/// <summary>
/// Read next fingerprint rec from file
/// </summary>
/// <param name="fi"></param>
/// <returns></returns>
public FingerprintRec ReadFingerprintRec(
int fi)
{
if (Rfpa == null || Rfpa.reader != ReadStreams[fi]) // start reading file
{
Rfpa = new ReadFingerprintRecArgs();
Rfpa.Initialize(ReadStreams[fi], FpLengthInLongs);
}
if (!ReadRawFingerprintRec(Rfpa))
{
return(null); // end of file
}
FingerprintRec r = new FingerprintRec();
r.molId = Rfpa.uci;
r.SrcId = Rfpa.src;
string cid = ASCIIEncoding.ASCII.GetString(Rfpa.cidBytes, 0, Rfpa.cidLength);
r.Cid = CompoundIdNormalizeForDatabase(cid);
r.Cardinality = Rfpa.cardinality;
r.Fingerprint = (long[])Rfpa.fingerprint.Clone();
return(r);
}
/// <summary>
/// ReadFingerprintRec
/// </summary>
/// <returns></returns>
public FingerprintRec ReadFingerprintRec()
{
if (Rsi < 0)
{
Rsi = 0; // first file
}
FingerprintRec r = ReadFingerprintRec(Rsi);
while (r == null) // if end of file try going to next
{
if (Rsi + 1 >= ReadStreams.Length)
{
return(null);
}
Rsi++;
Rfpa = new ReadFingerprintRecArgs();
Rfpa.Initialize(ReadStreams[Rsi], FpLengthInLongs);
r = ReadFingerprintRec(Rsi);
}
r.molId = Rfpa.uci;
r.SrcId = Rfpa.src;
string cid = ASCIIEncoding.ASCII.GetString(Rfpa.cidBytes, 0, Rfpa.cidLength);
r.Cid = CompoundIdNormalizeForDatabase(cid);
r.Cardinality = Rfpa.cardinality;
r.Fingerprint = (long[])Rfpa.fingerprint.Clone();
return(r);
}
/// <summary>
/// WriteFingerprintRec
/// </summary>
/// <param name="fpr"></param>
public void WriteFingerprintRec(
FingerprintRec fpr)
{
if (fpr.SrcId != LastSrcId || fpr.Cid != LastCid)
{ // keep all FPs for a Cid in the same file
Bwi++;
if (Bwi >= BinaryWriters.Length)
{
Bwi = 0;
}
}
WriteFingerprintRec(BinaryWriters[Bwi], fpr);
LastSrcId = fpr.SrcId;
LastCid = fpr.Cid;
return;
}
/// <summary>
/// GetMaxCorpId
/// </summary>
/// <returns></returns>
public static int GetMaxDestMolId()
{
int molId, maxMolId = 0;
FingerprintDao fpd = new FingerprintDao(Database, FingerprintType);
List <string> ids = new List <string>();
if (!fpd.DataFilesExist())
{
return(maxMolId);
}
fpd.OpenReaders();
while (true)
{
FingerprintRec rec = fpd.ReadFingerprintRec();
if (rec == null)
{
break;
}
//CorpIds.Add(rec.Cid); // debug
if (CorpDatabase)
{
int.TryParse(rec.Cid, out molId);
}
else
{
molId = rec.molId;
}
if (molId > maxMolId)
{
maxMolId = molId;
}
}
fpd.CloseReaders();
return(maxMolId);
}
/// <summary>
/// Get a set of the existing Cids
/// </summary>
/// <returns></returns>
public HashSet <string> GetExistingCidSet()
{
HashSet <string> cidSet = new HashSet <string>();
OpenReaders();
while (true)
{
FingerprintRec r = ReadFingerprintRec();
if (r == null)
{
break;
}
cidSet.Add(r.Cid);
}
CloseReaders();
return(cidSet);
}
/// <summary>
/// WriteFpRec
/// </summary>
/// <param name="bw"></param>
/// <param name="uci"></param>
/// <param name="src"></param>
/// <param name="cidString"></param>
/// <param name="fingerprint"></param>
public void WriteFingerprintRec(
BinaryWriter bw,
FingerprintRec fpr)
{
long l;
if (bw == null || fpr == null)
{
throw new InvalidDataException();
}
bw.Write(fpr.molId); // int - [4]
bw.Write(fpr.SrcId); // int - [4]
string cid = CompoundIdNormalizeForDatabase(fpr.Cid);
bw.Write((byte)cid.Length); // byte - [1]
