533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/annoStreamDbPslPlus.c src/hg/cgilib/annoStreamDbPslPlus.c
new file mode 100644
index 0000000..fb9e6ac
--- /dev/null
+++ src/hg/cgilib/annoStreamDbPslPlus.c
@@ -0,0 +1,256 @@
+/* annoStreamDbPslPlus -- subclass of annoStreamer for joining PSL+CDS+seq database tables */
+
+/* Copyright (C) 2017 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
+#include "annoStreamDbPslPlus.h"
+#include "annoStreamDb.h"
+#include "hdb.h"
+
+static char *pslPlusAutoSqlString =
+"table pslPlus"
+"\"transcript PSL, CDS and seq info\""
+"   ("
+"    uint    match;      \"Number of bases that match that aren't repeats\""
+"    uint    misMatch;   \"Number of bases that don't match\""
+"    uint    repMatch;   \"Number of bases that match but are part of repeats\""
+"    uint    nCount;       \"Number of 'N' bases\""
+"    uint    qNumInsert;   \"Number of inserts in query (transcript)\""
+"    int     qBaseInsert;  \"Number of bases inserted in query (transcript)\""
+"    uint    tNumInsert;   \"Number of inserts in target (chromosome/scaffold)\""
+"    int     tBaseInsert;  \"Number of bases inserted in target (chromosome/scaffold)\""
+"    char[2] strand;       \"+ or - for query strand (transcript to genome orientation)\""
+"    string  qName;        \"Transcript accession\""
+"    uint    qSize;        \"Transcript sequence size\""
+"    uint    qStart;       \"Alignment start position in query (transcript)\""
+"    uint    qEnd;         \"Alignment end position in query (transcript)\""
+"    string  tName;        \"Target (chromosome/scaffold) name\""
+"    uint    tSize;        \"Target (chromosome/scaffold) size\""
+"    uint    tStart;       \"Alignment start position in target\""
+"    uint    tEnd;         \"Alignment end position in target\""
+"    uint    blockCount;   \"Number of blocks in alignment\""
+"    uint[blockCount] blockSizes;  \"Size of each block\""
+"    uint[blockCount] qStarts;     \"Start of each block in query.\""
+"    uint[blockCount] tStarts;     \"Start of each block in target.\""
+"    string  cds;          \"CDS start and end in transcript (if applicable)\""
+"    string  protAcc;      \"Protein accession (if applicable)\""
+"    string  name2;        \"Gene symbolic name\""
+"    string  path;         \"Path to FASTA file containing transcript sequence\""
+"    uint    fileOffset;   \"Offset of transcript record in FASTA file\""
+"    uint    fileSize;     \"Number of bytes of transcript record in FASTA file\""
+"   )";
+
+struct annoStreamDbPslPlus
+    {
+    struct annoStreamer streamer;	// Parent class members & methods (external interface)
+    // Private members
+    char *gpTable;                      // Associated genePred (refGene, ncbiRefSeqCurated etc)
+    struct annoStreamer *mySource;	// Internal source of PSL+CDS+seq info
+    struct hash *idHash;		// Used to restrict PSL query result to curated/predicted
+    };
+
+// select p.*, c.cds, l.protAcc, l.name, e.path, s.file_offset, s.file_size 
+//   from (((ncbiRefSeqPsl p // NOT ANYMORE (#21770): join ncbiRefSeqCurated n on p.qName = n.name)
+//          left join ncbiRefSeqCds c on p.qName = c.id)
+//         join ncbiRefSeqLink l on p.qName = l.mrnaAcc)
+//        left join (seqNcbiRefSeq s left join extNcbiRefSeq e on s.extFile = e.id) on p.qName = s.acc
