/// <summary>
/// Performs a search against the Clinical Trials API
/// </summary>
/// <param name="searchParams">Search paramesters</param>
/// <param name="dynamicFilterParams">Deserialized dynamic search parameters</param>
/// <returns>Clinical Trials collection</returns>
public ClinicalTrialsCollection Search(CTSSearchParams searchParams, int pageNumber = 0, int itemsPerPage = 10)
{
int from = GetPageOffset(pageNumber, itemsPerPage);
Dictionary <string, object> filterCriteria = searchParams.ToFilterCriteria();
//Get our list of trials from the API client
ClinicalTrialsCollection rtnResults = new ClinicalTrialsCollection();
//Fetch results
rtnResults = Client.List(
searchParams: filterCriteria,
size: itemsPerPage,
from: from,
includeFields: CTSConstants.IncludeFields
);
//Remove all the inactive sites from all the trials.
foreach (ClinicalTrial trial in rtnResults.Trials)
{
RemoveNonRecruitingSites(trial);
}
return(rtnResults);
}
/// <summary>
/// Gets a selection of trials based on a query
/// </summary>
/// <param name="query">The Query without paging or include/exclude fields</param>
/// <param name="pageNumber">The current page number</param>
/// <param name="itemsPerPage">Items per page</param>
/// <param name="includeFields">A list of fields to include (DEFAULT: Return all fields)</param>
/// <returns></returns>
public ClinicalTrialsCollection GetClinicalTrials(JObject query, int pageNumber = 0, int itemsPerPage = 10, string[] includeFields = null)
{
int from = GetPageOffset(pageNumber, itemsPerPage);
ClinicalTrialsCollection rtnResults = new ClinicalTrialsCollection();
//Fetch results
rtnResults = Client.List(
searchParams: query,
size: itemsPerPage,
from: from,
includeFields: includeFields
);
//Remove all the inactive sites from all the trials.
foreach (ClinicalTrial trial in rtnResults.Trials)
{
RemoveNonRecruitingSites(trial);
}
return(rtnResults);
}
/// <summary>
/// Gets a collection of trials based on trial ids, batchVal at a time.
/// </summary>
/// <param name="ids">An array of trial IDs to fetch</param>
/// <param name="batchVal">The number of trials to retrieve at a time</param>
/// <returns>An enumerable list of ClinicalTrial objects</returns>
public IEnumerable <ClinicalTrial> GetMultipleTrials(List <String> ids, int batchVal = 5)
{
foreach (IEnumerable <string> batch in ids.Batch(batchVal))
{
Dictionary <string, object> filterCriteria = new Dictionary <string, object>();
filterCriteria.Add("nci_id", batch.ToArray());
ClinicalTrialsCollection ctColl = new ClinicalTrialsCollection();
ctColl = Client.List(
size: 100,
//from: 0,
searchParams: filterCriteria
);
foreach (ClinicalTrial c in ctColl.Trials)
{
//Remove all the inactive sites from the trial.
RemoveNonRecruitingSites(c);
yield return(c);
}
}
}
/// <summary>
/// Gets a collection of trials based on trial ids, batchVal at a time.
/// </summary>
/// <param name="ids">An array of trial IDs to fetch</param>
/// <param name="batchVal">The number of trials to retrieve at a time</param>
/// <returns>An enumerable list of ClinicalTrial objects</returns>
public IEnumerable <string> GetActiveTrialIDs(List <String> ids, int batchVal = 50)
{
foreach (IEnumerable <string> batch in ids.Batch(batchVal))
{
Dictionary <string, object> filterCriteria = new Dictionary <string, object>();
filterCriteria.Add("nci_id", batch.ToArray());
filterCriteria.Add("current_trial_status", CTSConstants.ActiveTrialStatuses);
ClinicalTrialsCollection ctColl = new ClinicalTrialsCollection();
string[] fieldsToInclude = { "nci_id" };
ctColl = Client.List(
size: 100,
includeFields: fieldsToInclude,
searchParams: filterCriteria
);
foreach (ClinicalTrial c in ctColl.Trials)
{
yield return(c.NCIID);
}
}
}
/// <summary>
/// CTSSearchParams -> filterCriterea mapping tests
/// </summary>
/// <param name="searchParams">An instance of a CTSSearchParams object</param>
/// <param name="expectedCriteria">The expected criteria for the search</param>
private void MappingTest(CTSSearchParams searchParams, Dictionary <string, object> expectedCriteria)
{
Dictionary <string, object> actualCriteria = null;
//When search gets called trap the criteria and set the actualCriteria
var mockClient = GetClientMock(
(filterCriteria, size, from, include, exclude) => actualCriteria = filterCriteria,
new ClinicalTrialsCollection()
{
TotalResults = 0, Trials = new ClinicalTrial[] { }
}
);
//Create a new instance of the factory, passing in the Mock's version of an implementation
//of our IClinicalTrialsAPIClient interface.
