public void TestMiddleAuthor()
{
string MedlineData = @"PMID- 14332364
OWN - NLM
STAT- OLDMEDLINE
DA - 19651101
DCOM- 19961201
LR - 20051116
PUBM- Print
IS - 0002-922X (Print)
VI - 110
DP - 1965 Sep
TI - CONGENITAL SCALP DEFECTS IN TWIN SISTERS.
PG - 293-5
FAU - HODGMAN, J E
AU - HODGMAN JE
FAU - MATHIES, A W Jr
AU - MATHIES AW Jr
FAU - LEVAN, N E
AU - LEVAN NE
LA - eng
PT - Journal Article
PL - UNITED STATES
TA - Am J Dis Child
JT - American journal of diseases of children (1960)
JID - 0370471
SB - OM
MH - *Abnormalities
MH - *Diseases in Twins
MH - *Infant, Newborn
MH - *Scalp
OTO - NLM
OT - *ABNORMALITIES
OT - *DISEASES IN TWINS
OT - *INFANT, NEWBORN
OT - *SCALP
EDAT- 1965/09/01
MHDA- 1965/09/01 00:01
PST - ppublish
SO - Am J Dis Child. 1965 Sep;110:293-5.";
// Add a person to the database
Database DB = new Database("Publication Harvester Unit Test");
Person Mathies = new Person("A5703161", "Allan", "W", "MATHIES", false,
new String[] { "MATHIES AW Jr" }, "MATHIES AW Jr[au]");
// Create the publication
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
Publications Pubs = new Publications(MedlineData, ptc);
Assert.IsTrue(Pubs.PublicationList.Length == 1);
Publication Pub = Pubs.PublicationList[0];
Assert.IsTrue(Pub.Authors[1] == "MATHIES AW Jr");
// Clear the database
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
// Write the person and publication to the database
// NOTE: The author position is determined in WritePeoplePublicationsToDB()
PublicationTypes PubTypes = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
Mathies.WriteToDB(DB);
Publications.WriteToDB(Pub, DB, PubTypes, new string[] { "eng" });
Publications.WritePeoplePublicationsToDB(DB, Mathies, Pub);
// Verify that Mathies is the middle author, not the second author
Publications PubsFromDB = new Publications(DB, Mathies, false);
Assert.IsTrue(PubsFromDB.PublicationList.Length == 1);
Assert.IsTrue(PubsFromDB.PublicationList[0].PMID == 14332364);
Harvester.AuthorPositions PositionType;
Assert.IsTrue(Publications.GetAuthorPosition(DB, 14332364, Mathies, out PositionType, "PeoplePublications") == 2);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Middle);
}
public void GetPublications()
{
// Set up the database
TestHarvester.GetPublicationsFromInput1XLS_Using_MockNCBI(false, new string[] { "eng" }, 22);
Database DB = new Database("Publication Harvester Unit Test");
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
// Verify the correct publications were written (including publication type and author position)
People people = new People(DB);
Assert.IsTrue(people.PersonList.Count == 4);
int FoundPublications = 0;
foreach (Person person in people.PersonList)
{
Publications pubs = new Publications(DB, person, false);
switch (person.Setnb)
{
case "A6009400": // Van Eys
Assert.IsTrue(pubs.PublicationList.Length == 8);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
switch (pub.PMID)
{
case 9876482:
FoundPublications++;
Assert.IsTrue(pub.Title == "Benefits of nutritional intervention on nutritional status, quality of life and survival.");
Assert.IsTrue(pub.Pages == "66-8");
Assert.IsTrue(pub.Year == 1998);
Assert.IsTrue(pub.Month == null);
Assert.IsTrue(pub.Day == null);
Assert.IsTrue(pub.Journal == "Int J Cancer Suppl");
Assert.IsTrue(pub.Volume == "11");
Assert.IsTrue(pub.Issue == null);
Assert.IsTrue(pub.Authors.Length == 1);
Assert.IsTrue(pub.Authors[0] == "Van Eys J");
// Verify publication type
Assert.IsTrue(pub.PubType == "Journal Article");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 3);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings.Count == 8);
Assert.IsTrue(pub.MeSHHeadings.Contains("Child"));
