public InMemoryProfileResolver(IConformanceResource profile) : this(new IConformanceResource[] { profile })
{
}
public void Reload(IConformanceResource profile) => Reload(new IConformanceResource[] { profile });
public void CanonicalizeAllResources()
{
Console.WriteLine("Canonicalizing All resources");
var parserJson = new FhirJsonParser();
var parserXml = new FhirXmlParser();
var serializerJson = new FhirJsonSerializer(new SerializerSettings()
{
Pretty = true
});
var serializerXml = new FhirXmlSerializer(new SerializerSettings()
{
Pretty = true
});
var testFilenames = Directory.EnumerateFiles(ResourcesDirectory, "*.*", SearchOption.AllDirectories);
// read the canonical URI for the guide
string igJsonText = System.IO.File.ReadAllText(_directory + "/ig.json");
var js = new JsonSerializer();
js.Formatting = Newtonsoft.Json.Formatting.Indented;
var igJson = js.Deserialize(new JsonTextReader(new StringReader(igJsonText)));
Newtonsoft.Json.Linq.JToken t = igJson as Newtonsoft.Json.Linq.JToken;
var igJsonCanonicalBase = t["canonicalBase"] as JValue;
string canonicalBase = igJsonCanonicalBase.Value.ToString();
if (string.IsNullOrEmpty(canonicalBase))
{
Console.Error.WriteLine("No canonical Base defined in the ig.json file");
return;
}
string namePrefix = canonicalBase.Substring(canonicalBase.LastIndexOf("/") + 1);
if (namePrefix.Contains("-"))
{
namePrefix = namePrefix.Substring(namePrefix.IndexOf("-") + 1);
}
namePrefix = namePrefix.Substring(0, 1).ToUpper() + namePrefix.Substring(1);
ImplementationGuide ig = parserXml.Parse <ImplementationGuide>(File.ReadAllText(Path.Combine(ResourcesDirectory, "ig.xml")));
List <Resource> resources = new List <Resource>();
Dictionary <string, Resource> fileResources = new Dictionary <string, Resource>();
foreach (var file in testFilenames)
{
if (ignoreResourceDirectoryFiles.Any(i => file.EndsWith(i)))
{
continue;
}
using (var stream = System.IO.File.Open(file, System.IO.FileMode.Open, System.IO.FileAccess.Read, System.IO.FileShare.Read))
{
System.IO.StreamReader sr = new System.IO.StreamReader(stream);
string oldContent = sr.ReadToEnd();
// Close the stream so we can re-write it
stream.Close();
try
{
Resource item = null;
if (file.EndsWith("json"))
{
Console.WriteLine($"Processing JSON {file}");
item = parserJson.Parse <Resource>(oldContent);
oldContent = serializerJson.SerializeToString(item);
}
else if (file.EndsWith("xml"))
{
Console.WriteLine($"Processing XML {file}");
item = parserXml.Parse <Resource>(oldContent);
oldContent = OutputResource(serializerXml, item);
}
else
{
// not a FHIR resource in STU3
Console.WriteLine($"XXX Not Processing {file}");
continue;
}
if (file.EndsWith(@"\ig.xml") && item is ImplementationGuide)
{
ig = item as ImplementationGuide;
}
else
{
resources.Add(item);
if (item is IConformanceResource)
{
fileResources.Add(file, item);
}
}
// --------------------------------------
// Cleanup the resources
// --------------------------------------
IConformanceResource conf = item as IConformanceResource;
if (conf != null)
{
// Cleanup the canonical URI
// e.g. http://fhir.telstrahealth.com.au/th-epd/StructureDefinition/epd-practitioner
string generateCanonical = $"{canonicalBase}/{item.ResourceType}/{item.Id}";
if (!conf.Url.StartsWith("http://hl7.org.au") && !(item is ImplementationGuide))
{
conf.Url = generateCanonical;
}
Regex r = new Regex("^[A-Z]([A-Za-z0-9_]){0,254}$", RegexOptions.Singleline);
if (conf.Name == null || !r.IsMatch(conf.Name))
{
conf.Name = $"{namePrefix}_{item.Id.Replace("searchparameter-", "_sp_").Replace("-", "_")}";
if (!r.IsMatch(conf.Name))
{
System.Diagnostics.Trace.WriteLine($"Replaced Name property is still invalid {conf.Name}");
}
}
if (conf.Publisher != ig.Publisher)
{
conf.Publisher = ig.Publisher;
}
//canonicalToSP.Add(item.Url, item);
//canonicalToLocalSP.Add(item.Url, item);
}
if (item is StructureDefinition sd)
{
// remove the snapshot - that get's regenerated anyway
sd.Snapshot = null;
// Cleanup StructureDefinition opening element that forge removes
if (sd.Type != sd.Differential.Element[0].Path)
{
sd.Differential.Element.Insert(0, new ElementDefinition()
{
ElementId = sd.Type, Path = sd.Type
});
}
// Check any extension URLs
var elemExtensionUrl = sd.Differential.Element.FirstOrDefault(e => e.Path == "Extension.url")?.Fixed as FhirUri;
if (elemExtensionUrl != null)
{
if (elemExtensionUrl.Value != conf.Url)
{
Console.WriteLine($"Fixed Extension URL from {elemExtensionUrl.Value} to {conf.Url}");
elemExtensionUrl.Value = conf.Url;
}
}
// Check for existence of the markdown files
string prefix = new FileInfo(file).Name;
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-intro.md");
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-summary.md");
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-search.md");
}
if (item is SearchParameter sp)
{
// Check for existence of the markdown files
string prefix = new FileInfo(file).Name;
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-intro.md");
