60e7358ad9239e80827ee2a9d95151ef5fc57946 angie Wed Sep 26 12:17:25 2018 -0700 Add fuzzy search of chromAlias to multi-region alt/fix autocomplete, so common haplotype name components like 'cox', 'apd', 'kir' can be matched. refs #18544 diff --git src/hg/hgSuggest/hgSuggest.c src/hg/hgSuggest/hgSuggest.c index ff81841..1e710fb 100644 --- src/hg/hgSuggest/hgSuggest.c +++ src/hg/hgSuggest/hgSuggest.c @@ -1,258 +1,263 @@ /* hgGeneSuggest - suggest a gene. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory 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" // Optional CGI param type can specify what kind of thing to suggest (default: gene) #define ALT_OR_PATCH "altOrPatch" void suggestGene(char *database, char *table, char *prefix) /* Print out a Javascript list of objects describing genes that start with prefix. */ { struct dyString *str = newDyString(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); } struct sqlConnection *conn = hAllocConn(database); 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)); } struct slName *queryQNames(struct sqlConnection *conn, char *table, char *term, boolean prefixOnly) /* If table exists, return qNames in table that match term, otherwise NULL. Exclude items whose * tName contains '_' 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)) { // 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: char *escapedTerm = sqlLikeFromWild(termCpy); char query[2048]; sqlSafef(query, sizeof query, "select distinct(qName) from %s where qName like '%s%s%%' " "and tName not rlike '.*_.*' order by qName", table, (prefixOnly ? "" : "%"), escapedTerm); 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) +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%%' " - "order by chrom", term); + sqlSafef(query, sizeof query, "select chrom, alias from chromAlias where alias like '%s%s%%' " + "order by chrom", (prefixOnly ? "" : "%"), 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 = queryQNames(conn, "fixSeqLiftOverPsl", term, TRUE); struct slName *altMatches = queryQNames(conn, "altSeqLiftOverPsl", term, 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 = queryQNames(conn, "fixSeqLiftOverPsl", term, FALSE); altMatches = queryQNames(conn, "altSeqLiftOverPsl", term, 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); + 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); } 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)) errAbort("'%s' is not a valid type", type); char *table = NULL; if (! sameOk(type, ALT_OR_PATCH)) { struct sqlConnection *conn = hAllocConn(database); 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 suggestGene(database, table, prefix); cgiExitTime("hgSuggest", enteredMainTime); return 0; }