/// <summary>
/// Adds examples for the profiles to the ZIP package. Only adds valid samples to the zip package.
/// </summary>
/// <remarks>Attempts to use the fhir-net-api to parse the resource as Xml and then as Json. If the sample
/// cannot be parsed successfully, then it is skipped and not added to the ZIP package.</remarks>
private void AddExamples()
{
// Validate that each of the samples associated with profiles has the required fields
var templateExamples = (from t in this.templates
join ts in this.tdb.TemplateSamples on t.Id equals ts.TemplateId
select new { Template = t, Sample = ts });
foreach (var templateExample in templateExamples)
{
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
string fileExtension = "";
try
{
resource = FhirParser.ParseResourceFromXml(templateExample.Sample.XmlSample);
fileExtension = "xml";
}
catch
{
}
try
{
if (resource == null)
{
resource = FhirParser.ParseResourceFromJson(templateExample.Sample.XmlSample);
fileExtension = "json";
}
}
catch
{
}
if (resource == null || string.IsNullOrEmpty(resource.Id))
{
continue;
}
string fileName = string.Format("resources/{0}/{1}.{2}", resource.ResourceType.ToString().ToLower(), resource.Id, fileExtension);
this.zip.AddEntry(fileName, templateExample.Sample.XmlSample);
}
}
/// <summary>
/// Adds individual FHIR Resource Instance files attached to the implementation guide being exported
/// to the ZIP package
/// </summary>
/// <remarks>Uses the mime-type of the file to determine if the attached file is xml or json.</remarks>
private void AddResourceInstances()
{
// Check that each FHIR resource instance is valid and has the required fields
foreach (var file in ig.Files)
{
var fileData = file.GetLatestData();
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
string fileExtension = "";
try
{
string fileContent = System.Text.Encoding.UTF8.GetString(fileData.Data);
if (file.MimeType == "application/xml" || file.MimeType == "text/xml")
{
resource = FhirParser.ParseResourceFromXml(fileContent);
fileExtension = "xml";
}
else if (file.MimeType == "application/json")
{
resource = FhirParser.ParseResourceFromJson(fileContent);
fileExtension = "json";
}
}
catch
{
}
if (resource == null || string.IsNullOrEmpty(resource.Id))
{
continue;
}
string fileName = string.Format("resources/{0}/{1}.{2}", resource.ResourceType.ToString().ToLower(), resource.Id, fileExtension);
this.zip.AddEntry(fileName, fileData.Data);
}
}
public override List <ValidationResult> ValidateTemplate(Template template, SimpleSchema igSchema, IEnumerable <Template> allContainedTemplates = null)
{
List <ValidationResult> results = base.ValidateTemplate(template, igSchema, allContainedTemplates);
var noHttpValueSets = (from tc in template.ChildConstraints
join vs in this.tdb.ValueSets on tc.ValueSetId equals vs.Id
where vs.Identifiers.Count(y => y.Type == ValueSetIdentifierTypes.HTTP) == 0
select new { ConstraintNumber = tc.Number, ValueSet = vs });
foreach (var noHttpValueSet in noHttpValueSets)
{
string vsIdentifier = noHttpValueSet.ValueSet.GetIdentifier(ValueSetIdentifierTypes.HTTP);
results.Add(new ValidationResult()
{
ConstraintNumber = noHttpValueSet.ConstraintNumber,
Level = ValidationLevels.Error,
Message = string.Format("The constraint references a value set ({0}) that does not have an HTTP identifier", vsIdentifier),
TemplateId = template.Id,
TemplateName = template.Name
});
}
foreach (var templateExample in template.TemplateSamples)
{
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
try
{
resource = fhirXmlParser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(templateExample.XmlSample);
}
catch
{
}
try
{
if (resource == null)
{
resource = fhirJsonParser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(templateExample.XmlSample);
}
}
catch
{
}
if (resource == null)
{
results.Add(new ValidationResult()
{
TemplateId = template.Id,
TemplateName = template.Name,
Level = ValidationLevels.Error,
Message = string.Format("Profile sample \"{0}\" cannot be parsed as a valid XML or JSON resource.", templateExample.Name)
});
}
else if (string.IsNullOrEmpty(resource.Id))
{
results.Add(new ValidationResult()
{
TemplateId = template.Id,
