├── .gitignore ├── CDMDataMaps ├── ACT2OMOP │ ├── ACT i2b2 ETL Quick Reference version ACT_SHRINE_ONTOLOGY_2018-1214.pdf │ ├── DRAFT i2b2 ACT 2.0 to OMOP 5.3.1 Mappings_Updated_June012020.xlsx │ ├── DRAFT i2b2 ACT 2.0 to OMOP 5.3.1 Mappings_Updated_June042020.xlsx │ ├── DRAFT i2b2 ACT 2.0 to OMOP 5.3.1 Mappings_Updated_June112020.xlsx │ ├── DRAFT i2b2 ACT 2.0 to OMOP 5.3.1 Mappings_Updated_June172020.xlsx │ ├── README.md │ └── act_omop_icd10cm.zip ├── DRAFT - CDMs to OMOP VSs Mapping (WIP-2020-05-28).xlsx ├── DRAFT - CDMs to OMOP VSs Mapping (WIP-2020-06-03).xlsx ├── DRAFT - CDMs to OMOP VSs Mapping (WIP-2020-06-03)_KK review_vF.xlsx ├── DRAFT OMOP to FHIR mappings 2021-09-23.xlsx ├── OMOP2OMOP │ └── README.md ├── PCORNet2OMOP │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (1).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (2).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (3).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (4).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (5).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (6).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (7).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings (7-changes).xlsx │ ├── DRAFT PCORNET 5.1 to OMOP 5.3.1 Mappings.xlsx │ └── README.md ├── READM.md └── TrinetX2OMOP │ ├── DRAFT TriNetX to OMOP 5.3.1 Mappings_Updated_03Jun2020.xlsx │ ├── DRAFT TriNetX to OMOP 5.3.1 Mappings_Updated_05June2020.xlsx │ ├── DRAFT TriNetX to OMOP 5.3.1 Mappings_Updated_23June2020.xlsx │ ├── DRAFT TriNetX to OMOP 5.3.1 Mappings_Updated_29May2020.xlsx │ ├── README.md │ └── test.txt ├── Data-Quality ├── DataQualityDashboard.md ├── N3C DQ Gates discussion #2 8MAY2020.pdf ├── N3C Data Quality Gates #3 11May20.pdf ├── N3C Data Quality Gates Series Kick-off 5May20.pdf ├── N3C_OHDSI_DQD_Example.xlsx ├── N3C_OHDSI_DQD_JHU.xlsx └── README ├── DataIntegrity └── README.md ├── DataSources ├── ACT │ ├── ACTDDL.sql │ ├── CRC_Design.pdf │ ├── README.md │ └── _readme_source.txt ├── PCORNet │ ├── 2018-12-05-PCORnet-Common-Data-Model-v4dot1-parseable.xlsx │ ├── PCORnet-Common-Data-Model-v51-2019_09_12(exported).docx │ ├── PCORnet-Common-Data-Model-v51-2019_09_12(exported).xlsx │ ├── PCORnet-Common-Data-Model-v51-2019_09_12.pdf │ ├── PCORnet_CDM_ValueSet_ReferenceFile_v1.5.xlsx │ ├── PCORnet_CDM_ValueSet_ReferenceFile_v1.6-2019_07_16.xlsx │ ├── README.md │ └── _readme_source.txt └── TriNetX │ ├── README.md │ ├── TriNetXResearchDataDictionaryMay2020.pdf │ ├── TriNetX_data_extract_dictionary_trinetx.xlsx │ ├── TrinetX Model.xlsx │ ├── TrinetX_FakeData │ ├── chemo_lines.csv │ ├── cohort_details.csv │ ├── dataset_details.csv │ ├── diagnosis.csv │ ├── encounter.csv │ ├── genomic.csv │ ├── lab_result.csv │ ├── medication.csv │ ├── oncology_treatment.csv │ ├── patient.csv │ ├── patient_cohort.csv │ └── procedure.csv │ ├── _readme_source.txt │ └── data_extract_sample_trinetx_12May20.xlsx ├── ETLProcess ├── Proposed Adeptia Workflow.md ├── README.md ├── pipeline_logic │ └── README.md ├── scripts │ ├── BUILD_P2O_CODE_XWALK.sql │ ├── Build_P2O_CODE_XWALK.pls │ ├── Deprecated │ │ ├── V_P2O_CONDITION_CODE_XWALK.sql │ │ ├── V_P2O_DEATH_CAUSE_CODE_XWALK.sql │ │ ├── V_P2O_DIAGNOSIS_CODE_XWALK.sql │ │ ├── V_P2O_DISPENSING_CODE_XWALK.sql │ │ ├── V_P2O_LAB_RESULT_CM_CODE_XWALK.sql │ │ ├── V_P2O_MED_ADMIN_CODE_XWALK.sql │ │ ├── V_P2O_OBSCLIN_CODE_XWALK.sql │ │ ├── V_P2O_OBS_GEN_CODE_XWALK.sql │ │ ├── V_P2O_PRESCRIBING_CODE_XWALK.sql │ │ └── V_P2O_PROCEDURE_CODE_XWALK.sql │ ├── DomainMap │ │ ├── SP_DM_OMOP_CARE_SITE.sql │ │ ├── sp_dm_i2b2Act_observation.sql │ │ ├── sp_dm_i2b2act_care_site.sql │ │ ├── sp_dm_i2b2act_condition_era.sql │ │ ├── sp_dm_i2b2act_patient.sql │ │ ├── sp_dm_i2b2act_provider.sql │ │ ├── sp_dm_i2b2act_visit.sql │ │ ├── sp_dm_omop_condition_occurr.sql │ │ ├── sp_dm_omop_death.sql │ │ ├── sp_dm_omop_device_exposure.sql │ │ ├── sp_dm_omop_drug_era.sql │ │ ├── sp_dm_omop_drug_exposure.sql │ │ ├── sp_dm_omop_location.sql │ │ ├── sp_dm_omop_measurement.sql │ │ ├── sp_dm_omop_observation.sql │ │ ├── sp_dm_omop_observation_period.sql │ │ ├── sp_dm_omop_payer_plan_period.sql │ │ ├── sp_dm_omop_person.sql │ │ ├── sp_dm_omop_procedure_occurr.sql │ │ ├── sp_dm_omop_provider.sql │ │ ├── sp_dm_omop_specimen.sql │ │ ├── sp_dm_omop_visit_occurrence.sql │ │ ├── sp_dm_pcornet_condition.sql │ │ ├── sp_dm_pcornet_death.sql │ │ ├── sp_dm_pcornet_death_cause.sql │ │ ├── sp_dm_pcornet_demographic.sql │ │ ├── sp_dm_pcornet_diagnosis.sql │ │ ├── sp_dm_pcornet_dispensing.sql │ │ ├── sp_dm_pcornet_encounter.sql │ │ ├── sp_dm_pcornet_immunization.sql │ │ ├── sp_dm_pcornet_lab_result_cm.sql │ │ ├── sp_dm_pcornet_lds_address_hist.sql │ │ ├── sp_dm_pcornet_med_admin.sql │ │ ├── sp_dm_pcornet_obs_clin.sql │ │ ├── sp_dm_pcornet_obs_gen.sql │ │ ├── sp_dm_pcornet_prescribing.sql │ │ ├── sp_dm_pcornet_pro_cm.sql │ │ ├── sp_dm_pcornet_procedures.sql │ │ ├── sp_dm_pcornet_provider.sql │ │ └── sp_dm_pcornet_vital.sql │ ├── SP_A2O_SRC_OBSERVATION_FACT.sql │ ├── SP_A2O_SRC_PATIENT_DIMENSION.sql │ ├── SP_A2O_SRC_VISIT_DIMENSION.sql │ ├── SP_P2O_SRC_CONDITION.sql │ ├── SP_P2O_SRC_DEATH.sql │ ├── SP_P2O_SRC_DEATH_CAUSE.sql │ ├── SP_P2O_SRC_DEMOGRAPHIC.sql │ ├── SP_P2O_SRC_DIAGNOSIS.sql │ ├── SP_P2O_SRC_DISPENSING.sql │ ├── SP_P2O_SRC_ENCOUNTER.sql │ ├── SP_P2O_SRC_IMMUNIZATION.sql │ ├── SP_P2O_SRC_LAB_RESULT_CM.sql │ ├── SP_P2O_SRC_LDS_ADDRESS_HISTORY.sql │ ├── SP_P2O_SRC_MED_ADMIN.sql │ ├── SP_P2O_SRC_OBS_CLIN.sql │ ├── SP_P2O_SRC_OBS_GEN.sql │ ├── SP_P2O_SRC_PRESCRIBING.sql │ ├── SP_P2O_SRC_PROCEDURES.sql │ ├── SP_P2O_SRC_PROVIDER.sql │ ├── SP_P2O_SRC_PRO_CM.sql │ ├── SP_P2O_SRC_VITAL.sql │ ├── V_P2O_LAB_RESULT_CM_CODE_XWALK.sql │ ├── V_P2O_PROCEDURE_CODE_XWALK.sql │ ├── a2o_term_xwalk.sql │ ├── adeptia │ │ ├── PythonScript.py │ │ └── README.md │ ├── build_a2o_code_xwalk.sql │ ├── build_t2o_code_xwalk.sql │ ├── dataload │ │ ├── SP_LD_INST2DS_CARE_SITE.sql │ │ ├── SP_LD_INST2DS_CONDITION_ERA.sql │ │ ├── SP_LD_INST2DS_CONDITION_OCCURR.sql │ │ ├── SP_LD_INST2DS_DEATH.sql │ │ ├── SP_LD_INST2DS_DEVICE_EXPOSURE.sql │ │ ├── SP_LD_INST2DS_DOSE_ERA.sql │ │ ├── SP_LD_INST2DS_DRUG_ERA.sql │ │ ├── SP_LD_INST2DS_DRUG_EXPOSURE.sql │ │ ├── SP_LD_INST2DS_LOCATION.sql │ │ ├── SP_LD_INST2DS_MEASUREMENT.sql │ │ ├── SP_LD_INST2DS_OBSERVATION.sql │ │ ├── SP_LD_INST2DS_OBSERVATION_PD.sql │ │ ├── SP_LD_INST2DS_PAYER_PLAN_PD.sql │ │ ├── SP_LD_INST2DS_PERSON.sql │ │ ├── SP_LD_INST2DS_PROCEDURE_OCCURR.sql │ │ ├── SP_LD_INST2DS_PROVIDER.sql │ │ ├── SP_LD_INST2DS_SPECIMEN.sql │ │ ├── SP_LD_INST2DS_VISIT_OCCURRENCE.sql │ │ ├── SP_LD_ST2INST_CARE_SITE.sql │ │ ├── SP_LD_ST2INST_CONDITION_ERA.sql │ │ ├── SP_LD_ST2INST_CONDITION_OCCURR.sql │ │ ├── SP_LD_ST2INST_DEATH.sql │ │ ├── SP_LD_ST2INST_DEVICE_EXPOSURE.sql │ │ ├── SP_LD_ST2INST_DOSE_ERA.sql │ │ ├── SP_LD_ST2INST_DRUG_ERA.sql │ │ ├── SP_LD_ST2INST_DRUG_EXPOSURE.sql │ │ ├── SP_LD_ST2INST_LOCATION.sql │ │ ├── SP_LD_ST2INST_MEASUREMENT.sql │ │ ├── SP_LD_ST2INST_OBSERVATION.sql │ │ ├── SP_LD_ST2INST_OBSERVATION_PD.sql │ │ ├── SP_LD_ST2INST_PAYER_PLAN_PD.sql │ │ ├── SP_LD_ST2INST_PERSON.sql │ │ ├── SP_LD_ST2INST_PROCEDURE_OCCURR.sql │ │ ├── SP_LD_ST2INST_PROVIDER.sql │ │ ├── SP_LD_ST2INST_SPECIMEN.sql │ │ └── SP_LD_ST2INST_VISIT_OCCURRENCE.sql │ ├── ethnicity_xwalk.sql │ ├── export │ │ ├── a2o_term_xwalk_export.tsv │ │ ├── deprecated │ │ │ ├── p2o_term_xwalk_export_09222020.tsv │ │ │ └── p2o_term_xwalk_export_101420_tsv.tsv │ │ └── t2o_term_xwalk_export.tsv │ ├── gender_xwalk.sql │ ├── generate_n3c_domain_id.sql │ ├── n3c_Ingested_data_table_count.sql │ ├── n3c_ddl.txt │ ├── n3c_dih_datacount_result.sql │ ├── n3c_domain_map.sql │ ├── n3c_manifest.sql │ ├── n3c_omop_person_clean.sql │ ├── n3c_xwalk.sql │ ├── n3c_xwalk_mapping.sql │ ├── p2o_admitting_source_xwalk.sql │ ├── p2o_death_term_xwalk.sql │ ├── p2o_demo_term_xwalk.sql │ ├── p2o_discharge_status_xwalk.sql │ ├── p2o_dispense_source_xwalk.sql │ ├── p2o_dispense_src_xwalk.sql │ ├── p2o_facility_type_xwalk.sql │ ├── p2o_medadmin_term_xwalk.sql │ ├── p2o_term_xwalk.sql │ ├── p2o_term_xwalk_v1.sql │ ├── p2o_vital_term_xwalk.sql │ ├── race_xwalk.sql │ ├── sp_st_trinetx_medication.sql │ ├── sp_t2o_src_diagnosis.sql │ ├── sp_t2o_src_encounter.sql │ ├── sp_t2o_src_medication.sql │ ├── sp_t2o_src_patient.sql │ ├── sp_t2o_src_procedure.sql │ ├── status.sql │ ├── t2o_term_xwalk.sql │ ├── us_state_xwalk.sql │ ├── v_P2O_OBS_CLIN_CODE_XWALK.sql │ └── visit_xwalk.sql ├── tools │ └── loinc-covid │ │ ├── README.md │ │ ├── TestNorm │ │ ├── __pycache__ │ │ │ ├── covid19_test_norm.cpython-36.pyc │ │ │ └── utils.cpython-36.pyc │ │ ├── covid19_test_norm.py │ │ └── utils.py │ │ ├── data │ │ ├── Covid19_lexicons.csv │ │ ├── Livd_sarscov2_testkits.csv │ │ ├── Loinc_2.68_License_4.1.txt │ │ └── Loinc_sarscov2_fulllist.csv │ │ ├── docs │ │ ├── coding_rules.png │ │ └── overview.png │ │ ├── loinc_update.py │ │ ├── requirements.txt │ │ └── test.py └── vocabimport │ ├── README.md │ └── cpt4_ddl_oracle.sql ├── README.md ├── TargetCDM ├── BigQuery │ ├── OMOP CDM bigquery ddl.txt │ └── README.md ├── CodeExcerpts │ ├── CodeExcerpts_README.md │ ├── DerivedTables │ │ ├── GenerateEra.sql │ │ ├── README.md │ │ ├── TranslateSnippet.R │ │ ├── impala │ │ │ └── GenerateEra.sql │ │ ├── netezza │ │ │ └── GenerateEra.sql │ │ ├── oracle │ │ │ └── GenerateEra.sql │ │ ├── pdw │ │ │ └── GenerateEra.sql │ │ ├── postgresql │ │ │ └── GenerateEra.sql │ │ └── redshift │ │ │ └── GenerateEra.sql │ └── Vocab_Mapping.sql ├── Documentation │ └── CommonDataModel_Wiki_Files │ │ ├── ATLAS_Persistence_Window.PNG │ │ ├── Athena_download_box.png │ │ ├── Background │ │ ├── Background.md │ │ ├── Data-Model-Conventions.md │ │ ├── Design-Principles.md │ │ └── The-Role-of-the-Common-Data-Model.md │ │ ├── Frequently-Asked-Questions.md │ │ ├── Glossary-of-Terms.md │ │ ├── Home.md │ │ ├── License.md │ │ ├── Sepsis_to_SNOMED.png │ │ ├── StandardizedClinicalDataTables │ │ ├── CONDITION_OCCURRENCE.md │ │ ├── DEATH.md │ │ ├── DEVICE_EXPOSURE.md │ │ ├── DRUG_EXPOSURE.md │ │ ├── FACT_RELATIONSHIP.md │ │ ├── MEASUREMENT.md │ │ ├── NOTE.md │ │ ├── NOTE_NLP.md │ │ ├── OBSERVATION.md │ │ ├── OBSERVATION_PERIOD.md │ │ ├── PERSON.md │ │ ├── PROCEDURE_OCCURRENCE.md │ │ ├── SPECIMEN.md │ │ ├── Standardized-Clinical-Data-Tables.md │ │ ├── VISIT_DETAIL.md │ │ └── VISIT_OCCURRENCE.md │ │ ├── StandardizedDerivedElements │ │ ├── COHORT.md │ │ ├── COHORT_ATTRIBUTE.md │ │ ├── CONDITION_ERA.md │ │ ├── DOSE_ERA.md │ │ ├── DRUG_ERA.md │ │ └── Standardized-Derived-Elements.md │ │ ├── StandardizedHealthEconomicsDataTables │ │ ├── COST.md │ │ ├── PAYER_PLAN_PERIOD.md │ │ └── Standardized-Health-Economics-Data-Tables.md │ │ ├── StandardizedHealthSystemDataTables │ │ ├── CARE_SITE.md │ │ ├── LOCATION.md │ │ ├── PROVIDER.md │ │ └── Standardized-Health-System-Data-Tables.md │ │ ├── StandardizedMetadata │ │ ├── CDM_SOURCE.md │ │ ├── METADATA.md │ │ └── Standardized-Metadata.md │ │ ├── StandardizedVocabularies │ │ ├── ATTRIBUTE_DEFINITION.md │ │ ├── COHORT_DEFINITION.md │ │ ├── CONCEPT.md │ │ ├── CONCEPT_ANCESTOR.md │ │ ├── CONCEPT_CLASS.md │ │ ├── CONCEPT_RELATIONSHIP.md │ │ ├── CONCEPT_SYNONYM.md │ │ ├── DOMAIN.md │ │ ├── DRUG_STRENGTH.md │ │ ├── RELATIONSHIP.md │ │ ├── SOURCE_TO_CONCEPT_MAP.md │ │ ├── Standardized-Vocabularies.md │ │ ├── VOCABULARY.md │ │ └── vocabulary_tables.png │ │ ├── Usagi.png │ │ ├── _Footer.md │ │ ├── _Sidebar.md │ │ └── images │ │ ├── ATLAS_Persistence_Window.PNG │ │ ├── Athena_download_box.png │ │ ├── Sepsis_to_SNOMED.png │ │ ├── Usagi.png │ │ └── drugdomain.jpg ├── Impala │ ├── DataImport │ │ └── OMOP_CDM_synpuf_load_Impala.sql │ ├── OMOP CDM impala ddl.txt │ ├── README.md │ └── VocabImport │ │ └── OMOP_CDM_vocabulary_load_Impala.sql ├── LICENSE ├── Netezza │ ├── OMOP CDM netezza ddl.txt │ ├── OMOP CDM netezza primary keys.txt │ └── README.md ├── OMOP CDM v5 COVID.pdf ├── OMOP_CDM_v5.3.1 COVID.xlsx ├── OMOP_CDM_v5_3_1.csv ├── OMOP_CDM_v5_3_1.pdf ├── Oracle │ ├── OMOP CDM oracle constraints.txt │ ├── OMOP CDM oracle ddl.txt │ ├── OMOP CDM oracle indexes.txt │ ├── README.md │ └── VocabImport │ │ ├── OMOP CDM vocabulary load - Oracle.bat │ │ ├── concept.ctl │ │ ├── concept_ancestor.ctl │ │ ├── concept_class.ctl │ │ ├── concept_relationship.ctl │ │ ├── concept_synonym.ctl │ │ ├── domain.ctl │ │ ├── drug_strength.ctl │ │ ├── relationship.ctl │ │ └── vocabulary.ctl ├── ParallelDataWarehouse │ ├── OMOP CDM pdw constraints.txt │ ├── OMOP CDM pdw ddl.txt │ ├── OMOP CDM pdw indexes.txt │ └── README.md ├── PostgreSQL │ ├── OMOP CDM postgresql constraints.txt │ ├── OMOP CDM postgresql ddl.txt │ ├── OMOP CDM postgresql indexes.txt │ ├── README.md │ └── VocabImport │ │ └── OMOP CDM vocabulary load - PostgreSQL.sql ├── README.md ├── Redshift │ ├── OMOP CDM redshift ddl.txt │ └── README.md ├── Sql Server │ ├── OMOP CDM sql server constraints.txt │ ├── OMOP CDM sql server ddl.txt │ ├── OMOP CDM sql server indexes.txt │ ├── README.md │ └── VocabImport │ │ └── OMOP CDM vocabulary load - SQL Server.sql ├── TheBookOfOhdsi.pdf ├── Vocabularies │ ├── CONCEPT.csv │ ├── CONCEPT_ANCESTOR.csv │ └── CONCEPT_CLASS.csv └── _readme_source.txt ├── Workflows ├── AdeptiaWorkFlowMay132020_DGEdits.jpg ├── IngestionWorkFlow24June20SH&DG_dDits.jpg ├── IngestionWorkFlowJune0120_update..png ├── IngestionWorkFlowMay182020_DGEdits.jpg ├── N3C - Cloud Infra. Overview.pdf ├── N3C DI&H workflow 12x12 layout.pptx ├── N3C DQ Gates discussion 11MAY20.jpg ├── N3C DQ Gates swimlane draft 14May20.jpg ├── N3C DQ Gates swimlane draft 6Jun20.jpg ├── N3C Data Ingestion & Harmonization Workstream_20APR2020_NoPrep.vsdx └── Simple Site payload state engine 30June20.jpg ├── cms_pipeline ├── README.md ├── medicaid-logic │ ├── README.md │ ├── templateConfig.json │ ├── transforms-python │ │ ├── conda-versions.run.linux-64.lock │ │ ├── conda_recipe │ │ │ └── meta.yaml │ │ └── src │ │ │ ├── .pylintrc │ │ │ ├── cms │ │ │ ├── __init__.py │ │ │ ├── configs │ │ │ │ ├── __init__.py │ │ │ │ ├── de_base.py │ │ │ │ ├── de_dates.py │ │ │ │ ├── de_dsb.py │ │ │ │ ├── de_hh_and_spo.py │ │ │ │ ├── de_mc.py │ │ │ │ ├── de_mfp.py │ │ │ │ ├── de_wvr.py │ │ │ │ ├── full_column_list.py │ │ │ │ ├── ip.py │ │ │ │ ├── lt.py │ │ │ │ ├── ot.py │ │ │ │ └── rx.py │ │ │ ├── datasets │ │ │ │ ├── __init__.py │ │ │ │ ├── metadata │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── care_site_datasets_marking_removed.py │ │ │ │ │ ├── cms_opt_in_only.py │ │ │ │ │ ├── errors_union.py │ │ │ │ │ └── person_map.py │ │ │ │ ├── step00_unzip │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── payload_filename.py │ │ │ │ │ ├── qc_latest_unzip.py │ │ │ │ │ ├── unzip.py │ │ │ │ │ └── unzip_pecos.py │ │ │ │ ├── step01_parsed │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── parse.py │ │ │ │ │ ├── parse_pecos.py │ │ │ │ │ └── union.py │ │ │ │ ├── step02_schema_applied │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── all-datasets.py │ │ │ │ ├── step03_melted │ │ │ │ │ ├── 1_initial.py │ │ │ │ │ ├── 2_datasets.py │ │ │ │ │ ├── 2_groups.py │ │ │ │ │ ├── 3_all.py │ │ │ │ │ └── __init__.py │ │ │ │ ├── step03_prepared │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── ip_prepared.py │ │ │ │ │ ├── long_prepared.py │ │ │ │ │ ├── lt_prepared.py │ │ │ │ │ ├── ndc_rx.py │ │ │ │ │ └── ot_prepared.py │ │ │ │ ├── step05_safe │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── all-datasets.py │ │ │ │ ├── step06_schema_check │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── all-datasets.py │ │ │ │ └── step07_staging │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── all-datasets.py │ │ │ │ │ ├── cms_mapping_table.py │ │ │ │ │ └── staged_cms_mapping_table.py │ │ │ ├── pipeline.py │ │ │ ├── repo_path.py │ │ │ └── utils.py │ │ │ ├── setup.cfg │ │ │ └── setup.py │ ├── transforms-shrinkwrap.yml │ ├── transforms-sql │ │ ├── CODEMAP.md │ │ └── src │ │ │ └── main │ │ │ └── sql │ │ │ ├── cms_medicaid_place_of_visit_xwalk.sql │ │ │ ├── codemap2_omop_target_domain.sql │ │ │ ├── codemap_medicaid_xwalk.sql │ │ │ ├── medicaid_valueset_xwalk.sql │ │ │ ├── step03_5_person_prepared │ │ │ ├── .gitkeep │ │ │ ├── person_with_multiple_bday.sql │ │ │ ├── person_with_multiple_demographic_values.sql │ │ │ ├── person_with_multiple_eth_values.sql │ │ │ ├── person_with_multiple_race_values.sql │ │ │ ├── person_with_multiple_sex.sql │ │ │ └── unique_person_id_most_recent_year_most_days.sql │ │ │ ├── step03_5_visit_prepared │ │ │ ├── .gitkeep │ │ │ ├── ip_dx_long_prepared.sql │ │ │ ├── ip_prepared.sql │ │ │ ├── ip_px_long_prepared.sql │ │ │ ├── lt_dx_long_prepared.sql │ │ │ ├── lt_prepared.sql │ │ │ ├── ot_dx_long_prepared.sql │ │ │ ├── ot_hcpcs_long_prepared.sql │ │ │ ├── ot_prepared.sql │ │ │ └── rx_prepared.sql │ │ │ ├── step04_domain_mapping │ │ │ ├── care_site.sql │ │ │ ├── care_site_2_include.sql │ │ │ ├── condition_era.sql │ │ │ ├── condition_occurrence.sql │ │ │ ├── death.sql │ │ │ ├── device_exposure.sql │ │ │ ├── drug_era.sql │ │ │ ├── drug_exposure.sql │ │ │ ├── health_system.sql │ │ │ ├── location.sql │ │ │ ├── location_history.sql │ │ │ ├── location_latest.sql │ │ │ ├── lt_visit_detail_with_spans.sql │ │ │ ├── macro_visit.sql │ │ │ ├── macro_visit_check.sql │ │ │ ├── macro_visit_with_micro_visit.sql │ │ │ ├── measurement.sql │ │ │ ├── observation.sql │ │ │ ├── observation_period.sql │ │ │ ├── person.sql │ │ │ ├── procedure_occurence.sql │ │ │ ├── provider.sql │ │ │ ├── provider_ext.sql │ │ │ ├── unit_test │ │ │ │ ├── .gitkeep │ │ │ │ └── medicaid_care_site_characterization.sql │ │ │ ├── visit_detail.sql │ │ │ ├── visit_detail_folder │ │ │ │ ├── .gitkeep │ │ │ │ ├── ip_visit_detail.sql │ │ │ │ ├── lt_visit_detail.sql │ │ │ │ └── ot_visit_detail.sql │ │ │ ├── visit_occurrence.sql │ │ │ └── visit_occurrence_with_macro_visit.sql │ │ │ └── step06_5_concept_name │ │ │ ├── .gitkeep │ │ │ ├── care_site.sql │ │ │ ├── condition_era.sql │ │ │ ├── condition_occurrence.sql │ │ │ ├── death.sql │ │ │ ├── device_exposure.sql │ │ │ ├── drug_era.sql │ │ │ ├── drug_exposure.sql │ │ │ ├── health_system.sql │ │ │ ├── location.sql │ │ │ ├── measurement.sql │ │ │ ├── observation.sql │ │ │ ├── observation_period.sql │ │ │ ├── person.sql │ │ │ ├── procedure_occurrence.sql │ │ │ ├── provider.sql │ │ │ └── visit_occurrence.sql │ └── versions.properties └── medicare-logic │ ├── README.md │ ├── templateConfig.json │ ├── transforms-python │ ├── conda-versions.run.linux-64.lock │ ├── conda_recipe │ │ └── meta.yaml │ └── src │ │ ├── .pylintrc │ │ ├── cms │ │ ├── __init__.py │ │ ├── configs │ │ │ ├── __init__.py │ │ │ ├── dm.py │ │ │ ├── full_column_list.py │ │ │ ├── hh.py │ │ │ ├── hs.py │ │ │ ├── ip.py │ │ │ ├── mbsf.py │ │ │ ├── opl.py │ │ │ ├── pb.py │ │ │ ├── pde.py │ │ │ └── sn.py │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site_datasets_marking_removed.py │ │ │ │ ├── cms_opt_in_only.py │ │ │ │ ├── errors_union.py │ │ │ │ └── person_map.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filename.py │ │ │ │ ├── qc_latest_unzip.py │ │ │ │ ├── unzip_medicare.py │ │ │ │ └── unzip_provider.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── all-files.py │ │ │ │ ├── parse_mapping.py │ │ │ │ └── parse_provider.py │ │ │ ├── step02_schema_applied │ │ │ │ ├── __init__.py │ │ │ │ ├── all-datasets.py │ │ │ │ └── pprl_mapping.py │ │ │ ├── step03_melted │ │ │ │ ├── 1_initial.py │ │ │ │ ├── 2_datasets.py │ │ │ │ ├── 2_groups.py │ │ │ │ ├── 3_all.py │ │ │ │ └── __init__.py │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── diagnoses_long.py │ │ │ │ ├── dm_hcpcs.py │ │ │ │ ├── hcpscd_long.py │ │ │ │ ├── hh_diagnosis_long.py │ │ │ │ ├── hh_rev_dt.py │ │ │ │ ├── hs_diagnosis_long.py │ │ │ │ ├── ip_diagnosis_long.py │ │ │ │ ├── ip_er_visits.py │ │ │ │ ├── ip_visit.py │ │ │ │ ├── opl_diagnoses_long.py │ │ │ │ ├── opl_procedures_long.py │ │ │ │ ├── pb_diagnosis_long.py │ │ │ │ ├── prcdrcd_long.py │ │ │ │ ├── sn_diagnosis_long.py │ │ │ │ ├── sn_hcpscd_long.py │ │ │ │ └── sn_prcdrcd_long.py │ │ │ ├── step05_safe │ │ │ │ ├── __init__.py │ │ │ │ └── all-datasets.py │ │ │ ├── step06_schema_check │ │ │ │ ├── __init__.py │ │ │ │ └── all-datasets.py │ │ │ └── step07_staging │ │ │ │ ├── __init__.py │ │ │ │ ├── all-datasets.py │ │ │ │ ├── cms_care_site_mapping_table.py │ │ │ │ ├── cms_mapping_table.py │ │ │ │ └── staged_cms_mapping_table.py │ │ ├── pipeline.py │ │ ├── repo_path.py │ │ └── utils.py │ │ ├── setup.cfg │ │ └── setup.py │ ├── transforms-shrinkwrap.yml │ ├── transforms-sql │ ├── README.md │ └── src │ │ ├── CODEMAP.md │ │ └── main │ │ ├── resources │ │ └── udfs.yml │ │ └── sql │ │ ├── .gitkeep │ │ ├── cms2omop_valueset_xwalk.sql │ │ ├── cms2omop_visit_xwalk.sql │ │ ├── cms_code_xwalk.sql │ │ ├── medicare_codemap_xwalk_ut.sql │ │ ├── step04_domain_mapping │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── care_site_characterization.sql │ │ ├── care_site_link2_health_system.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── health_system.sql │ │ ├── location.sql │ │ ├── macro_visit.sql │ │ ├── macro_visit_with_micro_visit.sql │ │ ├── macrovisit_check.