/// <summary>
/// Creates a list of actively recruiting sites only
/// </summary>
/// <param name="trial">Clinical trial</param>
private void RemoveNonRecruitingSites(ClinicalTrial trial)
{
if (trial.Sites != null)
{
trial.Sites = new List <ClinicalTrial.StudySite>(trial.Sites.Where(site => IsActivelyRecruiting(site)));
}
}
/// <summary>
/// Returns a Clinical Trial
/// </summary>
/// <param name="ID"></param>
/// <returns></returns>
public ClinicalTrial Get(string id)
{
ClinicalTrial trial = Client.Get(id);
RemoveNonRecruitingSites(trial);
return(trial);
}
/// <summary>
/// Gets the Primary Purpose and formats text
/// </summary>
/// <param name="trial"></param>
/// <returns>String - purpose</returns>
public string GetTrialType(ClinicalTrial trial)
{
///TODO: Verify if we need to add other_text and additioncal_qualifier_code to this text
string purpose = trial.GetPrimaryPurpose();
return(GetFormattedString(purpose));
}
public void FilterByHospital(ClinicalTrial trial, CTSSearchParams searchParams, IEnumerable <ClinicalTrial.StudySite> expectedSites)
{
SnippetControls.TrialVelocityTools tvt = new SnippetControls.TrialVelocityTools();
IEnumerable <ClinicalTrial.StudySite> actual = tvt.GetFilteredLocations(trial, searchParams);
Assert.Equal(expectedSites, actual, new ClinicalTrialsAPI.Test.StudySiteComparer());
}
private void SetupFieldAndUrlFilters(ClinicalTrial trial)
{
// Copying the Title & Short Title logic from Advanced Form
//set the page title as the protocol title
PageInstruction.AddFieldFilter("long_title", (fieldName, data) =>
{
data.Value = trial.BriefTitle;
});
PageInstruction.AddFieldFilter("short_title", (fieldName, data) =>
{
data.Value = trial.BriefTitle;
//Eh, When would this happen???
if (!string.IsNullOrWhiteSpace(trial.NCTID))
{
data.Value += " - " + trial.NCTID;
}
});
PageInstruction.AddFieldFilter("meta_description", (fieldname, data) =>
{
data.Value = trial.BriefTitle;
});
PageInstruction.AddUrlFilter("CurrentUrl", (name, url) =>
{
//Copy the params
//TODO: Really determine what to do with these params. If the search is invalid, we probably
//hsould not show them all.
foreach (KeyValuePair <string, string> param in this.ParsedReqUrlParams.QueryParameters)
{
url.QueryParameters.Add(param.Key, param.Value);
}
});
PageInstruction.AddUrlFilter("CanonicalUrl", (name, url) =>
{
// only the id should be provided for the canonical URL, so clear all query parameters and
// then add back id
url.QueryParameters.Clear();
url.QueryParameters.Add("id", trial.NCIID);
//url.QueryParameters.Add("id", TrialID);
});
// Override the social media URL (og:url)
PageInstruction.AddFieldFilter("og:url", (fieldName, data) =>
{
//Ok, this is weird, but... The OpenGraph URL is actually a field. It kind of makes sense,
//and it kind of does not. Really it should be a field that gets the og:url instead of the
//pretty URL.
//BUt here we are, and it is what we have. So let's replace the og:url with the canonical URL.
data.Value = PageInstruction.GetUrl(NCI.Web.CDE.PageAssemblyInstructionUrls.CanonicalUrl).ToString();
});
}
public static object GetAllSortedLocations(this ClinicalTrial trial)
{
return(new
{
USA = GetUSASortedLocations(trial),
Canada = GetCanadianSortedLocations(trial),
Other = GetOtherSortedLocations(trial)
});
}
/// <summary>
/// Loads a test trial from TrialExamples folder.
