/// <summary>
/// Add a row to PeoplePublications for a person and publication
/// </summary>
/// <param name="DB">Database to write to</param>
/// <param name="person">Person who is the author of the publication</param>
/// <param name="publication">Publication to write</param>
public static void WritePeoplePublicationsToDB(Database DB, Person person, Publication publication)
{
ArrayList Parameters;
int AuthorPosition = 0;
for (int i = 1; (AuthorPosition == 0) && (i <= publication.Authors.Length); i++)
{
foreach (string name in person.Names)
{
if (StringComparer.CurrentCultureIgnoreCase.Equals(
publication.Authors[i - 1], name //.ToUpper()
))
{
AuthorPosition = i;
}
else if (name == "*")
{
AuthorPosition = -1;
}
}
}
// From the SRS -- definition of position type:
// • 1 if the person is the first author
// • 2 if the person is the last author
// • 3 if the person is the second author -- only if # authors >= 5
// • 4 if the person is the next-to-last author -- only if # authors >= 5
// • 5 if the person is in the middle (and there are five or more authors for the publication)
Harvester.AuthorPositions PositionType;
if (AuthorPosition == 1)
{
PositionType = Harvester.AuthorPositions.First;
}
else if (AuthorPosition == publication.Authors.Length)
{
PositionType = Harvester.AuthorPositions.Last;
}
else if ((AuthorPosition == 2) && (publication.Authors.Length >= 5))
{
PositionType = Harvester.AuthorPositions.Second;
}
else if ((AuthorPosition == publication.Authors.Length - 1) && (publication.Authors.Length >= 5))
{
PositionType = Harvester.AuthorPositions.NextToLast;
}
else if (AuthorPosition == -1)
{
PositionType = Harvester.AuthorPositions.None;
}
else
{
PositionType = Harvester.AuthorPositions.Middle;
}
// Write the row to PeoplePublications
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(person.Setnb));
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(AuthorPosition));
Parameters.Add(Database.Parameter((int)PositionType));
DB.ExecuteNonQuery(@"INSERT INTO PeoplePublications
(Setnb, PMID, AuthorPosition, PositionType)
VALUES ( ? , ? , ? , ? )", Parameters);
}
/// <summary>
/// Add the current publication to the database
/// </summary>
/// <param name="publication">Publication to write</param>
/// <param name="DB">Database to add to</param>
/// <param name="PubTypes">PublicationTypes object</param>
/// <param name="Languages">The publication must match one of these languages or it will be rejected</param>
/// <returns>True if the publication was written or is in the database already, false otherwise</returns>
public static bool WriteToDB(Publication publication, Database DB, PublicationTypes PubTypes, string[] Languages)
{
ArrayList Parameters;
// If the object already exists in the database, do nothing
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
int Count = DB.GetIntValue(
@"SELECT Count(*) FROM Publications p
WHERE p.PMID = ?", Parameters
);
if (Count > 0)
{
return(true); // Return true because the publication is in the database
}
// Only write a publication if the language matches one of the languages
// passed in the Languages parameter -- if Languages is null, accept
// all values
if (Languages != null)
{
bool Found = false;
foreach (string Language in Languages)
{
if (publication.Language == Language)
{
Found = true;
}
}
if (!Found)
{
return(false); // Return false because the publication wasn't written
}
}
// Add the authors
// First delete any authors that are there, in case the add was
// interrupted partway through
for (int Position = 0; (publication.Authors != null) && (Position <= publication.Authors.GetUpperBound(0)); Position++)
{
int First = (Position == 0) ? 1 : 0;
int Last = (Position == publication.Authors.GetUpperBound(0)) ? 1 : 0;
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(Position + 1)); // The first author position is 1, not 0
Parameters.Add(Database.Parameter(Database.Left(publication.Authors[Position], 70)));
Parameters.Add(Database.Parameter(First));
Parameters.Add(Database.Parameter(Last));
DB.ExecuteNonQuery(
@"INSERT INTO PublicationAuthors
(PMID, Position, Author, First, Last)
VALUES (? , ? , ? , ? , ?)"
