/// <summary>
/// Gets URL upon calling which the required study data can be retrieved.
/// </summary>
/// <param name="studyUIDs">List of UIDs for the studies to be retrieved</param>
/// <param name="endPointUrl">URL of the NBIA Data Service to query. This is NOT the Data Transfer URL!</param>
/// <returns>URL that returns zip file with the studies</returns>
public string retrieveStudyURL(string[] studyUIDs, string endPointUrl)
{
TransferServiceContextService.DataTransferDescriptor dtd;
using (NCIACoreServicePortTypeClient proxy = new NCIACoreServicePortTypeClient("NCIACoreServicePortTypePort", endPointUrl))
{
try
{
TransferServiceContextReference tras = proxy.retrieveDicomDataByStudyUIDs(studyUIDs); // new TransferServiceContextReference();
EndpointReferenceType endPoint = tras.EndpointReference; // new EndpointReferenceType();
AddressHeader[] ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
for (int lcv = 0; lcv < ah.Length; lcv++)
{
XmlElement refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
EndpointAddress ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
// create binding by hand so we don't have to associate a config file with a dll
BasicHttpBinding binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
TransferServiceContextPortTypeClient transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (System.Net.WebException ex)
{
System.Console.WriteLine(ex.Message); //never gets here
throw new GridServicerException("Error querying NCIA Grid", ex);
}
catch (Exception e)
{
System.Console.WriteLine(e.Message); //never gets here
throw new GridServicerException("Error retrieving from NCIA Grid", e);
}
}
if (string.IsNullOrEmpty(dtd.url))
{
return(dtd.url);
}
else
{
return(null);
}
}
public string retrieveStudyURL(string[] studyUIDs, string endPointUrl)
{
TransferServiceContextService.DataTransferDescriptor dtd;
try
{
var proxy = new NCIACoreServicePortTypeClient();
var tras = proxy.retrieveDicomDataByStudyUIDs(studyUIDs);
var endPoint = tras.EndpointReference;
var ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
proxy.Endpoint.Address = new EndpointAddress(endPointUrl);
for (var lcv = 0; lcv < ah.Length; lcv++)
{
var refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
var ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
var binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
var transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (WebException ex)
{
Console.WriteLine(ex.Message);
throw new GridServicerException("Error querying NCIA Grid", ex);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
throw new GridServicerException("Error retrieving from NCIA Grid", e);
}
if (dtd.url != null || dtd.url.Equals(""))
{
return(dtd.url);
}
else
{
return(null);
}
}
/// <summary>
/// Gets URL upon calling which the required study data can be retrieved.
/// </summary>
/// <param name="studyUIDs">List of UIDs for the studies to be retrieved</param>
/// <param name="endPointUrl">URL of the NBIA Data Service to query. This is NOT the Data Transfer URL!</param>
/// <returns>URL that returns zip file with the studies</returns>
public string retrieveStudyURL(string[] studyUIDs, string endPointUrl)
{
TransferServiceContextService.DataTransferDescriptor dtd;
using (NCIACoreServicePortTypeClient proxy = new NCIACoreServicePortTypeClient("NCIACoreServicePortTypePort", endPointUrl))
{
try
{
TransferServiceContextReference tras = proxy.retrieveDicomDataByStudyUIDs(studyUIDs); // new TransferServiceContextReference();
EndpointReferenceType endPoint = tras.EndpointReference; // new EndpointReferenceType();
AddressHeader[] ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
for (int lcv = 0; lcv < ah.Length; lcv++)
{
XmlElement refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
EndpointAddress ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
// create binding by hand so we don't have to associate a config file with a dll
BasicHttpBinding binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
TransferServiceContextPortTypeClient transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (System.Net.WebException ex)
{
System.Console.WriteLine(ex.Message); //never gets here
throw new GridServicerException("Error querying NCIA Grid", ex);
}
catch (Exception e)
{
System.Console.WriteLine(e.Message); //never gets here
throw new GridServicerException("Error retrieving from NCIA Grid", e);
}
}
if (string.IsNullOrEmpty(dtd.url))
return dtd.url;
else
return null;
}
public string retrieveStudyURL(string[] studyUIDs, string endPointUrl)
{
TransferServiceContextService.DataTransferDescriptor dtd;
try
{
var proxy = new NCIACoreServicePortTypeClient();
var tras = proxy.retrieveDicomDataByStudyUIDs(studyUIDs);
var endPoint = tras.EndpointReference;
var ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
proxy.Endpoint.Address = new EndpointAddress(endPointUrl);
for (var lcv = 0; lcv < ah.Length; lcv++)
{
var refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
var ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
var binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
var transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (WebException ex)
{