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-summary.md");
CreateMarkdownStubIfMissing($"{PagesIncludesDirectory}/{item.Id}-search.md");
}
if (item is CodeSystem cs)
{
if (cs.Title == null)
{
cs.Title = cs.Name;
}
if (cs.Description == null)
{
cs.Description = new Markdown(cs.Name);
}
}
if (item is ValueSet vs)
{
if (vs.Title == null)
{
vs.Title = vs.Name;
}
if (vs.Description == null)
{
vs.Description = new Markdown(vs.Name);
}
}
string newContent;
if (file.EndsWith("json"))
{
newContent = serializerJson.SerializeToString(item);
}
else
{
newContent = OutputResource(serializerXml, item);
}
if (newContent != oldContent)
{
System.IO.File.WriteAllText(file, newContent);
Console.WriteLine($"Updated {file}");
}
}
catch (Exception ex)
{
Console.WriteLine($"Exception occurred processing {file} {ex.Message}");
}
}
}
// Everything has been processed, so lets check the IG.xml for all the resources
string oldIGContent = OutputResource(serializerXml, ig);
foreach (var item in resources)
{
string key = $"{item.ResourceType}/{item.Id}";
if (!ig.Definition.Resource.Any(r => r.Reference.Reference == key))
{
// This resource needs to be included
Console.WriteLine($"Added {key} to IG");
ig.Definition.Resource.Add(new ImplementationGuide.ResourceComponent()
{
Example = null, Reference = new ResourceReference(key)
});
}
else
{
// copy the name in
var res = ig.Definition.Resource.First(r => r.Reference.Reference == key);
if (resources.First(r => $"{r.TypeName}/{r.Id}" == key) is IConformanceResource conf)
{
res.Name = conf.Name;
}
}
}
// Update the sequencing of the resources in the IG.xml (and alphabetical by name within each type)
var packResource = new List <ImplementationGuide.ResourceComponent>();
var p = ig.Definition;
// Code Systems
packResource.AddRange(FilterResourcesToType(p.Resource, "CodeSystem").OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterResourcesToType(p.Resource, "CodeSystem"));
// ValueSets
packResource.AddRange(FilterResourcesToType(p.Resource, "ValueSet").OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterResourcesToType(p.Resource, "ValueSet"));
// Extension Definitions
packResource.AddRange(FilterStructureDefinitions(p.Resource, true, resources).OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterStructureDefinitions(p.Resource, true, resources));
// Profile Definitions
packResource.AddRange(FilterStructureDefinitions(p.Resource, false, resources).OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterStructureDefinitions(p.Resource, false, resources));
// Operation Definitions
packResource.AddRange(FilterResourcesToType(p.Resource, "OperationDefinition").OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterResourcesToType(p.Resource, "OperationDefinition"));
// Search Parameters
packResource.AddRange(FilterResourcesToType(p.Resource, "SearchParameter").OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterResourcesToType(p.Resource, "SearchParameter"));
// Capability Statements
packResource.AddRange(FilterResourcesToType(p.Resource, "CapabilityStatement").OrderBy(o => o.Name));
RemoveRange(p.Resource, FilterResourcesToType(p.Resource, "CapabilityStatement"));
// anything else
packResource.AddRange(p.Resource);
p.Resource = packResource;
// Now re-pack the manifest section
//if (ig.Manifest == null)
// ig.Manifest = new ImplementationGuide.ManifestComponent();
//ig.Manifest.Resource.Clear();
//foreach (var pair in fileResources)
//{
// ig.Manifest.Resource.Add(new ImplementationGuide.ManifestResourceComponent()
// {
// Reference = new ResourceReference($"{pair.Value.ResourceType.GetLiteral()}/{pair.Value.Id}"),
// RelativePath = $"{pair.Value.ResourceType.GetLiteral()}-{pair.Value.Id}.html"
// });
//}
string newIGContent = OutputResource(serializerXml, ig);
if (newIGContent != oldIGContent)
{
System.IO.File.WriteAllText(ResourcesDirectory + "/ig.xml", newIGContent);
Console.WriteLine($"Updated ig.xml");
}
// And re-process the IG.json file to generate the resources section
var igJsonResources = t["resources"] as JContainer;
igJsonResources.RemoveAll();
foreach (var pair in fileResources)
{
FileInfo fi = new FileInfo(pair.Key);
string htmlName = $"{pair.Value.ResourceType.GetLiteral()}-{fi.Name.Substring(0, fi.Name.Length - fi.Extension.Length)}.html";
htmlName = htmlName.Replace(pair.Value.ResourceType.GetLiteral().ToLower(), "");
htmlName = htmlName.Replace("--", "-");
htmlName = htmlName.Replace($"{pair.Value.ResourceType.GetLiteral()}-{pair.Value.ResourceType.GetLiteral()}-", $"{pair.Value.ResourceType.GetLiteral()}-");
string content = $"{{\r\n \"{pair.Value.ResourceType.GetLiteral()}/{pair.Value.Id}\": {{\r\n" +
$" \"source\" : \"{fi.Name}\",\r\n" +
$" \"base\" : \"{htmlName}\"\r\n" +
$" }}\r\n}}";
var newNode = Newtonsoft.Json.Linq.JObject.Parse(content) as JToken;
igJsonResources.Add(newNode.Children().First());
}
var sb = new StringBuilder();
js.Serialize(new JsonTextWriter(new StringWriter(sb)), igJson);
System.IO.File.WriteAllText(_directory + "/ig.json", sb.ToString());
}