public void ResetDatabase()
{
// Import "TestPeopleMaintenance/input1 plus testhyphens.xls" into the People table
People PeopleFromFile = new People(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPeopleMaintenance",
"input1 plus testhypens.xls");
DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
MockNCBI mockNCBI = new MockNCBI("medline");
mockNCBI.SearchThrowsAnError = false;
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
ptc.WriteToDB(DB);
// Anonymous callback functions for GetPublications
Harvester.GetPublicationsStatus StatusCallback = delegate(int number, int total, int averageTime)
{
//
};
Harvester.GetPublicationsMessage MessageCallback = delegate(string Message, bool StatusBarOnly)
{
//
};
Harvester.CheckForInterrupt InterruptCallback = delegate()
{
return(false);
};
// Write the people, then "harvest" the publications using MockNCBI
double AverageMilliseconds;
foreach (Person person in PeopleFromFile.PersonList)
{
person.WriteToDB(DB);
harvester.GetPublications(mockNCBI, ptc, person, StatusCallback, MessageCallback, InterruptCallback, out AverageMilliseconds);
}
People PeopleFromDB = new People(DB);
Assert.AreEqual(PeopleFromDB.PersonList.Count, 4);
}
public void TestOtherPeople()
{
// Note: Publication 14560782 was added to OtherPeople.dat to verify
// that the software handles the situation where a publication has
// no authors listed.
Database DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
MockNCBI mockNCBI = new MockNCBI("medline");
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
// Reinitialize the database
harvester.CreateTables();
// Make an anonymous callback function that keeps track of the callback data
int Callbacks = 0; // this will count all of the publications
Harvester.GetPublicationsStatus StatusCallback = delegate(int number, int total, int averageTime)
{
Callbacks++;
};
// 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);
};
// Create a new person to test
string[] names = new string[2];
names[0] = "Klein RG";
names[1] = "Guillemin R";
Person person = new Person("A1234567", "FIRST", "MIDDLE", "LAST",
false, names, "Special query for OtherPeople.dat");
person.WriteToDB(DB);
double AverageMilliseconds;
harvester.GetPublications(mockNCBI, ptc, person, StatusCallback, MessageCallback, InterruptCallback, out AverageMilliseconds);
// Verify that the data was written properly
int FoundPublications = 0;
Publications pubs = new Publications(DB, person, false);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
FoundPublications++;
switch (pub.PMID)
{
case 12679283:
// The weird part of this publication is the second MeSH heading, which is very long
Assert.IsTrue(pub.MeSHHeadings.Count == 23);
Assert.IsTrue(pub.MeSHHeadings.Contains(
"Attention Deficit and Disruptive Behavior Disorders/etiology/*prevention & control/psychology"));
break;
case 2417121:
// The weird part of this publication is the date, which has a weird format that causes
// the day to be long
Assert.IsTrue(pub.Day == "19-1986 Jan 1");
break;
case 6148773:
// One of the headers is long
Assert.IsTrue(pub.MeSHHeadings.Contains("Peptide Fragments/antagonists & inhibitors/chemical synthesis/diagnostic use/isolation & purification/pharmacology/*physiology"));
break;
case 16291338:
// One of the authors is long
Assert.IsTrue(pub.Authors.Length == 8);
Assert.IsTrue(pub.Authors[7] == "For The Michigan Alliance For The National Children's Study");
break;
case 15451956:
// Volume is long
Assert.IsTrue(pub.Volume == "Suppl Web Exclusives");
break;
case 14653276:
// Issue is long
Assert.IsTrue(pub.Issue == "5 Suppl Nitric Oxide");
break;
case 9965612:
// Journal name is long
Assert.IsTrue(pub.Journal == "PHYSICAL REVIEW. E. STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS");
break;
case 9469584:
// Title is long
Assert.IsTrue(pub.Title ==
Database.Left("Down-regulation of cholesterol biosynthesis in sitosterolemia: diminished activities of acetoacetyl-CoA thiolase, 3-hydroxy-3-methylglutaryl-CoA synthase, reductase, squalene synthase, and 7-dehydrocholesterol delta7-reductase in liver and mononuclear leukocytes."