, Parameters);
}
// Add the MeSH headings
for (int Heading = 0; (publication.MeSHHeadings != null) && (Heading < publication.MeSHHeadings.Count); Heading++)
{
// If the MeSH heading already exists in the MeSHHeadings table, reuse it,
// otherwise add it
int ID;
string MeSHHeading = Database.Left((string)publication.MeSHHeadings[Heading], 255);
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(MeSHHeading));
DataTable Results = DB.ExecuteQuery("SELECT ID FROM MeSHHeadings WHERE Heading = ?", Parameters);
if (Results.Rows.Count > 0)
{
ID = Convert.ToInt32(Results.Rows[0][0]);
}
else
{
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(MeSHHeading));
DB.ExecuteNonQuery("INSERT INTO MeSHHeadings (Heading) VALUES (?)", Parameters);
ID = DB.GetIntValue("SELECT LAST_INSERT_ID()");
}
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(ID));
DB.ExecuteNonQuery(
@"INSERT INTO PublicationMeSHHeadings (PMID, MeSHHeadingID)
VALUES ( ? , ? )", Parameters);
}
// Add the grants
for (int Grant = 0; (publication.Grants != null) && (Grant < publication.Grants.Count); Grant++)
{
// Some publications may have duplicate grants, so only add non-duplicates to avoid
// primary key problems
string GrantID = Database.Left((string)publication.Grants[Grant], 50);
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(GrantID));
if (DB.GetIntValue(
@"SELECT Count(*) FROM PublicationGrants
WHERE PMID = ? AND GrantID = ?", Parameters) == 0)
{
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(GrantID));
DB.ExecuteNonQuery(
@"INSERT INTO PublicationGrants (PMID, GrantID)
VALUES ( ? , ? )", Parameters);
}
}
// Strip the single and double quotes from the title before writing it
string title;
if (String.IsNullOrEmpty(publication.Title))
{
title = "";
}
else
{
title = publication.Title.Replace("\"", "").Replace("'", "");
}
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(publication.PMID));
Parameters.Add(Database.Parameter(Database.Left(publication.Journal, 128)));
Parameters.Add(Database.Parameter(publication.Year));
Parameters.Add(Database.Parameter(publication.Authors == null ? 0 : publication.Authors.Length));
Parameters.Add(Database.Parameter(Database.Left(publication.Month, 32)));
Parameters.Add(Database.Parameter(Database.Left(publication.Day, 32)));
Parameters.Add(Database.Parameter(Database.Left(title, 244)));
Parameters.Add(Database.Parameter(Database.Left(publication.Volume, 32)));
Parameters.Add(Database.Parameter(Database.Left(publication.Issue, 32)));
Parameters.Add(Database.Parameter(Database.Left(publication.Pages, 50)));
// Finally, add the publication. This is part of the publication fault
// tolerance system -- the headings and authors are not "final" until
// the publication is written, and can be cleared from the database using
// Harvester.ClearDataAfterInterruption().
// Publication type processing -- read the publication type file,
// create the publication type table, add the types, file types into bins
Parameters.Add(Database.Parameter(publication.PubType));
Parameters.Add(Database.Parameter(PubTypes.GetCategoryNumber(publication.PubType)));
DB.ExecuteNonQuery(
@"INSERT INTO Publications
(PMID, Journal, Year, Authors, Month, Day, Title,
Volume, Issue, Pages, PubType, PubTypeCategoryID)
VALUES
(? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? )", Parameters);
return(true);
}
/// <summary>
/// Initialize the publication from the database
/// </summary>
/// <param name="DB">Database to read from</param>
/// <param name="PMID">PMID of the publication</param>
/// <param name="publication">The publication to write</param>
/// <param name="SkipMeSHHeadingsAndGrants">Set SkipMeSHHeadingsAndGrants to true to skip reading MeSH headings and grants</param>
/// <returns>True if the publication was found, false otherwise</returns>
public static bool GetPublication(Database DB, int PMID, out Publication publication, bool SkipMeSHHeadingsAndGrants)
{
publication = new Publication();
publication.PMID = PMID;
// Read the publication information
ArrayList Parameters = new ArrayList();
Parameters.Add(Database.Parameter(PMID));
DataTable Results = DB.ExecuteQuery(
@"SELECT Journal, Year, Authors, Month, Day, Title, Volume,
Issue, Pages, PubType
FROM Publications
WHERE PMID = ?", Parameters);
if (Results.Rows.Count == 0)
{
throw new Exception("Article " + PMID.ToString() + " not found");
}
DataRow Row = Results.Rows[0];
publication.Year = (int)Row["Year"];
publication.Journal = Row["Journal"].Equals(DBNull.Value) ? null : Row["Journal"].ToString();
publication.Month = Row["Month"].Equals(DBNull.Value) ? null : Row["Month"].ToString();
publication.Day = Row["Day"].Equals(DBNull.Value) ? null : Row["Day"].ToString();
publication.Title = Row["Title"].Equals(DBNull.Value) ? null : Row["Title"].ToString();
publication.Volume = Row["Volume"].Equals(DBNull.Value) ? null : Row["Volume"].ToString();
publication.Issue = Row["Issue"].Equals(DBNull.Value) ? null : Row["Issue"].ToString();
publication.Pages = Row["Pages"].Equals(DBNull.Value) ? null : Row["Pages"].ToString();
publication.PubType = Row["PubType"].Equals(DBNull.Value) ? null : Row["PubType"].ToString();
// Strip single and double quotes from the title
publication.Title = publication.Title.Replace("\"", "").Replace("'", "");
// Read the authors
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(PMID));
Results = DB.ExecuteQuery(
@"SELECT Author
FROM PublicationAuthors
WHERE PMID = ?
