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| #!/bin/bash | |
| # This script attempts to build MIMIC on an Oracle instance. | |
| # You will likely need to modify it to fit your own system, for example, | |
| # you may need to change the authentication, e.g. replace '\ as SYSDBA' with 'myusername/mypassword' | |
| # The script requires sqlldr and sqlplus | |
| # Create the tables | |
| sqlplus '\ as SYSDBA' << EOF | |
| WHENEVER OSERROR EXIT 9; | |
| WHENEVER SQLERROR EXIT SQL.SQLCODE; | |
| ALTER SESSION SET CURRENT_SCHEMA = MIMICIII; | |
| @oracle_create_tables.sql | |
| EOF | |
| # Alternatively, you could specify a username/password here, and use the below snippet | |
| #db_username= | |
| #db_password= | |
| #sqlplus -s /nolog << EOF | |
| #WHENEVER OSERROR EXIT 9; | |
| #WHENEVER SQLERROR EXIT SQL.SQLCODE; | |
| #CONNECT ${db_username}/${db_password}; | |
| #@oracle_create_tables.sql | |
| #EOF | |
| # Call sqlldr to load the data | |
| sqlldr '\ as SYSDBA' control='controlfiles/admissions.ctl' log=admissions.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/callout.ctl' log=callout.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/caregivers.ctl' log=caregivers.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/chartevents.ctl' log=chartevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/cptevents.ctl' log=cptevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/d_cpt.ctl' log=d_cpt.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/d_icd_diagnoses.ctl' log=d_icd_diagnoses.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/d_icd_procedures.ctl' log=d_icd_procedures.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/d_items.ctl' log=d_items.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/d_labitems.ctl' log=d_labitems.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/datetimeevents.ctl' log=datetimeevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/diagnoses_icd.ctl' log=diagnoses_icd.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/drgcodes.ctl' log=drgcodes.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/icustays.ctl' log=icustays.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/inputevents_cv.ctl' log=inputevents_cv.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/inputevents_mv.ctl' log=inputevents_mv.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/labevents.ctl' log=labevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/microbiologyevents.ctl' log=microbiologyevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/noteevents_output.ctl' log=noteevents_output.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/outputevents.ctl' log=outputevents.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/patients.ctl' log=patients.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/prescriptions.ctl' log=prescriptions.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/procedureevents_mv.ctl' log=procedureevents_mv.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/procedures_icd.ctl' log=procedures_icd.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/services.ctl' log=services.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| sqlldr '\ as SYSDBA' control='controlfiles/transfers.ctl' log=transfers.log parallel=true direct=true multithreading=true skip_index_maintenance=true | |
| # Now, create the indexes and constraints | |
| sqlplus '\ as SYSDBA' << EOF | |
| WHENEVER OSERROR EXIT 9; | |
| WHENEVER SQLERROR EXIT SQL.SQLCODE; | |
| ALTER SESSION SET CURRENT_SCHEMA = MIMICIII; | |
| @oracle_add_indexes.sql | |
| @oracle_add_constraints.sql | |
| EOF |