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ ├── step04_drug │ │ │ ├── .gitkeep │ │ │ ├── ip_hcpcs_drug.sql │ │ │ └── pb_hcpcs_drug.sql │ │ ├── step04_visits │ │ │ ├── .gitkeep │ │ │ ├── SN_README.md │ │ │ ├── ip_visit.sql │ │ │ ├── pb_visit.sql │ │ │ ├── sn_visit_detail_prelim.sql │ │ │ ├── sn_visit_spans.sql │ │ │ └── sn_visit_spans_with_detail_id.sql │ │ ├── visit_detail.sql │ │ ├── visit_occurrence.sql │ │ └── visit_occurrence_with_macro_visit.sql │ │ ├── step06_5_concept_name │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── care_site_characterization.sql │ │ ├── condition_concept_name.sql │ │ ├── condition_era_concept_name.sql │ │ ├── death.sql │ │ ├── device_exposure_concept_name.sql │ │ ├── drug_era_concept_name.sql │ │ ├── drug_exposure_concept_name.sql │ │ ├── health_system.sql │ │ ├── measurement_concept_name.sql │ │ ├── observation_concept_name.sql │ │ ├── observation_period_concept_name.sql │ │ ├── person_concept_name.sql │ │ ├── procedure_concept_name.sql │ │ ├── provider.sql │ │ ├── visit_occurrence_concept_name.sql │ │ └── visit_occurrence_concept_name_and_macrovisit.sql │ │ └── test │ │ ├── .gitkeep │ │ ├── count_visit_types_persons.sql │ │ ├── count_visit_types_persons_w_join.sql │ │ ├── count_visit_types_visits.sql │ │ └── count_visit_types_visits_from_release.sql │ └── versions.properties ├── concept_sets ├── ATLAS SARS-CoV-2 rt-PCR and AG (v4).csv ├── Atlas #818 -N3C- CovidAntibody retry (v3).csv ├── CovidAmbiguous (v1).csv ├── Inpatient or critical care visit (v1).csv └── n3c-recommended-csets-json │ ├── ATLAS SARS-CoV-2 rt-PCR and AG (v4).386776576.json │ ├── AUTOIMMUNE DISEASEIMMUNODEFICIENCY (v1).595378384.json │ ├── Body weight (LG34372-9 and SNOMED) (v3).854721978.json │ ├── CARDIOMYOPATHIES (v3).35275316.json │ ├── CEREBROVASCULAR DISEASE (v2).718894835.json │ ├── CHRONIC LUNG DISEASE ​(v11).525604750.json │ ├── CONGESTIVE HEART FAILURE (v4).754910420.json │ ├── CORONARY ARTERY DISEASE (v3).139102200.json │ ├── DEMENTIA (v2).719082190.json │ ├── DEPRESSION (v3).38249145.json │ ├── DIABETES COMPLICATED (v3).530172631.json │ ├── DIABETES COMPLICATED (v5).18918743.json │ ├── DIABETES UNCOMPLICATED (v4).939771650.json │ ├── DIABETES UNCOMPLICATED (v7).248468138.json │ ├── DOWN SYNDROME (v3).566196507.json │ ├── HEART FAILURE (v4).882775108.json │ ├── HEMIPLEGIA or PARAPLEGIA (v2).157435065.json │ ├── HIV INFECTION (v2).865749288.json │ ├── HYPERTENSION (v2).834391873.json │ ├── Height (LG34373-7 + SNOMED) (v2).186671483.json │ ├── KIDNEY DISEASE (v2).579110282.json │ ├── Kostka - ECMO (v1).415149730.json │ ├── Long COVID Clinic Visit (v1).122805878.json │ ├── Long-COVID (PASC) (v2).708775231.json │ ├── MALIGNANT CANCER (v2).585389357.json │ ├── METASTATIC SOLID TUMOR CANCERS (v4).916369077.json │ ├── MILD LIVER DISEASE (v7).590841465.json │ ├── MODERATE OR SEVERE LIVER DISEASE (v5).437957818.json │ ├── MYOCARDIAL INFARCTION (v3).933777427.json │ ├── N3C Covid Diagnosis (v1).35486128.json │ ├── NIH Systemic Corticosteroids (v3).388662809.json │ ├── O2 device (v1).729941035.json │ ├── OBESITY (v5).581513221.json │ ├── PEPTIC ULCER (v3).413781282.json │ ├── PERIPHERAL VASCULAR DISEASE (v5).817711041.json │ ├── PREGNANT (v2).106000255.json │ ├── PSYCHOSIS (v2).173373426.json │ ├── PULMONARY EMBOLISM (v1).520581935.json │ ├── RHEUMATOLOGIC DISEASE (v2).903209001.json │ ├── Remdesivir (v2).719693192.json │ ├── ResultNeg (v3).21890932.json │ ├── ResultPos (v3).754723376.json │ ├── ResultPos (v5).23400628.json │ ├── SICKLE CELL DISEASE (v2).89178604.json │ ├── SUBSTANCE USE DISORDER (v2).703574576.json │ ├── THALASSEMIA (v7).763461643.json │ ├── TOBACCO SMOKER (v2).628969102.json │ ├── TRANSPLANT OF SOLID ORGAN OR BLOOD STEM CELL (v4).881464410.json │ ├── TUBERCULOSIS (v2).578545218.json │ ├── [ICUMODS]IMV (v2).469361388.json │ └── body mass index (v2).65622096.json ├── pipeline_logic ├── README.md ├── act │ ├── README.md │ ├── python │ │ ├── act_schemas.py │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ └── transform │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_status.py │ │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── concept_dimension.py │ │ │ │ ├── metadata │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── control_map.py │ │ │ │ │ ├── data_counts_check.py │ │ │ │ │ ├── local_code_map.py │ │ │ │ │ ├── manifest.py │ │ │ │ │ ├── n3c_vocab_map.py │ │ │ │ │ └── site_data_count.py │ │ │ │ ├── observation_fact.py │ │ │ │ ├── patient_dimension.py │ │ │ │ └── visit_dimension.py │ │ │ │ ├── step02_schema_applied │ │ │ │ ├── __init__.py │ │ │ │ ├── concept_dimension.py │ │ │ │ ├── observation_fact.py │ │ │ │ ├── patient_dimension.py │ │ │ │ └── visit_dimension.py │ │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── concept_dimension.py │ │ │ │ ├── observation_fact.py │ │ │ │ ├── patient_dimension.py │ │ │ │ └── visit_dimension.py │ │ │ │ ├── step05_pk_collision_check │ │ │ │ ├── __init__.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ └── visit_occurrence.py │ │ │ │ ├── step07_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ └── visit_occurrence.py │ │ │ │ └── step08_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ ├── omop_schemas.py │ │ ├── parsing.py │ │ ├── pipeline.py │ │ ├── pkey_utils.py │ │ ├── site_specific_utils.py │ │ └── utils.py │ └── sql │ │ ├── .gitkeep │ │ ├── a2o_code_xwalk.sql │ │ ├── step04_domain_mapping │ │ ├── .gitkeep │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ └── visit_occurrence.sql │ │ └── step06_id_generation │ │ ├── .gitkeep │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ └── visit_occurrence.sql ├── omop │ ├── README.md │ ├── python │ │ ├── __init__.py │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── control_map.py │ │ │ │ ├── data_counts.py │ │ │ │ ├── data_counts_check.py │ │ │ │ └── manifest.py │ │ │ ├── payload_status.