4 Getting Started

This section provides users with detailed information on program setup and configuration of the master program parameters. For more information on the technical requirements for running the QA Package, please refer to section 1.2: Technical Requirements.

4.1 Program Set-up

4.1.1 Download the QA Package from Sentinel git

1. Using git, clone the QA Package from the Sentinel git repo, into a folder using the package’s RequestID: git clone https://dev.sentinelsystem.org/scm/qa/qa_package.git soc_qar_wp999_nsdp_v01.

4.1.2 Configure the Master Program

2. Open the QA Package folder.

3. Open sasprograms.

4. Open the file 00.0_scdm_data_qa_review_master_file.sas in SAS or a text editor.

5. Find the parameter QAPackage_root and populate it with the path to the directory containing the QA Package. This should be the path from which the program will be run.

6. Populate the parameter Evaluate_ETL with the path or paths to the SCDM tables to be evaluated by the QA Program Package.

7. Review the SCDM table parameters, checking to make sure the defaults match the filenames of the datasets containing each SCDM table to be evaluated. If they do not, update to match the dataset filenames.

8. Populate table parameters for any optional SCDM tables being evaluated.

9. Locate the request parameters.

10. Populate ProjID, WPType, WPID, DPID, and VerID parameters. These parameters should match the RequestID of the program package.

11. Populate the parameter ETL with the number of this data refresh.

12. If the Mother-Infant Linkage table is to be populated, set Execute_MI to Y. Otherwise, set to N or leave blank.

13. Save 00.0_scdm_data_qa_review_master_file.sas and close.

4.1.3 Configure QA Package Control Flow

14. Navigate back to the root directory of the QA Package. Then open the folder inputfiles.

15. Open control_flow.csv in a text editor.

16. For any optional SCDM tables being evaluated, change the value of execute_flag to Y.

17. Save control_flow.csv and close.

4.1.4 Running the QA Package

18. Navigate back to the QA Package root directory and open the folder sasprograms.

19. Using the method appropriate for the system the package is being run on, submit 00.0_scdm_data_qa_review_master_file.sas to the SAS system as a batch job.

4.2 Master Program Parameters

The master SAS program found in sasprograms/00.0_scdm_data_qa_review_master_file.sas contains several parameters that must be specified by the user. These include the directory containing the QA Package, project, work plan, Data Partner identifiers, and a version identifier. Table 4.1 contains detailed specifications for master program parameters.