, 244));
break;
case 2545230:
// Month is long
Assert.IsTrue(pub.Month == "Spring-Summer");
break;
default:
break;
}
}
}
Assert.IsTrue(FoundPublications == 13);
}
public void TestTwoPeopleWithSameNames()
{
Database DB = new Database("Publication Harvester Unit Test");
// Set up the database
TestHarvester.GetPublicationsFromInput1XLS_Using_MockNCBI(false, new string[] { "eng" }, 22);
// Add two people to the database with the same names and search criteria
// (where the search should make MockNCBI use OtherPeople.dat)
string[] names = new string[2];
names[0] = "Guy JF";
names[1] = "Guy J";
Person Joe = new Person("A1234567", "JOE", "FIRST", "GUY",
false, names, "Special query for OtherPeople.dat");
Joe.WriteToDB(DB);
Person Jane = new Person("Z7654321", "JANE", "FIFTH", "GUY",
false, names, "Special query for OtherPeople.dat");
Jane.WriteToDB(DB);
// Also add Jim, but give him an error so we can make sure it's cleared
Person Jim = new Person("Q2222222", "JIM", "FOURTEENTH", "GUY",
false, names, "Special query for OtherPeople.dat");
Jim.WriteToDB(DB);
Jim.WriteErrorToDB(DB, "This is an error message");
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
// Make an anonymous callback function that keeps track of the callback data
int Callbacks = 0; // this will count all of the publications
Harvester.GetPublicationsStatus StatusCallback = delegate(int number, int total, int averageTime)
{
Callbacks++;
};
// Make an anonymous callback function to do nothing for GetPublicationsMessage
int MessageCallbacks = 0;
Harvester.GetPublicationsMessage MessageCallback = delegate(string Message, bool StatusBarOnly)
{
// Only increment MessageCallbacks if the message contains Joe's Setnb
// and the word "same"
if ((Message.Contains("A1234567") || (Message.Contains("Q2222222")) &&
Message.Contains("same")))
{
MessageCallbacks++;
}
};
// Make an anonymous callback function to return false for CheckForInterrupt
Harvester.CheckForInterrupt InterruptCallback = delegate()
{
return(false);
};
// More stuff for the harvester
Harvester harvester = new Harvester(DB);
MockNCBI mockNCBI = new MockNCBI("medline");
double AverageMilliseconds;
// Harvest the people
harvester.GetPublications(mockNCBI, ptc, Jane, StatusCallback, MessageCallback, InterruptCallback, out AverageMilliseconds);
// Make sure the harvester got Jane's publications
DataTable Results = DB.ExecuteQuery("SELECT PMID FROM PeoplePublications WHERE Setnb = 'Z7654321'");
Assert.AreEqual(Results.Rows.Count, 3);
foreach (DataRow Row in Results.Rows)
{
Assert.IsTrue(
(Row["PMID"].ToString() == "2417121") ||
(Row["PMID"].ToString() == "12679283") ||
(Row["PMID"].ToString() == "14653276"));
}
ArrayList Parameters = new ArrayList();
Parameters.Add(Database.Parameter(Jane.Setnb));
Results = DB.ExecuteQuery("SELECT Harvested, Error, ErrorMessage FROM People WHERE Setnb = ?", Parameters);
Assert.AreEqual(Results.Rows[0]["Harvested"], true);
Assert.AreEqual(Results.Rows[0]["Error"], DBNull.Value);
Assert.AreEqual(Results.Rows[0]["ErrorMessage"].ToString(), "");
// It should also get Joe's publications. It should call MessageCallback()
// twice to let us know Joe'and Jim's s publications were found, and it
// should add the appropriate rows to PeoplePublications.
Assert.AreEqual(MessageCallbacks, 2);
Results = DB.ExecuteQuery("SELECT PMID FROM PeoplePublications WHERE Setnb = 'A1234567'");
Assert.AreEqual(Results.Rows.Count, 3);
foreach (DataRow Row in Results.Rows)
{
Assert.IsTrue(
(Row["PMID"].ToString() == "2417121") ||
(Row["PMID"].ToString() == "12679283") ||
(Row["PMID"].ToString() == "14653276"));
}
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(Joe.Setnb));
Results = DB.ExecuteQuery("SELECT " + Database.PEOPLE_COLUMNS + " FROM People WHERE Setnb = ?", Parameters);
bool boolValue; // needed for GetBoolValue workaround for bit field bug in MySQL
Assert.IsTrue(Database.GetBoolValue(Results.Rows[0]["Harvested"], out boolValue));
Assert.IsTrue(boolValue);
Assert.IsTrue(Database.GetBoolValue(Results.Rows[0]["Error"], out boolValue));
Assert.IsFalse(boolValue);
Assert.AreEqual(Results.Rows[0]["Error"], DBNull.Value);
Assert.AreEqual(Results.Rows[0]["ErrorMessage"].ToString(), "");
// It should also get Jim's publications -- and it should also clear his error.
