21a6584e8ecdbba6d802ab30f3ec564c08b7dcc3 galt Sat Jun 29 02:11:16 2013 -0700 fixing callers of sqlGetField to use sqlSafeFrag diff --git src/hg/hgGene/pathways.c src/hg/hgGene/pathways.c index 0910d23..7e4bd89 100644 --- src/hg/hgGene/pathways.c +++ src/hg/hgGene/pathways.c @@ -1,406 +1,406 @@ /* pathways - do pathways section. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "hdb.h" #include "spDb.h" #include "hgGene.h" struct pathwayLink /* Info to link into a pathway. */ { char *name; /* Symbolic name */ char *shortLabel; /* Short label. */ char *longLabel; /* Long label. */ char *tables; /* Tables that must exist. */ int (*count)(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId); /* Count number of items referring to this gene. */ void (*printLinks)(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId); /* Print out links. */ }; static void keggLink(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Print out kegg database link. */ { char query[512], **row; struct sqlResult *sr; if (isRgdGene(conn)) { sqlSafef(query, sizeof(query), "select distinct k.locusID, k.mapID, keggMapDesc.description" " from rgdGene2KeggPathway k, keggMapDesc, rgdGene2 x" " where k.rgdId=x.name " " and x.name='%s'" " and k.mapID = keggMapDesc.mapID" , geneId); } else { sqlSafef(query, sizeof(query), "select k.locusID, k.mapID, keggMapDesc.description" " from keggPathway k, keggMapDesc, kgXref x" " where k.kgID=x.kgId " " and x.kgID='%s'" " and k.mapID = keggMapDesc.mapID" , geneId); } sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hPrintf("<A HREF=\"http://www.genome.ad.jp/kegg-bin/show_pathway?%s+%s\" TARGET=_blank>", row[1], row[0]); hPrintf("%s</A> - %s<BR>", row[1], row[2]); } sqlFreeResult(&sr); } static int keggCount(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[256]; if (!isRgdGene(conn)) { sqlSafef(query, sizeof(query), "select count(*) from keggPathway k, kgXref x where k.kgID=x.kgId and x.kgId='%s'", geneId); } else { sqlSafef(query, sizeof(query), "select count(*) from rgdGene2KeggPathway k, rgdGene2 x where k.rgdId=x.name and x.name='%s'", geneId); } return sqlQuickNum(conn, query); } static void bioCycLink(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Print out bioCyc database link. */ { char query[512], **row; struct sqlResult *sr; char *oldMapId = cloneString(""); char *upperCaseGenome = cloneString(genome); toUpperN(upperCaseGenome, strlen(upperCaseGenome)); sqlSafef(query, sizeof(query), "select bioCycPathway.mapId,description" " from bioCycPathway,bioCycMapDesc" " where bioCycPathway.kgId='%s'" " and bioCycPathway.mapId = bioCycMapDesc.mapId order by bioCycPathway.mapId" , geneId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { /* only print new ones */ if (!sameWord(oldMapId, row[0])) { hPrintf("<A HREF=\"http://biocyc.org/%s/new-image?type=PATHWAY&object=%s&detail-level=2\" TARGET=_blank>", upperCaseGenome, row[0]); hPrintf("%s</A> - %s<BR>\n", row[0], row[1]); } oldMapId = cloneString(row[0]); } sqlFreeResult(&sr); } static int bioCycCount(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[256]; sqlSafef(query, sizeof(query), "select count(*) from bioCycPathway where kgID='%s'", geneId); return sqlQuickNum(conn, query); } static char *getCgapId(struct sqlConnection *conn) /* Get cgap ID. */ { char query[256]; sqlSafef(query, sizeof(query), "select cgapId from cgapAlias where alias=\"%s\"", curGeneName); return sqlQuickString(conn, query); } static void