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adding tests to ensure that the same field with multiple modifiers is…
… correctly handled. adding IPS query logic. Adding IPS sections. TODO: tests broken.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,241 @@ | ||
| package database | ||
|
|
||
| import ( | ||
| "context" | ||
| "github.com/fastenhealth/fasten-onprem/backend/pkg" | ||
| "github.com/fastenhealth/fasten-onprem/backend/pkg/models" | ||
| databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database" | ||
| ) | ||
|
|
||
| // GetInternationalPatientSummary will generate an IPS bundle, which can then be used to generate a IPS QR code, PDF or JSON bundle | ||
| // The IPS bundle will contain a summary of all the data in the system, including a list of all sources, and the main Patient | ||
| // See: https://github.com/fastenhealth/fasten-onprem/issues/170 | ||
| // See: https://github.com/jddamore/fhir-ips-server/blob/main/docs/Summary_Creation_Steps.md | ||
| func (gr *GormRepository) GetInternationalPatientSummary(ctx context.Context) (*models.Summary, error) { | ||
| currentUser, currentUserErr := gr.GetCurrentUser(ctx) | ||
| if currentUserErr != nil { | ||
| return nil, currentUserErr | ||
| } | ||
|
|
||
| // we want a count of all resources for this user by type | ||
| var resourceCountResults []map[string]interface{} | ||
|
|
||
| resourceTypes := databaseModel.GetAllowedResourceTypes() | ||
| for _, resourceType := range resourceTypes { | ||
| tableName, err := databaseModel.GetTableNameByResourceType(resourceType) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
| var count int64 | ||
|
|
||
| gr.QueryResources(ctx, models.QueryResource{ | ||
| Use: "", | ||
| Select: nil, | ||
| From: "", | ||
| Where: nil, | ||
| Limit: nil, | ||
| Offset: nil, | ||
| Aggregations: nil, | ||
| }) | ||
|
|
||
| result := gr.GormClient.WithContext(ctx). | ||
| Table(tableName). | ||
| Where(models.OriginBase{ | ||
| UserID: currentUser.ID, | ||
| }). | ||
| Count(&count) | ||
| if result.Error != nil { | ||
| return nil, result.Error | ||
| } | ||
| if count == 0 { | ||
| continue //don't add resource counts if the count is 0 | ||
| } | ||
| resourceCountResults = append(resourceCountResults, map[string]interface{}{ | ||
| "resource_type": resourceType, | ||
| "count": count, | ||
| }) | ||
| } | ||
|
|
||
| // we want a list of all sources (when they were last updated) | ||
| sources, err := gr.GetSources(ctx) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
|
|
||
| // we want the main Patient for each source | ||
| patients, err := gr.GetPatientForSources(ctx) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
|
|
||
| if resourceCountResults == nil { | ||
| resourceCountResults = []map[string]interface{}{} | ||
| } | ||
| summary := &models.Summary{ | ||
| Sources: sources, | ||
| ResourceTypeCounts: resourceCountResults, | ||
| Patients: patients, | ||
| } | ||
|
|
||
| return summary, nil | ||
| } | ||
|
|
||
| // https://github.com/jddamore/fhir-ips-server/blob/main/docs/Summary_Creation_Steps.md | ||
| func generateIPSSectionQueries(sectionType pkg.IPSSections) ([]models.QueryResource, error) { | ||
|
|
||
| queries := []models.QueryResource{} | ||
| switch sectionType { | ||
| case pkg.IPSSectionsAllergiesIntolerances: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "AllergyIntolerance", | ||
| Where: map[string]interface{}{ | ||
| "clinicalStatus:not": []string{"inactive", "resolved"}, | ||
| "verificationStatus:not": []string{"entered-in-error"}, | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsProblemList: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Condition", | ||
| Where: map[string]interface{}{ | ||
| "clinicalStatus:not": []string{"inactive", "resolved"}, | ||
| "verificationStatus:not": []string{"entered-in-error"}, | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsMedicationSummary: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "MedicationStatement", | ||
| Where: map[string]interface{}{ | ||
| "status": "active,intended,unknown,on-hold", | ||
| }, | ||
| }) | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "MedicationRequest", | ||
| Where: map[string]interface{}{ | ||
| "status": "active,unknown,on-hold", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsDiagnosticResults: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "DiagnosticReport", | ||
| Where: map[string]interface{}{ | ||
| "category": "LAB", | ||
| }, | ||
| }) | ||
|
|
||
| //TODO: group by code, sort by date, limit to the most recent 3 | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Observation", | ||
| Where: map[string]interface{}{ | ||
| "category": "laboratory", | ||
| "status:not": "preliminary", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsVitalSigns: | ||
| //TODO: group by code, sort by date, limit to the most recent 3 | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Observation", | ||
| Where: map[string]interface{}{ | ||
| "category": "vital-signs", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsSocialHistory: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Observation", | ||
| Where: map[string]interface{}{ | ||
| "category": "social-history", | ||
| "status:not": "preliminary", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsPregnancy: | ||
| //TODO: determine the code for pregnancy from IPS specification | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Observation", | ||
| Where: map[string]interface{}{ | ||
| "status:not": "preliminary", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsImmunizations: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Immunization", | ||
| Where: map[string]interface{}{ | ||
| "status:not": "entered-in-error", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsAdvanceDirectives: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Consent", | ||
| Where: map[string]interface{}{ | ||
| "status": "active", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsFunctionalStatus: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "ClinicalImpression", | ||
| Where: map[string]interface{}{ | ||
| "status": "in-progress,completed", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsMedicalDevices: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Device", | ||
| Where: map[string]interface{}{ | ||
| "status": "entered-in-error", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsHistoryOfIllnesses: | ||
| //TODO: last updated date should be older than 5 years (dateTime or period.high) | ||
| //TODO: check if where clause with multiple modifiers for the same field works as expected | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Condition", | ||
| Where: map[string]interface{}{ | ||
| "clinicalStatus:not": []string{"entered-in-error"}, | ||
| "clinicalStatus": "inactive,remission,resolved", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsPlanOfCare: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "CarePlan", | ||
| Where: map[string]interface{}{ | ||
| "status": "active,on-hold,unknown", | ||
| }, | ||
| }) | ||
| break | ||
| case pkg.IPSSectionsHistoryOfProcedures: | ||
| queries = append(queries, models.QueryResource{ | ||
| Select: nil, | ||
| From: "Procedure", | ||
| Where: map[string]interface{}{ | ||
| "status:not": []string{"entered-in-error", "not-done"}, | ||
| }, | ||
| }) | ||
| } | ||
|
|
||
| return queries, nil | ||
| } |