748b06ac95ff2a3957be3845bd3594984e3cc3cf chmalee Wed Aug 17 19:21:48 2022 -0700 Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind diff --git src/hg/hgSuggest/hgSuggest.c src/hg/hgSuggest/hgSuggest.c index f073de4..8085dd7 100644 --- src/hg/hgSuggest/hgSuggest.c +++ src/hg/hgSuggest/hgSuggest.c @@ -1,273 +1,303 @@ /* hgGeneSuggest - suggest a gene. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "jksql.h" #include "hdb.h" #include "cheapcgi.h" #include "htmshell.h" #include "dystring.h" #include "jsonParse.h" #include "jsonWrite.h" #include "suggest.h" #include "genbank.h" +#include "hgFind.h" +#include "trix.h" // Optional CGI param type can specify what kind of thing to suggest (default: gene) #define ALT_OR_PATCH "altOrPatch" +#define HELP_DOCS "helpDocs" void suggestGene(char *database, char *table, char *prefix) /* Print out a Javascript list of objects describing genes that start with prefix. */ { struct dyString *str = dyStringNew(10000); dyStringPrintf(str, "[\n"); int exact = cgiOptionalInt("exact", 0); boolean hasKnownCanonical = sameString(table, "knownCanonical"); initGenbankTableNames(database); char query[2048]; if(exact) { // NOTE that exact is no longer used by the UI as of v271, but there are still some robots // using it so we still support it. if(hasKnownCanonical) sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description " "from knownCanonical k, knownGene kg, kgXref x " "where k.transcript = x.kgID and k.transcript = kg.name and x.geneSymbol = '%s' " "order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix); else sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name " "from %s r, %s g, %s d " "where r.name2 = '%s' and g.acc = r.name and g.description = d.id " "order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, prefix); } else { // We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql). // Also note that we take advantage of the fact that searches are case-insensitive in mysql. // Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical; // 3 POU5F1's in hg19); we return all of them (#5962). if(hasKnownCanonical) sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description " "from knownCanonical k, knownGene kg, kgXref x " "where k.transcript = x.kgID and k.transcript = kg.name " "and x.geneSymbol LIKE '%s%%' " "order by x.geneSymbol, k.chrom, kg.txStart", prefix); else sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name " "from %s r, %s g, %s d " "where r.name2 LIKE '%s%%' and g.acc = r.name and g.description = d.id " "order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix); } char *knownDatabase = hdbDefaultKnownDb(database); struct sqlConnection *conn = hAllocConn(knownDatabase); struct sqlResult *sr = sqlGetResult(conn, query); char **row; int count = 0; while ((row = sqlNextRow(sr)) != NULL) { // ignore funny chroms (e.g. _hap chroms. See redmine #4257. if(!strchr(row[1], '_')) { // We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate: const int maxDesc = 120; char *description = row[5]; if (strlen(description) > maxDesc + 4) strcpy(description + maxDesc, "..."); count++; dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", " "\"id\": \"%s:%d-%s\", " "\"geneSymbol\": \"%s\", " "\"internalId\": \"%s\"}", count == 1 ? "" : ",\n", row[0], jsonStringEscape(description), row[1], atoi(row[2])+1, row[3], jsonStringEscape(row[0]), jsonStringEscape(row[4])); } } hFreeConn(&conn); dyStringPrintf(str, "\n]\n"); puts(dyStringContents(str)); } char *escapeAltFixTerm(char *term) /* Special tweaks for SQL search of alt/fix terms that may include '.' and '_' characters. */ { // If there is a ".", make it into a single-character wildcard so that "GL383518.1" // can match "chr1_GL383518v1_alt". char termCpy[strlen(term)+1]; safecpy(termCpy, sizeof termCpy, term); subChar(termCpy, '.', '?'); // Escape '_' because that is an important character in alt/fix sequence names, and support // wildcards: return sqlLikeFromWild(termCpy); } struct slName *queryAltFixNames(struct sqlConnection *conn, char *table, char *term, char *excludeSuffix, boolean prefixOnly) /* If table exists, return names in table that match term, otherwise NULL. * Chop after ':' if there is one and exclude items that end with excludeSuffix so the * mappings between _alt and _fix sequences don't sneak into the wrong category's results. */ { struct slName *names = NULL; if (sqlTableExists(conn, table)) { char query[2048]; sqlSafef(query, sizeof query, "select distinct(substring_index(name, ':', 1)) from %s " "where name like '%s%s%%' " "and name not like '%%%s' and name not like '%%%s:%%'" "order by name", table, (prefixOnly ? "" : "%"), escapeAltFixTerm(term), excludeSuffix, excludeSuffix); names = sqlQuickList(conn, query); } return names; } void writeAltFixMatches(struct jsonWrite *jw, struct slName *matches, char *category) /* Append JSON objects containing alt or fix patch sequence names & optional category. */ { struct slName *match; for (match = matches; match != NULL; match = match->next) { if (strchr(match->name, '_')) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "value", match->name); if (isNotEmpty(category)) jsonWriteString(jw, "category", category); jsonWriteObjectEnd(jw); } } } struct