ORDER BY Position", Parameters);
if (Results.Rows.Count == 0)
{
publication.Authors = new string[] { };
}
else
{
publication.Authors = new string[Results.Rows.Count];
for (int i = 0; i < Results.Rows.Count; i++)
{
publication.Authors[i] = Results.Rows[i]["Author"].ToString();
}
}
if (SkipMeSHHeadingsAndGrants == false)
{
// Read the MeSH headings
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(PMID));
Results = DB.ExecuteQuery(
@"SELECT mh.Heading
FROM MeSHHEadings mh, PublicationMeSHHeadings pm
WHERE pm.PMID = ?
AND mh.ID = pm.MeSHHeadingID", Parameters);
// MeSHHeadings was initialized to null, so only set it if there are rows returned
if (Results.Rows.Count != 0)
{
publication.MeSHHeadings = new ArrayList();
for (int i = 0; i < Results.Rows.Count; i++)
{
publication.MeSHHeadings.Add(Results.Rows[i]["Heading"].ToString());
}
}
// Read the grants
Parameters = new ArrayList();
Parameters.Add(Database.Parameter(PMID));
Results = DB.ExecuteQuery(
@"SELECT GrantID
FROM PublicationGrants
WHERE PMID = ?", Parameters);
// Grants was initialized to null, so only set it if there are rows returned
if (Results.Rows.Count != 0)
{
publication.Grants = new ArrayList();
for (int i = 0; i < Results.Rows.Count; i++)
{
publication.Grants.Add(Results.Rows[i]["GrantID"].ToString());
}
}
}
return(true);
}
/// <summary>
/// Read a string containing a Medline tag and its data and populate the
/// appropriate property
/// </summary>
/// <param name="MedlineTag">A Medline tag and its data (with newlines stripped out)</param>
public static void ProcessMedlineTag(ref Publication publication, string MedlineTag, PublicationTypes pubTypes)
{
// Verify that the string is really a tag -- it must start with four characters
// followed by a dash and a space. If not, don't process it.
if ((MedlineTag.Length < 6) || (MedlineTag.Substring(4, 2) != "- "))
{
return;
}
string data = MedlineTag.Substring(5).Trim();
// Process the tags
switch (MedlineTag.Substring(0, 4).Trim())
{
case "PMID":
// "PMID- 16319490"
if (IsNumeric(data))
{
publication.PMID = Convert.ToInt32(data);
}
else
{
publication.PMID = int.MinValue;
}
break;
case "DP":
// "DP - 2005 Nov 24"
if (IsNumeric(data.Substring(0, 4)))
{
// Grab the year first, then the rest is month and day.
publication.Year = Convert.ToInt32(data.Substring(0, 4));
data = data.Substring(4).Trim();
if (data.Contains(" "))
{
publication.Month = data.Substring(0, data.IndexOf(" "));
publication.Day = data.Substring(data.IndexOf(" ") + 1);
}
else
{
if (data.Length != 0)
{
publication.Month = data;
}
}
}
break;
case "TI":
// "TI - Title..."
