public void TestColleaguesSetUp()
{
// Create the AAMC roster object
roster = new Roster(AppDomain.CurrentDomain.BaseDirectory + "\\Test Data\\TestRoster\\testroster.csv");
// Stuff for GetPublications()
// Make an anonymous callback function that keeps track of the callback data
Harvester.GetPublicationsStatus StatusCallback = delegate(int number, int total, int averageTime)
{
//
};
// Make an anonymous callback function to do nothing for GetPublicationsMessage
Harvester.GetPublicationsMessage MessageCallback = delegate(string Message, bool StatusBarOnly)
{
//
};
// Make an anonymous callback function to return false for CheckForInterrupt
Harvester.CheckForInterrupt InterruptCallback = delegate()
{
return(false);
};
double AverageMilliseconds;
// Read the people file
People PeopleFromFile = new People(
AppDomain.CurrentDomain.BaseDirectory + "\\Test Data\\TestColleagues",
"PeopleFile.xls");
// Drop all tables from the test database
DB = new Database("Colleague Generator Unit Test");
foreach (string Table in new string[]
{
"colleaguepublications", "colleagues", "meshheadings",
"people", "peoplepublications", "publicationauthors",
"publicationgrants", "publicationmeshheadings", "publications",
"pubtypecategories", "starcolleagues"
}
)
{
DB.ExecuteNonQuery("DROP TABLE IF EXISTS " + Table + ";");
}
// Create the test database
harvester = new Harvester(DB);
harvester.CreateTables();
ColleagueFinder.CreateTables(DB);
// Populate it using the Mock NCBI object
ncbi = new MockNCBI("Medline");
PubTypes = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Test Data\\TestColleagues",
"PublicationTypes.csv"
);
// Write each person and his publications to the database
foreach (Person person in PeopleFromFile.PersonList)
{
person.WriteToDB(DB);
harvester.GetPublications(ncbi, PubTypes, person, StatusCallback, MessageCallback, InterruptCallback, out AverageMilliseconds);
}
}
/// <summary>
/// Use the tests from TestColleagues to set up the database,
/// then find the colleagues, get their publications and
/// remove false colleagues.
///
/// This is a static void so that it can be called by other tests.
/// </summary>
public static void DoSetUp(out Database DB, out Harvester harvester, out PublicationTypes PubTypes, out NCBI ncbi, string[] Languages)
{
// First recreate the database
DB = new Database("Colleague Generator Unit Test");
ColleagueFinder.CreateTables(DB);
// Then use the test fixture setup in TestColleagues to populate it
TestColleagues testColleagues = new TestColleagues();
testColleagues.TestColleaguesSetUp();
// Write the publication types to the database
PubTypes = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Test Data\\TestColleagues",
"PublicationTypes.csv"
);
PubTypes.WriteToDB(DB);
// Create the other objects from the database
harvester = new Harvester(DB);
Roster roster = new Roster(AppDomain.CurrentDomain.BaseDirectory + "\\Test Data\\TestRoster\\testroster.csv");
ncbi = new MockNCBI("Medline");
// Find the colleagues and publications
ColleagueFinder finder = new ColleagueFinder(DB, roster, ncbi, null);
People people = new People(DB);
foreach (Person person in people.PersonList)
{
Person[] found = finder.FindPotentialColleagues(person);
if (found != null)
{
finder.GetColleaguePublications(found, new string[] { "eng" }, new List <int> {
1, 2, 3
});
}
}
// Remove false colleagues
ColleagueFinder.RemoveFalseColleagues(DB, null, "PeoplePublications");
// Create the extra articles for Bunn and Tobian.
// Verify that Bunn and Tobian have five articles in common, with years
// ranging from 1993 to 2001.
CreateExtraArticlesForTobianAndBunn(DB, PubTypes, Languages);
DataTable Result = DB.ExecuteQuery(
@"SELECT p.Year, p.PMID, pp.PositionType AS StarPositionType,
cp.PositionType AS ColleaguePositionType, p.Journal
FROM Publications p, ColleaguePublications cp, PeoplePublications pp
WHERE pp.Setnb = 'A5401532'
AND cp.Setnb = 'A4800524'
AND p.PMID = pp.PMID
AND p.PMID = cp.PMID
ORDER BY p.Year ASC");
Assert.AreEqual(Result.Rows.Count, 5);
Assert.AreEqual(Result.Rows[0]["Year"], 1993);
Assert.AreEqual(Result.Rows[4]["Year"], 2001);
}
public void GetColleaguesForTobian()
{
// We've seeded Tobian.dat with colleagues:
// Paul A. Bunn is in PMID 8931843. He has two articles in OtherPeople.dat, including
// article 8931843. (Also, PMID 15451956)
ColleagueFinder finder = new ColleagueFinder(DB, roster, ncbi, null);
People people = new People(DB);
Person[] found;
foreach (Person person in people.PersonList)
{
// Only look for a star's colleagues we've seeded that star's colleagues in the DAT files
switch (person.Last)
{
case "Tobian":
// Tobian has two apparent colleagues. Paul Bunn is a true colleague
// who has publications in common with Tobian. Sharon J. Bintliff
// is a false colleague with no common publications.