byte[] cidBytes = ASCIIEncoding.ASCII.GetBytes(cid);
bw.Write(cidBytes); // byte - [n]
bw.Write(fpr.Cardinality); // number of bits set in fp - int - [4]
long[] fp64 = fpr.Fingerprint; // FingerprintMx.ByteArrayToLongrray(fingerprint);
bw.Write((byte)FpLengthInLongs); // long count - byte - [1]
for (int li = 0; li < FpLengthInLongs; li++) // fingerprint long*3 -[24] (MACCS)
{
if (li < fp64.Length)
{
l = fp64[li];
}
else
{
l = 0; // pad to fixed length
}
bw.Write(l);
}
return;
}
/// <summary>
/// Merge existing .bin files with new records
/// 1. Copy .bin files to .mrg files filtering out cids that have been updated
/// 2. Append new records to .mrg files
/// 3. Rename .bin files to .bak files and .mrg files to new .bin files
/// </summary>
static void MergeRecordsIntoFiles(
List <FingerprintRec> fpRecList)
{
string date1, date2;
Progress.Show("Merging existing and new files...");
// Copy existing bin file entries filtering out cids that were updated
FpDao.OpenReaders("bin"); // open existing .bin files for input
FpDao.OpenWriters("mrg", FileMode.Create); // open new merge files for output
HashSet <string> fpRecHash = new HashSet <string>(); // build a hash of cids that shouldn't be copied
foreach (FingerprintRec fpr in fpRecList)
{
fpRecHash.Add(fpr.Cid);
}
int replacementCnt = 0;
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++) // copy each file
{
BinaryWriter bw = FpDao.BinaryWriters[fi];
while (true)
{
FingerprintRec fpr = FpDao.ReadFingerprintRec(fi);
if (fpr == null)
{
break;
}
if (fpRecHash.Contains(fpr.Cid))
{
//Log("Removing " + fpr.Cid); // debug
replacementCnt++;
continue; // skip if this cid is was updated in the incoming list
}
FpDao.WriteFingerprintRec(bw, fpr);
}
}
FpDao.CloseReaders();
// Append the new records to the merge files
foreach (FingerprintRec fpr in fpRecList) // write out buffered recs
{
FpDao.WriteFingerprintRec(fpr);
}
FpDao.CloseWriters();
// Backup old files and activate new files
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++) // check that we can backup all bin files
{
string fileName = FpDao.GetFpFileName(fi) + ".bin";
bool backupOk = FileUtil.CanRename(fileName);
if (!backupOk)
{
throw new Exception("Unable to rename file: " + fileName + ", aborting update");
}
}
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++)
{
string fileName = FpDao.GetFpFileName(fi);
bool backupOk = FileUtil.BackupAndReplaceFile(fileName + ".bin", fileName + ".bak", fileName + ".mrg");
if (!backupOk)
{
throw new Exception("Error replacing file: " + fileName + ".bin");
}
}
if (ByCheckpoint)
{
string checkPointDate = String.Format("{0:dd-MMM-yyyy HHmmss}", MoleculeDateTime); // format last new/updated date time in a format that works with Oracle
FpDao.WriteFingerPrintSimMxDataUpdateCheckpointDate(checkPointDate); // update checkpoint
}
Progress.Show("Merging complete...");
int cnt = fpRecList.Count;
string cid1 = fpRecList[0].Cid;
string cid2 = fpRecList[cnt - 1].Cid;
if (CidUpdateDateDict.ContainsKey(cid1))
{
date1 = CidUpdateDateDict[cid1].ToString();
}
else
{
date1 = "Missing";
}
if (CidUpdateDateDict.ContainsKey(cid2))
{
date2 = CidUpdateDateDict[cid1].ToString();
}
else
{
date2 = "Missing";
}
Log("Records stored: " + cnt + ", Adds: " + (cnt - replacementCnt) + ", Replacements: " + replacementCnt +