publication.Title = data;
break;
case "TA":
// "TA - Hum Hered"
publication.Journal = data;
break;
case "GR":
// "GR - GM 28356/GM/NIGMS"
// GrantID should contain a comma-delimit list of grant IDs
if (publication.Grants == null)
{
publication.Grants = new ArrayList();
}
publication.Grants.Add(data);
break;
case "PT":
// "PT - Clinical Trial"
// Only copy PubType if it's the first PT tag encountered in this
// publication or if the publication type is flagged as an
// "override first category" publication type
if (publication.PubType == null)
{
publication.PubType = data;
}
else if (pubTypes.OverrideFirstCategory.ContainsKey(data))
{
publication.PubType = data;
}
break;
case "IP":
// "IP - 3"
publication.Issue = data;
break;
case "PG":
// "PG - 134-142"
publication.Pages = data;
break;
case "LA":
// "LA - eng"
publication.Language = data.ToLower();
break;
case "VI":
// "VI - 60"
publication.Volume = data;
break;
case "AU":
// "AU - Wang T"
// If this is the first author, create the Authors array
if (publication.Authors == null)
{
publication.Authors = new string[1];
publication.Authors[0] = data;
}
else
{
// Otherwise, copy the author to the end of the Authors array
string[] temp = new string[publication.Authors.Length + 1];
publication.Authors.CopyTo(temp, 0);
publication.Authors = temp;
publication.Authors[publication.Authors.GetUpperBound(0)] = data;
}
break;
case "MH":
// "AU - Wang T"
// If this is the first MeSH heading, create the new ArrayList
if (publication.MeSHHeadings == null)
{
publication.MeSHHeadings = new ArrayList();
}
publication.MeSHHeadings.Add(data.ToString());
break;
}
}
/// <summary>
/// Retrieve counts from a publication list
/// </summary>
/// <param name="PublicationList">Publication list to retrieve counts from,
/// sorted by year, publication type and author position</param>
/// <param name="Index">Offset in the publication list of the first publication
/// matching the year and publication type</param>
/// <param name="Year">Year to match for</param>
/// <param name="PublicationType">Publication type to match for</param>
public Counts(Publication[] PublicationList, ref int Index, int Year, int PublicationType,
PublicationTypes PubTypes, Database DB, Person person, Hashtable Weights, string PeoplePublicationsTable)
{
// Return zero counts if the publication list is empty
if (PublicationList.Length == 0)
{
return;
}
// Return zero counts if the index is out of bounds
if ((Index < 0) || (Index >= PublicationList.Length))
{
return;
}
// Return zero counts if the index doesn't point to a match -- that means
// there are no matches
Publication pub = PublicationList[Index];
int PubType = PubTypes.GetCategoryNumber(pub.PubType);
if ((pub.Year != Year) || (PubType != PublicationType))
{
return;
}
// If we get this far, we have a match. Move forward through the publication
// list, adding to the counts, until we find a non-matching publication or
// the list runs out.
do
{
// Get the weight for the journal
float Weight = 0;
if (pub.Journal != null && Weights.ContainsKey(pub.Journal))
{
Weight += (float)Weights[pub.Journal];
}
// Get the position type, and increment the correct counter
Harvester.AuthorPositions PositionType;
Publications.GetAuthorPosition(DB, pub.PMID, person, out PositionType, PeoplePublicationsTable);
switch (PositionType)
{
case Harvester.AuthorPositions.First:
First++;
FirstWeighted += Weight;
break;
case Harvester.AuthorPositions.Last:
Last++;
LastWeighted += Weight;
break;
case Harvester.AuthorPositions.Second:
Second++;
SecondWeighted += Weight;
break;
case Harvester.AuthorPositions.NextToLast:
NextToLast++;
NextToLastWeighted += Weight;
break;
case Harvester.AuthorPositions.Middle:
case Harvester.AuthorPositions.None:
Middle++;
MiddleWeighted += Weight;
break;
}
Index++;
if (Index < PublicationList.Length)
{
pub = PublicationList[Index];
PubType = PubTypes.GetCategoryNumber(pub.PubType);
}
} while ((Index < PublicationList.Length) &&
(PublicationList[Index].Year == Year) &&
(PubType == PublicationType));
}
