protected string[] processCQLObjectResult(AIMTCGAService.CQLQueryResults response)
{
var results = new ArrayList();
foreach (CQLObjectResult result in response.Items)
{
results.Add(XMLSerializingDeserializing.Serialize(result.Any).InnerXml);
}
return((string[])results.ToArray(typeof(string)));
}
private CQLQueryResults getAnnotationOfAnnotationCQLInfo()
{
object[] obj = null;
Attribute attrTemp = null;
Association assoTemp = null;
var proxy = new AIM3DataServicePortTypeClient();
proxy.Endpoint.Address = new System.ServiceModel.EndpointAddress(AIMDataServiceSettings.Default.AIMDataServiceUrl);
var associationList = new ArrayList();
obj = null;
Association aecAssociation = null;
foreach (var queryData in _queryParameters.AecQueryParameters)
{
var results = new ArrayList();
if (!queryData.CodeValue.IsEmpty)
{
results.Add(CreateAttribute("codeValue", queryData.CodeValue));
}
if (!queryData.CodeMeaning.IsEmpty)
{
results.Add(CreateAttribute("codeMeaning", queryData.CodeMeaning));
}
if (!queryData.CodingSchemeDesignator.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeDesignator", queryData.CodingSchemeDesignator));
}
if (!queryData.CodingSchemeVersion.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeVersion", queryData.CodingSchemeVersion));
}
if (!queryData.Confidence.IsEmpty)
{
results.Add(CreateAttribute("annotatorConfidence", queryData.Confidence));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
Group grpAnnatomicEntityCharacteristic = null;
if (obj.Length > 1)
{
grpAnnatomicEntityCharacteristic = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
obj = null;
}
else
{
attrTemp = obj[0] as Attribute;
}
aecAssociation = CreateQRAttrAssoGroup.createAssociation("edu.northwestern.radiology.aim.AnatomicEntityCharacteristic", "anatomicEntityCharacteristicCollection", grpAnnatomicEntityCharacteristic, attrTemp, null);
}
}
obj = null;
if (aecAssociation != null && _queryParameters.AeQueryParameters.Count == 0)
{
var queryData = new AimAnatomicEntityQueryData();
queryData.CodeMeaning = new QueryData(String.Empty, QueryPredicate.LIKE);
_queryParameters.AeQueryParameters.Add(queryData);
}
foreach (var queryData in _queryParameters.AeQueryParameters)
{
var results = new ArrayList();
if (!queryData.CodeValue.IsEmpty)
{
results.Add(CreateAttribute("codeValue", queryData.CodeValue));
}
//if (!queryData.CodeMeaning.IsEmpty)
results.Add(CreateAttribute("codeMeaning", queryData.CodeMeaning));
if (!queryData.CodingSchemeDesignator.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeDesignator", queryData.CodingSchemeDesignator));
}
if (!queryData.CodingSchemeVersion.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeVersion", queryData.CodingSchemeVersion));
}
if (!queryData.Confidence.IsEmpty)
{
results.Add(CreateAttribute("annotatorConfidence", queryData.Confidence));
}
if (aecAssociation != null)
{
results.Add(aecAssociation);
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
Group grpAnnatomicEntity = null;
if (obj.Length > 1)
{
grpAnnatomicEntity = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
obj = null;
}
else
{
attrTemp = obj[0] as Attribute;
}
associationList.Add(CreateQRAttrAssoGroup.createAssociation("edu.northwestern.radiology.aim.AnatomicEntity", "anatomicEntityCollection", grpAnnatomicEntity, attrTemp, null));
}
}
obj = null;
Association iocAssociation = null;
foreach (var queryData in _queryParameters.ImcQueryParameters)
{
var results = new ArrayList();
if (!queryData.CodeValue.IsEmpty)
{
results.Add(CreateAttribute("codeValue", queryData.CodeValue));
}
if (!queryData.CodeMeaning.IsEmpty)
{
results.Add(CreateAttribute("codeMeaning", queryData.CodeMeaning));
}
if (!queryData.CodingSchemeDesignator.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeDesignator", queryData.CodingSchemeDesignator));
}
if (!queryData.CodingSchemeVersion.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeVersion", queryData.CodingSchemeVersion));
}
if (!queryData.Confidence.IsEmpty)
{
results.Add(CreateAttribute("annotatorConfidence", queryData.Confidence));
}
if (!queryData.Comment.IsEmpty)
{
results.Add(CreateAttribute("comment", queryData.Comment));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
Group grpImagingObservationCharacteristic = null;
if (obj.Length > 1)
{
grpImagingObservationCharacteristic = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
obj = null;
}
else
{
attrTemp = obj[0] as Attribute;
}
iocAssociation = CreateQRAttrAssoGroup.createAssociation("edu.northwestern.radiology.aim.ImagingObservationCharacteristic", "imagingObservationCharacteristicCollection", grpImagingObservationCharacteristic, attrTemp, null);
}
}
obj = null;
if (iocAssociation != null && _queryParameters.ImQueryParameters.Count == 0)
{
var queryData = new AimImagingObservationQueryData();
queryData.CodeMeaning = new QueryData(String.Empty, QueryPredicate.LIKE);
_queryParameters.ImQueryParameters.Add(queryData);
}
foreach (var queryData in _queryParameters.ImQueryParameters)
{
var results = new ArrayList();
if (!queryData.CodeValue.IsEmpty)
{
results.Add(CreateAttribute("codeValue", queryData.CodeValue));
}