/// </summary>
/// <param name="trialName">The name of the file to load.</param>
/// <returns></returns>
public static ClinicalTrial LoadTrial(string trialName)
{
string path = Path.Combine(AssemblyPath, "TrialExamples", trialName);
ClinicalTrial trial = JsonConvert.DeserializeObject <ClinicalTrial>(
File.ReadAllText(path)
);
return(trial);
}
/// <summary>
/// Gets the Phase number from the API and formats it for presentation
/// </summary>
/// <param name="trial"></param>
/// <returns>String </returns>
public string GetPhase(ClinicalTrial trial)
{
string phase = trial.GetTrialPhase();
if (!String.IsNullOrWhiteSpace(phase))
{
phase = "Phase " + phase.Replace("_", "/");
}
return(phase);
}
/// <summary>
/// Gets the Lead Organization
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public static string GetLeadOrg(this ClinicalTrial trial)
{
string leadOrg = String.Empty;
if (!String.IsNullOrEmpty(trial.LeadOrganizationName))
{
leadOrg = trial.LeadOrganizationName;
}
return(leadOrg);
}
public void TestDeserialize()
{
string path = Path.Combine(AssemblyPath, "TrialExamples", "NCT02194738.json");
ClinicalTrial trial = JsonConvert.DeserializeObject <ClinicalTrial>(
File.ReadAllText(path)
);
Assert.Equal("NCT02194738", trial.NCTID);
//TODO: Check all the fields.
}
/// <summary>
/// Gets the Principal Investigator
/// </summary>
/// <param name="trial"></param>
/// <returns>string - principal</returns>
public static string GetPrincipalInvestigator(this ClinicalTrial trial)
{
string principal = String.Empty;
if (!String.IsNullOrEmpty(trial.PrincipalInvestigator))
{
principal = trial.PrincipalInvestigator;
}
return(principal);
}
/// <summary>
/// Get formatted age range string. Based on the max and min age for the trial, display the
/// resulting age in a pretty format and with units specified.
/// TODO: Handle any edge cases with redundant units
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public String GetAgeString(ClinicalTrial trial)
{
int minAgeNum = trial.GetMinAgeNum();
int maxAgeNum = trial.GetMaxAgeNum();
string minAgeUnit = trial.GetMinAgeUnit().ToLower();
string maxAgeUnit = trial.GetMaxAgeUnit().ToLower();
string minAgeText = CleanAgeText(minAgeNum, minAgeUnit);
string maxAgeText = CleanAgeText(maxAgeNum, maxAgeUnit);
string ageRange = minAgeText + " to " + maxAgeText;
// Set age range string for years if both max and min units are years
if ((maxAgeUnit == "years") && (minAgeUnit == "years"))
{
ageRange = minAgeNum.ToString() + " to " + maxAgeNum.ToString() + " years";
if (minAgeNum < 1 && maxAgeNum <= 120)
{
ageRange = maxAgeText + " and under";
}
else if (minAgeNum > 0 && maxAgeNum > 120)
{
ageRange = minAgeText + " and over";
}
else if (minAgeNum < 1 && maxAgeNum > 120)
{
ageRange = "Not specified";
}
}
// Set age range string for max and min if units match
else if (maxAgeUnit == minAgeUnit)
{
ageRange = minAgeNum.ToString() + " to " + maxAgeNum.ToString() + maxAgeUnit;
if (minAgeNum < 1 && maxAgeNum <= 999)
{
ageRange = maxAgeText + " and under";
}
else if (minAgeNum > 0 && maxAgeNum >= 999)
{
ageRange = minAgeText + " and over";
}
}
// Set age range string if units do not match
else
{
if (maxAgeNum > 120 && maxAgeUnit == "years")
{
ageRange = minAgeText + " and over";
}
}
ageRange = ageRange.Replace("year to", "to").Replace("years to", "to");
return(GetFormattedString(ageRange));
}
/// <summary>
/// Get formatted gender string
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public string GetGenderString(ClinicalTrial trial)
{
String gender = trial.GetGender();
if (gender.ToLower() == "both")
{
gender = "Male or Female";
return(gender);
}
return(GetFormattedString(gender));
}
/// <summary>
