private string GetContentAs(string content, FhirMimeType mimeType)
{
var serializer = new SerializationWrapper(_arguments.FhirVersion);
var resource = serializer.Parse(content);
return(serializer.Serialize(resource, mimeType));
}
private async IAsyncEnumerable <ResourceWrapper> ExpandInputFiles()
{
var serializer = new SerializationWrapper(_arguments.FhirVersion);
var content = await File.ReadAllTextAsync(_arguments.QuestionnairePath);
var resource = serializer.Parse(content, _arguments.MimeType);
if (resource == null)
{
_issues.Add(new Issue
{
Details = $"Failed to deserialize Questionnaire from file\nLocation: '{_arguments.QuestionnairePath}'.",
Severity = IssueSeverityEnum.Error,
});
yield break;
}
if (resource.ResourceType == ResourceTypeWrapper.Bundle)
{
var bundle = resource.CastToBundle();
foreach (var r in bundle.GetResources())
{
if (r.ResourceType != ResourceTypeWrapper.Questionnaire)
{
continue;
}
yield return(r);
}
}
else
{
yield return(resource);
}
}
private async Tasks.Task <BundleWrapper> CreateBundle(IEnumerable <string> batch, FhirVersion fhirVersion)
{
var serializer = new SerializationWrapper(fhirVersion);
var bundle = new BundleWrapper(fhirVersion);
foreach (var file in batch)
{
ResourceWrapper resource = null;
try
{
var content = await File.ReadAllTextAsync(file);
resource = serializer.Parse(content, _arguments.MimeType);
}
catch (Exception e)
{
_logger.LogError($"Could not read and parse {file}. Skipping: {e.Message}");
}
var entry = bundle.AddResourceEntry(resource, null);
var request = new RequestComponentWrapper(fhirVersion);
request.Method = HTTPVerbWrapper.PUT;
request.Url = $"/{resource.ResourceType}/{resource.Id}";
entry.Request = request;
_logger.LogInformation($" Added {request.Url} to bundle");
}
return(bundle);
}
public string Convert(string fromString)
{
var parser = new SerializationWrapper(FromVersion);
var serializer = new SerializationWrapper(ToVersion);
var fromObject = parser.Parse(fromString);
var converted = Convert <Base, Base>(fromObject.Resource);
return(serializer.Serialize(converted));
}
//[InlineData(@"TestData\account.profile-r4.json")]
//[InlineData(@"TestData\activitydefinition.profile-r4.json")]
//[InlineData(@"TestData\adverseevent.profile-r4.json")]
//[InlineData(@"TestData\allergyintolerance.profile-r4.json")]
//[InlineData(@"TestData\appointment.profile-r4.json")]
//[InlineData(@"TestData\appointmentresponse.profile-r4.json")]
//[InlineData(@"TestData\consent.profile-r4.json")]
public async Task CanConvert_Questionnaire_FromR4ToR3_RoundTrip(string path)
{
var converterFromR4ToR3 = new FhirConverter(to: FhirVersion.R3, from: FhirVersion.R4);
var converterFromR3ToR4 = new FhirConverter(to: FhirVersion.R4, from: FhirVersion.R3);
var r4Serializer = new SerializationWrapper(FhirVersion.R4);
var r4Resource = r4Serializer.Parse(await File.ReadAllTextAsync(path));
var r3Resource = converterFromR4ToR3.Convert <Resource, Resource>(r4Resource.Resource);
var r4ResourceRoundTrip = converterFromR3ToR4.Convert <Resource, Resource>(r3Resource);
var r4ResourceContent = r4Serializer.Serialize(r4Resource);
var r4ResourceRoundTripContent = r4Serializer.Serialize(r4ResourceRoundTrip);
Assert.Equal(r4ResourceContent, r4ResourceRoundTripContent);
}
public override async Task <OperationResultEnum> Execute()
{
_logger.LogInformation($"Starting conversion of source file: '{_arguments.Source}' from format: '{_arguments.FromMimeType}' to format '{_arguments.ToMimeType}'.");
var serializer = new SerializationWrapper(_arguments.FhirVersion);
var resource = serializer.Parse(_arguments.SourceContent, _arguments.FromMimeType, true);
var outContent = serializer.Serialize(resource, _arguments.ToMimeType.GetValueOrDefault());
var fileName = Path.GetFileName(_arguments.Source);
var outPath = GetOutPath(_arguments.OutPath, fileName, _arguments.ToMimeType.GetValueOrDefault());
if (!string.IsNullOrWhiteSpace(outContent))
{
using var stream = File.Open(outPath, FileMode.OpenOrCreate, FileAccess.Write);
await stream.WriteAsync(Encoding.UTF8.GetBytes(outContent));
_logger.LogInformation($"Converted file stored at: '{outPath}'.");
}
return(await Task.FromResult(OperationResultEnum.Succeeded));
}
public override async Tasks.Task <OperationResultEnum> Execute()
{
var serializer = new SerializationWrapper(_arguments.FhirVersion);
var lines = await File.ReadAllLinesAsync(_arguments.DumpFile.Path);
var linenr = 0;
var versionMap = new Dictionary <string, Data>();
foreach (var entry in lines)
{
linenr++;
try
{
var json = JObject.Parse(entry);
var versionPath = json["_id"].ToString();
json.Property("_id").Remove();
var id = $"{json["resourceType"]}/{json["id"]}";
if (_arguments.SkipIds.Contains(id))
{
_logger.LogInformation($"Skipping {id} as requested");
continue;
}
RemoveUnwantedMongoDbElements(json);
var dataEntry = new Data
{
Id = id,
JObject = json,
Line = linenr,
RawContent = entry,
VersionPath = versionPath
};
if (versionMap.TryGetValue(id, out Data other))
{
var version = GetVersion(json);
var otherVersion = GetVersion(other.JObject);
if (version > otherVersion)
{
versionMap.Remove(id);
versionMap.Add(id, dataEntry);
}
}
else
{
versionMap.Add(id, dataEntry);
}
}
catch (Exception e)
{
_logger.LogError($"line {linenr}: Not valid json{Environment.NewLine}{e.Message}");
if (_arguments.ShowOriginalJson)
{
_logger.LogInformation(entry);
}
continue;
}
}
foreach (var key in versionMap.Keys)
{
var data = versionMap[key];
try
{
var content = data.JObject.ToString();
var resource = serializer.Parse(content, permissiveParsing: _arguments.PermissiveParsing);
}
catch (Exception e)
{
_logger.LogError($"line {data.Line}: resource {key} is not a valid FHIR object (was {data.VersionPath}){Environment.NewLine}{e.Message}");
if (_arguments.ShowOriginalJson)
{
_logger.LogInformation(data.RawContent);
}
continue;
}
}
return(await Tasks.Task.FromResult(OperationResultEnum.Succeeded));
}