", Date range: " + date1 + " - " + date2 + ", CIDs: First = " + cid1 + ", Last = " + cid2);
return;
}
static ICdkMol CdkMolUtil => StaticCdkMol.I; // static molecule shortcut for utility methods
/// <summary>
/// UpdateCorpFingerprintDatabaseMx
/// ///////////////////////////////////////////////////////
/// Syntax: Update FingerprintDatabaseMx [Corp | ChEMBL] [MACCS | ECFP4] [Load | ByCidRange | SinceLastCheckpoint | LoadMissing | <SingleCorpId>]
///
/// Corp Examples:
/// Update FingerprintDatabaseMx Corp MACCS Load
/// Update FingerprintDatabaseMx Corp MACCS LoadMissing
/// Update FingerprintDatabaseMx Corp MACCS SinceLastCheckpoint
///
/// Update FingerprintDatabaseMx Corp ECFP4 Load
/// Update FingerprintDatabaseMx Corp ECFP4 LoadMissing
/// Update FingerprintDatabaseMx Corp ECFP4 SinceLastCheckpoint
///
/// ChEMBL Examples:
/// Update FingerprintDatabaseMx Chembl MACCS Load
/// Update FingerprintDatabaseMx Chembl MACCS LoadMissing
///
/// Update FingerprintDatabaseMx Chembl ECFP4 Load
/// Update FingerprintDatabaseMx Chembl ECFP4 LoadMissing
/// ///////////////////////////////////////////////////////
/// </summary>
/// <param name="argString"></param>
/// <returns></returns>
static public string Update(
string argString)
{
MoleculeMx mol;
double mw;
string chime, smiles, molString, molFile = "";
string msg = "", sql = "", chemblId, cid = "", maxCorpIdSql, maxIdSql2, mf, missingFixCriteria = "", CorpIdList = "";
int storeChunkCount = 0, CorpId, molregno, molId, lowId = 0, highId = 0, maxDestId = 0, maxSrcId = 0;
int readCount = 0, storeCount = 0;
ByCheckpoint = ByCidRange = ByCidList = LoadIfMissing = false;
ReadChunkSize = DefaultReadChunkSize;
WriteChunkSize = DefaultWriteChunkSize;
Failures = new Dictionary <string, string>();
NewUndefinedStructureCids = new List <string>();
LastFailure = "";
FailureCount = 0;
// global try loop
try
{
////////////////////////
/// Parse Parameters ///
////////////////////////
// See which database
argString = argString.Trim();
if (Lex.StartsWith(argString, "Corp"))
{
Database = "Corp";
argString = argString.Substring(5).Trim();
}
else if (Lex.StartsWith(argString, "Chembl"))
{
Database = "ChEMBL";
argString = argString.Substring(6).Trim();
}
else
{
return(SyntaxMsg);
}
// See which fingerprint type
FingerprintType = FingerprintType.MACCS; // default to MACCS if type not defined
if (Lex.TryReplace(ref argString, "MACCS", ""))
{
FingerprintType = FingerprintType.MACCS;
argString = argString.Trim();
}
else if (Lex.TryReplace(ref argString, "ECFP4", ""))
{
FingerprintType = FingerprintType.Circular; // (i.e. ECFP4)
argString = argString.Trim();
}
FpDao = new FingerprintDao(Database, FingerprintType);
List <FingerprintRec> fpRecList = new List <FingerprintRec>();
string args = argString.Trim();
string initialMsg = "Update FingerprintDatabase started: " + args;
CidList = new List <string>(); // init empty list
//////////////////////
/// Corp Database ///
//////////////////////
if (CorpDatabase)
{
if (Lex.Eq(args, "Load"))
{
ByCidRange = true;
ShowProgress("Getting range of CorpIds to insert...");
maxCorpIdSql = SelectMaxCorpId; // get highest id in source db
maxSrcId = SelectSingleValueDao.SelectInt(maxCorpIdSql);
if (maxSrcId < 0)
{
maxSrcId = 0;
}
maxDestId = GetMaxDestMolId();