/// Gets the list of secondary IDs from extension method as comma separated string
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public string GetSecondaryIDsString(ClinicalTrial trial)
{
string[] ids = trial.GetSecondaryIDs();
if (ids.Length == 0)
{
return(string.Empty);
}
else
{
return(string.Join(", ", ids));
}
}
/// <summary>
/// Gets an array of all of the collaborator names
/// </summary>
/// <param name="trial"></param>
/// <returns>string[] collaborators</returns>
public static string[] GetCollaborators(this ClinicalTrial trial)
{
List <String> collaborators = new List <String>();
if (trial.Collaborators != null)
{
collaborators.AddRange(
from collab in trial.Collaborators
select collab.Name
);
}
return(collaborators.ToArray());
}
/// <summary>
/// Gets the phase number only
/// </summary>
/// <param name="trial"></param>
/// <returns>String - phase</returns>
public static String GetTrialPhase(this ClinicalTrial trial)
{
string rtnPhase = String.Empty;
if (trial.TrialPhase != null)
{
if (!String.IsNullOrEmpty(trial.TrialPhase.PhaseNumber))
{
rtnPhase = trial.TrialPhase.PhaseNumber;
}
}
return(rtnPhase);
}
/// <summary>
/// Gets the eligibility criteria for exclusion form this trial
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public static string[] GetExclusionCriteria(this ClinicalTrial trial)
{
if (trial.EligibilityInfo != null && trial.EligibilityInfo.UnstructuredCriteria != null)
{
return((
from criterion in trial.EligibilityInfo.UnstructuredCriteria
where !criterion.IsInclusionCriterion
select criterion.Description
).ToArray());
}
else
{
return(new string[0]);
}
}
internal void SeedDoctorsClinicalTrialsAndSpecialties(ApplicationDbContext context)
{
if (!context.Doctors.Any() || !context.ClinicalTrials.Any() || !context.Specialities.Any())
{
for (int i = 1; i < 5; i++)
{
var clinicalTrial = new ClinicalTrial
{
Title = "Trial - " + i + ".1",
Price = random.RandomDataInt(25, 4587),
IsAvailable = IsAvailable.Yes,
};
var clinicalTrial2 = new ClinicalTrial
{
Title = "Trial - " + i + ".2",
Price = random.RandomDataInt(48, 565),
IsAvailable = IsAvailable.No,
};
var listDoctors = new List <Doctor>();
for (int j = 0; j < random.RandomDataInt(2, 6); j++)
{
var doctor = new Doctor
{
Name = "Doctor - " + random.RandomDataString(6, 10) + " " + random.RandomDataString(10, 13),
Image = CreateImage(),
Description = random.RandomDataString(400, 1000)
};
listDoctors.Add(doctor);
}
var specialty = new Speciality
{
Title = "Specialty - " + i,
Description = random.RandomDataString(200, 500),
ClinicalTrials = new HashSet <ClinicalTrial>()
{
clinicalTrial,
clinicalTrial2
},
Doctors = listDoctors
};
context.Specialities.Add(specialty);
context.SaveChanges();
}
}
}
/// <summary>
/// Gets Principal Investigator strings and joins them into an array
/// </summary>
/// <param name="trial"></param>
/// <returns>string - principal</returns>
public string[] GetPrincipalArray(ClinicalTrial trial)
{
List <String> principal = new List <String>();
if (!String.IsNullOrWhiteSpace(trial.GetPrincipalInvestigator()))
{
principal.Add(trial.GetPrincipalInvestigator());
}
/* TODO - Verify if there actually any instances where we
* have more than one Principal Investigator - OR if there
* is another value from the API that we should combine with
* this
*/
// principal.Add(trial.GetSomeOtherValue());
return(principal.ToArray());
}
/// <summary>
/// Gets the Primary Purpose
/// </summary>
/// <param name="trial"></param>
/// <returns>String - purpose</returns>
public static String GetPrimaryPurpose(this ClinicalTrial trial)
{
string purpose = String.Empty;
if (trial.PrimaryPurpose != null)
{
if (!String.IsNullOrEmpty(trial.PrimaryPurpose.Code))