+//   where p.tName = "chr1"
+//   order by p.tName, p.tStart
+//  limit 5;
+
+static char *ncbiRefSeqConfigJsonFormat =
+    "{ \"naForMissing\": false,"
+    "  \"relatedTables\": [ { \"table\": \"ncbiRefSeqCds\","
+    "                         \"fields\": [\"cds\"] },"
+    "                       { \"table\": \"ncbiRefSeqLink\","
+    "                         \"fields\": [\"protAcc\", \"name\"] },"
+    "                       { \"table\": \"extNcbiRefSeq\","
+    "                         \"fields\": [\"path\"] },"
+    "                       { \"table\": \"seqNcbiRefSeq\","
+    "                         \"fields\": [\"file_offset\", \"file_size\"] } ] }";
+
+//select p.*,c.name,l.protAcc,l.name,e.path,s.file_offset,s.file_size, i.version
+//from refSeqAli p
+//  join (hgFixed.gbCdnaInfo i
+//        left join hgFixed.cds c on i.cds = c.id) on i.acc = p.qName
+//       left join (hgFixed.gbSeq s
+//                  join hgFixed.gbExtFile e on e.id = s.gbExtFile) on s.acc = p.qName
+//       join hgFixed.refLink l on p.qName = l.mrnaAcc
+//  where p.tName = "chr1"
+//   order by p.tName, p.tStart
+//  limit 5;
+
+static char *refSeqAliConfigJson =
+    "{ \"naForMissing\": false,"
+    "  \"relatedTables\": [ { \"table\": \"hgFixed.cds\","
+    "                         \"fields\": [\"name\"] },"
+    "                       { \"table\": \"hgFixed.refLink\","
+    "                         \"fields\": [\"protAcc\", \"name\"] },"
+    "                       { \"table\": \"hgFixed.gbExtFile\","
+    "                         \"fields\": [\"path\"] },"
+    "                       { \"table\": \"hgFixed.gbSeq\","
+    "                         \"fields\": [\"file_offset\", \"file_size\"] } ] }";
+
+struct asObject *annoStreamDbPslPlusAsObj()
+/* Return an autoSql object with PSL, gene name, protein acc, CDS and sequence file info fields.
+ * An annoStreamDbPslPlus instance may return additional additional columns if configured, but
+ * these columns will always be present. */
+{
+return asParseText(pslPlusAutoSqlString);
+}
+
+static void asdppSetRegion(struct annoStreamer *sSelf, char *chrom, uint rStart, uint rEnd)
+/* Pass setRegion down to internal source. */
+{
+annoStreamerSetRegion(sSelf, chrom, rStart, rEnd);
+struct annoStreamDbPslPlus *self = (struct annoStreamDbPslPlus *)sSelf;
+self->mySource->setRegion(self->mySource, chrom, rStart, rEnd);
+}
+
+static struct annoRow *asdppNextRow(struct annoStreamer *sSelf, char *minChrom, uint minEnd,
+				    struct lm *lm)
+/* Return next psl+ row. */
+{
+struct annoStreamDbPslPlus *self = (struct annoStreamDbPslPlus *)sSelf;
+char **ppWords;
+lmAllocArray(lm, ppWords, sSelf->numCols);
+struct annoRow *ppRow;
+boolean rightJoinFail = FALSE;
+while ((ppRow = self->mySource->nextRow(self->mySource, minChrom, minEnd, lm)) != NULL)
+    {
+    ppWords = ppRow->data;
+    // If self->idHash is non-NULL, check PSL qName; skip this row if qName not found.
+    char *qName = ppWords[9];
+    if (self->idHash && ! hashLookup(self->idHash, qName))
+        continue;
+    // If there are filters, apply them, otherwise just return aRow.
+    if (sSelf->filters)
+	{
+	boolean fails = annoFilterRowFails(sSelf->filters, ppWords, sSelf->numCols,
+					   &rightJoinFail);
+	// If this row passes the filter, or fails but is rightJoin, then we're done looking.