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step02_clean │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step04_id_collision_check │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step06_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ └── step07_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ ├── parsing.py │ │ ├── pipeline.py │ │ ├── schemas.py │ │ ├── site_specific_utils.py │ │ └── utils.py │ └── sql │ │ ├── .gitkeep │ │ └── transform │ │ ├── .gitkeep │ │ ├── step03_local_id_generation │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql │ │ └── step05_global_id_generation │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql ├── pcornet │ ├── README.md │ ├── python │ │ ├── __init__.py │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ └── transform │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_status.py │ │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── condition.py │ │ │ │ ├── death.py │ │ │ │ ├── death_cause.py │ │ │ │ ├── demographic.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── dispensing.py │ │ │ │ ├── encounter.py │ │ │ │ ├── immunization.py │ │ │ │ ├── lab_result_cm.py │ │ │ │ ├── lds_address_history.py │ │ │ │ ├── med_admin.py │ │ │ │ ├── metadata │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── control_map.py │ │ │ │ │ ├── data_counts_check.py │ │ │ │ │ ├── manifest.py │ │ │ │ │ └── site_data_count.py │ │ │ │ ├── obs_clin.py │ │ │ │ ├── obs_gen.py │ │ │ │ ├── prescribing.py │ │ │ │ ├── pro_cm.py │ │ │ │ ├── procedures.py │ │ │ │ ├── provider.py │ │ │ │ └── vital.py │ │ │ │ ├── step02_schema_applied │ │ │ │ ├── __init__.py │ │ │ │ ├── condition.py │ │ │ │ ├── death.py │ │ │ │ ├── death_cause.py │ │ │ │ ├── demographic.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── dispensing.py │ │ │ │ ├── encounter.py │ │ │ │ ├── immunization.py │ │ │ │ ├── lab_result_cm.py │ │ │ │ ├── lds_address_history.py │ │ │ │ ├── med_admin.py │ │ │ │ ├── obs_clin.py │ │ │ │ ├── obs_gen.py │ │ │ │ ├── prescribing.py │ │ │ │ ├── pro_cm.py │ │ │ │ ├── procedures.py │ │ │ │ ├── provider.py │ │ │ │ └── vital.py │ │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── condition.py │ │ │ │ ├── death.py │ │ │ │ ├── death_cause.py │ │ │ │ ├── demographic.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── dispensing.py │ │ │ │ ├── encounter.py │ │ │ │ ├── immunization.py │ │ │ │ ├── lab_result_cm.py │ │ │ │ ├── lds_address_history.py │ │ │ │ ├── med_admin.py │ │ │ │ ├── obs_clin.py │ │ │ │ ├── obs_gen.py │ │ │ │ ├── prescribing.py │ │ │ │ ├── pro_cm.py │ │ │ │ ├── procedures.py │ │ │ │ ├── provider.py │ │ │ │ └── vital.py │ │ │ │ ├── step05_pk_collision_check │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── payer_plan_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ │ ├── step07_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── payer_plan_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ │ └── step08_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ ├── omop_schemas.py │ │ ├── parsing.py │ │ ├── pcornet_schemas.py │ │ ├── pipeline.py │ │ ├── pkey_utils.py │ │ ├── site_specific_utils.py │ │ └── utils.py │ └── sql │ │ ├── .gitkeep │ │ ├── p2o_code_xwalk.sql │ │ ├── step04_domain_mapping │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── payer_plan_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql │ │ └── step06_id_generation │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── payer_plan_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql ├── pedsnet │ ├── python │ │ ├── __init__.py │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── control_map.py │ │ │ │ ├── data_counts.py │ │ │ │ ├── data_counts_check.py │ │ │ │ └── manifest.py │ │ │ ├── payload_status.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step02_clean │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step05_id_collision_check │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ ├── step07_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ ├── care_site.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── dose_era.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ ├── provider.py │ │ │ │ └── visit_occurrence.py │ │ │ └── step08_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ ├── parsing.py │ │ ├── pipeline.py │ │ ├── schemas.py │ │ ├── site_specific_utils.py │ │ └── utils.py │ └── sql │ │ ├── .gitkeep │ │ └── transform │ │ ├── .gitkeep │ │ ├── step04_mapping │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql │ │ └── step06_global_id_generation │ │ ├── .gitkeep │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql ├── reference_tables │ ├── TriNetX Vocab Correction Mapping Table.csv │ ├── a2o_valueset_mapping_table.csv │ ├── act_vocab_id_mapping_table.csv │ ├── ethnicity_xwalk_table.csv │ ├── gender_xwalk_table.csv │ ├── p2o_valueset_mapping_table.csv │ ├── pcornet_vocab_id_mapping_table.csv │ ├── pedsnet_visit_xwalk_table.csv │ ├── race_xwalk_table.csv │ ├── t2o_valueset_mapping_table.csv │ ├── testnorm_covid19_mapping_table.csv │ ├── visit_xwalk_mapping_table.csv │ └── visit_xwalk_table.csv ├── trinetx │ ├── README.md │ ├── python │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ └── transform │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_status.py │ │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── encounter.py │ │ │ │ ├── lab_result.py │ │ │ │ ├── medication.py │ │ │ │ ├── metadata │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── control_map.py │ │ │ │ │ ├── data_counts_check.py │ │ │ │ │ ├── manifest.py │ │ │ │ │ └── site_data_count.py │ │ │ │ ├── patient.py │ │ │ │ ├── procedure.py │ │ │ │ └── vital_signs.py │ │ │ │ ├── step02_schema_applied │ │ │ │ ├── __init__.