{
purpose = trial.PrimaryPurpose.Code;
if (purpose.ToLower() == "other")
{
purpose = trial.PrimaryPurpose.OtherText;
}
}
}
return(purpose);
}
public void TestGet()
{
string baseUrl = "https://example.org/v1/";
string trialID = "NCT02194738";
string trialFilePath = TestFileTools.GetPathToTestFile(typeof(ClinicalTrialsAPIClientTests), Path.Combine(new string[] { "TrialExamples", trialID + ".json" }));
HttpClient mockedClient = HttpClientMockHelper.GetClientMockForURLWithFileResponse(String.Format("{0}clinical-trial/{1}", baseUrl, trialID), trialFilePath);
mockedClient.BaseAddress = new Uri(baseUrl);
ClinicalTrialsAPIClient client = new ClinicalTrialsAPIClient(mockedClient);
ClinicalTrial trial = client.Get(trialID);
Assert.Equal(trialID, trial.NCTID);
}
/// <summary>
/// Gets the Phase number and adds glossification markup
/// </summary>
/// <param name="trial"></param>
/// <returns>String glossifedPhase</returns>
public string GetGlossifiedPhase(ClinicalTrial trial)
{
string phase = trial.GetTrialPhase();
string cdrID = "";
string htmlBlobOpen;
string htmlBlobClose;
// Check the API trial values and assign to a CDR ID if valid
switch (phase)
{
case "I": cdrID = "45830";
break;
case "I_II": cdrID = "45832";
break;
case "II": cdrID = "45831";
break;
case "II_III": cdrID = "45834";
break;
case "III": cdrID = "45833";
break;
case "IV": cdrID = "45835";
break;
}
if (String.IsNullOrEmpty(cdrID))
{
phase = "No phase specified";
}
else
{
htmlBlobOpen = @"<a onclick=""javascript:popWindow('defbyid','CDR00000" + cdrID +
@"&version=Patient&language=English'); return false;"" href=""/Common/PopUps/popDefinition.aspx?id=CDR00000" + cdrID +
@"45830&version=Patient&language=English"" class=""definition"">";
htmlBlobClose = @"</a>";
phase = htmlBlobOpen + "Phase " + phase.Replace("_", "/") + htmlBlobClose;
}
return(phase);
}
/// <summary>
/// Send 404 error if the trial is invalid or does not have a view-able status.
/// </summary>
/// <param name="trial">The trial to check</param>
private void RedirectIfTrialNotValid(ClinicalTrial trial)
{
// If trial value is null, redirect to the 404 page
//TODO: Determine if a null trial should be a 404, or redirect to CT.gov
if (trial == null)
{
throw new HttpException(404, "Trial cannot be found.");
}
if (Config.RedirectIfInactive)
{
string[] actives = CTSConstants.ActiveTrialStatuses;
if (Array.IndexOf(actives, trial.CurrentTrialStatus) < 0)
{
throw new HttpException(404, "Trial status is not active.");
}
if (string.IsNullOrWhiteSpace(trial.NCTID))
{
throw new HttpException(404, "Trial does not have an NCT ID.");
}
}
}
/// <summary>
/// Gets an array of all of the secondary IDs, which are those that are not the NCT ID or the Primary ID
/// </summary>
/// <param name="trial"></param>
/// <returns></returns>
public static string[] GetSecondaryIDs(this ClinicalTrial trial)
{
List <String> rtnIds = new List <String>();
String[] secIds = { trial.CTEPID, trial.DCPID, trial.CCRID, trial.NCIID };
String dupe = "";
// Add secondary IDs (NCI, CCR, CTEP, DCP) to list
foreach (String sid in secIds)
{
if (!String.IsNullOrEmpty(sid))
{
rtnIds.Add(sid);
}
}
// Add other secondary IDs to list
if (trial.OtherTrialIDs != null)
{
rtnIds.AddRange(
from id in trial.OtherTrialIDs
where !String.IsNullOrEmpty(id.Value)
select id.Value
);
}
// Remove any duplicate found in Primary or Secondary IDs
foreach (String rtnid in rtnIds.ToList())
{
if (rtnid == trial.NCTID || rtnid == trial.ProtocolID || rtnid == dupe)
{
rtnIds.Remove(rtnid);
}
dupe = rtnid;
}
return(rtnIds.ToArray());
}
public IEnumerable <ClinicalTrial.StudySite> GetAllStudySites(ClinicalTrial trial)
{
IEnumerable <ClinicalTrial.StudySite> sites = null;
