4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/makeDb/schema/joinerGraph/joinerGraph.c src/hg/makeDb/schema/joinerGraph/joinerGraph.c index 3c0a259..0b511ec 100644 --- src/hg/makeDb/schema/joinerGraph/joinerGraph.c +++ src/hg/makeDb/schema/joinerGraph/joinerGraph.c @@ -1,296 +1,296 @@ /* joinerGraph - Make graph out of joiner by creating a .dot file for * Graphvis.. */ /* Copyright (C) 2004 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "dystring.h" #include "options.h" #include "joiner.h" #include "asParse.h" /* Variable that can be set from command line. */ char *genoDb = "hg16"; /* Genomic database. */ char *asFile = NULL; /* autoSql file with field definitions if any. */ void usage() /* Explain usage and exit. */ { errAbort( "joinerGraph - Make graph out of joiner via Graphvis .dot file\n" "usage:\n" " joinerGraph file.joiner graph.dot\n" "options:\n" " -as=file.as - Create graph with fields as well as tables using .as file\n" " -db=db - Use given database primarily (default is %s)\n" , genoDb ); } char *ourDb(struct slName *list) /* Return TRUE if it contains one of our databases. */ { static char *dbs[] = {"hg16", "swissProt", "go", "hgFixed"}; int i; dbs[0] = genoDb; for (i=0; i<ArraySize(dbs); ++i) { char *db = dbs[i]; if (slNameInList(list, db)) return db; } return NULL; } struct hash *readAs(char *fileName) /* Read in .as file and put objects in hash keyed both * by table name, and by comma-separated field list. */ { struct asObject *as, *asList = asParseFile(fileName); struct hash *asHash = hashNew(10); struct dyString *dy = dyStringNew(0); for (as = asList; as != NULL; as = as->next) { struct asColumn *col; hashAdd(asHash, as->name, as); dyStringClear(dy); for (col = as->columnList; col != NULL; col = col->next) { dyStringAppend(dy, col->name); dyStringAppendC(dy, ','); } hashAdd(asHash, dy->string, as); } dyStringFree(&dy); return asHash; } struct hash *makeTypeLookupHash(struct joiner *joiner) /* Make hash keyed by table names with autoSql table type * values. */ { struct joinerType *type; struct joinerTable *table; struct hash *hash = hashNew(0); for (type = joiner->typeList; type != NULL; type = type->next) { for (table = type->tableList; table != NULL; table = table->next) { hashAdd(hash, table->table, type->name); } } return hash; } void edgeColor(FILE *f, char *primaryDb, struct joinerField *primary) /* Write color of edge so that knownGene and refLink show up special. */ { if (sameString(primary->table, "knownGene") || sameString(primary->table, "sgdGene") || sameString(primary->table, "bdgpGene") || sameString(primary->table, "sangerGene") ) fprintf(f, " [color=purple]"); else if (sameString(primary->table, "refLink")) fprintf(f, " [color=blue]"); else if (sameString(primary->table, "ensGene") || sameString(primary->table, "ensTranscript")) fprintf(f, " [color=forestGreen]"); else if (sameString(primaryDb, "swissProt")) fprintf(f, " [color=red]"); else if (sameString(primaryDb, "hgFixed")) fprintf(f, " [color=orange]"); } char *nodeColor(FILE *f, char *db, struct joinerField *jf) /* Write color of database. */ { char *col = NULL; if (sameString("swissProt", db)) col = "red"; else if (sameString("hgFixed", db)) col = "orange"; else if (startsWith("ens", jf->table)) col = "forestGreen"; else if (startsWith("ref", jf->table)) col = "blue"; else if (startsWith("known", jf->table) || startsWith("kg", jf->table)) col = "purple"; return col; } void edgeArrow(FILE *f, struct joinerField *jf) /* Figure out what type of fancy arrow if any to make. */ { if (jf->full && jf->unique) fprintf(f, "[arrowhead=invdot]"); else if (jf->full) fprintf(f, "[arrowhead=dot]"); else if (jf->unique) fprintf(f, "[arrowhead=invodot]"); } void