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── encounter.py │ │ │ │ ├── lab_result.py │ │ │ │ ├── medication.py │ │ │ │ ├── patient.py │ │ │ │ ├── procedure.py │ │ │ │ └── vital_signs.py │ │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── diagnosis.py │ │ │ │ ├── encounter.py │ │ │ │ ├── lab_result.py │ │ │ │ ├── medication.py │ │ │ │ ├── patient.py │ │ │ │ ├── procedure.py │ │ │ │ └── vital_signs.py │ │ │ │ ├── step05_pk_collision_check │ │ │ │ ├── __init__.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ └── visit_occurrence.py │ │ │ │ ├── step07_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ ├── condition_era.py │ │ │ │ ├── condition_occurrence.py │ │ │ │ ├── death.py │ │ │ │ ├── device_exposure.py │ │ │ │ ├── drug_era.py │ │ │ │ ├── drug_exposure.py │ │ │ │ ├── location.py │ │ │ │ ├── measurement.py │ │ │ │ ├── observation.py │ │ │ │ ├── observation_period.py │ │ │ │ ├── person.py │ │ │ │ ├── procedure_occurrence.py │ │ │ │ └── visit_occurrence.py │ │ │ │ └── step08_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ ├── omop_schemas.py │ │ ├── parsing.py │ │ ├── pipeline.py │ │ ├── pkey_utils.py │ │ ├── site_specific_utils.py │ │ ├── trinetx_schemas.py │ │ └── utils.py │ └── sql │ │ ├── .gitkeep │ │ ├── data_counts.sql │ │ ├── step04_domain_mapping │ │ ├── .gitkeep │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ └── visit_occurrence.sql │ │ ├── step06_id_generation │ │ ├── .gitkeep │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ └── visit_occurrence.sql │ │ └── t2o_code_xwalk.sql └── v2 │ ├── README.md │ ├── act │ ├── README.md │ ├── transform-python │ │ └── src │ │ │ └── act │ │ │ ├── __init__.py │ │ │ ├── anchor │ │ │ ├── __init__.py │ │ │ ├── generate-anchor.py │ │ │ └── path.py │ │ │ ├── local_schemas.py │ │ │ ├── parsing.py │ │ │ ├── pipeline.py │ │ │ ├── pkey_utils.py │ │ │ ├── site_specific_utils.py │ │ │ └── utils.py │ └── transform-sql │ │ └── src │ │ └── main │ │ ├── a2o_code_xwalk.sql │ │ ├── sdoh_answer_code_xwalk.sql │ │ ├── sql │ │ ├── a2o_code_xwalk.sql │ │ ├── sdoh_answer_code_xwalk.sql │ │ ├── step04_domain_mapping │ │ │ ├── condition_era.sql │ │ │ ├── condition_occurrence.sql │ │ │ ├── control_map.sql │ │ │ ├── death.sql │ │ │ ├── device_exposure.sql │ │ │ ├── drug_era.sql │ │ │ ├── drug_exposure.sql │ │ │ ├── location.sql │ │ │ ├── measurement.sql │ │ │ ├── note.sql │ │ │ ├── note_nlp.sql │ │ │ ├── observation.sql │ │ │ ├── observation_period.sql │ │ │ ├── person.sql │ │ │ ├── procedure_occurrence.sql │ │ │ ├── visit_detail.sql │ │ │ ├── visit_dimension_excluded.sql │ │ │ └── visit_occurrence.sql │ │ ├── step06_id_generation │ │ │ ├── condition_era.sql │ │ │ ├── condition_occurrence.sql │ │ │ ├── control_map.sql │ │ │ ├── death.sql │ │ │ ├── device_exposure.sql │ │ │ ├── drug_era.sql │ │ │ ├── drug_exposure.sql │ │ │ ├── location.sql │ │ │ ├── measurement.sql │ │ │ ├── note.sql │ │ │ ├── note_nlp.sql │ │ │ ├── observation.sql │ │ │ ├── observation_period.sql │ │ │ ├── person.sql │ │ │ ├── procedure_occurrence.sql │ │ │ ├── visit_detail.sql │ │ │ └── visit_occurrence.sql │ │ └── vent_code_xwalk.sql │ │ └── vent_code_xwalk.sql │ ├── omop │ ├── README.md │ ├── transform-python │ │ └── myproject │ │ │ ├── __init__.py │ │ │ ├── anchor │ │ │ ├── __init__.py │ │ │ ├── generate-anchor.py │ │ │ └── path.py │ │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── control_map.py │ │ │ │ ├── data_counts_check.py │ │ │ │ ├── data_counts_filtered.py │ │ │ │ ├── manifest.py │ │ │ │ └── payload_status.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── cached_domains.py │ │ │ │ ├── metadata_files.py │ │ │ │ ├── optional_domains.py │ │ │ │ └── required_domains.py │ │ │ ├── step02_clean │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step04_id_collision_check │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step06b_pre_clean │ │ │ │ ├── 1-removed_person_ids.py │ │ │ │ ├── 2-all-domains.py │ │ │ │ └── __init__.py │ │ │ ├── step07b_clean │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step08_final_health_check │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ └── step09_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── local_schemas.py │ │ │ ├── local_utils.py │ │ │ └── pipeline.py │ └── transform-sql │ │ └── src │ │ └── main │ │ └── sql │ │ └── transform │ │ ├── step03_local_id_generation │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ │ └── step05_global_id_generation │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ ├── pcornet │ ├── README.md │ ├── transform-python │ │ └── src │ │ │ └── pcornet │ │ │ ├── __init__.py │ │ │ ├── local_schemas.py │ │ │ ├── pipeline.py │ │ │ ├── pkey_utils.py │ │ │ ├── site_specific_utils.py │ │ │ └── utils.py │ └── transform-sql │ │ └── src │ │ └── main │ │ └── sql │ │ ├── answer_code_xwalk.sql │ │ ├── p2o_code_xwalk.sql │ │ ├── step04_domain_mapping │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── payer_plan_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ │ ├── step06_id_generation │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── payer_plan_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ │ └── vent_code_xwalk.sql │ ├── pedsnet │ ├── README.md │ ├── transform-python │ │ └── src │ │ │ └── pedsnet │ │ │ ├── __init__.py │ │ │ ├── anchor │ │ │ ├── __init__.py │ │ │ ├── generate-anchor.py │ │ │ └── path.py │ │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── control_map.py │ │ │ │ ├── data_counts_check.py │ │ │ │ ├── manifest.py │ │ │ │ └── payload_status.