRabbit_lib/dom4j-1.6.1.jar WhiteRabbit_lib/poi-3.9-20121203.jar WhiteRabbit_lib/poi-excelant-3.9-20121203.jar WhiteRabbit_lib/poi-ooxml-3.9-20121203.jar WhiteRabbit_lib/poi-ooxml-schemas-3.9-20121203.jar WhiteRabbit_lib/stax-api-1.0.1.jar WhiteRabbit_lib/xmlbeans-2.3.0.jar WhiteRabbit_lib/postgresql-9.4-1201.jdbc4.jar WhiteRabbit_lib/postgresql-9.4-1201.jdbc41.jar WhiteRabbit_lib/json-io-3.0.1.jar WhiteRabbit_lib/commons-csv-1.1.jar WhiteRabbit_lib/commons-lang-2.0.jar WhiteRabbit_lib/commons-logging-1.2.jar WhiteRabbit_lib/hsqldb-2.2.5.jar WhiteRabbit_lib/jackcess-2.1.3.jar WhiteRabbit_lib/ucanaccess-3.0.3.1.jar WhiteRabbit_lib/RedshiftJDBC4-1.1.10.1010.jar"/>
</manifest>
<fileset dir="${build.dir}"/>
<fileset dir="${src.dir}" includes="**/*.csv,**/*.png" />
Expand All @@ -40,7 +40,7 @@
</copy>
<delete dir="${build.dir}/WhiteRabbit_lib"/>
<mkdir dir="${build.dir}/WhiteRabbit_lib"/>
<copy file="lib/ojdbc7.jar" todir="${build.dir}/WhiteRabbit_lib"/>
<copy file="lib/ojdbc14.jar" todir="${build.dir}/WhiteRabbit_lib"/>
<copy file="lib/sqljdbc4.jar" todir="${build.dir}/WhiteRabbit_lib"/>
<copy file="lib/mysql-connector-java-5.1.37-bin.jar" todir="${build.dir}/WhiteRabbit_lib"/>
<copy file="lib/dom4j-1.6.1.jar" todir="${build.dir}/WhiteRabbit_lib"/>
Expand Down
Binary file added lib/ojdbc14.jar
View file
Binary file not shown.
Binary file removed lib/ojdbc7.jar
View file
Binary file not shown.
57 changes: 0 additions & 57 deletions src/org/ohdsi/whiteRabbit/scan/SourceDataScan.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,6 @@
public class SourceDataScan {

public static int MAX_VALUES_IN_MEMORY = 100000;
// public static int MAX_VALUES_TO_REPORT = 25000;
public static int MIN_CELL_COUNT_FOR_CSV = 1000000;
public static int N_FOR_FREE_TEXT_CHECK = 1000;
public static int MIN_AVERAGE_LENGTH_FOR_FREE_TEXT = 100;
Expand All @@ -61,62 +60,6 @@ public class SourceDataScan {
private DbType dbType;
private String database;

public static void main(String[] args) {
DbSettings dbSettings = new DbSettings();
dbSettings.dataType = DbSettings.DATABASE;
dbSettings.dbType = DbType.POSTGRESQL;
dbSettings.server = "127.0.0.1/ohdsi";
dbSettings.database = "ars";
dbSettings.tables.add("drugs");
dbSettings.user = "postgres";
dbSettings.password = "";
SourceDataScan scan = new SourceDataScan();
scan.process(dbSettings, 100000, true, 5, 1000, "s:/temp/ScanReport.xlsx");

// DbSettings dbSettings = new DbSettings();
// dbSettings.dataType = DbSettings.DATABASE;
// dbSettings.dbType = DbType.ORACLE;
// dbSettings.server = "127.0.0.1/xe";
// dbSettings.database = "test";
// dbSettings.tables.add("test_table");
// dbSettings.user = "system";
// dbSettings.password = "F1r3starter";
// SourceDataScan scan = new SourceDataScan();
// scan.process(dbSettings, 1000000, "s:/data/ScanReport.xlsx");

// DbSettings dbSettings = new DbSettings();
// dbSettings.dataType = DbSettings.DATABASE;
// dbSettings.dbType = DbType.MSSQL;
// dbSettings.server = "RNDUSRDHIT04";
// dbSettings.database = "[HCUP-NIS]";
// dbSettings.tables.add("hospital");
// dbSettings.tables.add("severity");
// dbSettings.tables.add("dx_pr_grps");
// dbSettings.tables.add("core");
// SourceDataScan scan = new SourceDataScan();
// scan.process(dbSettings, 1000000, true, 25, "s:/data/ScanReport.xlsx");

// DbSettings dbSettings = new DbSettings();
// dbSettings.dataType = DbSettings.DATABASE;
// dbSettings.dbType = DbType.MYSQL;
// dbSettings.server = "127.0.0.1";
// dbSettings.database = "CDM_v4";
// dbSettings.user = "root";
// dbSettings.password = "F1r3starter";
// dbSettings.tables.add("person");
// dbSettings.tables.add("provider");
// SourceDataScan scan = new SourceDataScan();
// scan.process(dbSettings, 100000, true, 25, "c:/temp/ScanReport.xlsx");
//
// DbSettings dbSettings = new DbSettings();
// dbSettings.dataType = DbSettings.CSVFILES;
// dbSettings.delimiter = ',';
// dbSettings.tables.add("S:/Data/ARS/Simulation/DDRUG.csv");
// dbSettings.tables.add("S:/Data/ARS/Simulation/HOSP.csv");
// SourceDataScan scan = new SourceDataScan();
// scan.process(dbSettings, 100000, false, 25, "c:/temp/ScanReport.xlsx");
}

public void process(DbSettings dbSettings, int sampleSize, boolean scanValues, int minCellCount, int maxValues, String filename) {
this.sampleSize = sampleSize;
this.scanValues = scanValues;
Expand Down

0 comments on commit 3cebf14

Please sign in to comment.