a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/hg/hgGene/links.c src/hg/hgGene/links.c index f71ab6f..8179ad3 100644 --- src/hg/hgGene/links.c +++ src/hg/hgGene/links.c @@ -1,282 +1,281 @@ /* links.c - Handle links section. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "dystring.h" #include "web.h" #include "hui.h" #include "hdb.h" #include "hgGene.h" #include "wikiTrack.h" -static char const rcsid[] = "$Id: links.c,v 1.38 2009/06/18 20:19:18 hiram Exp $"; struct link /* A link to another web site. */ { struct link *next; /* Next in list. */ double priority; /* Order to print in. */ char *name; /* Symbolic name. */ char *shortLabel; /* Short human-readable label. */ char *idSql; /* SQL to create ID. */ char *nameSql; /* SQL to create name. */ char *nameFormat; /* Text formatting for name. */ char *url; /* URL of link. */ boolean useHgsid; /* If true add hgsid to link. */ boolean useDb; /* If true add db= to link. */ char *preCutAt; /* String to chop at before sql. */ char *postCutAt; /* String to chop at after sql. */ }; static int linkCmpPriority(const void *va, const void *vb) /* Compare to sort links based on priority. */ { const struct link *a = *((struct link **)va); const struct link *b = *((struct link **)vb); float dif = a->priority - b->priority; if (dif < 0) return -1; else if (dif > 0) return 1; else { return differentWord(b->shortLabel, a->shortLabel); } } static char *linkRequiredField(struct hash *hash, char *name) /* Return required field in link hash. Squawk and die if it doesn't exist. */ { char *s = hashFindVal(hash,name); if (s == NULL) errAbort("Couldn't find %s field in %s in links.ra", name, (char *)hashFindVal(hash, "name")); return s; } static char *linkOptionalField(struct hash *hash, char *name) /* Return field in hash if it exists or NULL otherwise. */ { return hashFindVal(hash, name); } static struct link *getLinkList(struct sqlConnection *conn, char *raFile) /* Get list of links - starting with everything in .ra file, * and making sure any associated tables and databases exist. */ { struct hash *ra, *raList = readRa(raFile, NULL); struct link *linkList = NULL, *link; for (ra = raList; ra != NULL; ra = ra->next) { if (linkOptionalField(ra, "hide") == NULL) { if (checkDatabases(linkOptionalField(ra, "databases")) && sqlTablesExist(conn, linkOptionalField(ra, "tables"))) { /* only include the wikiTrack if it is enabled */ if (sameWord(linkRequiredField(ra, "name"), "wikiTrack") && ! wikiTrackEnabled(database, NULL)) continue; AllocVar(link); link->priority = atof(linkRequiredField(ra, "priority")); link->name = linkRequiredField(ra, "name"); link->shortLabel = linkRequiredField(ra, "shortLabel"); link->idSql = linkRequiredField(ra, "idSql"); link->nameSql = linkOptionalField(ra, "nameSql"); link->nameFormat = linkOptionalField(ra, "nameFormat"); link->url = linkRequiredField(ra, "url"); link->useHgsid = (linkOptionalField(ra, "hgsid") != NULL); link->useDb = (linkOptionalField(ra, "dbInUrl") != NULL); link->preCutAt = linkOptionalField(ra, "preCutAt"); link->postCutAt = linkOptionalField(ra, "postCutAt"); slAddHead(&linkList, link); } } } slSort(&linkList, linkCmpPriority); return linkList; } static char *cloneAndCut(char *s, char *cutAt) /* Return copy of string that may have stuff cut off end. */ { char *clone = cloneString(s); if (cutAt != NULL) { char *end = stringIn(cutAt, clone); if (end != NULL) *end = 0; } return clone; } static void addLinkExtras(struct link *link, struct dyString *dy) /* Add extra identifiers if specified in the .ra. */ { if (link->useHgsid) dyStringPrintf(dy, "&%s", cartSidUrlString(cart)); if (link->useDb) dyStringPrintf(dy, "&db=%s", database); } char *linkGetUrl(struct link *link, struct sqlConnection *conn, char *geneId) /* Return URL string if possible or NULL if not. FreeMem