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PEDSnet / pedsnetdcc

CLI tool for PEDSnet data coordinating center ETL tasks
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Adjust Indexes & Copy Map Id #108

Closed piglet25 closed 6 years ago

piglet25 commented 6 years ago

Adjust indexes to match new specifications.

Table Old Indexes New Indexes
adt_occurrence adt_type_concept_idadt_type_concept_namenext_adt_occurrence_idservice_concept_idservice_concept_namesitevisit_occurrence_id adt_type_concept_idperson_idservice_concept_idvisit_occurrence_idadt_datesite
care_site sitespecialty_concept_name place_of_service_concept_idspecialty_concept_idsite
condition_occurrence condition_concept_idcondition_concept_namecondition_source_concept_namecondition_start_age_in_monthscondition_status_concept_namecondition_type_concept_nameperson_idsitevisit_occurence_id condition_concept_idcondition_start_age_in_monthscondition_start_datecondition_type_concept_idperson_idsitevisit_occurrence_idcondition_source_valuecondition_concept_name
drug_exposure dose_unit_concept_namedrug_concept_iddrug_concept_namedrug_exposure_start_age_in_monthsdrug_source_concept_namedrug_type_concept_nameperson_idroute_concept_namesitevisit_occurrence_id drug_concept_iddrug_type_concept_iddrug_exposure_start_age_in_monthsdrug_exposure_start_dateperson_idvisit_occurrence_iddrug_concept_name
fact_relationship domain_concept_id_1domain_concept_id_2relationship_concept_idsite fact_id_1fact_id_2relationship_concept_id
location site sitezipstate
measurement measurement_age_in_monthsmeasurement_concept_idmeasurement_concept_namemeasurement_result_age_in_monthsmeasurement_source_concept_namemeasurement_type_concept_nameoperator_concept_nameperson_idpriority_concept_namerange_high_operator_concept_namerange_low_operator_concept_namesiteunit_concept_namevalue_as_concept_namevisit_occurrence_id measurement_age_in_monthsmeasurement_concept_idmeasurement_datemeasurement_type_concept_idperson_idsitevisit_occurrence_idmeasurement_source_valuemeasurement_concept_namevalue_as_concept_idvalue_as_number
measurement_organism organism_concept_namesite organism_concept_idperson_idvisit_occurrence_idmeasurement_id
observation observation_age_in_monthsobservation_concept_idobservation_concept_nameobservation_source_concept_nameperson_idqualifier_concept_namesiteunit_concept_namevalue_as_concept_namevisit_occurrence_id observation_age_in_monthsobservation_concept_idobservation_dateperson_idsitevisit_occurrence_id
observation_period person_idperiod_type_concept_namesite observation_period_start_dateobservation_period_end_dateperson_idsite
person ethnicity_concept_nameethnicity_source_concept_namegender_concept_namegender_source_concept_namelanguage_concept_namelanguage_source_concept_namerace_concept_namerace_source_concept_namesite birth_datetimeethnicity_concept_idrace_concept_idgender_concept_idethnicity_concept_namerace_concept_namegender_concept_namesite
procedure_occurrence modifier_concept_nameperson_idprocedure_age_in_monthsprocedure_concept_idprocedure_concept_nameprocedure_source_concept_nameprocedure_type_concept_nameprovider_idsitevisit_occurrence_id person_idprocedure_age_in_monthsprocedure_concept_idprocedure_datesitevisit_occurrence_idprocedure_concept_name
provider gender_concept_namegender_source_concept_namesitespecialty_concept_namespecialty_source_concept_name specialty_concept_idsite
visit_occurrence admitting_source_concept_namedischarge_to_concept_nameperson_idsitevisit_concept_idvisit_concept_namevisit_start_age_in_monthsvisit_type_concept_name person_idcare_site_idprovider_idsitevisit_start_datevisit_concept_idvisit_start_age_in_months
visit_payer   visit_occurrence_idplan_type
vocabulary.concept concept_class_idconcept_codedomain_idvocabulary_id concept_class_idconcept_codeconcept_namestandard_conceptvocabulary_id
vocabulary.concept_ancestor ancestor_concept_iddecendant_concept_id  
vocabulary.concept_relationship relationship_id concept_id_1concept_id_2relationship_id
piglet25 commented 6 years ago

Copy Map Ids wasn't working due to the Postgres version installed on the server. No code changes needed. Postgres < 9.3 doesn't support --dbname=connection_string syntax. Updated Docker file to include newer Postgres version.