private IMongoQuery ParametersToQuery(IEnumerable<IParameter> parameters)
{
List<IMongoQuery> queries = new List<IMongoQuery>();
queries.Add(M.Query.EQ(InternalField.LEVEL, 0)); // geindexeerde contained documents overslaan
IEnumerable<IMongoQuery> q = parameters.Select(p => ParameterToQuery(p));
queries.AddRange(q);
return M.Query.And(queries);
}
public IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
foreach (var tag in Category)
result.AddRange(tag.Validate(validationContext));
return result;
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (!result.Any()) result.Add(ValidationResult.Success);
return result;
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (When == null)
result.Add(new ValidationResult("A DeletedEntry must have a non-null deletion time (When)"));
if (!result.Any()) result.Add(ValidationResult.Success);
return result;
}
public static void SetTextTag(this BundleEntry entry, string text)
{
var result = new List<Tag>();
if (entry.Tags != null) result.AddRange(entry.Tags);
result.RemoveAll(t => Equals(t.Scheme,Tag.FHIRTAGSCHEME_GENERAL) &&
(t.Term != null && t.Term.StartsWith(TAG_TERM_TEXT)));
result.Add(new Tag(TAG_TERM_TEXT + Uri.EscapeUriString(text), Tag.FHIRTAGSCHEME_GENERAL, text));
entry.Tags = result;
}
public override IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
result.AddRange(base.Validate(validationContext));
if (Content == null)
result.Add(new ValidationResult("Entry must contain (possibly 0-length) data in Content element"));
if (ContentType == null)
result.Add(new ValidationResult("Entry must contain a ContentType"));
return result;
}
public static List<Tag> GetFhirTags(this HttpHeaders headers)
{
IEnumerable<string> tagstrings;
List<Tag> tags = new List<Tag>();
if (headers.TryGetValues(FhirHeader.CATEGORY, out tagstrings))
{
foreach (string tagstring in tagstrings)
{
tags.AddRange(HttpUtil.ParseCategoryHeader(tagstring));
}
}
return tags;
}
public virtual IEnumerable<ValidationResult> Validate(ValidationContext validationContext)
{
var result = new List<ValidationResult>();
if (!Bundle.UriHasValue(Id))
result.Add(new ValidationResult("Entry must have an id"));
else
if (!Id.IsAbsoluteUri)
result.Add(new ValidationResult("Entry id must be an absolute URI"));
if (Bundle.UriHasValue(SelfLink) && !SelfLink.IsAbsoluteUri)
result.Add(new ValidationResult("Entry selflink must be an absolute URI"));
if (Links.FirstLink != null || Links.LastLink != null || Links.PreviousLink != null || Links.NextLink != null)
result.Add(new ValidationResult("Paging links can only be used on feeds, not entries"));
if (Tags != null)
result.AddRange(new TagList(Tags).Validate(validationContext));
return result;
}
/// <summary>
/// Unpacks zip-files containing the artifact files, and enumerates all (zipped/nonzipped) files.
/// </summary>
/// <remarks>This is an expensive operations and should be run once. As well, it unpacks files on the
/// file system and is not thread-safe.</remarks>
public void Prepare()
{
#if !PORTABLE45
_artifactFiles = new List<string>();
var zips = Directory.GetFiles(_contentDirectory, "*.zip");
// Get the files in each *.zip files present in the content directory
// The ZipCacher will avoid re-extracting these files.
foreach (string zipPath in zips)
{
ZipCacher zc = new ZipCacher(zipPath, CACHE_KEY);
_artifactFiles.AddRange(zc.GetContents());
}
_isPrepared = true;
#else
throw Error.NotImplemented("File based Core artifact source is not supported on the portable runtime");
#endif
}
public static IEnumerable<Tag> Merge(this IEnumerable<Tag> tags, IEnumerable<Tag> that)
{
var result = new List<Tag>(tags.Remove(that));
result.AddRange(that);
return result;
}
private static List<string> GetTargetedReferenceTypes(ModelInfo.SearchParamDefinition parameter, String modifier)
{
var allowedResourceTypes = ModelInfo.SupportedResources; //TODO: restrict to parameter.ReferencedResources. This means not making this static, because you want to use IFhirModel.
