10 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 MIL Package, please refer to section 1.2: Technical Requirements.

To run this package, users must supply the following:

A Mother-Infant Linkage Table⁶ in Sentinel Common Data Model format.⁷
A computing environment which meets the Minimum Technical Specifications

10.1 Program Set-up

Clone the QA MIL Package: git clone https://dev.sentinelsystem.org/scm/qa/qa_package.git⁸
In the QA MIL Package directory, open the file sasprograms/00.0_scdm_data_qa_review_master_file.sas
1. Edit the parameters as directed by the code comments (for detailed specifications for the master program file parameters, see Table 4.1) and then save.
When distributed, the QA MIL Package should be executed in Batch mode.

10.1.1 Master Program Parameters

The master SAS Program found in sasprograms/00.0_scdm_mil_data_qa_review_master_file.sas contains several parameters that must be specified by the user. These include the directory containing the QA MIL Package, project, work plan, Data Partner identifiers, and a version identifier. Table 10.1 contains detailed specifications for master program parameters.

Table 10.1: List and description of parameters to be populated for program set-up
Parameter	Details
EVALUATE_MIL	Description: Location of staged MIL table under review.
	Note 1: If multiple paths are necessary, delimit with a single space
	Format: Alphanumeric
	Example: `/sentinel/etl22/phaseB`
DPL_MI	Description: Path name for location of [Mother-Infant Identify] results in Phase A dplocal folder
	Note 1: Created by the QA Program Package or a standalone Mother-Infant Identification request (mir)
	Format: Alphanumeric
	Example: `/sentinel/etl22/phaseA/soc_qar_wp999_nsdp_v01/dplocal/`
_MILTABLE	Description: Specifies the mother-infant linkage table name. Value should exclude the .sas7bdat file name. Default values are provided.
	Format: Alphanumeric
	Example: `mother_infant_linkage`
SCC	Description: Path to directory containing executed Phase A Common Components (cca) associated with this ETL
	Note 1: Request ID should be included in path name Note 2: Data Partners who do not have Common Components output related to their Phase A ETL should leave this blank and populate parameters specified in Table 10.2.
	Format: Alphanumeric
	Example: `/sentinel/etl22/soc_cca_wp001_xxxx_v01/`
_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: `qmr`: Used for package distributions aimed at Sentinel Distributed Database Data Partners `qcm`: Used for package distributions aimed at Rapid COVID Distributed Database Data Partners `qmd`: Used for beta test packages
	Format: Alphanumeric
	Example: `qmr`
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.
	Note 1: : This needs to be the same ETL number for Phase A
	Format: Alphanumeric
	Example: `22`
Execute_CC	Description: Parameter indicating if the Common Components module should run.
	Note 1: If left blank, parameter will default to N Note 2: If Phase A Common Components are not available or being bypassed, this parameter should be set to `N`. If Phase A Common Components are bypassed and this parameter is set to `Y`, the program will error out during at the start of the package run and print an error the log instructing the user to provide Phase A Common Components.
	Valid Values: Y: Yes N: No
	Format: Alphanumeric
	Example: `Y`

Table 10.2 contains detailed specifications for master program parameters which need to be filled out only by Data Partners who lack Common Components Phase A output.

