public object GetValueFor(ItemsChoiceType choice)
{
var idx = GetIndexFor(choice);
if (idx == -1)
return null;
return Items[idx];
}
private int GetIndexFor(ItemsChoiceType choice)
{
for (int i = 0; i != ItemsElementName.Length; ++i)
if (ItemsElementName[i] == choice)
return i;
return -1;
}
protected virtual CodeExpression BuildConditionalExpression(
conditionalContainer container, ItemsChoiceType choiceType)
{
//grab the children
List<CodeExpression> children = new List<CodeExpression>();
for (int i = 0; i < container.Items.Length; i++)
{
if (container.Items[i] is conditionalContainer)
{
children.Add(BuildConditionalExpression((conditionalContainer)container.Items[i],
container.ItemsElementName[i]));
}
else if (container.Items[i] is actionEquals)
{
children.Add(BuildConditionalExpression((actionEquals)container.Items[i]));
}
else if (container.Items[i] is valueEquals)
{
children.Add(BuildConditionalExpression((valueEquals)container.Items[i],
container.ItemsElementName[i]));
}
else
{
throw new GatException("Unrecognized conditional item type: " +
container.Items[i].GetType());
}
}
//get the full expression
CodeExpression expr = null;
if (choiceType == ItemsChoiceType.none)
{
expr = new CodeBinaryOperatorExpression(children[0],
CodeBinaryOperatorType.IdentityEquality, new CodePrimitiveExpression(false));
for (int i = 1; i < children.Count; i++)
{
expr = new CodeBinaryOperatorExpression(expr,
CodeBinaryOperatorType.BooleanAnd,
new CodeBinaryOperatorExpression(children[i],
CodeBinaryOperatorType.IdentityEquality, new CodePrimitiveExpression(false)));
}
}
else if (choiceType == ItemsChoiceType.all ||
choiceType == ItemsChoiceType.any)
{
CodeBinaryOperatorType opType = choiceType == ItemsChoiceType.all ?
CodeBinaryOperatorType.BooleanAnd : CodeBinaryOperatorType.BooleanOr;
expr = children[0];
for (int i = 1; i < children.Count; i++)
{
expr = new CodeBinaryOperatorExpression(expr,
CodeBinaryOperatorType.BooleanOr, children[i]);
}
}
else
{
throw new GatException("Unrecognized choice type: " + choiceType);
}
return expr;
}
public static QueryRequestCqlQuery createQueryRequestCqlQuery(string name, string[] queryModifierItems, ItemsChoiceType[] queryModifierItemsChoiceType1,
Association targetAssociation, Group targetGroup)
{
QueryRequestCqlQuery arg = new QueryRequestCqlQuery();
arg.CQLQuery = new CQLQuery();
arg.CQLQuery.Target = new Object();
arg.CQLQuery.Target.name = name;
if ((queryModifierItems != null) && (queryModifierItemsChoiceType1 != null))
{
arg.CQLQuery.QueryModifier = new QueryModifier();
arg.CQLQuery.QueryModifier.countOnly = false;
arg.CQLQuery.QueryModifier.Items = queryModifierItems;
arg.CQLQuery.QueryModifier.ItemsElementName = queryModifierItemsChoiceType1;
}
if (targetAssociation != null)
arg.CQLQuery.Target.Item = targetAssociation;
else if (targetGroup != null)
arg.CQLQuery.Target.Item = targetGroup;
return arg;
}
public static CQLQueryResults getAnnotationOfAnnotationInfo()
{
object[] obj;
AIMTCGADataServicePortTypeClient proxy = new AIMTCGADataServicePortTypeClient();
string[] items = new string[] { "codeValue", "codeMeaning", "codingSchemeDesignator", "codingSchemeVersion", "annotatorConfidence" };
ItemsChoiceType[] itemsChoiceType1 = new ItemsChoiceType[] {
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames,
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames };
// Anatomic Entity
obj = null;
Attribute attrCodeValue = null;
Attribute attrCodeMeaning = null;
Attribute attrCodingSchemeDesignator = null;
Attribute attrCodingSchemeVersion = null;
Attribute attrAnnotatorConfidence = null;
return null;
}
public bool HasValueFor(ItemsChoiceType choice)
{
return GetValueFor(choice) != null;
}
private int GetIndexOf(ItemsChoiceType type)
{