Table 4.1: List and description of parameters to be populated for program set-up

Parameter	Details
QAPACKAGE_ROOT	Description: Location of the QA Package root directory.
	Format: Alphanumeric
	Example: /apps/socrequests/
EVALUATE_SCDM	Description: Location of staged SCDM tables under review.
	Note 1: If multiple paths are necessary, delimit with a single space
	Format: Alphanumeric
	Example: /sentinel/etl14/tables
NumSession	Description: Required. Number of parallel sessions (SAS Grid or SAS/CONNECT) that may be spawned by the master program.
	Note 1: Default is 0. Note 2: Unless the ETL has been approved for parallel sessions by Sentinel DMQA, do not change. Otherwise, the query may fail.
	Format: Numeric
	Example: 4
ENRTABLE	Description: Specifies the enrollment table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: enrollment
DEMTABLE	Description: Specifies the demographic table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: demographic
DISTABLE	Description: Specifies the dispensing table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: dispensing
ENCTABLE	Description: Specifies the encounter table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: encounter
DIATABLE	Description: Specifies the diagnosis table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: diagnosis
PROCTABLE	Description: Specifies the procedure table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: procedure
FACTABLE	Description: Specifies the facility table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: facility
PVDTABLE	Description: Specifies the provider table name. Value should exclude the .sas7bdat extension part of the file name. Default values are provided.
	Example: provider
LABTABLE	Description: Specifies the laboratory results table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: lab_results
DEATHTABLE	Description: Specifies the death table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: death
CODTABLE	Description: Specifies the cause of death table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: cause_of_death
VITTABLE	Description: Specifies the vital signs table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: vital_signs
IPHARMTABLE	Description: Specifies the inpatient pharmacy table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: ip_rx
ITRANSTABLE	Description: Specifies the inpatient transfusion table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: ip_trx
PRETABLE	Description: Specifies the prescribing table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: prescribing
PRSTABLE	Description: Specifies the patient reported measures survey table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: prs
PRRTABLE	Description: Specifies the patient reported measures response table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: prr
FEATABLE	Description: Specifies the feature engineering table name. Value should exclude the .sas7bdat extension part of the file name.
	Example: feature_engineering
PTSTOEXCLUDE	Description: Name of file, including library reference, that lists patients to be excluded from snapshot-specific output files
	Note 1: Do not alter this parameter unless instructed to do so by the Sentinel DMQA team.
	Format: Alphanumeric
	Example: PTSTOEXCLUDE = infolder.PtsToExclude
Execute_CC	Description: Parameter indicating if the Common Components module should run.
	Note 1: If left blank, parameter will default to N
	Valid Values: Y: Yes N: No
	Format: Alphanumeric
	Example: Y
_ROOT_DPLOCAL	Description: Local ETL and Phase-specific (NOT request specific) request folder root for DPLOCAL subfolder. When combined with parameters from the master program file for a specific production request, the full path(s) specific to that request are dynamically generated.
	Note 1: For most Data Partners, all root-path parameters will point to the same directory.
	Format: Alphanumeric
	Example: _ROOT_DPLOCAL = /sentinel/etl22/PhaseA/requests/
_ROOT_INPUTFILES	Description: Local ETL and Phase-specific (NOT request specific) request folder root for INPUTFILES subfolder. When combined with parameters from the master program file for a specific production request, the full path(s) specific to that request are dynamically generated.
	Note 1: For most Data Partners, all root-path parameters will point to the same directory.
	Format: Alphanumeric
	Example: _ROOT_INPUTFILES = &_ROOT_DPLOCAL
_ROOT_MSOC	Description: Local ETL and Phase-specific (NOT request specific) request folder root for MSOC subfolder. When combined with parameters from the master program file for a specific production request, the full path(s) specific to that request are dynamically generated.
	Note 1: For most Data Partners, all root-path parameters will point to the same directory.
	Format: Alphanumeric
	Example: _ROOT_MSOC = &_ROOT_DPLOCAL
_ROOT_SASPROGRAMS	Description: Local ETL and Phase-specific (NOT request specific) request folder root for SASPROGRAMS subfolder. When combined with parameters from the master program file for a specific production request, the full path(s) specific to that request are dynamically generated.
	Note 1: For most Data Partners, all root-path parameters will point to the same directory.
	Format: Alphanumeric
	Example: _ROOT_SASPROGRAMS = &_ROOT_DPLOCAL
PROJID	Description: Project identifier for internal SOC identification and tracking
	Format: Alphanumeric
	Example: soc
WPTYPE	Description: Work plan type for internal SOC identification and tracking.
	Note 1: This value is used to conditionally select the appropriate inputfiles for the distributed database type.
	Valid Values: qar: Used for package distributions aimed at Sentinel Distributed Database Data Partners qcr: Used for package distributions aimed at Rapid COVID Distributed Database Data Partners qad: Used for beta test packages
	Format: Alphanumeric
	Example: qar
WPID	Description: Work plan identifier for internal SOC identification and tracking.
	Note 1: Should follow the format wp[###]. Note 2: Should be used to uniquely identify packages distributed against given ETL
	Format: Alphanumeric
	Example: wp001
DPID	Description: Data Partner identifier for internal SOC identification and tracking.
	Format: Alphanumeric
	Example: nsdp
VERID	Description: Version identifier for internal SOC identification and tracking. Should track each re-distribution of the package (if multiple distributions are required).
	Note 1: Should follow the format v[##].
	Format: Alphanumeric
	Example: v01
ETL	Description: ETL Number for this request.
	Format: Numeric
	Example: 22
EXECUTE_MI	Description: Parameter indicating whether the Mother-Infant Identification Program should run.
	Note 1: If left blank, parameter will default to N
	Valid Values: Y: Yes N: No
	Format: Alphanumeric
	Example: Y
ZIP3	Description: Specifies whether a three or five digit ZIP code value is available.
	Valid Values: Y: Yes N: No
	Example: Y
SCDMVER	Description: Parameter indicating the version of the Sentinel Common Data Model in which the data the QA Package is to run against is formated.
	Format: Alphanumeric
	Example: 8.2.0

The following parameters are option parameters for Data Partners running a special version of the package capable of running on partitioned data. These should only be populated upon specific instructions from Sentinel Operations Center.

Table 4.2: List and description of option parameters to be populated for program set-up in a partitioned environment

Parameter	Details
_SASCMD	Description: Command used to start new SAS session.
	Note 1: Do not specify unless instructed to by SOC.
	Format: Alphanumeric
	Example: sas
_SASCONNECT	Description: Specifies if SAS/Connect can be used.
	Note 1: Do not specify unless instructed to by SOC.
	Valid Values: Y: Use SAS Connect. N: Do not use SAS Connect.
	Format: Alphanumeric
	Example: Y
_SASGRID	Description: Specifies if SAS Grid can be used.
	Note 1: Do not specify unless instructed to by SOC.
	Valid Values: Y: Use SAS Grid. N: Do not use SAS Grid.
	Format: Alphanumeric
	Example: Y
_GRIDSRV	Description: Specifies the name of the SAS Grid server if available.
	Note 1: _SASGRID must be set to Y. Note 2: Do not specify unless instructed to by SOC.
	Format: Alphanumeric
	Example: gridsrv1
_NumPartitions	Description: Specifies the number of partitions for the partitioned SCDM Tables.
	Note 1: If left blank, will default to 1. Note 2: Do not specify unless instructed to by SOC.
	Format: Numeric
	Example: 13
_PARTABLE	Description: Name of the PartitionID to PatID crosswalk table.
	Note 1: Must contain a column PatID and a column PartitionID where a unique row is PatID and Partition ID. Should be sorted by PartitionID and then PatID. Note 2: Do not specify unless instructed to by SOC.
	Format: Alphanumeric
	Example: patid2partitionid