Assert.AreEqual(MessageCallbacks, 2);
Results = DB.ExecuteQuery("SELECT PMID FROM PeoplePublications WHERE Setnb = 'A1234567'");
Assert.AreEqual(Results.Rows.Count, 3);
foreach (DataRow Row in Results.Rows)
{
Assert.IsTrue(
(Row["PMID"].ToString() == "2417121") ||
(Row["PMID"].ToString() == "12679283") ||
(Row["PMID"].ToString() == "14653276"));
}
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(Jim.Setnb));
Results = DB.ExecuteQuery("SELECT " + Database.PEOPLE_COLUMNS + "FROM People WHERE Setnb = ?", Parameters);
Assert.IsTrue(Database.GetBoolValue(Results.Rows[0]["Harvested"], out boolValue));
Assert.AreEqual(boolValue, true);
Assert.AreEqual(Results.Rows[0]["Error"], DBNull.Value);
Assert.AreEqual(Results.Rows[0]["ErrorMessage"].ToString(), "");
}
/// <summary>
/// Set up the database with data from Input1.XLS using the Mock NCBI object
/// (this is also called from TestReports())
/// </summary>
/// <param name="NCBISearchThrowsAnError">True if the MockNCBI object is supposed to throw an error</param>
public static void GetPublicationsFromInput1XLS_Using_MockNCBI(bool NCBISearchThrowsAnError, string[] Languages, int ExpectedPublications)
{
bool TablesCreated;
int NumPeople;
int NumHarvestedPeople;
int NumPublications;
int NumErrors;
Database DB = new Database("Publication Harvester Unit Test");
// Drop all tables and make sure the database reports as empty
foreach (string Table in new string[] {
"meshheadings", "people", "peoplepublications", "publicationauthors",
"publicationmeshheadings", "publications", "pubtypecategories"
})
{
DB.ExecuteNonQuery("DROP TABLE IF EXISTS " + Table);
DB.GetStatus(out TablesCreated, out NumPeople, out NumHarvestedPeople, out NumPublications, out NumErrors);
Assert.IsFalse(TablesCreated);
Assert.AreEqual(NumPeople, 0);
Assert.AreEqual(NumHarvestedPeople, 0);
Assert.AreEqual(NumPublications, 0);
Assert.AreEqual(NumErrors, 0);
}
// Create and populate the tables
Harvester harvester = new Harvester(DB);
harvester.Languages = Languages;
MockNCBI mockNCBI = new MockNCBI("medline");
mockNCBI.SearchThrowsAnError = NCBISearchThrowsAnError;
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
// Reinitialize the database
harvester.CreateTables();
ptc.WriteToDB(DB);
// Retrieve the publications for each person in input1.xls using GetPublications()
People PeopleFromFile = new People(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPeople",
"input1.xls");
// Make an anonymous callback function that keeps track of the callback data
int Callbacks = 0; // this will count all of the publications
Harvester.GetPublicationsStatus StatusCallback = delegate(int number, int total, int averageTime)
{
Callbacks++;
};
// 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);
};
// Verify that the database was created and populated properly
DB.GetStatus(out TablesCreated, out NumPeople, out NumHarvestedPeople, out NumPublications, out NumErrors);
Assert.IsTrue(TablesCreated);
Assert.AreEqual(NumPeople, 0);
Assert.AreEqual(NumHarvestedPeople, 0);
Assert.AreEqual(NumPublications, 0);
Assert.AreEqual(NumErrors, 0);
int PeopleCount = 0;
int HarvestedCount = 0;
int PubCount = 0;
foreach (Person person in PeopleFromFile.PersonList)
{
double AverageMilliseconds;
// First write the person to the database
person.WriteToDB(DB);
PeopleCount++;
// Check that the database status is updated properly
DB.GetStatus(out TablesCreated, out NumPeople, out NumHarvestedPeople, out NumPublications, out NumErrors);
Assert.IsTrue(TablesCreated);
Assert.AreEqual(NumPeople, PeopleCount);
if (!NCBISearchThrowsAnError)
{
Assert.AreEqual(NumHarvestedPeople, HarvestedCount);
}
else
{
Assert.AreEqual(NumHarvestedPeople, 0);
}
Assert.AreEqual(NumPublications, PubCount);
if (!NCBISearchThrowsAnError)
{
Assert.AreEqual(NumErrors, 0);
}
else
{
Assert.AreEqual(NumErrors, PeopleCount - 1);
}
// Harvest the person's publications
PubCount += harvester.GetPublications(mockNCBI, ptc, person, StatusCallback, MessageCallback, InterruptCallback, out AverageMilliseconds);
HarvestedCount++;
// Check the status again after the people were harvested
DB.GetStatus(out TablesCreated, out NumPeople, out NumHarvestedPeople, out NumPublications, out NumErrors);
Assert.IsTrue(TablesCreated);
Assert.AreEqual(NumPeople, PeopleCount);
if (!NCBISearchThrowsAnError)
{
Assert.AreEqual(NumHarvestedPeople, HarvestedCount);
}
else
{
Assert.AreEqual(NumHarvestedPeople, 0);
}
Assert.AreEqual(NumPublications, PubCount);
if (!NCBISearchThrowsAnError)
{
Assert.AreEqual(NumErrors, 0);
}
else
{
Assert.AreEqual(NumErrors, PeopleCount);
}
}
// Verify that the database was written properly
if (!NCBISearchThrowsAnError)
{
Assert.IsTrue(Callbacks == 24);
}
else
{
Assert.IsTrue(Callbacks == 0);
}
DB.GetStatus(out TablesCreated, out NumPeople, out NumHarvestedPeople, out NumPublications, out NumErrors);
Assert.IsTrue(TablesCreated);
Assert.AreEqual(NumPeople, 4);
if (!NCBISearchThrowsAnError)
{
Assert.AreEqual(NumHarvestedPeople, 4);
Assert.AreEqual(NumPublications, ExpectedPublications);
Assert.AreEqual(NumErrors, 0);
}
else
{
Assert.AreEqual(NumHarvestedPeople, 0);
Assert.AreEqual(NumPublications, 0);
Assert.AreEqual(NumErrors, 4);
}
}