found = finder.FindPotentialColleagues(person);
Assert.AreEqual(found.Length, 2);
Person PaulBunn = found[0];
Assert.AreEqual(PaulBunn.Setnb, "A4800524");
Assert.AreEqual(PaulBunn.Last, "BUNN");
Assert.AreEqual(PaulBunn.First, "PAUL");
Assert.AreEqual(PaulBunn.Middle, "A.");
Assert.AreEqual(PaulBunn.Names.Length, 4);
Assert.AreEqual(PaulBunn.Names[0], "bunn p jr");
Assert.AreEqual(PaulBunn.Names[1], "bunn pa jr");
Assert.AreEqual(PaulBunn.Names[2], "bunn pa");
Assert.AreEqual(PaulBunn.Names[3], "bunn p");
Assert.AreEqual(PaulBunn.MedlineSearch, "((\"bunn pa jr\"[au] or \"bunn p jr\"[au]) or ((\"bunn p\"[au] or \"bunn pa\"[au]) and (lymphoma or cancer)) and 1970:2005[dp])");
Person SharonBintliff = found[1];
Assert.AreEqual(SharonBintliff.Setnb, "A2700156");
Assert.AreEqual(SharonBintliff.Last, "BINTLIFF");
Assert.AreEqual(SharonBintliff.First, "SHARON");
Assert.AreEqual(SharonBintliff.Middle, "J");
Assert.AreEqual(SharonBintliff.Names.Length, 1);
Assert.AreEqual(SharonBintliff.Names[0], "bintliff sj");
Assert.AreEqual(SharonBintliff.MedlineSearch, "\"bintliff sj\"[au]");
// Make sure that Paul and Sharon were really added as a colleague
DataTable result = DB.ExecuteQuery("SELECT StarSetnb, Setnb FROM StarColleagues ORDER BY Setnb DESC");
Assert.AreEqual(result.Rows.Count, 2);
DataRow row = result.Rows[0];
Assert.AreEqual(row[0].ToString(), "A5401532");
Assert.AreEqual(row[1].ToString(), "A4800524");
row = result.Rows[1];
Assert.AreEqual(row[0].ToString(), "A5401532");
Assert.AreEqual(row[1].ToString(), "A2700156");
// Get the colleague's publications, make sure they're written to the database
finder.GetColleaguePublications(found, new string[] { "eng" }, new List <int> {
0, 1, 2, 3, 4, 5, 6
});
Assert.AreEqual(DB.GetIntValue("SELECT Count(*) FROM Colleagues"), 2);
Assert.AreEqual(DB.GetIntValue("SELECT Count(*) FROM StarColleagues"), 2);
Assert.AreEqual(DB.GetIntValue("SELECT Count(*) FROM ColleaguePublications"), 2);
Assert.AreEqual(DB.GetIntValue("SELECT Count(*) FROM ColleaguePublications WHERE PMID = 8931843"), 1);
Assert.AreEqual(DB.GetIntValue("SELECT Count(*) FROM ColleaguePublications WHERE PMID = 15451956"), 1);
// Remove false colleagues, make sure Sharon was deleted
ColleagueFinder.RemoveFalseColleagues(DB, null, "PeoplePublications");
result = DB.ExecuteQuery("SELECT StarSetnb, Setnb FROM StarColleagues ORDER BY Setnb DESC");
Assert.AreEqual(result.Rows.Count, 1);
row = result.Rows[0];
Assert.AreEqual(row[0].ToString(), "A5401532");
Assert.AreEqual(row[1].ToString(), "A4800524");
break;
}
}
}
/// <summary>
/// Add five extra articles to the database for Tobian and Bunn
/// </summary>
public static void CreateExtraArticlesForTobianAndBunn(Database DB, PublicationTypes PubTypes, string[] Languages)
{
// Create people objects for Tobian and Bunn
Person Tobian = new Person("A5401532", "Louis", "", "Tobian", true,
new String[] { "tobian l", "tobian l jr", "tobian lj" },
"(\"tobian l\"[au] OR \"tobian l jr\"[au] OR \"tobian lj\"[au])");
Person Bunn = new Person("A4800524", "PAUL", "A.", "BUNN", true,
new String[] { "bunn p jr", "bunn pa jr", "bunn pa", "bunn p" },
"((\"bunn pa jr\"[au] or \"bunn p jr\"[au]) or ((\"bunn p\"[au] or \"bunn pa\"[au]) and (lymphoma or cancer)) and 1970:2005[dp])");
// First, add a few more publications to the colleague.
Publication pub = new Publication();
string[] Authors = new String[] { "TOBIAN L", "BUNN P" };
pub.Year = 1993;
pub.Journal = "Fake Journal";
pub.Authors = Authors;
pub.PMID = 22222222;
pub.Title = "Fake article #1";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "BUNN P", "TOBIAN L" };
pub.Year = 1996;
pub.Journal = "Xenotransplantation";
pub.Authors = Authors;
pub.PMID = 12345678;
pub.Title = "Fake article #2";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "TOBIAN L", "BUNN P" };
pub.Year = 1996;
pub.Journal = "Fake Journal";
pub.Authors = Authors;
pub.PMID = 98765432;
pub.Title = "Fake article #3";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
pub = new Publication();
Authors = new String[] { "TOBIAN L", "BUNN P", "SCHMOE J" };
pub.Year = 2001;
pub.Journal = "Nature";
pub.Authors = Authors;
pub.PMID = 55555555;
pub.Title = "Fake article #4";
pub.Language = "eng";
pub.PubType = "Journal Article";
Publications.WriteToDB(pub, DB, PubTypes, Languages);
Publications.WritePeoplePublicationsToDB(DB, Tobian, pub);
ColleagueFinder.WriteColleaguePublicationsToDB(DB, Bunn, pub, PubTypes, new string[] { "eng" });
}