List<string> searchResourceTypes = new List<string>();
if (String.IsNullOrEmpty(modifier))
searchResourceTypes.AddRange(allowedResourceTypes);
else if (allowedResourceTypes.Contains(modifier))
{
searchResourceTypes.Add(modifier);
}
else
{
throw new NotSupportedException(String.Format("Referenced type cannot be of type %s.", modifier));
}
return searchResourceTypes;
}
public IEnumerable<string> ListArtifactNames()
{
var result = new List<string>();
foreach (var source in Sources)
{
try
{
result.AddRange(source.ListArtifactNames());
}
catch (NotImplementedException)
{
// Don't do anything, just try the next IArtifactSource
}
}
return result;
}
/// <summary>
/// CloseCriterium("patient.name=\"Teun\"") -> "patient=id1,id2"
/// </summary>
/// <param name="resourceType"></param>
/// <param name="crit"></param>
/// <returns></returns>
private Criterium CloseCriterium(Criterium crit, string resourceType)
{
List<string> targeted = crit.GetTargetedReferenceTypes(resourceType);
List<string> allKeys = new List<string>();
foreach (var target in targeted)
{
var keys = CollectKeys(target, new List<Criterium> { (Criterium)crit.Operand }); //Recursive call to CollectKeys!
allKeys.AddRange(keys.Select(k => k.ToString()));
}
crit.Type = Operator.IN;
crit.Operand = ChoiceValue.Parse(String.Join(",", allKeys));
return crit;
}
private static IEnumerable<Bookmark> locateChildren(BaseElementNavigator nav, IEnumerable<string> path, bool partial)
{
var child = path.First();
var rest = path.Skip(1);
var bm = nav.Bookmark();
if (nav.MoveToChild(child))
{
var result = new List<Bookmark>();
do
{
if (!rest.Any())
{
// Exact match!
result.Add(nav.Bookmark());
}
else if (!nav.HasChildren && partial)
{
// This is as far as we can get in this structure,
// so this is a hit too if partial hits are OK
result.Add(nav.Bookmark());
}
else
{
// So, no hit, but we have children that might fit the bill.
result.AddRange(locateChildren(nav, rest, partial));
}
// Try this for the other matching siblings too...
}
while (nav.MoveToNext(child));
// We've scanned all my children and collected the results,
// move the navigator back to where we were before
nav.ReturnToBookmark(bm);
return result;
}
else
return Enumerable.Empty<Bookmark>();
}
/// <summary>
/// CloseCriterium("patient.name=\"Teun\"") -> "patient IN (id1,id2)"
/// </summary>
/// <param name="resourceType"></param>
/// <param name="crit"></param>
/// <returns></returns>
private Criterium CloseCriterium(Criterium crit, string resourceType, int level)
{
List<string> targeted = crit.GetTargetedReferenceTypes(resourceType);
List<string> allKeys = new List<string>();
var errors = new List<Exception>();
foreach (var target in targeted)
{
try {
Criterium innerCriterium = (Criterium)crit.Operand;
var keys = CollectKeys(target, new List<Criterium> { innerCriterium }, ++level); //Recursive call to CollectKeys!
allKeys.AddRange(keys.Select(k => k.ToString()));
}
catch (Exception ex)
{
errors.Add(ex);
}
}
if (errors.Count == targeted.Count())
{
//It is possible that some of the targets don't support the current parameter. But if none do, there is a serious problem.
throw new ArgumentException(String.Format("None of the possible target resources support querying for parameter {0}", crit.ParamName));
}
crit.Operator = Operator.IN;
crit.Operand = ChoiceValue.Parse(String.Join(",", allKeys));
return crit;
}
/// <summary>
/// Will match up the children of the current element in diffNav to the children of the element in snapNav.
/// </summary>
/// <param name="snapNav"></param>
/// <param name="diffNav"></param>
/// <returns>Returns a list of Bookmark combinations, the first bookmark pointing to an element in the base,
/// the second a bookmark in the diff that matches the bookmark in the base.</returns>
/// <remarks>Will match slices to base elements, re-sliced slices to slices and type-slice shorthands to choie elements.
/// Note that this function may expand snapNav when it encounters paths in the differential that move into the complex types
/// of one of snap's elements. (NO NEED, it just has to match direct children, not deeper)
/// This function assumes the differential is not sparse: it must have parent nodes for all child constraint paths.