var index = ItemsElementName.Select((x, i) => Tuple.Create(x, i)).Where(x => x.Item1 == type).Select(x => x.Item2 + 1).SingleOrDefault() - 1;
return index;
}
protected virtual CodeExpression BuildConditionalExpression(
valueEquals valEquals, ItemsChoiceType choiceType)
{
int regexIndex = -1;
if (valEquals.regex)
{
regexIndex = _regexes.Count;
_regexes.Add(valEquals.value);
}
if (choiceType == ItemsChoiceType.columnEquals) {
if (!valEquals.regex)
{
//context.Columns.Contains(VALUE_LITERAL)
return new CodeMethodInvokeExpression(new CodePropertyReferenceExpression(
new CodeVariableReferenceExpression("context"), "Columns"), "Contains",
new CodePrimitiveExpression(valEquals.value));
}
else
{
//context.IsRegexColumnPresent(_regexes[REGEX_INDEX])
return new CodeMethodInvokeExpression(new CodeMethodReferenceExpression(
new CodeVariableReferenceExpression("context"), "IsRegexColumnPresent"),
new CodeArrayIndexerExpression(new CodeFieldReferenceExpression(
null, "_regexes"), new CodePrimitiveExpression(regexIndex)));
}
}
else if (choiceType == ItemsChoiceType.schemaEquals ||
choiceType == ItemsChoiceType.tableEquals)
{
CodePropertyReferenceExpression propRef;
if (choiceType == ItemsChoiceType.schemaEquals)
{
propRef = new CodePropertyReferenceExpression(
new CodeVariableReferenceExpression("context"), "Schema");
}
else
{
propRef = new CodePropertyReferenceExpression(
new CodeVariableReferenceExpression("context"), "Table");
}
if (!valEquals.regex)
{
//VALUE_LITERAL.Equals(context.Schema/Table)
return new CodeMethodInvokeExpression(new CodeMethodReferenceExpression(
new CodePrimitiveExpression(valEquals.value), "Equals"),
propRef);
}
else
{
//_regexes[REGEX_INDEX].IsMatch(context.Schema/Table)
return new CodeMethodInvokeExpression(new CodeMethodReferenceExpression(
new CodeArrayIndexerExpression(new CodeFieldReferenceExpression(null,
"_regexes"), new CodePrimitiveExpression(regexIndex)), "IsMatch"),
propRef);
}
}
else
{
throw new GatException("Unrecognized choice type: " + choiceType);
}
}
private CQLQueryResults getClinicalTrialProtocolCQLInfo(string endPointUrl)
{
object[] obj;
CQLQueryResults result;
Association assoTrialDataProvenance = null;
Association assoClinicalTrialSubject = null;
Association assoClinicalTrialSite = null;
Association assoImage = null;
Association assoSeries = null;
Association assoStudy = null;
Association assoPatient = null;
ArrayList results = new ArrayList();
NCIACoreServicePortTypeClient proxy = new NCIACoreServicePortTypeClient();
proxy.Endpoint.Address = new System.ServiceModel.EndpointAddress(endPointUrl);
string[] items = new string[] { "protocolId", "protocolName" };
ItemsChoiceType[] itemsChoiceType1 = new ItemsChoiceType[] {
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames};
// Image
assoImage = null;
if (!_queryParameters.SliceThickness.IsEmpty)
{
Attribute attrPatient = this.CreateAttribute("sliceThickness", _queryParameters.SliceThickness);
Group grpPatient = CreateQRAttrAssoGroup.createGroup(attrPatient, LogicalOperator.AND);
assoImage = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Image", "imageCollection", grpPatient);
}
// Series
results = new ArrayList();
assoSeries = null;
obj = null;
if (assoImage != null)
results.Add(assoImage);
if (!_queryParameters.Modality.IsEmpty)
results.Add(this.CreateAttribute("modality", _queryParameters.Modality));
if (results.Count > 0)
obj = (object[])results.ToArray(typeof(object));
if (obj != null)
{
Group grpSeries = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoSeries = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Series", "seriesCollection", grpSeries);
}
// Study
obj = null;
assoStudy = null;
results = new ArrayList();
if (assoSeries != null)
results.Add(assoSeries);
if (!_queryParameters.StudyInstanceUID.IsEmpty)
