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Issues/468 filter getproperty for all processors #591

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51 changes: 51 additions & 0 deletions src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/Filters/GeneralFiltersTests.cs
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Expand Up @@ -58,6 +58,57 @@ public void GetPropertyTest()
Assert.Null(Filters.GetProperty(context, "M", string.Empty, "code"));
}

[Fact]
public void GetProperty_WhenCodeMappingIsAppended_ReturnsMappedValue()
{
// empty context
var context = new Context(CultureInfo.InvariantCulture);
Assert.Null(Filters.GetProperty(context, null, null, null));

// context with null CodeMapping
context = new Context(
environments: new List<Hash>(),
outerScope: new Hash(),
registers: new Hash(),
errorsOutputMode: ErrorsOutputMode.Rethrow,
maxIterations: 0,
formatProvider: CultureInfo.InvariantCulture,
cancellationToken: CancellationToken.None);
context["CodeMapping"] = null;

// First CodeMapping from CodeSystem
var firstMapping = new CodeMapping(new Dictionary<string, Dictionary<string, Dictionary<string, string>>>
{
{
"CodeSystem/Gender", new Dictionary<string, Dictionary<string, string>>
{
{ "M", new Dictionary<string, string> { { "code", "male" } } },
}
},
});

// Additional CodeMapping from ValueSet
var additionalMapping = new CodeMapping(new Dictionary<string, Dictionary<string, Dictionary<string, string>>>
{
{
"ValueSet/Gender", new Dictionary<string, Dictionary<string, string>>
{
{ "F", new Dictionary<string, string> { { "code", "female" } } },
{ "O", new Dictionary<string, string> { { "code", "other" } } },
}
},
});

// Append ValueSet to CodeMapping
firstMapping.Append(additionalMapping);
context["CodeMapping"] = firstMapping;

// Assert both CodeSystem/Gender and ValueSet/Gender
Assert.Equal("male", Filters.GetProperty(context, "M", "CodeSystem/Gender", "code"));
Assert.Equal("female", Filters.GetProperty(context, "F", "ValueSet/Gender", "code"));
Assert.Equal("other", Filters.GetProperty(context, "O", "ValueSet/Gender", "code"));
}

[Fact]
public void EvaluateTest()
{
Expand Down
48 changes: 48 additions & 0 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Models/CodeMapping.cs
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Expand Up @@ -3,6 +3,7 @@
// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
// -------------------------------------------------------------------------------------------------

using System;
using System.Collections.Generic;
using DotLiquid;

Expand All @@ -16,5 +17,52 @@ public CodeMapping(Dictionary<string, Dictionary<string, Dictionary<string, stri
}

public Dictionary<string, Dictionary<string, Dictionary<string, string>>> Mapping { get; set; }

/// <summary>
/// Appends mappings from another CodeMapping instance.
/// Throws InvalidOperationException if any key path already exists with a different value.
/// </summary>
/// <param name="additionalMapping">The CodeMapping to append.</param>
/// <exception cref="ArgumentNullException">Thrown if <paramref name="mappingToAppend"/> is null.</exception>
/// <exception cref="InvalidOperationException">Thrown if any key path already exists with a different value.</exception>
public void Append(CodeMapping additionalMapping)
{
ArgumentNullException.ThrowIfNull(additionalMapping, nameof(additionalMapping));

foreach (var level1 in additionalMapping.Mapping)
{
if (!Mapping.TryGetValue(level1.Key, out var level2Dict))
{
Mapping[level1.Key] = new Dictionary<string, Dictionary<string, string>>(level1.Value);
continue;
}

foreach (var level2 in level1.Value)
{
if (!level2Dict.TryGetValue(level2.Key, out var level3Dict))
{
level2Dict[level2.Key] = new Dictionary<string, string>(level2.Value);
continue;
}