/// </remarks>
public List<MatchInfo> Match(ElementNavigator snapNav, ElementNavigator diffNav)
{
if (!snapNav.HasChildren) throw Error.Argument("snapNav", "Cannot match base to diff: element '{0}' in snap has no children".FormatWith(snapNav.PathName));
if (!diffNav.HasChildren) throw Error.Argument("diffNav", "Cannot match base to diff: element '{0}' in diff has no children".FormatWith(diffNav.PathName));
// These bookmarks are used only in the finally {} to make sure we don't alter the position of the navs when leaving the merger
var baseStartBM = snapNav.Bookmark();
var diffStartBM = diffNav.Bookmark();
snapNav.MoveToFirstChild();
diffNav.MoveToFirstChild();
var choiceNames = listChoiceElements(snapNav);
var result = new List<MatchInfo>();
try
{
do
{
// First, match directly -> try to find the child in base with the same name as the path in the diff
if (snapNav.PathName != diffNav.PathName && !snapNav.MoveToNext(diffNav.PathName))
{
// Not found, maybe this is a type slice shorthand, look if we have a matching choice prefix in snap
var typeSliceShorthand = diffNav.PathName;
// Try to match nameXXXXX to name[x]
var matchingChoice = choiceNames.SingleOrDefault(prefix => isPossibleTypeSlice(prefix, typeSliceShorthand));
if (matchingChoice != null)
snapNav.MoveToNext(matchingChoice);
else
throw Error.InvalidOperation("Differential has a constraint for path '{0}', which does not exist in its base".FormatWith(diffNav.Path));
}
result.AddRange(constructMatch(snapNav, diffNav));
}
while (diffNav.MoveToNext());
}
finally
{
snapNav.ReturnToBookmark(baseStartBM);
diffNav.ReturnToBookmark(diffStartBM);
}
return result;
}
/// <summary>
/// Scan all xml files found by prepareFiles and find conformance resources + their id
/// </summary>
private void prepareResources()
{
if (_resourcesPrepared) return;
prepareFiles();
_resourceInformation = new List<ConformanceInformation>();
foreach (var file in _artifactFilePaths.Where(af => Path.GetExtension(af) == ".xml"))
{
if (file.EndsWith("dataelements.xml")) continue; // buggy file
try
{
var conformanceResources = readInformationFromFile(file).Where(ci =>
ResourceIdentity.IsRestResourceIdentity(ci.Url) &&
ModelInfo.IsConformanceResource((new ResourceIdentity(ci.Url)).ResourceType));
_resourceInformation.AddRange(conformanceResources);
}
catch(XmlException)
{
throw;
}
}
// Check for duplicate canonical urls, this is forbidden within a single source (and actually, universally,
// but if another source has the same url, the order of polling in the MultiArtifactSource matters)
var doubles = _resourceInformation.Where(ci=>ci.Url != null).GroupBy(ci => ci.Url).Where(group => group.Count() > 1);
if (doubles.Any())
{
throw Error.InvalidOperation("The source has found multiple Conformance Resource artifacts with the same canonical url: {0} appears at {1}"
.FormatWith(doubles.First().Key, String.Join(", ", doubles.First().Select(hit => hit.Origin))));
}
_resourcesPrepared = true;
}
public static IEnumerable<Tag> Remove(this IEnumerable<Tag> tags, IEnumerable<Tag> that)
{
var result = new List<Tag>();
result.AddRange(tags);
if (that != null)
result.RemoveAll(t => that.HasTag(t.Term, t.Scheme));
return result;
}
/// <summary>
/// Prepares the source by reading all files present in the directory (matching the mask, if given)
/// </summary>
private void prepareFiles()
{
if (_filesPrepared) return;
IEnumerable<string> masks;
if (Mask == null)
masks = new string[] { "*.*" };
else
masks = Mask.Split('|').Select(s => s.Trim()).Where(s => !String.IsNullOrEmpty(s));
// Add files present in the content directory
var allFiles = new List<string>();
foreach (var mask in masks)
{
allFiles.AddRange(Directory.GetFiles(_contentDirectory, mask, _includeSubs ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly));
}
allFiles.RemoveAll(name => Path.GetExtension(name) == ".exe" || Path.GetExtension(name) == ".dll");
_artifactFilePaths = new List<string>(allFiles);
_filesPrepared = true;
}
/// <summary>
/// Prepares the source by reading all files present in the directory (matching the mask, if given)
/// </summary>
public void Prepare()
{
#if !PORTABLE45
_artifactFiles = new List<string>();
IEnumerable<string> masks;
if (Mask == null)
masks = new string[] { "*.*" };
else
masks = Mask.Split('|').Select(s => s.Trim()).Where(s => !String.IsNullOrEmpty(s));
// Add files present in the content directory
var allFiles = new List<string>();
foreach (var mask in masks)
{
allFiles.AddRange(Directory.GetFiles(_contentDirectory, mask, _includeSubs ? SearchOption.AllDirectories : SearchOption.TopDirectoryOnly));
}
var files = allFiles.Where(name => Path.GetExtension(name) != "exe" && Path.GetExtension(name) != "dll");
_artifactFiles.AddRange(files);
_isPrepared = true;
#else
throw Error.NotImplemented("File based artifact source is not supported on the portable runtime");
#endif
}
public void SearchPatientByGenderMissing()
{
var patients = new List<ResourceEntry<Patient>>();
var bundle = client.Search<Patient>();
while (bundle != null && bundle.Entries.ByResourceType<Patient>().Count() > 0)
{
patients.AddRange(bundle.Entries.ByResourceType<Patient>());
bundle = client.Continue(bundle);
}
var patientsNoGender = patients.Where(p => p.Resource.Gender == null);
var nrOfPatientsWithMissingGender = patientsNoGender.Count();
var actual = client.Search<Patient>(new string[] { "gender:missing=true" }, pageSize: 500).Entries.ByResourceType<Patient>();
HttpTests.AssertCorrectNumberOfResults(nrOfPatientsWithMissingGender, actual.Count(), "Expected {0} patients without gender, but got {1}.");
}