Assert.IsTrue(pub.MeSHHeadings.Contains("Nutrition Disorders/*complications/*therapy"));
Assert.IsTrue(pub.MeSHHeadings.Contains("Survival Rate"));
// Verify position type
Harvester.AuthorPositions PositionType;
int AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
break;
case 8403744:
FoundPublications++;
Assert.IsTrue(pub.Title == "Early hospital discharge and the timing of newborn metabolic screening.");
Assert.IsTrue(pub.Pages == "463-6");
Assert.IsTrue(pub.Year == 1993);
Assert.IsTrue(pub.Month == "Aug");
Assert.IsTrue(pub.Day == null);
Assert.IsTrue(pub.Journal == "Clin Pediatr (Phila)");
Assert.IsTrue(pub.Volume == "32");
Assert.IsTrue(pub.Issue == "8");
Assert.IsTrue(pub.Authors.Length == 4);
Assert.IsTrue(pub.Authors[0] == "Coody D");
Assert.IsTrue(pub.Authors[1] == "Yetman RJ");
Assert.IsTrue(pub.Authors[2] == "Montgomery D");
Assert.IsTrue(pub.Authors[3] == "van Eys J");
// Verify publication type
Assert.IsTrue(pub.PubType == "Consensus Development Conference, NIH");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 1);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings.Count == 15);
Assert.IsTrue(pub.MeSHHeadings.Contains("Cesarean Section"));
Assert.IsTrue(pub.MeSHHeadings.Contains("Hospitals, Private"));
Assert.IsTrue(pub.MeSHHeadings.Contains("*Insurance, Health"));
Assert.IsTrue(pub.MeSHHeadings.Contains("United States"));
// Verify position type
AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 4);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Last);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 4);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Last);
break;
}
}
}
break;
case "A5401532": // Tobian
Assert.IsTrue(pubs.PublicationList.Length == 5);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
switch (pub.PMID)
{
case 9931073:
FoundPublications++;
Assert.IsTrue(pub.Title == "Story of the birth of the journal called Hypertension.");
Assert.IsTrue(pub.Pages == "7");
Assert.IsTrue(pub.Year == 1999);
Assert.IsTrue(pub.Month == "Jan");
Assert.IsTrue(pub.Day == null);
Assert.IsTrue(pub.Volume == "33");
Assert.IsTrue(pub.Issue == "1");
Assert.IsTrue(pub.Authors.Length == 1);
Assert.IsTrue(pub.Authors[0] == "Tobian L");
// Verify publication type
Assert.IsTrue(pub.PubType == "Historical Article");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 0);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings.Count == 5);
Assert.IsTrue(pub.MeSHHeadings.Contains("American Heart Association/*history"));
Assert.IsTrue(pub.MeSHHeadings.Contains("*Hypertension"));
Assert.IsTrue(pub.MeSHHeadings.Contains("United States"));
// Verify position type
Harvester.AuthorPositions PositionType;
int AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
break;
}
}
}
break;
case "A5501586": // Reemtsma
Assert.IsTrue(pubs.PublicationList.Length == 3);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
switch (pub.PMID)
{
case 11528018:
FoundPublications++;
Assert.IsTrue(pub.Title == "Xenotransplantation: A Historical Perspective.");
Assert.IsTrue(pub.Pages == "9-12");
Assert.IsTrue(pub.Year == 1995);
Assert.IsTrue(pub.Month == null);
Assert.IsTrue(pub.Day == null);
Assert.IsTrue(pub.Volume == "37");
Assert.IsTrue(pub.Issue == "1");
Assert.IsTrue(pub.Authors.Length == 1);
Assert.IsTrue(pub.Authors[0] == "Reemtsma K");
// Verify publication type
Assert.IsTrue(pub.PubType == "JOURNAL ARTICLE");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 3);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings == null);
// Verify position type
Harvester.AuthorPositions PositionType;
int AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 1);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.First);
