/// <summary>
/// Retrieve the IDs from the XML results from ELink
/// </summary>
/// <param name="xml">XML results from ELink</param>
/// <param name="relatedRanks">Ouput - dictionary that maps PMIDs to map for looking up rank in related results</param>
/// <returns>Dictionary that maps source PMIds to a list of IDs extracted from the XML (or an empty list of none)</returns>
private static Dictionary <int, List <int> > GetIdsFromXml(string xml, out Dictionary <int, Dictionary <int, RankAndScore> > relatedRanks)
{
Dictionary <int, List <int> > result = new Dictionary <int, List <int> >();
relatedRanks = new Dictionary <int, Dictionary <int, RankAndScore> >();
List <int> ids = new List <int>();
XmlDocument xmlDoc = new XmlDocument();
xmlDoc.LoadXml(xml);
XmlNodeList linkSets = xmlDoc["eLinkResult"].ChildNodes;
foreach (XmlNode linkSet in linkSets)
{
// There's one <LinkSet> for each PMID from the search
int pmid;
if (int.TryParse(linkSet["IdList"]["Id"].InnerText, out pmid))
{
Dictionary <int, RankAndScore> relatedRank = null;
if (relatedRanks.ContainsKey(pmid))
{
relatedRank = relatedRanks[pmid];
}
else
{
relatedRank = new Dictionary <int, RankAndScore>();
relatedRanks.Add(pmid, relatedRank);
}
XmlNodeList linkSetDbs = linkSet.SelectNodes("LinkSetDb");
// Find the "pubmed_pubmed" link set
foreach (XmlNode linkSetDb in linkSetDbs)
{
if (linkSetDb["LinkName"].InnerText == "pubmed_pubmed")
{
// We've found the link set of related PubMed publications. Add it to the results.
List <int> linkList;
if (result.ContainsKey(pmid))
{
linkList = result[pmid] as List <int>;
}
else
{
linkList = new List <int>();
result[pmid] = linkList;
}
int rank = 0;
foreach (XmlNode link in linkSetDb.SelectNodes("Link"))
{
int score;
if (!int.TryParse(link["Score"].InnerText, out score))
{
score = -1;
}
int relatedPmid;
if (int.TryParse(link["Id"].InnerText, out relatedPmid))
{
linkList.Add(relatedPmid);
RankAndScore rankAndScore = new RankAndScore()
{
Rank = ++rank, Score = score
};
relatedRank.Add(relatedPmid, rankAndScore);
}
}
}
}
}
}
return(result);
}
/// <summary>
/// Go through all of the ranks and scores retrieved from the server for each PMID and write them to the output file and the database.
/// </summary>
/// <param name="db">Database to write to</param>
/// <param name="relatedTableName">Name of the related table</param>
/// <param name="relatedSearchResults">NCBI search results parsed into a dictionary that maps queried PMIDs to a list of related PMIDs</param>
/// <param name="relatedRanks">Dictionary parsed from NCBI search results that maps each queried PMID to a dictionary of related PMIDs and their ranks and scores</param>
/// <param name="outputFilename">Output file to append to</param>
/// <param name="inputQueue">Input queue for marking success or error</param>
/// <returns>True if a lines were successfully added to the file and table, false if an error occurred</returns>
private bool WriteRelatedRanksToOutputFileAndDatabase(Database db, string relatedTableName,
Dictionary <int, List <int> > relatedSearchResults, Dictionary <int, Dictionary <int, RankAndScore> > relatedRanks,
string outputFilename, InputQueue inputQueue)
{
if (BackgroundWorker != null && BackgroundWorker.CancellationPending)
{
Trace.WriteLine(DateTime.Now + " - stopped");
return(false);
}
foreach (int pmid in relatedSearchResults.Keys)
{
List <int> relatedPmids = relatedSearchResults[pmid];
if (relatedPmids == null)
{
Trace.WriteLine($"{DateTime.Now} - found empty related PMID list for PMID {pmid} ({++_pmidsProcessed} of {inputQueue.TotalPmidsAdded})");
}
else if (!relatedRanks.ContainsKey(pmid))
{
Trace.WriteLine($"{DateTime.Now} - no ranks or scores found for PMID {pmid} ({++_pmidsProcessed} of {inputQueue.TotalPmidsAdded})");
}
else
{
Trace.WriteLine($"{DateTime.Now} - found {relatedPmids.Count} results for PMID {pmid} ({++_pmidsProcessed} of {inputQueue.TotalPmidsAdded})");
Dictionary <int, RankAndScore> ranksAndScores = relatedRanks[pmid];
foreach (int relatedPmid in relatedPmids)
{
if (!ranksAndScores.ContainsKey(relatedPmid))
{
Trace.WriteLine(DateTime.Now + " - unable to find related ranks and scores for PMID " + pmid + ", related PMID " + relatedPmid);
}
else
{
RankAndScore rankAndScore = ranksAndScores[relatedPmid];
string line = String.Format("{0},{1},{2},{3}", pmid, relatedPmid, rankAndScore.Rank, rankAndScore.Score);
string output = line + Environment.NewLine;
try
{
File.AppendAllText(outputFilename, output);
}
catch (Exception ex)
{
Trace.WriteLine(DateTime.Now + " - unable to append '" + line + "' to the output file: " + ex.Message);
Trace.WriteLine(ex.StackTrace);
Trace.WriteLine(DateTime.Now + " - stopping the run, use the Resume button to resume");
inputQueue.MarkError(pmid);
return(false);
}
bool written = WriteRelatedRankToDatabase(db, relatedTableName, pmid, relatedPmid, rankAndScore.Rank, rankAndScore.Score);
if (!written)
{
return(false);
}
}
}
}
// Mark the PMID processed in the queue
inputQueue.MarkProcessed(pmid);
}
return(true);
}