//maxIdSql2 = "select max(src_compound_id_nbr) from dev_mbs_owner.corp_uc_xref where src_id = 0"; // get highest id in UniChemDb db
//highCorpId = SelectSingleValueDao.SelectInt(maxIdSql2);
if (maxDestId < 0)
{
maxDestId = 0;
}
}
else if (Lex.Eq(args, "SinceLastCheckpoint"))
{
ByCheckpoint = true;
ShowProgress("Getting list of CorpIds updated since last checkpoint...");
CidList = GetNewAndModifiedCorpIdList(out CidUpdateDateDict);
//CidUpdateList = new List<string>(); // debug with single cmpd
//CidUpdateList.Add("03435269");
if (CidList.Count == 0)
{
return("There have been no updates since the last checkpoint");
}
initialMsg += ", CorpIds to add/update: " + CidList.Count;
}
else if (Lex.StartsWith(args, "ByCorpIdList"))
{
ByCidList = true;
CorpIdList = args.Substring("ByCorpIdList".Length).Trim();
if (Lex.IsUndefined(CorpIdList))
{
throw new Exception("Undefined CorpId list");
}
}
else if (Lex.StartsWith(args, "LoadMissing"))
{
LoadIfMissing = true;
if (args.Contains(" "))
{
missingFixCriteria = args.Substring("LoadMissing".Length).Trim();
}
ShowProgress("Getting list of missing CorpIds...");
CidList = GetMissingCidList();
if (CidList.Count == 0)
{
return("There are no missing CorpIds");
}
initialMsg += ", Missing CorpIds: " + CidList.Count;
}
else if (int.TryParse(args, out maxSrcId)) // single CorpId
{
ByCidRange = true;
maxDestId = maxSrcId - 1; // say 1 less is the max we have
}
else
{
return(SyntaxMsg);
}
}
///////////////////////
/// ChEMBL Database ///
///////////////////////
else if (ChemblDatabase)
{
if (Lex.Eq(args, "Load"))
{
ByCidRange = true;
ShowProgress("Getting range of MolRegNos to insert...");
sql = "select max(molregno) from chembl_owner.compound_struct_xxxxxx";
maxSrcId = SelectSingleValueDao.SelectInt(sql);
if (maxSrcId < 0)
{
maxSrcId = 0;
}
maxDestId = GetMaxDestMolId();
if (maxDestId < 0)
{
maxDestId = 0;
}
}
else if (Lex.StartsWith(args, "LoadMissing"))
{
LoadIfMissing = true;
ShowProgress("Getting list of missing ChEMBL Ids...");
CidList = GetMissingCidList();
if (CidList.Count == 0)
{
return("There are no missing Ids");
}
initialMsg += ", Missing Chembl Ids: " + CidList.Count;
}
else
{
return(SyntaxMsg);
}
}
else
{
return(SyntaxMsg);
}
CidListOriginalCount = CidList.Count;
Log(initialMsg);
/////////////////////////////
// Loop over chunks of data
/////////////////////////////
for (int chunk = 1; ; chunk++)
{
//////////////////////
/// Corp Database ///
//////////////////////
if (CorpDatabase)
{
if (ByCheckpoint) // single chunk
{
string cidList = GetNextListChunk();
if (Lex.IsUndefined(cidList))
{
break;
}
sql = SelectByCorpIdCriteria;
sql = Lex.Replace(sql, "<CorpIdCriteria>", "in (" + cidList + ")");
string matchString = "order by m.corp_nbr";
if (!Lex.Contains(sql, matchString))
{
throw new Exception(matchString + " not found");
}
sql = Lex.Replace(sql, matchString, "order by m.molecule_date");
msg = "Processing " + CidListOriginalCount + " updates since " + CheckpointDateTime;
// + " (" + Mobius.Data.CidList.FormatCidListForDisplay(null, chunkCidList) + ")";
}
else if (ByCidRange) // by CorpId range
{
if (maxDestId >= maxSrcId)
{
break; // done
}
lowId = maxDestId + 1; // start of next chunk
highId = lowId + ReadChunkSize;
maxDestId = highId;
//lowCorpId = highCorpId = 12345; // debug
if (highId >= maxSrcId)