Console.WriteLine(ex.Message);
throw new GridServicerException("Error querying NCIA Grid", ex);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
throw new GridServicerException("Error retrieving from NCIA Grid", e);
}
if (dtd.url != null || dtd.url.Equals(""))
return dtd.url;
else
return null;
}
private CQLQueryResults getClinicalTrialSiteCQLInfo(string endPointUrl)
{
object[] obj;
CQLQueryResults result;
Association assoTrialDataProvenance = null;
Association assoClinicalTrialProtocol = null;
Association assoClinicalTrialSubject = 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[] { "siteId", "siteName" };
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);
}
assoClinicalTrialProtocol = null;
obj = null;
results = new ArrayList();
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));
if (obj != null)
{
var grpClinicalTrialProtocol = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
assoClinicalTrialProtocol = CreateQRAttrAssoGroup.createAssociation("gov.nih.nci.ncia.domain.ClinicalTrialProtocol",
"protocol", grpClinicalTrialProtocol);
}
results = new ArrayList();
if (assoClinicalTrialProtocol != null)
results.Add(assoClinicalTrialProtocol);
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.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 groupClinicalTrialSite = null;
if (obj != null)
groupClinicalTrialSite = CreateQRAttrAssoGroup.createGroup(obj, LogicalOperator.AND);
var arg = CreateQRAttrAssoGroup.createQueryRequestCqlQuery("gov.nih.nci.ncia.domain.ClinicalTrialSite", items, itemsChoiceType1, null, groupClinicalTrialSite);
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 void retrieveStudyUID(string[] str)
{
TransferServiceContextService.DataTransferDescriptor dtd =null;
TransferServiceContextPortTypeClient transProxy = null;
NCIACoreServicePortTypeClient proxy = null;
try
{
proxy = new NCIACoreServicePortTypeClient();
TransferServiceContextReference tras = proxy.retrieveDicomDataByStudyUIDs(str); // new TransferServiceContextReference();
EndpointReferenceType endPoint = tras.EndpointReference; // new EndpointReferenceType();
AddressHeader[] ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
for (int lcv = 0; lcv < ah.Length; lcv++)
{
XmlElement refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
EndpointAddress ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
// create binding by hand so we don't have to associate a config file with a dll
BasicHttpBinding binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (System.Net.WebException ex)
{
System.Console.WriteLine(ex.Message);
}
catch (Exception e)
{
System.Console.WriteLine(e.Message);
throw new GridServicerException("Error querying NCIA Grid", e);
}
if (dtd.url != null && dtd.url.Equals(""))
{
WebRequest wr = WebRequest.Create(dtd.url);
WebResponse resp = wr.GetResponse();
byte[] buf = new byte[8192];
int read;
if (transProxy != null && proxy != null)
{
try
{
Stream stream = resp.GetResponseStream();
FileStream fs = new FileStream(_directory + "/" + str[0] + ".zip", FileMode.Create, FileAccess.Write);
while ((read = stream.Read(buf, 0, buf.Length)) > 0)
{
fs.Write(buf, 0, read);
}
fs.Close();
stream.Close();
resp.Close();
proxy.Close();
transProxy.Close();
}
catch (IOException ioe)
{
throw new GridServicerException("Error writting zip file from caGrid", ioe);
}
}
}
}
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 void retrieveStudyUID(string[] str)
{
TransferServiceContextService.DataTransferDescriptor dtd = null;
TransferServiceContextPortTypeClient transProxy = null;
NCIACoreServicePortTypeClient proxy = null;
try
{
proxy = new NCIACoreServicePortTypeClient();
var tras = proxy.retrieveDicomDataByStudyUIDs(str);
var endPoint = tras.EndpointReference;
var ah = new AddressHeader[endPoint.ReferenceProperties.Any.Length];
for (var lcv = 0; lcv < ah.Length; lcv++)
{
var refProp = endPoint.ReferenceProperties.Any[lcv];
ah[lcv] = AddressHeader.CreateAddressHeader(refProp.LocalName, refProp.NamespaceURI, refProp.InnerText);
}
var ea = new EndpointAddress(new Uri(endPoint.Address.Value), ah);
var binding = new BasicHttpBinding(BasicHttpSecurityMode.None);
binding.Name = "TransferServiceContextPortTypePort";
transProxy = new TransferServiceContextPortTypeClient(binding, ea);
dtd = transProxy.getDataTransferDescriptor();
}
catch (WebException ex)
{
Console.WriteLine(ex.Message);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
throw new GridServicerException("Error querying NCIA Grid", e);
}
if (dtd.url != null && dtd.url.Equals(""))
{
var wr = WebRequest.Create(dtd.url);
var resp = wr.GetResponse();
var buf = new byte[8192];
int read;
if (transProxy != null && proxy != null)
{
try
{
var stream = resp.GetResponseStream();
var fs = new FileStream(_directory + "/" + str[0] + ".zip", FileMode.Create, FileAccess.Write);
while ((read = stream.Read(buf, 0, buf.Length)) > 0)
{
fs.Write(buf, 0, read);
}
fs.Close();
stream.Close();
resp.Close();
proxy.Close();
transProxy.Close();
}
catch (IOException ioe)
{
throw new GridServicerException("Error writting zip file from caGrid", ioe);
}
}
}
}
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;
}
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);
}