Table 10.2: Parameters to be populated for program set-up in the absence of Common Components
Parameter	Details
PTSTOEXCLUDE	Description: Name of file, including library reference, that lists patients to be excluded from snapshot-specific output files
	Format: Alphanumeric
	Example: `PTSTOEXCLUDE = infolder.PtsToExclude`
_DP	Description: A descriptive identifier for the Data Partner organization.
	Note 1: This should be a 3-6 UPPERCASE character abbreviation.
	Format: Alphanumeric
	Example: `NSDP`
_PACKAGEROOT	Description: Location of this request package’s root directory.
	Format: Alphanumeric
	Example: `/apps/sentinel/`
PROD_SCDM	Description: Specify the file path to the location of this ETL’s Phase A Sentinel Common Data Model (SCDM) datasets.
	Format: Alphanumeric
	Example: `/apps/sentinel/ETL22/PhaseA/SCDM`
_DP_MINDATE	Description: The overall SCDM minimum date.
	Note 1: Value can be found in QA Package output. Note 2: Defaults to `“01Jan2000”d`
	Format: SASDate (“DDMMMYYYY”d)
	Example: `“01Jan2000”d`
_DP_MAXDATE	Description: The overall SCDM maximum date.
	Note 1: Value can be found in QA Package output.
	Format: SASDate (“DDMMMYYYY”d)
	Example: `“31Jan2022”d`
_ETL_	Description: ETL number for the current Phase A production ETL.
	Format: Alphanumeric
	Example: `22`
_SCDMVER	Description: Parameter indicating the version of the Sentinel Common Data Model associated with this ETL.
	Format: Alphanumeric
	Example: `8.1.0`
ENRTABLE	Description: Specifies the enrollment table name. Value should exclude the .sas7bdat file name. Default values are provided.
ENRTABLE	Example: `enrollment`
DEMTABLE	Description: Specifies the demographic table name. Value should exclude the .sas7bdat file name. Default values are provided.
DEMTABLE	Example: `demographic`
DISTABLE	Description: Specifies the dispensing table name. Value should exclude the .sas7bdat file name. Default values are provided.
DISTABLE	Example: `dispensing`
ENCTABLE	Description: Specifies the encounter table name. Value should exclude the .sas7bdat file name. Default values are provided.
ENCTABLE	Example: `encounter`
DIATABLE	Description: Specifies the diagnosis table name. Value should exclude the .sas7bdat file name. Default values are provided.
DIATABLE	Example: `diagnosis`
PROCTABLE	Description: Specifies the procedure table name. Value should exclude the .sas7bdat file name. Default values are provided.
PROCTABLE	Example: `procedure`
FACTABLE	Description: Specifies the facility table name. Value should exclude the .sas7bdat file name. Default values are provided.
FACTABLE	Example: `facility`
PVDTABLE	Description: Specifies the provider table name. Value should exclude the .sas7bdat file name. Default values are provided.
PVDTABLE	Example: `provider`
LABTABLE	Description: Specifies the Lab Results table name. Value should exclude the .sas7bdat file name.
LABTABLE	Example: `lab_results`
DEATHTABLE	Description: Specifies the death table name. Value should exclude the .sas7bdat file name.
DEATHTABLE	Example: `death`
CODTABLE	Description: Specifies the cause of death table name. Value should exclude the .sas7bdat file name.
CODTABLE	Example: `cause_of_death`
VITTABLE	Description: Specifies the vital signs table name. Value should exclude the .sas7bdat file name.
VITTABLE	Example: `vital_signs`
IPHARMTABLE	Description: Specifies the inpatient pharmacy table name. Value should exclude the .sas7bdat file name.
IPHARMTABLE	Example: `ip_rx`
ITRANSTABLE	Description: Specifies the inpatient transfusion table name. Value should exclude the .sas7bdat file name.
ITRANSTABLE	Example: `ip_trx`
PRETABLE	Description: Specifies the prescribing table name. Value should exclude the .sas7bdat file name.
PRETABLE	Example: `prescribing`
PRSTABLE	Description: Specifies the patient reported measures survey table name. Value should exclude the .sas7bdat file name.
PRSTABLE	Example: `prs`
PRRTABLE	Description: Specifies the patient reported measures response table name. Value should exclude the .sas7bdat file name.
PRRTABLE	Example: `prr`
FEATABLE	Description: Specifies the feature engineering table name. Value should exclude the .sas7bdat extension part of the file name.
FEATABLE	Example: `feature_engineering`

All information in the Mother-Infant Linkage Table will be pulled from the Quality Assurance Program output files r01_mother_deliveries and / or r02_infants, created by a separate Mother-Infant Identification Program run as part of the core Quality Assurance Package (see Mother-Infant Identification Module). Please note that this does not include the variable MatchMethod. MatchMethod is a DP populated field that indicates the method used to match mothers and infants.↩︎
Please refer to the Sentinel Common Data Model documentation for the Mother-Infant Linkage Table specifications.↩︎
Please note that the QA MIL Package folder should correspond to the Request ID of the QA MIL Package.↩︎