results.Add(this.CreateAttribute("studyInstanceUID", _queryParameters.StudyInstanceUID));
assoStudy = null;
if (results.Count > 0)
obj = (object[])results.ToArray(typeof(object));
if (obj != null)
{
Group groupStudy = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoStudy = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Study", "studyCollection", groupStudy);
}
// TrialDataProvenance
assoTrialDataProvenance = null;
if (!_queryParameters.ProjectName.IsEmpty)
{
Attribute attrTrialDataProvenance = this.CreateAttribute("project", _queryParameters.ProjectName);
Group grpTrialDataProvenance = CreateQRAttrAssoGroup.createGroup(attrTrialDataProvenance, LogicalOperator.AND);
assoTrialDataProvenance = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.TrialDataProvenance", "dataProvenance", grpTrialDataProvenance);
}
// Patient
obj = null;
results = new ArrayList();
if (assoStudy != null)
results.Add(assoStudy);
if (assoTrialDataProvenance != null)
results.Add(assoTrialDataProvenance);
if (!_queryParameters.PatientBirthDate.IsEmpty)
results.Add(this.CreateAttribute("patientBirthDate", _queryParameters.PatientBirthDate));
if (!_queryParameters.PatientId.IsEmpty)
results.Add(this.CreateAttribute("patientId", _queryParameters.PatientId));
if (!_queryParameters.PatientName.IsEmpty)
results.Add(this.CreateAttribute("patientName", _queryParameters.PatientName));
if (!_queryParameters.PatientSex.IsEmpty)
results.Add(this.CreateAttribute("patientSex", _queryParameters.PatientSex));
if (results.Count > 0)
obj = (object[])results.ToArray(typeof(object));
if (obj != null)
{
Group patientGroup = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoPatient = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Patient", "patient", patientGroup);
}
// Clinical Trial Site
obj = null;
results = new ArrayList();
if (!_queryParameters.SiteId.IsEmpty)
results.Add(this.CreateAttribute("siteId", _queryParameters.SiteId));
if (!_queryParameters.SiteName.IsEmpty)
results.Add(this.CreateAttribute("siteName", _queryParameters.SiteName));
if (results.Count > 0)
obj = (object[])results.ToArray(typeof(object));
Group grpClinicalTrialSite = null;
if (obj != null)
{
grpClinicalTrialSite = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSite = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSite", "site", grpClinicalTrialSite);
}
// Clinical Trial Subject
results = new ArrayList();
if (assoClinicalTrialSite != null)
results.Add(assoClinicalTrialSite);
if (assoPatient != null)
results.Add(assoPatient);
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
Group grpClinicalTrialSubject = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSubject = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSubject", "subjectCollection", grpClinicalTrialSubject);
}
// Clinical Trial Protocol (Root)
obj = null;
results = new ArrayList();
if (assoClinicalTrialSubject != null)
results.Add(assoClinicalTrialSubject);
if (!_queryParameters.ProtocolId.IsEmpty)
results.Add(this.CreateAttribute("protocolId", _queryParameters.ProtocolId));
if (!_queryParameters.ProtocolName.IsEmpty)
results.Add(this.CreateAttribute("protocolName", _queryParameters.ProtocolName));
if (results.Count > 0)
obj = (object[])results.ToArray(typeof(object));
Group grpClinicalTrialProtocol = null;
if (obj != null)
{
grpClinicalTrialProtocol = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
}
QueryRequestCqlQuery arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("gov.nih.nci.ncia.domain.ClinicalTrialProtocol", items, itemsChoiceType1, null, grpClinicalTrialProtocol);
XmlDocument doc = XMLSerializingDeserializing.Serialize(arg);
Console.WriteLine(((System.Xml.XmlDocument)((System.Xml.XmlNode)(doc))).InnerXml);
try
{
result = proxy.query(arg);
}
catch (System.Net.WebException ex)