BasicCTSManager manager = new BasicCTSManager(mockClient.Object);
//Get the results of parsing the URL
ClinicalTrialsCollection returnedCol = manager.Search(searchParams);
//Test the actual result to the expected. NOTE: If you add fields to the CTSSearchParams, you need
//to also modify the comparer
Assert.Equal(expectedCriteria, actualCriteria);
}
/// <summary>
/// Gets a mock that can be used for a IClinicalTrialsAPIClient
/// See https://github.com/moq/moq4 for more details on the mock library.
/// (You can do cool thinks like make sure a method was called a certain number of times too...)
/// (You can pretend to throw an exception if this are not right...)
/// </summary>
///
/// <returns>A mock to be used as the service.</returns>
private Mock <IClinicalTrialsAPIClient> GetClientMock(
Action <Dictionary <string, object>, int, int, string[], string[]> criteriaIntercept, ClinicalTrialsCollection rtnCollection)
{
Mock <IClinicalTrialsAPIClient> rtnMock = new Mock <IClinicalTrialsAPIClient>();
//Handle the case when a string of C4872 is passed in to GetTitleCase and return the label "Breast Cancer"
//This makes it so that we do not have to create a fake class that returns fake data.
rtnMock.Setup(client => client.List(
It.IsAny <Dictionary <string, object> >(),
It.IsAny <int>(),
It.IsAny <int>(),
It.IsAny <string[]>(),
It.IsAny <string[]>()))
.Callback(criteriaIntercept) //This should be fleshed out to accept more params
.Returns(rtnCollection);
return(rtnMock);
}
/// <summary>
/// Goes and fetches the data from the API & Returns the results to base class to be bound to the template.
/// </summary>
/// <returns></returns>
protected override object GetDataForTemplate()
{
//TODO: Don't do a search if there are param errors.
if (SearchParams.HasInvalidParams() == true)
{
_results = new ClinicalTrialsCollection();
_results.TotalResults = 0;
}
else
{
_results = CTSManager.Search(SearchParams, this.PageNum, this.ItemsPerPage);
}
//Let's setup some helpful items for the template, so they do not need to be helper functions
//The start is either 0 if there are no results, or a 1 based offset based on Page number and items per page.
int startItemNumber = _results.TotalResults == 0 ? _results.TotalResults : ((this.PageNum - 1) * this.ItemsPerPage) + 1;
//Determine the last item.
long lastItemNumber = (this.PageNum * this.ItemsPerPage);
if (lastItemNumber > _results.TotalResults)
{
lastItemNumber = _results.TotalResults;
}
//Determine the max page
int maxPage = (int)Math.Ceiling((double)_results.TotalResults / (double)this.ItemsPerPage);
// Add URL filters
PageInstruction.AddUrlFilter("CurrentUrl", (name, url) =>
{
//Convert the current search parameters into a NciUrl
NciUrl paramsUrl = CTSSearchParamFactory.ConvertParamsToUrl(this.SearchParams);
//Add or replace the currentURL params based on the *validated* query params.
foreach (KeyValuePair <string, string> qp in paramsUrl.QueryParameters)
{
if (!url.QueryParameters.ContainsKey(qp.Key))
{
url.QueryParameters.Add(qp.Key, qp.Value);
}
else
{
url.QueryParameters[qp.Key] = qp.Value;
}
}
url.QueryParameters.Add("ni", this.ItemsPerPage.ToString());
});
//Return the object for binding.
return(new
{
Results = _results,
Control = this,
Parameters = SearchParams,
PageInfo = new {
CurrentPage = this.PageNum,
MaxPage = maxPage,
ItemsPerPage = this.ItemsPerPage,
StartItemNumber = startItemNumber,
LastItemNumber = lastItemNumber
},
TrialTools = new TrialVelocityTools()
});
}