foreach (var level3 in level2.Value)
{
if (level3Dict.TryGetValue(level3.Key, out var existingValue))
{
if (!string.Equals(existingValue, level3.Value, StringComparison.Ordinal))
{
throw new InvalidOperationException(
$"Conflict at path [{level1.Key}][{level2.Key}][{level3.Key}]: " +
$"existing='{existingValue}', new='{level3.Value}'");
}
}
else
{
level3Dict[level3.Key] = level3.Value;
}
}
}
}
}
}
}
58 changes: 51 additions & 7 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Processors/BaseProcessor.cs
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Expand Up @@ -6,6 +6,7 @@
using System;
using System.Collections.Generic;
using System.Globalization;
using System.Linq;
using System.Threading;
using DotLiquid;
using EnsureThat;
Expand Down Expand Up @@ -63,7 +64,23 @@ public string Convert(string data, string rootTemplate, ITemplateProvider templa

protected abstract string InternalConvert(string data, string rootTemplate, ITemplateProvider templateProvider, TraceInfo traceInfo = null);

protected virtual Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
protected Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
{
Context context = CreateBaseContext(templateProvider, data);

// Load filters
context.AddFilters(typeof(Filters));

// Add root template's parent path to context.
AddRootTemplatePathScope(context, templateProvider, rootTemplate);

// Inject of codemapping into context.
InjectCodeMappingIntoContext(context, templateProvider);

return context;
}

protected virtual Context CreateBaseContext(ITemplateProvider templateProvider, IDictionary<string, object> data)
{
// Load data and templates
var cancellationToken = Settings.TimeOut > 0 ? new CancellationTokenSource(Settings.TimeOut).Token : CancellationToken.None;
Expand All @@ -76,12 +93,6 @@ protected virtual Context CreateContext(ITemplateProvider templateProvider, IDic
formatProvider: CultureInfo.InvariantCulture,
cancellationToken: cancellationToken);

// Load filters
context.AddFilters(typeof(Filters));

// Add root template's parent path to context.
AddRootTemplatePathScope(context, templateProvider, rootTemplate);

return context;
}

Expand Down Expand Up @@ -182,5 +193,38 @@ protected void LogTelemetry(string telemetryName, double duration)
Logger.LogInformation("{Metric}: {Duration} milliseconds.", telemetryName, duration);
}
}

protected void InjectCodeMappingIntoContext(Context context, ITemplateProvider templateProvider)
{
var rootTemplateParentPath = context[TemplateUtility.RootTemplateParentPathScope]?.ToString();
List<string> codeMappings = new List<string> { "ValueSet/ValueSet", "CodeSystem/CodeSystem", };
var allPaths = codeMappings
.Select(name => TemplateUtility.GetFormattedTemplatePath(name, rootTemplateParentPath))
.ToList();

CodeMapping combinedMapping = null;

foreach (var path in allPaths)
{
var template = templateProvider.GetTemplate(path);
var node = template?.Root?.NodeList?.FirstOrDefault() as CodeMapping;
if (node != null)
{
if (combinedMapping == null)
{
combinedMapping = node;
}
else
{
combinedMapping.Append(node);
}
}
}

if (combinedMapping != null)
{
context["CodeMapping"] = combinedMapping;
}
}
}
}
20 changes: 0 additions & 20 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Processors/CcdaProcessor.cs
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Expand Up @@ -36,25 +36,5 @@ protected override string InternalConvert(string data, string rootTemplate, ITem

return InternalConvertFromObject(ccdaData, rootTemplate, templateProvider, traceInfo);
}

protected override Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
{
// Load value set mapping
var context = base.CreateContext(templateProvider, data, rootTemplate);
var codeMapping = templateProvider.GetTemplate(GetCodeMappingTemplatePath(context));
if (codeMapping?.Root?.NodeList?.First() != null)
{
context["CodeMapping"] = codeMapping.Root.NodeList.First();
}

return context;
}

private string GetCodeMappingTemplatePath(Context context)
{
var rootTemplateParentPath = context[TemplateUtility.RootTemplateParentPathScope]?.ToString();
var codeSystemTemplateName = "ValueSet/ValueSet";
return TemplateUtility.GetFormattedTemplatePath(codeSystemTemplateName, rootTemplateParentPath);
}
}
}
9 changes: 2 additions & 7 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Processors/FhirToHl7v2Processor.cs
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Expand Up @@ -225,11 +225,11 @@ public string ConvertHl7MessageToString(Hl7v2Data message)
return sb.ToString();
}