{
highId = maxSrcId;
}
sql = SelectByCorpIdCriteria;
sql = Lex.Replace(sql, "<CorpIdCriteria>", "between " + lowId + " and " + highId);
msg = "Processing CorpId range: " + lowId + " to " + highId;
}
else if (ByCidList) // by single user-supplied CorpId list
{
if (chunk > 1)
{
break; // break 2nd time through
}
sql = SelectByCorpIdCriteria;
sql = Lex.Replace(sql, "<CorpIdCriteria>", "in (" + CorpIdList + ")");
msg = "Processing CorpId list: " + CorpIdList;
}
else if (LoadIfMissing)
{
string cidList = GetNextListChunk();
if (Lex.IsUndefined(cidList))
{
break; // all done
}
sql = SelectByCorpIdCriteria;
sql = Lex.Replace(sql, "<CorpIdCriteria>", "in (" + cidList + ")");
msg = "Processing missing CorpId Chunk: " + Mobius.Data.CidList.FormatAbbreviatedCidListForDisplay(null, cidList) +
", Total Ids: " + CidListOriginalCount;
Log(msg);
}
else
{
return(SyntaxMsg);
}
}
///////////////////////
/// ChEMBL Database ///
///////////////////////
else if (ChemblDatabase)
{
if (ByCidRange) // by CID range
{
if (maxDestId >= maxSrcId)
{
break; // done
}
lowId = maxDestId + 1; // start of next chunk
highId = lowId + ReadChunkSize;
maxDestId = highId;
//lowId = highId = 12345; // debug
if (maxDestId >= maxSrcId)
{
maxDestId = maxSrcId;
}
sql = SelectChemblSql;
sql = Lex.Replace(sql, "<molregnoCriteria>", "between " + lowId + " and " + highId);
msg = "Processing ChEMBL MolRegNo range: " + lowId + " to " + highId;
}
else if (LoadIfMissing)
{
string cidList = GetNextListChunk();
if (Lex.IsUndefined(cidList))
{
break; // all done
}
sql = SelectByCorpIdCriteria;
sql = Lex.Replace(sql, "<CorpIdCriteria>", "in (" + cidList + ")");
msg = "Processing missing ChEMBL Id Chunk: " + Mobius.Data.CidList.FormatAbbreviatedCidListForDisplay(null, cidList) +
", Total Ids: " + CidListOriginalCount;
}
else
{
return(SyntaxMsg);
}
}
else
{
return(SyntaxMsg);
}
ShowProgress(msg);
// Execute the SQL to get the rows for the chunk
DbCommandMx rdr = DbCommandMx.PrepareAndExecuteReader(sql);
DateTime lastShowProgressTime = DateTime.MinValue;
///////////////////////////////////////////
/// Loop over rows in the current chunk ///
///////////////////////////////////////////
while (true)
{
// Update progress display
if (DateTime.Now.Subtract(lastShowProgressTime).TotalSeconds > 1) // show progress
{
int storeTotalCount = storeCount + storeChunkCount;
string msg2 = msg + "\r\n" +
"Reads: " + readCount + "\r\n" +
"Undefined: " + NewUndefinedStructureCids.Count + "\r\n" +
"Insert/Updates: " + storeTotalCount + "\r\n" +
"Failures: " + FailureCount + "\r\n" +
"Failure Types: " + Failures.Count + "\r\n" +
"Last Failure: " + LastFailure;
ShowProgress(msg2);
lastShowProgressTime = DateTime.Now;
}
// Read and process next compound
bool readOk = rdr.Read();
if (readOk)
{
readCount++;
try
{
double t1 = 0, t2 = 0, t3 = 0, t4 = 0;
DateTime t0 = DateTime.Now;
mol = null;
//t2 = TimeOfDay.Delta(ref t0);
//////////////////////
/// Corp Database ///
//////////////////////
if (CorpDatabase)
{
CorpId = rdr.GetInt(0); // corp_nbr
//Log("CorpId: " + CorpId); // debug
molId = CorpId;
cid = CorpId.ToString();
cid = CompoundId.NormalizeForDatabase(cid);
if (!rdr.IsNull(1)) // be sure chime field isn't null
{
chime = rdr.GetClob(1);
if (Lex.IsDefined(chime))
{