makeEdge(FILE *f, struct hash *asHash, char *primaryDb, struct joinerField *primary, char *otherDb, struct joinerField *jf) /* Cause a single edge to be drawn between primary and jf. */ { if (asHash) { fprintf(f, " %s_%s:%s -> %s_%s:%s", primaryDb, primary->table, primary->field, otherDb, jf->table, jf->field); } else { fprintf(f, " %s_%s -> %s_%s", primaryDb, primary->table, otherDb, jf->table); } edgeColor(f, primaryDb, primary); edgeArrow(f, jf); fprintf(f, ";\n"); } void makeGraph(struct joiner *joiner, struct hash *asHash, char *dotFile) /* Make graph out of joiner and as records showing fields. */ { struct joinerSet *js; struct hash *uniqHash = hashNew(0); struct hash *typeLookupHash = makeTypeLookupHash(joiner); FILE *f = mustOpen(dotFile, "w"); static char *dbs[] = {"go", "swissProt", NULL, "hgFixed"}; int dbIx; char *db; dbs[2] = genoDb; fprintf(f, "digraph %s {\n", "schema"); if (asHash != NULL) { fprintf(f, " rankdir=LR;\n"); fprintf(f, " node [shape=record];\n"); } fprintf(f, " edge [arrowhead=odot];\n"); for (dbIx = 0; dbIx < ArraySize(dbs); ++dbIx) { db = dbs[dbIx]; if (sameString(db, "swissProt") || sameString(db, "go")) { fprintf(f, " subgraph cluster_%s {\n", db); fprintf(f, " label=\"%s database\";\n", db); } else { fprintf(f, " subgraph %s {\n", db); } for (js = joiner->jsList; js != NULL; js = js->next) { struct joinerField *jf, *primary = js->fieldList; /* Draw nodes. */ for (jf = js->fieldList; jf != NULL; jf = jf->next) { if (slNameInList(jf->dbList, db)) { char dbTable[512]; safef(dbTable, sizeof(dbTable), "%s.%s", db, jf->table); if (!hashLookup(uniqHash, dbTable)) { char tableName[128]; hashAdd(uniqHash, dbTable, NULL); struct asObject *as; char *dbCol; char *type = hashFindVal(typeLookupHash, jf->table); if (type == NULL) type = jf->table; if (sameString(db, "hgFixed")) safef(tableName, sizeof(tableName), "%s\\n%s", db, jf->table); else safef(tableName, sizeof(tableName), "%s", jf->table); if (asHash) { as = hashFindVal(asHash, type); fprintf(f, " %s_%s [label=\"*%s*", db, jf->table, tableName); if (as != NULL) { struct asColumn *col; if (!sameString(as->name, jf->table)) fprintf(f, "|(%s)", as->name); for (col = as->columnList; col != NULL; col = col->next) { fprintf(f, "|<%s>%s", col->name, col->name); } } fprintf(f, "\""); } else { fprintf(f, "%s_%s [label=\"%s\"", db, jf->table, tableName); } dbCol = nodeColor(f, db, jf); if (dbCol != NULL) fprintf(f, ", color=%s", dbCol); fprintf(f, "];\n"); } } } /* Draw edges within database. */ if (primary != NULL && slNameInList(primary->dbList, db)) { for (jf = primary->next; jf != NULL; jf = jf->next) { if (slNameInList(jf->dbList, db)) makeEdge(f, asHash, db, primary, db, jf); } } } fprintf(f, " }\n"); } /* Draw edges between databases. */ for (js = joiner->jsList; js != NULL; js = js->next) { struct joinerField *jf, *primary = js->fieldList; if (primary != NULL) { char *primaryDb = ourDb(primary->dbList); if (primaryDb != NULL) { for (jf = primary; jf != NULL; jf = jf->next) { char *otherDb = ourDb(jf->dbList); if (otherDb != NULL && !sameString(otherDb, primaryDb)) { if (jf != primary) { makeEdge(f, asHash, primaryDb, primary, otherDb, jf); } } } } } } fprintf(f, "}\n"); carefulClose(&f); } void joinerGraph(char *joinerFile, char *asFile, char *dotFile) /* joinerGraph - Make graph out of joiner. */ { struct joiner *joiner = joinerRead(joinerFile); struct hash *asHash = NULL; if (asFile != NULL) asHash = readAs(asFile); makeGraph(joiner, asHash, dotFile); } int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); genoDb = optionVal("db", genoDb); asFile = optionVal("as", asFile); if (argc != 3) usage(); joinerGraph(argv[1], asFile, argv[2]); return 0; }