reactomeLink(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) { char condStr[255]; char *spID, *chp; struct sqlConnection *conn2; char query2[256]; struct sqlResult *sr2; char **row2; char *eventDesc; char *eventID; /* check the existence of kgXref table first */ if (isRgdGene(conn)) { if (!sqlTableExists(conn, "rgdGene2Xref")) return; } else { if (!sqlTableExists(conn, "kgXref")) return; } if (isRgdGene(conn)) { - safef(condStr, sizeof(condStr), "name='%s'", geneId); + sqlSafefFrag(condStr, sizeof(condStr), "name='%s'", geneId); spID = sqlGetField(database, "rgdGene2ToUniProt", "value", condStr); } else { - safef(condStr, sizeof(condStr), "kgID='%s'", geneId); + sqlSafefFrag(condStr, sizeof(condStr), "kgID='%s'", geneId); spID = sqlGetField(database, "kgXref", "spID", condStr); } if (spID != NULL) { /* convert splice variant UniProt ID to its main root ID */ chp = strstr(spID, "-"); if (chp != NULL) *chp = '\0'; hPrintf( "<BR>Protein %s (<A href=\"http://www.reactome.org/cgi-bin/link?SOURCE=UniProt&ID=%s\" TARGET=_blank>Reactome details)</A> participates in the following event(s):<BR><BR>" , spID, spID); conn2= hAllocConn(database); sqlSafef(query2,sizeof(query2), "select eventID, eventDesc from proteome.spReactomeEvent where spID='%s'", spID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); while (row2 != NULL) { eventID = row2[0]; eventDesc = row2[1]; hPrintf( "<A href=\"http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s\" TARGET=_blank>%s</A> %s<BR>\n", eventID, eventID, eventDesc); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn2); } } static void rgdPathwayLink(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Print out bioCarta database link. */ { char query[512], **row; struct sqlResult *sr; char *rgdId = geneId; sqlSafef(query, sizeof(query), "select x.pathwayId, description from rgdPathway p, rgdGenePathway x " " where p.pathwayId = x.pathwayId " " and x.geneId = '%s'" , rgdId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hPrintf("<A HREF=\"http://rgd.mcw.edu/tools/ontology/ont_annot.cgi?ontology=wo&ont_id=%s\" TARGET=_blank>", row[0]); hPrintf("%s</A> - %s<BR>\n", row[0], row[1]); } sqlFreeResult(&sr); } static void bioCartaLink(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Print out bioCarta database link. */ { char *cgapId = getCgapId(conn); if (cgapId != NULL) { struct hash *uniqHash = newHash(8); char query[512], **row; struct sqlResult *sr; sqlSafef(query, sizeof(query), "select cgapBiocDesc.mapID,cgapBiocDesc.description " " from cgapBiocPathway,cgapBiocDesc" " where cgapBiocPathway.cgapID='%s'" " and cgapBiocPathway.mapID = cgapBiocDesc.mapID" , cgapId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; if (!hashLookup(uniqHash, name)) { hashAdd(uniqHash, name, NULL); hPrintf("<A HREF=\"http://cgap.nci.nih.gov/Pathways/BioCarta/%s\" TARGET=_blank>", row[0]); hPrintf("%s</A> - %s<BR>\n", row[0], row[1]); } } freez(&cgapId); hashFree(&uniqHash); } } static int bioCartaCount(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { int ret = 0; char *cgapId = getCgapId(conn); if (cgapId != NULL) { char query[256]; sqlSafef(query, sizeof(query), "select count(*) from cgapBiocPathway where cgapID='%s'", cgapId); ret = sqlQuickNum(conn, query); freez(&cgapId); } return ret; } static int rgdPathwayCount(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { char query[256]; sqlSafef(query, sizeof(query), "select count(*) from rgdGenePathway