protected override Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
protected override Context CreateBaseContext(ITemplateProvider templateProvider, IDictionary<string, object> data)
{
// Load data and templates
var cancellationToken = Settings.TimeOut > 0 ? new CancellationTokenSource(Settings.TimeOut).Token : CancellationToken.None;
var context = new JSchemaContext(
return new JSchemaContext(
environments: new List<Hash> { Hash.FromDictionary(data) },
outerScope: new Hash(),
registers: Hash.FromDictionary(new Dictionary<string, object> { { "file_system", templateProvider.GetTemplateFileSystem() } }),
Expand All @@ -240,11 +240,6 @@ protected override Context CreateContext(ITemplateProvider templateProvider, IDi
{
ValidateSchemas = new List<JsonSchema>(),
};

// Load filters
context.AddFilters(typeof(Filters));

return context;
}

protected override void CreateTraceInfo(object data, Context context, TraceInfo traceInfo)
Expand Down
20 changes: 0 additions & 20 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Processors/Hl7v2Processor.cs
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Expand Up @@ -40,32 +40,12 @@ protected override string InternalConvert(string data, string rootTemplate, ITem
return InternalConvertFromObject(hl7v2Data, rootTemplate, templateProvider, traceInfo);
}

protected override Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
{
// Load code system mapping
var context = base.CreateContext(templateProvider, data, rootTemplate);
var codeMapping = templateProvider.GetTemplate(GetCodeMappingTemplatePath(context));
if (codeMapping?.Root?.NodeList?.First() != null)
{
context["CodeMapping"] = codeMapping.Root.NodeList.First();
}

return context;
}

protected override void CreateTraceInfo(object data, Context context, TraceInfo traceInfo)
{
if (traceInfo is Hl7v2TraceInfo hl7v2TraceInfo)
{
hl7v2TraceInfo.UnusedSegments = Hl7v2TraceInfo.CreateTraceInfo(data as Hl7v2Data).UnusedSegments;
}
}

private string GetCodeMappingTemplatePath(Context context)
{
var rootTemplateParentPath = context[TemplateUtility.RootTemplateParentPathScope]?.ToString();
var codeSystemTemplateName = "CodeSystem/CodeSystem";
return TemplateUtility.GetFormattedTemplatePath(codeSystemTemplateName, rootTemplateParentPath);
}
}
}
12 changes: 2 additions & 10 deletions src/Microsoft.Health.Fhir.Liquid.Converter/Processors/JsonProcessor.cs
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Expand Up @@ -54,11 +54,11 @@ public string Convert(JObject data, string rootTemplate, ITemplateProvider templ
return InternalConvertFromObject(jsonData, rootTemplate, templateProvider, traceInfo);
}

protected override Context CreateContext(ITemplateProvider templateProvider, IDictionary<string, object> data, string rootTemplate)
protected override Context CreateBaseContext(ITemplateProvider templateProvider, IDictionary<string, object> data)
{
// Load data and templates
var cancellationToken = Settings.TimeOut > 0 ? new CancellationTokenSource(Settings.TimeOut).Token : CancellationToken.None;
var context = new JSchemaContext(
return new JSchemaContext(
environments: new List<Hash> { Hash.FromDictionary(data) },
outerScope: new Hash(),
registers: Hash.FromDictionary(new Dictionary<string, object> { { "file_system", templateProvider.GetTemplateFileSystem() } }),
Expand All @@ -69,14 +69,6 @@ protected override Context CreateContext(ITemplateProvider templateProvider, IDi
{
ValidateSchemas = new List<JsonSchema>(),
};

// Load filters
context.AddFilters(typeof(Filters));

// Add root template's parent path to context.
AddRootTemplatePathScope(context, templateProvider, rootTemplate);

return context;
}

protected override void CreateTraceInfo(object data, Context context, TraceInfo traceInfo)
Expand Down