TemplateName = template.Name,
Level = ValidationLevels.Error,
Message = string.Format("Profile sample \"{0}\" does not have an \"id\" property.", templateExample.Name)
});
}
}
return(results);
}
protected override ValidationResults ValidateImplementationGuide(ImplementationGuide implementationGuide, SimpleSchema igSchema)
{
ValidationResults results = base.ValidateImplementationGuide(implementationGuide, igSchema);
// Check that the implementation guide has a base identifier/url
if (string.IsNullOrEmpty(implementationGuide.Identifier))
{
results.Messages.Add("Implementation guide does not have a base identifier/url.");
}
// Check that each FHIR resource instance is valid and has the required fields
foreach (var file in implementationGuide.Files)
{
var fileData = file.GetLatestData();
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
string fileContent = System.Text.Encoding.UTF8.GetString(fileData.Data);
try
{
resource = this.fhirXmlParser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(fileContent);
}
catch (Exception ex)
{
if (file.MimeType == "application/xml" || file.MimeType == "text/xml")
{
results.Messages.Add("FHIR Resource instance \"" + file.FileName + "\" cannot be parsed as valid XML: " + ex.Message);
}
}
try
{
if (resource == null)
{
resource = this.fhirJsonParser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(fileContent);
}
}
catch (Exception ex)
{
if (file.MimeType == "binary/octet-stream" || file.MimeType == "application/json")
{
results.Messages.Add("FHIR Resource instance \"" + file.FileName + "\" cannot be parsed as valid JSON: " + ex.Message);
}
}
if (resource != null && string.IsNullOrEmpty(resource.Id))
{
string msg = string.Format("FHIR resource instance \"" + file.FileName + "\" does not have an \"id\" property.");
results.Messages.Add(msg);
}
}
List <string> resourceIds = new List <string>();
// Go through each of the FHIR Resource Instance files associated with the implementation guide and get the resource type and id for each one
foreach (var file in implementationGuide.Files.Where(y => y.ContentType == ImplementationGuideFile.ContentTypeFHIRResourceInstance))
{
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
string fileContent = Encoding.UTF8.GetString(file.GetLatestData().Data);
try
{
if (file.MimeType.Contains("json"))
{
fhir_stu3.Hl7.Fhir.Serialization.FhirJsonParser parser = new FhirJsonParser();
resource = parser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(fileContent);
}
else if (file.MimeType.Contains("xml"))
{
fhir_stu3.Hl7.Fhir.Serialization.FhirXmlParser parser = new FhirXmlParser();
resource = parser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(fileContent);
}
}
catch
{
// Do nothing? Skip?
}
if (resource != null)
{
// Ex: Questionnaire/ssi-questionnaire
resourceIds.Add(resource.ResourceType + "/" + resource.Id);
}
}
// Go through each of the profile samples, and do the same thing. Loop through each template in the IG, and Template.TemplateSamples
var allTemplateSamples = implementationGuide.ChildTemplates.SelectMany(y => y.TemplateSamples);
foreach (var templateSample in allTemplateSamples)
{
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
string fileContent = templateSample.XmlSample;
try
{
fhir_stu3.Hl7.Fhir.Serialization.FhirXmlParser parser = new FhirXmlParser();
resource = parser.Parse <fhir_stu3.Hl7.Fhir.Model.Resource>(fileContent);
}
catch
{
// Do nothing
}
if (resource != null)
{
resourceIds.Add(resource.ResourceType + "/" + resource.Id);
}
}
// Go through each of the profiles and determine their StructureDefinition/<id> as well, add to list
foreach (var template in implementationGuide.ChildTemplates)
{
String resourceId = template.Oid.Substring(template.Oid.IndexOf("StructureDefinition/") + 20);
resourceIds.Add(template.PrimaryContextType + "/" + resourceId);
}
// Check the list of resourceIds for duplicates (suggest using some form of linq query - search online)
var duplicateCheck = resourceIds.GroupBy(x => x)
.Where(g => g.Count() > 1)
.Select(d => d.Key).ToList();
// For each duplicate, create a resources.Messages error. Flag results.RestrictDownload if any duplicates, cause the exports will error out.