where geneId ='%s'", geneId); return sqlQuickNum(conn, query); } static int reactomeCount(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Count up number of hits. */ { int ret = 0; char query[256]; char *spID, *chp; char condStr[256]; char *origSpID; /* check the existence of kgXref table first */ if (!isRgdGene(conn)) { if (!sqlTableExists(conn, "kgXref")) return(0); } else { if (!sqlTableExists(conn, "rgdGene2Xref")) return(0); } if (isRgdGene(conn)) { - safef(condStr, sizeof(condStr), "name='%s'", geneId); + sqlSafefFrag(condStr, sizeof(condStr), "name='%s'", geneId); spID = sqlGetField(database, "rgdGene2ToUniProt", "value", condStr); } else { - safef(condStr, sizeof(condStr), "kgID='%s'", geneId); + sqlSafefFrag(condStr, sizeof(condStr), "kgID='%s'", geneId); spID = sqlGetField(database, "kgXref", "spID", condStr); } if (spID != NULL) { origSpID = cloneString(spID); /* convert splice variant UniProt ID to its main root ID */ chp = strstr(spID, "-"); if (chp != NULL) *chp = '\0'; if (!isRgdGene(conn)) { sqlSafef(query, sizeof(query), "select count(*) from %s.spReactomeEvent, %s.spVariant, %s.kgXref where kgID='%s' and kgXref.spID=variant and variant = '%s' and spReactomeEvent.spID=parent", PROTEOME_DB_NAME, PROTEOME_DB_NAME, database, geneId, origSpID); } else { sqlSafef(query, sizeof(query), "select count(*) from %s.spReactomeEvent, %s.spVariant, %s.rgdGene2ToUniProt where name='%s' and value=variant and variant = '%s' and spReactomeEvent.spID=parent", PROTEOME_DB_NAME, PROTEOME_DB_NAME, database, geneId, origSpID); } ret = sqlQuickNum(conn, query); } return ret; } struct pathwayLink pathwayLinks[] = { { "kegg", "KEGG", "KEGG - Kyoto Encyclopedia of Genes and Genomes", "keggPathway keggMapDesc", keggCount, keggLink}, { "bioCyc", "BioCyc", "BioCyc Knowledge Library", "bioCycPathway bioCycMapDesc", bioCycCount, bioCycLink}, { "bioCarta", "BioCarta", "BioCarta from NCI Cancer Genome Anatomy Project", "cgapBiocPathway cgapBiocDesc cgapAlias", bioCartaCount, bioCartaLink}, { "reactome", "Reactome", "Reactome (by CSHL, EBI, and GO)", "proteome.spReactomeEvent", reactomeCount, reactomeLink}, { "rgdPathway", "RGDPathway", "RGD Pathway", "rgdPathway rgdGenePathway", rgdPathwayCount, rgdPathwayLink}, }; static boolean pathwayExists(struct pathwayLink *pl, struct sqlConnection *conn, char *geneId) /* Return TRUE if pathway exists and has data. */ { if (!sqlTablesExist(conn, pl->tables)) return FALSE; return pl->count(pl, conn, geneId) > 0; } static boolean pathwaysExists(struct section *section, struct sqlConnection *conn, char *geneId) /* Return TRUE if there's some pathway info on this one. */ { int i; for (i=0; i<ArraySize(pathwayLinks); ++i) { if (pathwayExists(&pathwayLinks[i], conn, geneId)) return TRUE; } return FALSE; } static void pathwaysPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print out pathway links. */ { int plIx; struct pathwayLink *pl; boolean isFirst = TRUE; for (plIx=0; plIx < ArraySize(pathwayLinks); ++plIx) { pl = &pathwayLinks[plIx]; if (pathwayExists(pl, conn, geneId)) { if (isFirst) isFirst = !isFirst; else hPrintf("<BR>\n"); hPrintf("<B>%s</B><BR>", pl->longLabel); pl->printLinks(pl, conn, geneId); } } } struct section *pathwaysSection(struct sqlConnection *conn, struct hash *sectionRa) /* Create pathways section. */ { struct section *section = sectionNew(sectionRa, "pathways"); section->exists = pathwaysExists; section->print = pathwaysPrint; return section; }