public void ReadAndWritePublicationTypes()
{
// Read the publication types from the CSV file
PublicationTypes ptc = new PublicationTypes(
AppDomain.CurrentDomain.BaseDirectory + "\\Unit Tests\\TestPublicationTypes",
"PublicationTypes.csv"
);
Assert.AreEqual(ptc.Categories.Count, 52);
Assert.AreEqual(ptc.GetCategoryNumber("Legislation"), 0);
Assert.AreEqual(ptc.GetCategoryNumber("Consensus Development Conference, NIH"), 1);
Assert.AreEqual(ptc.GetCategoryNumber("Review, Multicase"), 2);
Assert.AreEqual(ptc.GetCategoryNumber("Technical Report"), 3);
Assert.AreEqual(ptc.GetCategoryNumber("Comment"), 4);
// Verify OverrideFirstCategory values
Assert.IsTrue(ptc.OverrideFirstCategory.ContainsKey("Review"));
Assert.IsTrue(ptc.OverrideFirstCategory.ContainsKey("Review, Multicase"));
Assert.AreEqual(ptc.OverrideFirstCategory.ContainsKey("Comment"), false);
// First recreate the database, then write the publication types to it
Database DB = new Database("Publication Harvester Unit Test");
Harvester harvester = new Harvester(DB);
harvester.CreateTables();
ptc.WriteToDB(DB);
// Read the publication types from the database
PublicationTypes ptcFromDB =
new PublicationTypes(DB);
Assert.AreEqual(ptcFromDB.Categories.Count, 52);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Overall"), 0);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Clinical Trial, Phase II"), 1);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Review of Reported Cases"), 2);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Technical Report"), 3);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Letter"), 4);
Assert.AreEqual(ptcFromDB.GetCategoryNumber("Comment"), 4);
// Verify OverrideFirstCategory values
Assert.IsTrue(ptcFromDB.OverrideFirstCategory.ContainsKey("Review"));
Assert.IsTrue(ptcFromDB.OverrideFirstCategory.ContainsKey("Review, Multicase"));
Assert.AreEqual(ptcFromDB.OverrideFirstCategory.ContainsKey("Comment"), false);
}
/// <summary>
/// Check a publication against the filter
/// </summary>
/// <param name="publication">Publication to check</param>
/// <param name="linkRanking">Link ranking for the publication</param>
/// <param name="referencePublication">Reference publication to compare against</param>
/// <param name="publicationTypes">PublicationTypes object for the current database</param>
/// <returns>True if the publication matches the filter, false otherwise</returns>
public bool FilterPublication(Publication publication, int linkRanking, Publication referencePublication, PublicationTypes publicationTypes)
{
if (SameJournal && (publication.Journal != referencePublication.Journal))
{
return(false);
}
if (PubWindowLowerBound.HasValue && (referencePublication.Year - PubWindowLowerBound > publication.Year))
{
return(false);
}
if (PubWindowUpperBound.HasValue && (referencePublication.Year + PubWindowUpperBound < publication.Year))
{
return(false);
}
if (linkRanking > MaximumLinkRanking)
{
return(false);
}
if (((IncludeCategories != null) && (IncludeCategories.Count() > 0)) &&
((String.IsNullOrEmpty(publication.PubType) ||
!IncludeCategories.Contains(publicationTypes.GetCategoryNumber(publication.PubType)))))
{
return(false);
}
if ((IncludeLanguages != null) && (IncludeLanguages.Count() > 0) &&
(String.IsNullOrEmpty(publication.Language) ||
!IncludeLanguages.Contains(publication.Language)))
{
return(false);
}
return(true);
}
/// <summary>
/// Retrieve all of the publications a set of colleagues
/// </summary>
/// <param name="Star">Star whose colleagues are being retrieved</param>
/// <param name="Colleagues">List of colleagues whose publications should be retrieved</param>
public void GetColleaguePublications(Person[] Colleagues, string[] Languages, List <int> AllowedPubTypeCategories)
{
// Keep a list of written Setnbs, just to make sure we don't write the
// same colleage twice
ArrayList WrittenSetnbs = new ArrayList();
// Process each colleague
foreach (Person Colleague in Colleagues)
{
// Only process a colleague that hasn't yet been touched
if (!WrittenSetnbs.Contains(Colleague.Setnb))
{
WrittenSetnbs.Add(Colleague.Setnb);
// Get the colleague's publications
// Search NCBI -- if an error is thrown, write that error to the database
string results;
try
{
results = ncbi.Search(Colleague.MedlineSearch);
}
catch (Exception ex)
{
string Message = "Error reading publications for "
+ Colleague.Last + " (" + Colleague.Setnb + ex.Message;
ColleagueFinder.WriteErrorToDB(Message, DB, Colleague);
throw new Exception(Message);
}
// Turn the results into a set of publications for the colleague
if ((results != null) && (results.Trim() != ""))
{
Publications ColleaguePublications = new Publications(results, pubTypes);
// Write the publications to the database -- but only if they
// actually belong to the colleague.
if (ColleaguePublications.PublicationList != null)
{
foreach (Publication pub in ColleaguePublications.PublicationList)
{
// If the publication has no authors, it's clearly not actually
// a publication that belongs to this colleague.
// Also, since the publication harvester only harvests
// English publications, we exclude any non-English ones as well.
if ((pub.Authors != null) && (pub.Language == "eng") &&
(AllowedPubTypeCategories.Contains(pubTypes.GetCategoryNumber(pub.PubType))))
{
// Add a row to the ColleaguePublications table -- this will
// return False if the publication doesn't actually belong
// to the colleague
bool PubBelongsToColleague = WriteColleaguePublicationsToDB(DB, Colleague, pub, pubTypes, Languages);
if (PubBelongsToColleague)
{
// Make sure the publication doesn't already exist, then write
// it to the database.
if (DB.GetIntValue("SELECT Count(*) FROM Publications WHERE PMID = " + pub.PMID.ToString()) == 0)
{
Publications.WriteToDB(pub, DB, pubTypes, Languages);
}
}
}
}
}
// Update the Harvested column in the Colleagues table
ArrayList Parameters = new ArrayList();
Parameters.Add(Database.Parameter(Colleague.Setnb));
DB.ExecuteNonQuery("UPDATE Colleagues SET Harvested = 1 WHERE Setnb = ?", Parameters);
}
}
}
}
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);
}
}