{
System.Console.WriteLine(ex.Message);
result = null;
}
catch (Exception e)
{
System.Console.WriteLine(e.Message);
result = null;
throw new GridServicerException("Error querying NCIA Grid", e);
}
return result;
}
private static string GetStringItemFromPosition(Position position, ItemsChoiceType itemsChoice)
{
var indItemChoice = position.ItemsElementName.ToList().FindIndex(x => x == itemsChoice);
return indItemChoice >= 0 ? position.Items[indItemChoice] : null;
}
private string Write3_ItemsChoiceType(ItemsChoiceType v)
{
switch (v)
{
case ItemsChoiceType.ExcludeQuery:
return "ExcludeQuery";
case ItemsChoiceType.MaxValueQuery:
return "MaxValueQuery";
case ItemsChoiceType.MinValueQuery:
return "MinValueQuery";
case ItemsChoiceType.RegularQuery:
return "RegularQuery";
}
long num = (long) v;
throw base.CreateInvalidEnumValueException(num.ToString(CultureInfo.InvariantCulture), "Microsoft.PowerShell.Cmdletization.Xml.ItemsChoiceType");
}
private MessageRefType FindMessage(InterfaceOperationType op2, ItemsChoiceType type)
{
for (int i = 0; i < op2.ItemsElementName.Length; i++)
{
if (op2.ItemsElementName[i] == type)
return op2.Items[i] as MessageRefType;
}
return null;
}
public void Init()
{
Items = new object[] { 1, 2 };
ItemsElementName = new ItemsChoiceType[] { ItemsChoiceType.In, ItemsChoiceType.Es };
}
public RightNowFieldAttribute(string name, ItemsChoiceType type)
{
CanUpdate = true;
FieldType = type;
Name = name;
}
private CQLQueryResults getPatientCQLInfo(string endPointUrl)
{
object[] obj;
CQLQueryResults result = null;
Association assoClinicalTrialSite = null;
Association assoClinicalTrialProtocol = null;
Association assoClinicalTrialSubject = null;
Association assoImage = null;
Association assoTrialDataProvenance = null;
Association assoSeries = null;
Association assoStudy = null;
ArrayList results = new ArrayList();
NCIACoreServicePortTypeClient proxy = new NCIACoreServicePortTypeClient();
proxy.Endpoint.Address = new System.ServiceModel.EndpointAddress(endPointUrl);
string[] items = new string[] { "ethnicGroup", "patientBirthDate", "patientId", "patientName", "patientSex" };
ItemsChoiceType[] itemsChoiceType1 = new ItemsChoiceType[] {
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames,
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames
};
// TrialDataProvenance
assoTrialDataProvenance = null;
if (!_queryParameters.ProjectName.IsEmpty)
{
Attribute attrTrialDataProvenance = this.CreateAttribute("project", _queryParameters.ProjectName);
Group grpTrialDataProvenance = CreateQRAttrAssoGroup.createGroup(attrTrialDataProvenance, LogicalOperator.AND);
assoTrialDataProvenance = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.TrialDataProvenance", "dataProvenance", grpTrialDataProvenance);
}
// ClinicalTrial Site
assoClinicalTrialSite = null;
obj = null;
results = new ArrayList();
if (!_queryParameters.SiteId.IsEmpty)
{
results.Add(this.CreateAttribute("siteId", _queryParameters.SiteId));
}
if (!_queryParameters.SiteName.IsEmpty)
{
results.Add(this.CreateAttribute("siteName", _queryParameters.SiteName));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
Group grpClinicalTrialSite = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSite = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSite", "site", grpClinicalTrialSite);
}
// ClinicalTrial Protocol
assoClinicalTrialProtocol = null;
obj = null;
results = new ArrayList();
if (!_queryParameters.ProtocolId.IsEmpty)
{
results.Add(this.CreateAttribute("protocolId", _queryParameters.ProtocolId));
}
if (!_queryParameters.ProtocolName.IsEmpty)
{
results.Add(this.CreateAttribute("protocolName", _queryParameters.ProtocolName));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