slPair *queryChromAlias(struct sqlConnection *conn, char *term, boolean prefixOnly) /* Search chromAlias for prefix matches for term. */ { struct slPair *matches = NULL; if (sqlTableExists(conn, "chromAlias")) { char query[1024]; sqlSafef(query, sizeof query, "select chrom, alias from chromAlias where alias like '%s%s%%' " "order by chrom", (prefixOnly ? "" : "%"), escapeAltFixTerm(term)); matches = sqlQuickPairList(conn, query); } return matches; } void writeValLabelMatches(struct jsonWrite *jw, struct slPair *matches, char *category) /* Append JSON objects containing alt/fix seqs with extra label info & optional category. */ { struct slPair *match; for (match = matches; match != NULL; match = match->next) { char *seqName = match->name; if (strchr(seqName, '_') && !endsWith(seqName, "_random") && !startsWith("chrUn", seqName)) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "value", seqName); char *extraInfo = match->val; if (isNotEmpty(extraInfo)) { int len = strlen(seqName) + strlen(extraInfo) + 32; char label[len]; safef(label, sizeof label, "%s (%s)", seqName, extraInfo); jsonWriteString(jw, "label", label); } if (isNotEmpty(category)) jsonWriteString(jw, "category", category); jsonWriteObjectEnd(jw); } } } void suggestAltOrPatch(char *database, char *term) /* Print out a Javascript list of objects describing alternate haplotype or fix patch sequences * from database that match term. */ { struct jsonWrite *jw = jsonWriteNew(); jsonWriteListStart(jw, NULL); struct sqlConnection *conn = hAllocConn(database); // First, search for prefix matches struct slName *fixMatches = queryAltFixNames(conn, "fixLocations", term, "alt", TRUE); struct slName *altMatches = queryAltFixNames(conn, "altLocations", term, "fix", TRUE); // Add category labels only if we get both types of matches. writeAltFixMatches(jw, fixMatches, altMatches ? "Fix Patches" : ""); writeAltFixMatches(jw, altMatches, fixMatches ? "Alt Patches" : ""); // If there are no prefix matches, look for partial matches if (fixMatches == NULL && altMatches == NULL) { fixMatches = queryAltFixNames(conn, "fixLocations", term, "alt", FALSE); altMatches = queryAltFixNames(conn, "altLocations", term, "fix", FALSE); writeAltFixMatches(jw, fixMatches, altMatches ? "Fix Patches" : ""); writeAltFixMatches(jw, altMatches, fixMatches ? "Alt Patches" : ""); } // If there are still no matches, try chromAlias. if (fixMatches == NULL && altMatches == NULL) { struct slPair *aliasMatches = queryChromAlias(conn, term, TRUE); writeValLabelMatches(jw, aliasMatches, ""); if (aliasMatches == NULL) { struct slPair *aliasMatches = queryChromAlias(conn, term, FALSE); writeValLabelMatches(jw, aliasMatches, ""); } } hFreeConn(&conn); jsonWriteListEnd(jw); puts(jw->dy->string); jsonWriteFree(&jw); } +void suggestHelpPage(char *prefix) +/* Print out a Javascript list of objects describing help pages that start with prefix. */ +{ +struct jsonWrite *jw = jsonWriteNew(); +jsonWriteListStart(jw, NULL); +char *lowered = cloneString(prefix); +char *keyWords[16]; +int keyCount; +tolowers(lowered); +keyCount = chopLine(lowered, keyWords); +struct trix *helpTrix = openStaticTrix(helpDocsTrix); +struct trixSearchResult *tsr, *tsrList = trixSearch(helpTrix, keyCount, keyWords, tsmExpand); +int i; +for (i = 0, tsr = tsrList; i < 25 && tsr != NULL; i++, tsr = tsr->next) + { + jsonWriteObjectStart(jw, NULL); + jsonWriteString(jw, "value", tsr->itemId); // value is necessary + jsonWriteString(jw, "category", "helpDocs"); // hardcode this for client + jsonWriteObjectEnd(jw); + } +jsonWriteListEnd(jw); +puts(jw->dy->string); +jsonWriteFree(&jw); +} + char *checkParams(char *database, char *prefix, char *type) /* If we don't have valid CGI parameters, quit with a Bad Request HTTP response. */ { pushWarnHandler(htmlVaBadRequestAbort); pushAbortHandler(htmlVaBadRequestAbort); if(prefix == NULL || database == NULL) errAbort("%s", "Missing prefix and/or db CGI parameter"); if (! hDbIsActive(database)) errAbort("'%s' is not a valid, active database", htmlEncode(database)); -if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH)) +if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH) && differentString(type, HELP_DOCS)) errAbort("'%s' is not a valid type", type); char *table = NULL; -if (! sameOk(type, ALT_OR_PATCH)) +if (! sameOk(type, ALT_OR_PATCH) && !sameOk(type, HELP_DOCS)) { char *knownDatabase = hdbDefaultKnownDb(database); struct sqlConnection *conn = hAllocConn(knownDatabase); table = connGeneSuggestTable(conn); hFreeConn(&conn); if(table == NULL) errAbort("gene autosuggest is not supported for db '%s'", database); } popWarnHandler(); popAbortHandler(); return table; } int main(int argc, char *argv[]) { long enteredMainTime = clock1000(); cgiSpoof(&argc, argv); char *database = cgiOptionalString("db"); char *prefix = cgiOptionalString("prefix"); char *type = cgiOptionalString("type"); char *table = checkParams(database, prefix, type); puts("Content-Type:text/plain"); puts("\n"); if (sameOk(type, ALT_OR_PATCH)) suggestAltOrPatch(database, prefix); +else if (sameOk(type, HELP_DOCS)) + suggestHelpPage(prefix); else suggestGene(database, table, prefix); cgiExitTime("hgSuggest", enteredMainTime); return 0; }