this when done. */ { char query[512]; struct sqlResult *sr; char **row; char *url = NULL; /* Some special case code here for things that need to * do more than check a table. */ if (sameString(link->name, "family")) { if (!hgNearOk(database)) return NULL; } if (sameString(link->name, "protBrowser")) { if (!hgPbOk(database)) return NULL; /* special processing for PB, since we need the protein ID, instead everything key off from gene ID */ /* use UniProt accession instead of displayID, because display ID sometimes changes */ if (swissProtAcc == NULL || swissProtAcc[0] == 0) return NULL; if (isRgdGene(conn)) { safef(query, sizeof(query), "../cgi-bin/pbGlobal?proteinID=%s", swissProtAcc); } else { safef(query, sizeof(query), "../cgi-bin/pbTracks?db=%s&proteinID=%s", database, swissProtAcc); } return(cloneString(query)); } if (sameString(link->name, "tbSchema")) { char *geneTable = genomeSetting("knownGene"); struct trackDb *tdb = hTrackDbForTrack(sqlGetDatabase(conn), geneTable); struct dyString *dy = NULL; if (tdb == NULL) return NULL; dy = newDyString(256); dyStringPrintf(dy, link->url, tdb->grp, geneTable, geneTable); trackDbFree(&tdb); addLinkExtras(link, dy); return dyStringCannibalize(&dy); } geneId = cloneAndCut(geneId, link->preCutAt); safef(query, sizeof(query), link->idSql, geneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL && row[0][0] != 0) /* If not null or empty */ { struct dyString *dy = newDyString(0); char *name = cloneAndCut(row[0], link->postCutAt); dyStringPrintf(dy, link->url, name, row[1], row[2], row[3]); addLinkExtras(link, dy); url = dyStringCannibalize(&dy); freez(&name); } sqlFreeResult(&sr); freeMem(geneId); return url; } char *linkGetName(struct link *link, struct sqlConnection *conn, char *geneId) /* Return name string if possible or NULL if not. */ { char *nameSql = link->nameSql; char *format = link->nameFormat; char query[512]; struct sqlResult *sr; char **row; char *name = NULL; if (nameSql == NULL) nameSql = link->idSql; if (format == NULL) format = "%s"; safef(query, sizeof(query), nameSql, geneId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { char buf[256]; safef(buf, sizeof(buf), format, row[0], row[1], row[2]); name = cloneString(buf); } sqlFreeResult(&sr); return name; } static boolean linksExists(struct section *section, struct sqlConnection *conn, char *geneId) /* Return TRUE if necessary database exists and has something * on this one. */ { section->items = getLinkList(conn, section->raFile); return TRUE; } static void linksPrint(struct section *section, struct sqlConnection *conn, char *geneId) /* Print the links section. */ { int maxPerRow = 6, itemPos = 0; int rowIx = 0; struct link *link, *linkList = section->items; webPrintLinkTableStart(); printGenomicSeqLink(conn, geneId, curGeneChrom, curGeneStart, curGeneEnd); printMrnaSeqLink(conn,geneId); printProteinSeqLink(conn,geneId); hPrintf("</TR>\n<TR>"); ++rowIx; for (link = linkList; link != NULL; link = link->next) { char *url = linkGetUrl(link, conn, geneId); if (url != NULL) { boolean fakeOut = link->useHgsid && differentWord(link->name,"wikiTrack"); char *target = (fakeOut ? "" : " TARGET=_blank"); if (++itemPos > maxPerRow) { hPrintf("</TR>\n<TR>"); itemPos = 1; ++rowIx; } if (fakeOut) webPrintLinkCellStart(); else webPrintLinkOutCellStart(); hPrintf("<A HREF=\"%s\"%s class=\"toc\">", url, target); hPrintf("%s", link->shortLabel); hPrintf("</A>"); webPrintLinkCellEnd(); freez(&url); } } webFinishPartialLinkOutTable(rowIx, itemPos, maxPerRow); webPrintLinkTableEnd(); } struct section *linksSection(struct sqlConnection *conn, struct hash *sectionRa) /* Create links section. */ { struct section *section = sectionNew(sectionRa, "links"); section->exists = linksExists; section->print = linksPrint; section->raFile = "links.ra"; return section; }