//BasicCTSManager mgr = new BasicCTSManager();
// Assemble list of trial sites to be printed by the Velocity template:
// 1. Filter inactive study sites out of our sites list
// 2. Make a list of USA sites, sorted by state, then city
// 3. Make a list of Canada sites, sorted by province, then city
// 4. Make a list of international sites, sorted by country, then city
// 5. Join the lists with USA as the first group of items and all other countries alphabetized afterward
if (trial.Sites != null)
{
trial.Sites = new List <ClinicalTrial.StudySite>(trial.Sites.Where(site => CTSConstants.ActiveRecruitmentStatuses.Any(status => status.ToLower() == site.RecruitmentStatus.ToLower())));
var usaSites = trial.Sites.Where(s => s.Country == "United States").OrderBy(s => s.StateOrProvince).ThenBy(s => s.City).ThenBy(s => s.Name).ToArray();
var canadaSites = trial.Sites.Where(s => s.Country == "Canada").OrderBy(s => s.StateOrProvince).ThenBy(s => s.City).ThenBy(s => s.Name).ToArray();
var otherSites = trial.Sites.Where(s => s.Country != "United States" && s.Country != "Canada").OrderBy(s => s.City).ThenBy(s => s.Name).ToArray();
sites = canadaSites.Concat(otherSites).OrderBy(s => s.Country);
sites = usaSites.Concat(sites);
}
return(sites);
}
/// <summary>
/// Checks whether the given trial ID exists in the API.
/// </summary>
/// <param name="idString">NCT ID</param>
/// <returns>True if trial is found in API.</returns>
private bool IsValidTrial(string idString)
{
// If the ID is a valid NCTID, go to web service and see if trial exists
try
{
ClinicalTrialsAPIClient client = APIClientHelper.GetV1ClientInstance();
ClinicalTrial trial = client.Get(idString);
if (trial != null)
{
return(true);
}
}
catch (ArgumentNullException nx)
{
log.DebugFormat("Error retrieving trial - value cannot be null. idString = " + idString, nx);
return(false);
}
catch (Exception ex)
{
log.Error("Error retrieving trial object from API", ex);
return(false);
}
return(false);
}
private static object GetOtherSortedLocations(ClinicalTrial trial)
{
OrderedDictionary locations = new OrderedDictionary();
if (trial.Sites != null)
{
var sortedSites = from site in trial.Sites
where (site.Country != "United States" &&
site.Country != "Canada")
orderby site.Country, site.StateOrProvince, site.Name
select site;
foreach (ClinicalTrial.StudySite site in sortedSites)
{
if (!locations.Contains(site.Country))
{
locations.Add(site.Country, new List <ClinicalTrial.StudySite>());
}
((List <ClinicalTrial.StudySite>)locations[site.Country]).Add(site);
}
}
return(locations);
}
private static object GetNASortedLocations(ClinicalTrial trial, string country)
{
OrderedDictionary locations = new OrderedDictionary();
if (trial.Sites != null)
{
var sortedSites = from site in trial.Sites
where site.Country == country
orderby site.StateOrProvince, site.Name
select site;
foreach (ClinicalTrial.StudySite site in sortedSites)
{
if (!locations.Contains(site.StateOrProvince))
{
locations.Add(site.StateOrProvince, new List <ClinicalTrial.StudySite>());
}
((List <ClinicalTrial.StudySite>)locations[site.StateOrProvince]).Add(site);
}
}
return(locations);
}
/// <summary>
/// Get min age unit info for trial
/// </summary>
/// <param name="site"></param>
/// <returns></returns>
public static String GetMinAgeUnit(this ClinicalTrial trial)
{
string unit = trial.EligibilityInfo.StructuredCriteria.MinAgeUnits;
return(unit);
}
/// <summary>
/// Get min age eligibility info for trial
/// </summary>
/// <param name="site"></param>
/// <returns></returns>
public static int GetMinAgeNum(this ClinicalTrial trial)
{
int age = trial.EligibilityInfo.StructuredCriteria.MinAgeInt;
return(age);
}