//if (!queryData.CodeMeaning.IsEmpty)
results.Add(CreateAttribute("codeMeaning", queryData.CodeMeaning));
if (!queryData.CodingSchemeDesignator.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeDesignator", queryData.CodingSchemeDesignator));
}
if (!queryData.CodingSchemeVersion.IsEmpty)
{
results.Add(CreateAttribute("codingSchemeVersion", queryData.CodingSchemeVersion));
}
if (!queryData.Comment.IsEmpty)
{
results.Add(CreateAttribute("comment", queryData.Comment));
}
if (!queryData.Confidence.IsEmpty)
{
results.Add(CreateAttribute("annotatorConfidence", queryData.Confidence));
}
if (iocAssociation != null)
{
results.Add(iocAssociation);
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
attrTemp = null;
Group grpImagingObservation = null;
if (obj.Length > 1)
{
grpImagingObservation = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
obj = null;
}
else
{
attrTemp = obj[0] as Attribute;
}
associationList.Add(CreateQRAttrAssoGroup.createAssociation("edu.northwestern.radiology.aim.ImagingObservation", "imagingObservationCollection", grpImagingObservation, attrTemp, null));
}
}
obj = null;
foreach (var queryData in _queryParameters.UserParameters)
{
var results = new ArrayList();
if (!queryData.IsEmpty)
{
results.Add(CreateAttribute("loginName", queryData));
results.Add(CreateAttribute("name", queryData));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(Attribute));
}
if (obj != null && obj.Length > 0)
{
Group grpAnnatomicEntityCharacteristic = null;
if (obj.Length > 1)
{
grpAnnatomicEntityCharacteristic = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.OR);
obj = null;
}
else
{
attrTemp = obj[0] as Attribute;
}
associationList.Add(CreateQRAttrAssoGroup.createAssociation("edu.northwestern.radiology.aim.User", "user", grpAnnatomicEntityCharacteristic, attrTemp, null));
}
}
obj = null;
Group grpAnnotationOfAnnotation = null;
if (associationList.Count > 0)
{
obj = (object[])associationList.ToArray(typeof(Association));
}
if (obj != null && obj.Length > 0)
{
assoTemp = null;
if (obj.Length > 1)
{
grpAnnotationOfAnnotation = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
}
else
{
assoTemp = obj[0] as Association;
}
}
var arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("edu.northwestern.radiology.aim.AnnotationOfAnnotation", null, null, assoTemp, grpAnnotationOfAnnotation);
var doc = XMLSerializingDeserializing.Serialize(arg);
Console.WriteLine(doc.InnerXml);
CQLQueryResults result;
try
{
result = proxy.query(arg);
}
catch (System.Net.WebException ex)
{
Console.WriteLine(ex.Message);
result = null;
}
catch (Exception e)
{
Console.WriteLine(e.Message);
result = null;
throw new GridServicerException("Error querying AIM data service", e);
}
return(result);
}
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;
var results = new ArrayList();
var proxy = new NCIACoreServicePortTypeClient();
proxy.Endpoint.Address = new System.ServiceModel.EndpointAddress(endPointUrl);
var items = new[] { "protocolId", "protocolName" };
var itemsChoiceType1 = new[] {
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames
};
assoImage = null;
if (!_queryParameters.SliceThickness.IsEmpty)
{
var attrPatient = CreateAttribute("sliceThickness", _queryParameters.SliceThickness);
var grpPatient = CreateQRAttrAssoGroup.createGroup(attrPatient, LogicalOperator.AND);
assoImage = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Image", "imageCollection", grpPatient);
}
results = new ArrayList();
assoSeries = null;
obj = null;
if (assoImage != null)
{
results.Add(assoImage);
}
if (!_queryParameters.Modality.IsEmpty)
{
results.Add(CreateAttribute("modality", _queryParameters.Modality));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
var grpSeries = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoSeries = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Series", "seriesCollection", grpSeries);
}
obj = null;
assoStudy = null;
results = new ArrayList();
if (assoSeries != null)
{
results.Add(assoSeries);
}
if (!_queryParameters.StudyInstanceUID.IsEmpty)
{
results.Add(CreateAttribute("studyInstanceUID", _queryParameters.StudyInstanceUID));
}
assoStudy = null;
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
var groupStudy = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoStudy = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Study", "studyCollection", groupStudy);
}
assoTrialDataProvenance = null;
if (!_queryParameters.ProjectName.IsEmpty)
{
var attrTrialDataProvenance = CreateAttribute("project", _queryParameters.ProjectName);
var grpTrialDataProvenance = CreateQRAttrAssoGroup.createGroup(attrTrialDataProvenance, LogicalOperator.AND);
assoTrialDataProvenance = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.TrialDataProvenance", "dataProvenance", grpTrialDataProvenance);
}
obj = null;
results = new ArrayList();
if (assoStudy != null)
{
results.Add(assoStudy);
}
if (assoTrialDataProvenance != null)
{
results.Add(assoTrialDataProvenance);
}
if (!_queryParameters.PatientBirthDate.IsEmpty)
{
results.Add(CreateAttribute("patientBirthDate", _queryParameters.PatientBirthDate));
}
if (!_queryParameters.PatientId.IsEmpty)
