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Update Incremental Load authored by Henke, Elisa's avatar Henke, Elisa
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Incremental-Load.md
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...@@ -20,7 +20,7 @@ The following sections provide an overview of the data flow and processing of re ...@@ -20,7 +20,7 @@ The following sections provide an overview of the data flow and processing of re
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When a Patient resource is read in, the job first checks whether this Patient resource is marked as 'deleted'. If so, this Patient record in OMOP CDM and all other records referenced to this will be delted. If not, the job checks whether this Patient resource already exists in OMOP CDM. This is done in the PERSON table using `fhir_logical_id` or `fhir_identifier`. If the Patient resource already exists in OMOP CDM, an update will take place in OMOP CDM based on the corresponding `person_id`. If the Patient resource does not exist in OMOP CDM, it will be written to OMOP CDM as a new resource. When a Patient resource is read in, the job first checks whether this Patient resource is marked as 'deleted'. If so, this Patient record in OMOP CDM and all other records referenced to this will be delted. If not, the job checks whether this Patient resource already exists in OMOP CDM. This is done in the PERSON table using `fhir_logical_id` or `fhir_identifier`. If the Patient resource already exists in OMOP CDM, an update will take place in OMOP CDM based on the corresponding `person_id`. If the Patient resource does not exist in OMOP CDM, it will be written to OMOP CDM as a new resource.
![inkrementellesLaden-Patient](uploads/77f47e4e66bd89a56a20589273e43ec6/inkrementellesLaden-Patient.png) ![inkrementellesLaden-Patient](uploads/df39ac051b2e0b4ed8661fbfd4089ce7/inkrementellesLaden-Patient.png)
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...@@ -35,7 +35,7 @@ When an Encounter resource is read in, the job first checks whether this Encount ...@@ -35,7 +35,7 @@ When an Encounter resource is read in, the job first checks whether this Encount
Next, the job checks if the Encounter resource already exists in OMOP CDM. This is done in the VISIT_OCCURRENCE table using `fhir_logical_id` or `fhir_identifier`. If the Encounter resource does not exist in OMOP CDM, it will be written to OMOP CDM as a new resource. If the Encounter resource already exists in OMOP CDM, an update will take place in OMOP CDM based on the corresponding `visit_occurrence_id`. Next, the job checks if the Encounter resource already exists in OMOP CDM. This is done in the VISIT_OCCURRENCE table using `fhir_logical_id` or `fhir_identifier`. If the Encounter resource does not exist in OMOP CDM, it will be written to OMOP CDM as a new resource. If the Encounter resource already exists in OMOP CDM, an update will take place in OMOP CDM based on the corresponding `visit_occurrence_id`.
![inkrementellesLaden-Encounter](uploads/01a6ed9adef20ab02ef195b0fc05c808/inkrementellesLaden-Encounter.png) ![inkrementellesLaden-Encounter](uploads/a0e34018ceb4052f63f46083578cb006/inkrementellesLaden-Encounter.png)
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...@@ -59,7 +59,7 @@ Next, it checks whether the referenced Medication resource already exists in OMO ...@@ -59,7 +59,7 @@ Next, it checks whether the referenced Medication resource already exists in OMO
If the referenced Medication resource is not yet available in OMOP CDM, the Medication reference of the MedicationAdministration/MedicationStatement resource is set as `drug_source_value` in DRUG_EXPOSURE. After all resources have been processed, post-processing takes place. During a next incremental loading, the referenced Medication resource is searched in the MEDICATION_ID_MAP table using the Medication reference in `drug_source_value`. If this Medication resource exists in OMOP CDM, an update in DRUG_EXPOSURE takes place. If the referenced Medication resource is not yet available in OMOP CDM, the Medication reference of the MedicationAdministration/MedicationStatement resource is set as `drug_source_value` in DRUG_EXPOSURE. After all resources have been processed, post-processing takes place. During a next incremental loading, the referenced Medication resource is searched in the MEDICATION_ID_MAP table using the Medication reference in `drug_source_value`. If this Medication resource exists in OMOP CDM, an update in DRUG_EXPOSURE takes place.
![inkrementellesLaden-Medication](uploads/c09f5ef17bc8c1e280eb641d11cf835c/inkrementellesLaden-Medication.png) ![inkrementellesLaden-Medication](uploads/a82c647fe5004faefab31978d4e31d5e/inkrementellesLaden-Medication.png)
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...@@ -74,7 +74,7 @@ When an Encounter/Procedure/Observation/MedicationAdministration/MedicationState ...@@ -74,7 +74,7 @@ When an Encounter/Procedure/Observation/MedicationAdministration/MedicationState
The job checks whether the referenced Patient resource already exists in OMOP CDM. This is done in PERSON and table using `fhir_logical_id` or `fhir_identifier`. If the referenced Patient resource is not available in OMOP CDM, the read Encounter/Procedure/Observation/MedicationAdministration/MedicationStatement/Condition resource is skipped. If the referenced Patient resource already exists in OMOP CDM, the existing `person_id` will be used. After this step, the further processing of the read resource is done analog to bulk load. The job checks whether the referenced Patient resource already exists in OMOP CDM. This is done in PERSON and table using `fhir_logical_id` or `fhir_identifier`. If the referenced Patient resource is not available in OMOP CDM, the read Encounter/Procedure/Observation/MedicationAdministration/MedicationStatement/Condition resource is skipped. If the referenced Patient resource already exists in OMOP CDM, the existing `person_id` will be used. After this step, the further processing of the read resource is done analog to bulk load.
![inkrementellesLaden-Others](uploads/ade06d6eddcdbb70c4314382a5ff0526/inkrementellesLaden-Others.png) ![inkrementellesLaden-Others](uploads/5d43c97e8c0c8606c0ca32573de21b61/inkrementellesLaden-Others.png)
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