break;
}
}
}
break;
case "A5702471": // Guillemin
Assert.IsTrue(pubs.PublicationList.Length == 6);
if (pubs.PublicationList != null)
{
foreach (Publication pub in pubs.PublicationList)
{
switch (pub.PMID)
{
case 15642779:
// For this publication, we're just concerned that
// the publication type is "Review" -- even though
// it's the second publication type in the citation,
// it's flagged as an "override first pubtype"
// in PublicationTypes.csv
Assert.IsTrue(pub.PubType == "Review");
break;
// NOTE: The title has a quote (laureates') that gets stripped off
case 12462241:
FoundPublications++;
Assert.IsTrue(pub.Title == "Nobel laureates letter to President Bush.");
Assert.IsTrue(pub.Pages == "A02");
Assert.IsTrue(pub.Year == 2001);
Assert.IsTrue(pub.Month == "Feb");
Assert.IsTrue(pub.Day == "22");
Assert.IsTrue(pub.Journal == "Washington Post");
Assert.IsTrue(pub.Volume == null);
Assert.IsTrue(pub.Issue == null);
Assert.IsTrue(pub.Authors.Length == 82);
Assert.IsTrue(pub.Authors[0] == "Arrow KJ");
Assert.IsTrue(pub.Authors[26] == "Guillemin R");
Assert.IsTrue(pub.Authors[81] == "Wilson RW");
// Verify publication type
Assert.IsTrue(pub.PubType == "Newspaper Article");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 0);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings.Count == 9);
Assert.IsTrue(pub.MeSHHeadings.Contains("Embryo Disposition"));
Assert.IsTrue(pub.MeSHHeadings.Contains("National Institutes of Health (U.S.)"));
Assert.IsTrue(pub.MeSHHeadings.Contains("United States"));
// Verify position type
Harvester.AuthorPositions PositionType;
int AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 27);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Middle);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 27);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Middle);
break;
case 3086749:
// This publication was altered to contain six GrantIDs in order to
// test the GrantID column length in the database
FoundPublications++;
Assert.IsTrue(pub.Title == "Pituitary FSH is released by a heterodimer of the beta-subunits from the two forms of inhibin.");
Assert.IsTrue(pub.Pages == "779-82");
Assert.IsTrue(pub.Year == 1986);
Assert.IsTrue(pub.Month == "Jun");
Assert.IsTrue(pub.Day == "19-25");
Assert.IsTrue(pub.Journal == "Nature");
Assert.IsTrue(pub.Volume == "321");
Assert.IsTrue(pub.Issue == "6072");
Assert.IsTrue(pub.Authors.Length == 7);
Assert.IsTrue(pub.Authors[0] == "Ling N");
Assert.IsTrue(pub.Authors[4] == "Esch F");
Assert.IsTrue(pub.Authors[6] == "Guillemin R");
// Verify publication type
Assert.IsTrue(pub.PubType == "Journal Article");
Assert.IsTrue(ptc.GetCategoryNumber(pub.PubType) == 3);
// Verify MeSH headings
Assert.IsTrue(pub.MeSHHeadings.Count == 14);
Assert.IsTrue(pub.MeSHHeadings.Contains("Amino Acid Sequence"));
Assert.IsTrue(pub.MeSHHeadings.Contains("Follicle Stimulating Hormone/*secretion"));
Assert.IsTrue(pub.MeSHHeadings.Contains("Swine"));
// Verify position type
AuthorPosition = Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, "PeoplePublications");
Assert.IsTrue(AuthorPosition == 7);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Last);
AuthorPosition = person.GetAuthorPosition(DB, pub, out PositionType);
Assert.IsTrue(AuthorPosition == 7);
Assert.IsTrue(PositionType == Harvester.AuthorPositions.Last);
break;
}
}
}
break;
}
}
Assert.IsTrue(FoundPublications == 6);
// Verify that People.Harvested has been updated for each person
DataTable Results = DB.ExecuteQuery("SELECT Setnb, Harvested FROM People");
Assert.IsTrue(Results.Rows.Count == 4);
foreach (DataRow Row in Results.Rows)
{
Assert.IsTrue((bool)Row["Harvested"] == true);
}
}