{
results.Add(CreateAttribute("patientId", _queryParameters.PatientId));
}
if (!_queryParameters.PatientName.IsEmpty)
{
results.Add(CreateAttribute("patientName", _queryParameters.PatientName));
}
if (!_queryParameters.PatientSex.IsEmpty)
{
results.Add(CreateAttribute("patientSex", _queryParameters.PatientSex));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null)
{
var patientGroup = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoPatient = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Patient", "patient", patientGroup);
}
obj = null;
results = new ArrayList();
if (!_queryParameters.SiteId.IsEmpty)
{
results.Add(CreateAttribute("siteId", _queryParameters.SiteId));
}
if (!_queryParameters.SiteName.IsEmpty)
{
results.Add(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);
}
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));
var grpClinicalTrialSubject = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSubject = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSubject", "subjectCollection", grpClinicalTrialSubject);
}
obj = null;
results = new ArrayList();
if (assoClinicalTrialSubject != null)
{
results.Add(assoClinicalTrialSubject);
}
if (!_queryParameters.ProtocolId.IsEmpty)
{
results.Add(CreateAttribute("protocolId", _queryParameters.ProtocolId));
}
if (!_queryParameters.ProtocolName.IsEmpty)
{
results.Add(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);
}
var arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("gov.nih.nci.ncia.domain.ClinicalTrialProtocol", items, itemsChoiceType1, null, grpClinicalTrialProtocol);
var doc = XMLSerializingDeserializing.Serialize(arg);
Console.WriteLine(doc.InnerXml);
try
{
result = proxy.query(arg);
}
catch (System.Net.WebException ex)
{
Console.WriteLine(ex.Message);
result = null;
}
catch (Exception e)
{
Console.WriteLine(e.Message);
result = null;
throw new GridServicerException("Error querying NCIA Grid", e);
}
return(result);
}
private CQLQueryResults getStudyCQLInfo(string endPointUrl)
{
object[] obj;
CQLQueryResults result;
Association assoImage = null;
Association assoTrialDataProvenance = null;
Association assoSeries = null;
Association assoClinicalTrialSite = null;
Association assoClinicalTrialProtocol = null;
Association assoClinicalTrialSubject = null;
Association assoPatient = null;
ArrayList results = new ArrayList();
NCIACoreServicePortTypeClient proxy = new NCIACoreServicePortTypeClient();
proxy.Endpoint.Address = new System.ServiceModel.EndpointAddress(endPointUrl);
string[] items = new string[] { "additionalPatientHistory",
"admittingDiagnosesCodeSequence", "occupation", "patientAge", "patientSize", "patientWeight",
"studyDate", "studyId", "studyInstanceUID", "studyTime", "timePointDescription", "timePointId" };
ItemsChoiceType[] itemsChoiceType1 = new ItemsChoiceType[] {
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames,
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames,
ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames, ItemsChoiceType.AttributeNames,
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
assoSeries = null;
obj = null;
results = new ArrayList();
if (assoImage != null)
{
results.Add(assoImage);
}
if (!_queryParameters.Modality.IsEmpty)
{
results.Add(this.CreateAttribute("modality", _queryParameters.Modality));
}
if (results.Count > 0 || assoImage != null)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
Group grpSeries = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoSeries = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Series", "seriesCollection", grpSeries);
}
// 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 && obj.Length > 0)
{
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 && obj.Length > 0)
{
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 && obj.Length > 0)
{
Group grpClinicalTrialSubject = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialSubject = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialSubject",
"subjectCollection", grpClinicalTrialSubject);
}
// Patient
obj = null;
results = new ArrayList();
if (assoClinicalTrialSubject != null)
{
results.Add(assoClinicalTrialSubject);
}
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 && obj.Length > 0)
{
Group patientGroup = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoPatient = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.Patient", "patient", patientGroup);
}
// Study
obj = null;
results = new ArrayList();
Group groupStudy = null;
if (assoSeries != null)
{
results.Add(assoSeries);
}
if (assoPatient != null)
{
results.Add(assoPatient);
}
if (!_queryParameters.StudyInstanceUID.IsEmpty)
{
results.Add(this.CreateAttribute("studyInstanceUID", _queryParameters.StudyInstanceUID));
}
if (results.Count > 0)
{
obj = (object[])results.ToArray(typeof(object));
}
if (obj != null && obj.Length > 0)
{
groupStudy = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
}
QueryRequestCqlQuery arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("gov.nih.nci.ncia.domain.Study", items, itemsChoiceType1, null, groupStudy);
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);
}