molFile = MoleculeMx.ChimeStringToMolfileString(chime); // convert Chime to MolFile
mol = new MoleculeMx(MoleculeFormat.Molfile, molFile);
}
}
MoleculeDateTime = rdr.GetDateTimeByName("Molecule_Date"); // Date molecule was updated in the CorpDB cartridge DB
}
///////////////////////
/// ChEMBL Database ///
///////////////////////
else // chembl
{
molId = molregno = rdr.GetInt(0);
cid = chemblId = rdr.GetString(1);
smiles = rdr.GetString(2);
if (Lex.IsDefined(smiles))
{
mol = new MoleculeMx(MoleculeFormat.Smiles, smiles);
}
}
if (MoleculeMx.IsUndefined(mol) || mol.AtomCount <= 1)
{
NewUndefinedStructureCids.Add(cid);
continue;
//mol = new AtomContainer(); // write empty structure
}
bool includeOverallFingerprint = true;
List <BitSetFingerprint> fps = CdkMol.BuildBitSetFingerprints(mol.MolfileString, includeOverallFingerprint, FingerprintType);
//t3 = TimeOfDay.Delta(ref t0);
foreach (BitSetFingerprint fp in fps)
{
FingerprintRec fpr = new FingerprintRec();
fpr.molId = molId;
fpr.SrcId = SrcDbId;
fpr.Cid = cid;
fpr.Cardinality = fp.cardinality();
fpr.Fingerprint = fp.asBitSet().toLongArray();
fpRecList.Add(fpr);
}
//t4 = TimeOfDay.Delta(ref t0);
t4 = t4;
}
catch (Exception ex)
{
if (!Failures.ContainsKey(ex.Message))
{
Failures.Add(ex.Message, cid);
}
else
{
Failures[ex.Message] += ", " + cid;
}
LastFailure = "Cid: " + cid + " - " + ex.Message;
Log(LastFailure);
//ShowProgress(ex.Message + "\r\n" + ex.StackTrace.ToString()); // debug
FailureCount++;
continue;
}
storeChunkCount++;
}
bool commitTransaction = (storeChunkCount >= WriteChunkSize || (!readOk && storeChunkCount > 0));
if (commitTransaction) // end of chunk of data to store?
{
// if updating by CheckPoint date range then merge existing data with new/updated data
if (ByCheckpoint)
{
if (readCount > 0 && (storeCount > 0 || FailureCount == 0)) // make sure not everything has failed)
{
MergeRecordsIntoFiles(fpRecList);
}
}
// Simple append of records to files
else
{
FpDao.OpenWriters("bin", FileMode.Append); // open bin files for append
foreach (FingerprintRec fpr in fpRecList) // write out buffered recs
{
FpDao.WriteFingerprintRec(fpr);
}
FpDao.CloseWriters();
int cnt = fpRecList.Count;
if (cnt > 0)
{
string cid1 = fpRecList[0].Cid;
string cid2 = fpRecList[cnt - 1].Cid;
Log("Records Appended: " + cnt + ", CIDS: " + cid1 + " - " + cid2);
}
else
{
Log("Records Appended: 0");
}
}
fpRecList.Clear();
storeCount += storeChunkCount;
storeChunkCount = 0;
}
if (!readOk)
{
break;
}
} // end of read loop for rows in a chunk
rdr.Dispose();
} // end for loop of chunks
DeleteTempFiles();
if (LoadIfMissing) // update list of cids with missing structures
{
ExistingUndefinedStructureCids.UnionWith(NewUndefinedStructureCids);
FpDao.WriteUndefinedStructuresCids(ExistingUndefinedStructureCids);
}
msg = "*** Update Complete ***\r\n\r\n" + msg;
ShowProgress(msg);
System.Threading.Thread.Sleep(100);
string logMsg = "UpdateFingerprintDb - CIDs stored: " + storeCount + ", Undefined structures: " + NewUndefinedStructureCids.Count + ", failures: " + FailureCount + "\r\n";
foreach (string key in Failures.Keys)
{
logMsg += key + " - CIDs: " + Failures[key] + "\r\n";
}
Log(logMsg);
return(logMsg);
} // end of main try loop
catch (Exception ex)
{
Log(DebugLog.FormatExceptionMessage(ex));
throw new Exception(ex.Message, ex);
}
}