Group grpClinicalTrialProtocol = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialProtocol = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialProtocol",
"protocol", grpClinicalTrialProtocol);
}
// Clinical Trial Subject
obj = null;
results = new ArrayList();
assoClinicalTrialSubject = null;
if (assoClinicalTrialSite != null)
{
results.Add(assoClinicalTrialSite);
}
if (assoClinicalTrialProtocol != null)
{
results.Add(assoClinicalTrialProtocol);
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
Group grpClinicalTrialSubject = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSubject = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSubject",
"subjectCollection", grpClinicalTrialSubject);
}
// Image
assoImage = null;
if (!_queryParameters.SliceThickness.IsEmpty)
{
Attribute attrPatient = this.CreateAttribute("sliceThickness", _queryParameters.SliceThickness);
Group grpPatient = CreateQRAttrAssoGroup.createGroup(attrPatient, LogicalOperator.AND);
assoImage = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Image", "imageCollection", grpPatient);
}
// Series
assoSeries = null;
obj = null;
results = new ArrayList();
Attribute attrSeries = null;
if (assoImage != null)
{
results.Add(assoImage);
}
if (!_queryParameters.Modality.IsEmpty)
{
attrSeries = this.CreateAttribute("modality", _queryParameters.Modality);
}
if (attrSeries != null)
{
results.Add(attrSeries);
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
Group grpSeries = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoSeries = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Series", "seriesCollection", grpSeries);
}
// Study
obj = null;
assoStudy = null;
results = new ArrayList();
if (assoSeries != null)
{
results.Add(assoSeries);
}
if (!_queryParameters.StudyInstanceUID.IsEmpty)
{
results.Add(this.CreateAttribute("studyInstanceUID", _queryParameters.StudyInstanceUID));
}
assoStudy = null;
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
Group groupStudy = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoStudy = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Study", "studyCollection", groupStudy);
}
// Patient
obj = null;
results = new ArrayList();
if (assoClinicalTrialSubject != null)
{
results.Add(assoClinicalTrialSubject);
}
if (assoTrialDataProvenance != null)
{
results.Add(assoTrialDataProvenance);
}
if (assoStudy != null)
{
results.Add(assoStudy);
}
if (!_queryParameters.PatientBirthDate.IsEmpty)
{
results.Add(this.CreateAttribute("patientBirthDate", _queryParameters.PatientBirthDate));
}
if (!_queryParameters.PatientId.IsEmpty)
{
results.Add(this.CreateAttribute("patientId", _queryParameters.PatientId));
}
if (!_queryParameters.PatientName.IsEmpty)
{
results.Add(this.CreateAttribute("patientName", _queryParameters.PatientName));
}
if (!_queryParameters.PatientSex.IsEmpty)
{
results.Add(this.CreateAttribute("patientSex", _queryParameters.PatientSex));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
Group groupPatient = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
QueryRequestCqlQuery arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("gov.nih.nci.ncia.domain.Patient", items, itemsChoiceType1, null, groupPatient);
XmlDocument doc = XMLSerializingDeserializing.Serialize(arg);
try
{
result = proxy.query(arg);
}
catch (System.Net.WebException ex)
{
System.Console.WriteLine(ex.Message);
result = null;
}
catch (Exception e)
{
System.Console.WriteLine(e.Message);
result = null;
throw new GridServicerException("Error querying NCIA Grid", e);
}
return(result);
}
public object GetSingleItemByEnum(ItemsChoiceType choiceType)
{
if (itemList == null)
itemList = new List<ItemsChoiceType>(this.ItemsElementName);
var returnvalue = itemList.FindIndex(x => x == choiceType);
if (returnvalue > -1)
return this.Items[returnvalue];
return null;
}