if (duplicateCheck.Count != 0)
{
results.RestrictDownload = true;
foreach (var duplicate in duplicateCheck)
{
results.Messages.Add("Export Restricted: Entry with type and id " + duplicate.ToString() + " appears more than once within this implementation guide as an IG sample file, as a sample associated with a profile within the IG, or a profile");
}
}
return(results);
}
public IEnumerable <string> ValidateXml(XMLSettingsModel model)
{
List <string> messages = new List <string>();
ImplementationGuide ig = this.tdb.ImplementationGuides.SingleOrDefault(y => y.Id == model.ImplementationGuideId);
var templates = (from t in this.tdb.Templates
join tid in model.TemplateIds on t.Id equals tid
select t);
if (ig == null)
{
messages.Add("Could not find implementation guide with id " + model.ImplementationGuideId);
return(messages);
}
switch (model.XmlType)
{
case XMLSettingsModel.ExportTypes.FHIRBuild:
// Check that the implementation guide has a base identifier/url
if (string.IsNullOrEmpty(ig.Identifier))
{
messages.Add("Implementation guide does not have a base identifier/url.");
}
// Check that each FHIR resource instance is valid and has the required fields
foreach (var file in ig.Files)
{
var fileData = file.GetLatestData();
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
try
{
string fileContent = System.Text.Encoding.UTF8.GetString(fileData.Data);
if (file.MimeType == "application/xml" || file.MimeType == "text/xml")
{
resource = fhir_stu3.Hl7.Fhir.Serialization.FhirParser.ParseResourceFromXml(fileContent);
}
else if (file.MimeType == "application/json")
{
resource = fhir_stu3.Hl7.Fhir.Serialization.FhirParser.ParseResourceFromJson(fileContent);
}
}
catch
{
}
if (resource == null)
{
string msg = string.Format("FHIR resource instance \"" + file.FileName + "\" cannot be parsed as a valid XML or JSON resource.");
messages.Add(msg);
}
if (string.IsNullOrEmpty(resource.Id))
{
string msg = string.Format("FHIR resource instance \"" + file.FileName + "\" does not have an \"id\" property.");
messages.Add(msg);
}
}
// Validate that each of the samples associated with profiles has the required fields
var templateExamples = (from t in templates
join ts in this.tdb.TemplateSamples on t.Id equals ts.TemplateId
select new { Template = t, Sample = ts });
foreach (var templateExample in templateExamples)
{
fhir_stu3.Hl7.Fhir.Model.Resource resource = null;
try
{
resource = fhir_stu3.Hl7.Fhir.Serialization.FhirParser.ParseResourceFromXml(templateExample.Sample.XmlSample);
}
catch
{
}
try
{
if (resource == null)
{
resource = fhir_stu3.Hl7.Fhir.Serialization.FhirParser.ParseResourceFromJson(templateExample.Sample.XmlSample);
}
}
catch
{
}
if (resource == null)
{
string msg = string.Format("Profile sample \"" + templateExample.Sample.Name + "\" cannot be parsed as a valid XML or JSON resource.");
messages.Add(msg);
}
else if (string.IsNullOrEmpty(resource.Id))
{
string msg = string.Format("Profile sample \"" + templateExample.Sample.Name + "\" does not have an \"id\" property.");
messages.Add(msg);
}
}
break;
}
return(messages);
}