+	if (!fails || rightJoinFail)
+	    break;
+	}
+    else
+	// no filtering to do, just use this row
+	break;
+    }
+if (ppRow != NULL)
+    return annoRowFromStringArray(ppRow->chrom, ppRow->start, ppRow->end, rightJoinFail,
+				  ppWords, sSelf->numCols, lm);
+else
+    return NULL;
+}
+
+static void asdppClose(struct annoStreamer **pSSelf)
+/* Free up state. */
+{
+if (pSSelf == NULL)
+    return;
+struct annoStreamDbPslPlus *self = *(struct annoStreamDbPslPlus **)pSSelf;
+freez(&self->gpTable);
+self->mySource->close(&(self->mySource));
+annoStreamerFree(pSSelf);
+}
+
+static struct asColumn *asColumnClone(struct asColumn *colIn)
+/* Return a full clone of colIn, or NULL if colIn is NULL. */
+{
+if (colIn == NULL)
+    return NULL;
+if (colIn->obType != NULL || colIn->index != NULL)
+    errAbort("asColumnClone: support for obType and index not implemented");
+struct asColumn *colOut;
+AllocVar(colOut);
+colOut->name = cloneString(colIn->name);
+colOut->comment = cloneString(colIn->comment);
+colOut->lowType = colIn->lowType; // static struct in asParse.c
+colOut->obName = cloneString(colIn->obName);
+colOut->fixedSize = colIn->fixedSize;
+colOut->linkedSizeName = cloneString(colIn->linkedSizeName);
+colOut->linkedSize = asColumnClone(colIn->linkedSize);
+colOut->isSizeLink = colIn->isSizeLink;
+colOut->isList = colIn->isList;
+colOut->isArray = colIn->isArray;
+colOut->autoIncrement = colIn->autoIncrement;
+colOut->values = slNameCloneList(colIn->values);
+return colOut;
+}
+
+static void asObjAppendExtraColumns(struct asObject *asObjTarget, struct asObject *asObjSource)
+/* If asObjSource has more columns than asObjTarget then clone and append those additional columns
+ * to asObjTarget. */
+{
+int tColCount = slCount(asObjTarget->columnList);
+int sColCount = slCount(asObjSource->columnList);
+if (tColCount < 1)
+    errAbort("asObjAppendExtraColumns: support for empty target columnList not implemented");
+if (sColCount > tColCount)
+    {
+    struct asColumn *tCol = asObjTarget->columnList, *sCol = asObjSource->columnList;
+    int i;
+    for (i = 0;  i < tColCount-1;  i++)
+        {
+        tCol = tCol->next;
+        sCol = sCol->next;
+        }
+    while (sCol->next != NULL)
+        {
+        tCol->next = asColumnClone(sCol->next);
+        tCol = tCol->next;
+        sCol = sCol->next;
+        }
+    }
+}
+
+struct annoStreamer *annoStreamDbPslPlusNew(struct annoAssembly *aa, char *gpTable, int maxOutRows,
+                                            struct jsonElement *extraConfig)
+/* Create an annoStreamer (subclass) object that streams PSL, CDS and seqFile info.
+ * gpTable is a genePred table that has associated PSL, CDS and sequence info
+ * (i.e. refGene, ncbiRefSeq, ncbiRefSeqCurated or ncbiRefSeqPredicted). */
+{
+char *pslTable = NULL, *configJson = NULL;
+if (sameString("refGene", gpTable))
+    {
+    pslTable = "refSeqAli";
+    configJson = refSeqAliConfigJson;
+    }
+else if (startsWith("ncbiRefSeq", gpTable))
+    {
+    pslTable = "ncbiRefSeqPsl";
+    struct dyString *dy = dyStringCreate(ncbiRefSeqConfigJsonFormat, gpTable);
+    configJson = dyStringCannibalize(&dy);
+    }
+else
+    errAbort("annoStreamDbPslPlusNew: unrecognized table \"%s\"", gpTable);
+struct annoStreamDbPslPlus *self;
+AllocVar(self);
+// Get internal streamer for joining PSL with other tables.
+struct jsonElement *config = jsonParse(configJson);
+if (extraConfig)
+    jsonObjectMerge(config, extraConfig);
+self->mySource = annoStreamDbNew(aa->name, pslTable, aa, maxOutRows, config);
+struct asObject *asObj = annoStreamDbPslPlusAsObj();
+if (extraConfig)
+    asObjAppendExtraColumns(asObj, self->mySource->asObj);
+if (startsWith("ncbiRefSeq", gpTable) && differentString("ncbiRefSeq", gpTable))
+    {
+    // Load up an ID hash to restrict PSL query results to the subset in gpTable:
+    struct sqlConnection *conn = hAllocConn(aa->name);
+    char query[1024];
+    sqlSafef(query, sizeof(query), "select name, 1 from %s", gpTable);
+    self->idHash = sqlQuickHash(conn, query);
+    hFreeConn(&conn);
+    }
+// Set up external streamer interface
+struct annoStreamer *streamer = &(self->streamer);
+annoStreamerInit(streamer, aa, asObj, pslTable);
+streamer->rowType = arWords;
+self->gpTable = cloneString(gpTable);
+// Override methods that need to pass through to internal source:
+streamer->setRegion = asdppSetRegion;
+streamer->nextRow = asdppNextRow;
+streamer->close = asdppClose;
+return (struct annoStreamer *)self;
+}