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── metadata_datasets.py │ │ │ │ ├── optional_datasets.py │ │ │ │ └── required_datasets.py │ │ │ ├── step02_clean │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step05_id_collision_check │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step07b_pre_clean │ │ │ │ ├── 1-removed_person_ids.py │ │ │ │ ├── 2-all-domains.py │ │ │ │ └── __init__.py │ │ │ ├── step08b_clean │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step09_final_health_checks │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ └── step10_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── local_schemas.py │ │ │ ├── local_utils.py │ │ │ └── pipeline.py │ └── transform-sql │ │ └── src │ │ └── main │ │ └── sql │ │ └── transform │ │ ├── step04_mapping │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql │ │ └── step06_global_id_generation │ │ ├── care_site.sql │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── dose_era.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── provider.sql │ │ └── visit_occurrence.sql │ ├── shared-logic │ ├── README.md │ └── src │ │ ├── setup.cfg │ │ ├── setup.py │ │ └── source_cdm_utils │ │ ├── __init__.py │ │ ├── clean.py │ │ ├── collision_check.py │ │ ├── manifest.py │ │ ├── parse.py │ │ ├── person_ids.py │ │ ├── pre_clean.py │ │ ├── schema.py │ │ ├── status.py │ │ └── unzip.py │ ├── trinetx │ ├── README.md │ ├── transforms-python │ │ └── src │ │ │ └── trinetx │ │ │ ├── __init__.py │ │ │ ├── anchor │ │ │ ├── __init__.py │ │ │ ├── generate-anchor.py │ │ │ └── path.py │ │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ ├── metadata │ │ │ │ ├── __init__.py │ │ │ │ ├── control_map.py │ │ │ │ ├── data_counts_check.py │ │ │ │ ├── data_counts_filtered.py │ │ │ │ ├── manifest.py │ │ │ │ └── payload_status.py │ │ │ ├── step00_unzip │ │ │ │ ├── __init__.py │ │ │ │ ├── payload_filenames.py │ │ │ │ └── unzip.py │ │ │ ├── step01_parsed │ │ │ │ ├── __init__.py │ │ │ │ ├── cached_domains.py │ │ │ │ ├── metadata_files.py │ │ │ │ ├── optional_domains.py │ │ │ │ └── required_domains.py │ │ │ ├── step02_schema_applied │ │ │ │ ├── __init__.py │ │ │ │ ├── encounter.py │ │ │ │ └── simple_domains.py │ │ │ ├── step03_prepared │ │ │ │ ├── __init__.py │ │ │ │ ├── encounter.py │ │ │ │ └── simple_domains.py │ │ │ ├── step05_pk_collision_check │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step07b_pre_clean │ │ │ │ ├── 1-removed_person_ids.py │ │ │ │ ├── 2-all-domains.py │ │ │ │ └── __init__.py │ │ │ ├── step08b_clean │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── step09_final_health_check │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ └── step10_union_staging │ │ │ │ ├── __init__.py │ │ │ │ └── all_domains.py │ │ │ ├── local_schema.py │ │ │ ├── pipeline.py │ │ │ ├── pkey_utils.py │ │ │ ├── site_specific_utils.py │ │ │ └── utils.py │ └── transforms-sql │ │ └── src │ │ └── main │ │ └── sql │ │ ├── sdoh_answer_code_xwalk.sql │ │ ├── step04_domain_mapping │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── step04.5_deduping │ │ │ ├── observation_dupes.sql │ │ │ ├── observation_raw.sql │ │ │ ├── visit_detail_dups.sql │ │ │ └── visit_detail_raw.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ │ ├── step06_id_generation │ │ ├── condition_era.sql │ │ ├── condition_occurrence.sql │ │ ├── control_map.sql │ │ ├── death.sql │ │ ├── device_exposure.sql │ │ ├── drug_era.sql │ │ ├── drug_exposure.sql │ │ ├── location.sql │ │ ├── measurement.sql │ │ ├── note.sql │ │ ├── note_nlp.sql │ │ ├── observation.sql │ │ ├── observation_period.sql │ │ ├── person.sql │ │ ├── procedure_occurrence.sql │ │ ├── visit_detail.sql │ │ └── visit_occurrence.sql │ │ ├── t2o_code_xwalk.sql │ │ └── vent_code_xwalk.sql │ └── unit-harmonization-and-inference │ └── UHI-tool-for-sites │ ├── README.md │ ├── pipeline-code │ └── transforms-python │ │ ├── conda-versions.run.linux-64.lock │ │ ├── conda_recipe │ │ └── meta.yaml │ │ └── src │ │ ├── get_unit_inference_calculation_file_site_tool.py │ │ ├── get_unit_inference_file_site_tool.py │ │ ├── get_unit_mapping_file.py │ │ └── harmonization_pipeline.py │ └── pipeline-input │ ├── cannonical_unit_of_measure.csv │ ├── code-to-update-input │ ├── conda_recipe │ │ └── meta.yaml │ ├── conversionsLib │ │ └── unitConversions │ │ │ ├── README_edit_conversions.md │ │ │ └── conversionsDictionary.py │ ├── deprecated │ │ ├── canonical_units.py │ │ ├── conversionsDictionary.py │ │ ├── conversions_table.py │ │ └── invalid_units_table.py │ └── unit-standards │ │ ├── canonical_units.py │ │ ├── codeset_members.py │ │ ├── conversions_table.py │ │ ├── invalid_units_table.py │ │ └── utils.py │ ├── filtered_percentiles_table.xlsx │ ├── invalid_units_of_measure.csv │ └── unit_harmonization_conversion.csv └── sssom_mapping_commons └── example ├── sssom_mappings_1411icd10cm.csv ├── sssom_mappings_1507icd10cm.csv ├── sssom_mappings_1578icd10cm.csv ├── sssom_mappings_1678icd10cm.csv ├── sssom_mappings_1688icd10cm.csv ├── sssom_mappings_1726icd10cm.csv ├── sssom_mappings_1726icd10cm_a.csv ├── sssom_mappings_1726icd10cm_b.csv ├── sssom_mappings_177icd10cm.csv ├── sssom_mappings_1793icd10cm.csv ├── sssom_mappings_1798icd10cm.csv └── sssom_sample_1507icd10cm.csv /.gitignore: -------------------------------------------------------------------------------- 1 | *_local_test.py 2 | 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