/// <summary>
/// Search PubMed for all of the related publications and add them to the database, keep trying until search is successful
/// </summary>
/// <param name="relatedPmids">Related publications</param>
/// <returns>NCBI search results</returns>
private string SearchPubMedForRelatedPublications(List <int> relatedPmids)
{
StringBuilder searchQuery = new StringBuilder();
foreach (int relatedPmid in relatedPmids)
{
// Build the search query to issue the PubMed search for related IDs
searchQuery.AppendFormat("{0}{1}[uid]", searchQuery.Length == 0 ? String.Empty : " OR ", relatedPmid);
}
NCBI.UsePostRequest = true;
// If ncbi.Search() throws an exception, retry -- web connection may be temporarily down
bool searchSuccessful = false;
string searchResults = null;
while (!searchSuccessful)
{
try
{
searchResults = ncbi.Search(searchQuery.ToString());
searchSuccessful = true;
}
catch (Exception ex)
{
Trace.WriteLine(DateTime.Now + " - web request error during NCBI search, retrying search. Error message: " + ex.Message);
System.Threading.Thread.Sleep(2000);
}
}
return(searchResults);
}
/// <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);
}
}
}
}