async Task <Dataset> ExecuteDatasetAsync(DatasetExecutionContext context, CancellationToken token)
{
var sql = context.CompiledQuery;
var parameters = context.SqlParameters();
var pepper = context.QueryContext.Pepper;
using (var cn = new SqlConnection(opts.ConnectionString))
{
await cn.OpenAsync();
using (var cmd = new SqlCommand(sql, cn))
{
cmd.Parameters.AddRange(parameters);
using (var reader = await cmd.ExecuteReaderAsync(token))
{
var dbSchema = GetShapedSchema(context, reader);
var marshaller = DatasetMarshaller.For(context.Shape, dbSchema, pepper);
var data = marshaller.Marshal(reader, user.Anonymize());
var resultSchema = ShapedDatasetSchema.From(dbSchema);
return(new Dataset
{
Schema = resultSchema,
Results = data.GroupBy(d => d.PersonId).ToDictionary(g => g.Key, g => g.Select(r => r))
});
}
}
}
}
public static DatasetMarshaller For(DatasetExecutionContext context, DatasetResultSchema schema, Guid pepper)
{
switch (context.Shape)
{
case Shape.Dynamic:
return(new DynamicMarshaller(context, schema, pepper));
case Shape.Observation:
return(new ObservationMarshaller(schema, pepper));
case Shape.Encounter:
return(new EncounterMarshaller(schema, pepper));
case Shape.Condition:
return(new ConditionMarshaller(schema, pepper));
case Shape.Procedure:
return(new ProcedureMarshaller(schema, pepper));
case Shape.Immunization:
return(new ImmunizationMarshaller(schema, pepper));
case Shape.Allergy:
return(new AllergyMarshaller(schema, pepper));
case Shape.MedicationRequest:
return(new MedicationRequestMarshaller(schema, pepper));
case Shape.MedicationAdministration:
return(new MedicationAdministrationMarshaller(schema, pepper));
default:
throw new ArgumentException($"{context.Shape.ToString()} switch branch not implemented");
}
}
public async Task <Dataset> ExecuteDatasetAsync(DatasetExecutionContext context, CancellationToken token)
{
var sql = context.CompiledQuery;
var parameters = context.SqlParameters();
var pepper = context.QueryContext.Pepper;
var deidentify = deidentOpts.Patient.Enabled && user.Anonymize();
using (var cn = new SqlConnection(dbOpts.ConnectionString))
{
await cn.OpenAsync();
using (var cmd = new SqlCommand(sql, cn))
{
cmd.Parameters.AddRange(parameters);
using (var reader = await cmd.ExecuteReaderAsync(token))
{
var dbSchema = GetShapedSchema(context, reader);
var marshaller = DatasetMarshaller.For(context, dbSchema, pepper);
var data = marshaller.Marshal(reader, deidentify, deidentOpts);
var resultSchema = ShapedDatasetSchema.From(dbSchema, context);
return(new Dataset(resultSchema, data));
}
}
}
}
public static ShapedDatasetSchema From(DatasetResultSchema resultSchema, DatasetExecutionContext context)
{
var contract = ShapedDatasetContract.For(resultSchema.Shape, context.DatasetQuery);
var fields = resultSchema.Fields.Where(f => contract.Fields.Any(cf => cf.Name == f.Name)).ToArray();
return(new ShapedDatasetSchema
{
Shape = resultSchema.Shape,
Fields = fields,
Contract = contract
});
}
public DatasetExecutionContext BuildDatasetSql(DatasetCompilerContext compilerContext)
{
executionContext = new DatasetExecutionContext(compilerContext.Shape, compilerContext.QueryContext, compilerContext.DatasetQuery.Id.Value);
var cohort = CteCohortInternals(compilerContext.QueryContext);
new SqlValidator(Dialect.ILLEGAL_COMMANDS).Validate(compilerContext.DatasetQuery);
var dataset = CteDatasetInternals(compilerContext.DatasetQuery);
var filter = CteFilterInternals(compilerContext);
var select = SelectFromCTE();
executionContext.CompiledQuery = Compose(cohort, dataset, filter, select);
return(executionContext);
}
public DatasetExecutionContext BuildDatasetSql(DatasetCompilerContext compilerContext)
{
executionContext = new DatasetExecutionContext(compilerContext.Shape, compilerContext.QueryContext, compilerContext.DatasetQuery.Id.Value);
var cohort = CteCohortInternals(compilerContext);
new SqlValidator(Dialect.IllegalCommands).Validate(compilerContext.DatasetQuery.SqlStatement);
var dataset = CteDatasetInternals(compilerContext.DatasetQuery);
var filter = CteFilterInternals(compilerContext);
var select = SelectFromCTE(compilerContext);
var parameters = compiler.BuildContextParameterSql();
executionContext.DatasetQuery = compilerContext.DatasetQuery;
executionContext.CompiledQuery = Compose(parameters, cohort, dataset, filter, select);
return(executionContext);
}
DatasetResultSchema GetShapedSchema(DatasetExecutionContext context, SqlDataReader reader)
{
var shape = context.Shape;
var actualSchema = GetResultSchema(shape, reader);
var validationSchema = ValidationSchema.For(shape);
var result = validationSchema.Validate(actualSchema);
switch (result.State)
{
case SchemaValidationState.Warning:
log.LogWarning("Dataset Schema Validation Warning. Context:{@Context} Messages:{Messages}", context, result.Messages);
break;
case SchemaValidationState.Error:
log.LogError("Dataset Schema Validation Error. Context:{@Context} Messages:{Messages}", context, result.Messages);
throw new LeafCompilerException($"Dataset {context.DatasetId} failed schema validation");
}
return(validationSchema.GetShapedSchema(actualSchema));
}
public DynamicMarshaller(DatasetExecutionContext context, DatasetResultSchema schema, Guid pepper) : base(pepper)
{
_context = context;
_schema = schema;
}