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/near/hgNear/search.c src/hg/near/hgNear/search.c index 3ebbede..ee70a8b 100644 --- src/hg/near/hgNear/search.c +++ src/hg/near/hgNear/search.c @@ -1,292 +1,292 @@ /* search - manage simple searches - ones based on just a single name. */ /* Copyright (C) 2013 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 "hash.h" #include "jksql.h" #include "hdb.h" #include "obscure.h" #include "hgNear.h" int searchResultCmpShortLabel(const void *va, const void *vb) /* Compare to sort based on short label. */ { const struct searchResult *a = *((struct searchResult **)va); const struct searchResult *b = *((struct searchResult **)vb); return strcmp(a->shortLabel, b->shortLabel); } static struct genePos *findGenePredPos(struct sqlConnection *conn, char *table, char *search) /* Find out gene ID from search term. */ { char query[256]; struct sqlResult *sr; char **row; struct genePos *gpList = NULL, *gp; if (search != NULL) { sqlSafef(query, sizeof(query), "select name,chrom,txStart,txEnd from %s where name = '%s'", table, search); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(gp); gp->name = cloneString(row[0]); gp->chrom = cloneString(row[1]); gp->start = sqlUnsigned(row[2]); gp->end = sqlUnsigned(row[3]); slAddHead(&gpList, gp); } sqlFreeResult(&sr); } slReverse(&gpList); return gpList; } struct columnSearchResults /* Search results for one column. */ { struct columnSearchResults *next; /* next in list. */ char *label; /* Description of column - not allocated here. */ struct searchResult *results; /* List of results. */ }; static void transformToCanonical(struct searchResult *list, struct sqlConnection *conn) /* Transform search results to canonical versions. */ { struct dyString *dy = newDyString(1024); char *cannon = genomeSetting("canonicalTable"); char *isoform = genomeSetting("isoformTable"); struct sqlResult *sr; char **row; struct searchResult *el; for (el = list; el != NULL; el = el->next) { dyStringClear(dy); sqlDyStringPrintf(dy, "select %s.transcript,%s.chrom,%s.chromStart,%s.chromEnd,%s.protein ", cannon, cannon, cannon, cannon, cannon); sqlDyStringPrintf(dy, "from %s,%s ", isoform, cannon); sqlDyStringPrintf(dy, "where %s.transcript = '%s' ", isoform, el->gp.name); sqlDyStringPrintf(dy, "and %s.clusterId = %s.clusterId", isoform, cannon); sr = sqlGetResult(conn, dy->string); if ((row = sqlNextRow(sr)) != NULL) genePosFillFrom5(&el->gp, row); sqlFreeResult(&sr); } dyStringFree(&dy); } static struct searchResult *removeDupes(struct searchResult *list) /* Remove duplicates from list. Return weeded list. */ { struct searchResult *el, *next, *newList = NULL; struct hash *dupHash = newHash(0); for (el = list; el != NULL; el = next) { next = el->next; if (!hashLookup(dupHash, el->gp.name)) { hashAdd(dupHash, el->gp.name, NULL); slAddHead(&newList, el); } } hashFree(&dupHash); slReverse(&newList); return newList; } static void fillInMissingLabels(struct sqlConnection *conn, struct column *colList, struct searchResult *srList) /* Fill in missing columns by looking up name and description * if possible. */ { struct column *nameColumn = findNamedColumn("name"); struct column *desColumn = findNamedColumn("description"); struct searchResult *sr; for (sr = srList; sr != NULL; sr = sr->next) { if (sr->shortLabel == NULL) { if (nameColumn != NULL) sr->shortLabel = nameColumn->cellVal(nameColumn, &sr->gp, conn); if (sr->shortLabel == NULL) sr->shortLabel = cloneString(sr->gp.name); } if (sr->longLabel == NULL) { if (desColumn != NULL) sr->longLabel = desColumn->cellVal(desColumn, &sr->gp, conn); else sr->longLabel = cloneString(""); } } } static boolean allSame(struct columnSearchResults *csrList) /* Return TRUE if all search results point to the same place. */ { struct hash *dupeHash = newHash(0); char hashName[512]; int sepCount = 0; struct columnSearchResults *csr; struct searchResult *sr; for (csr = csrList; csr != NULL && sepCount < 2; csr = csr->next) { for (sr = csr->results; sr != NULL && sepCount < 2; sr = sr->next) { char *chrom = sr->gp.chrom; if (chrom == NULL) chrom = "n/a"; safef(hashName, sizeof(hashName), "%s %s:%d-%d", sr->gp.name, chrom, sr->gp.start, sr->gp.end); if (!hashLookup(dupeHash, hashName)) { hashAdd(dupeHash, hashName, NULL); ++sepCount; } } } hashFree(&dupeHash); return sepCount <= 1; } static void searchAllColumns(struct sqlConnection *conn, struct column *colList, char *search) /* Call search on each column. */ { struct column *col; struct searchResult *srList, *sr; struct columnSearchResults *csrList = NULL, *csr; int totalCount = 0; struct searchResult *srOne = NULL; for (col = colList; col != NULL; col = col->next) { if (col->simpleSearch) { srList = col->simpleSearch(col, conn, search); if (showOnlyCanonical() && srList != NULL) { transformToCanonical(srList, conn); srList = removeDupes(srList); } if (srList != NULL) { srOne = srList; fillInMissingLabels(conn, colList, srList); AllocVar(csr); csr->label = columnSetting(col, "searchLabel", col->longLabel); csr->results = srList; slAddTail(&csrList, csr); totalCount += slCount(srList); } } } if (totalCount == 0) { displayData(conn, colList, NULL); if (anyWild(search)) warn("Sorry, the search box doesn't take wildcards, " "though in most cases it will find things without " "them. Try entering your search without * or ? " "characters."); else warn("Sorry, couldn't find '%s'", search); } else if (totalCount == 1 || allSame(csrList)) // else if (totalCount == 1) displayData(conn, colList, &srOne->gp); else { makeTitle("Simple Search Results", NULL); for (csr = csrList; csr != NULL; csr = csr->next) { hPrintf("<H2>%s</H2>\n", csr->label); slSort(&csr->results, searchResultCmpShortLabel); for (sr = csr->results; sr != NULL; sr = sr->next) { selfAnchorSearch(&sr->gp); if (sr->matchingId != NULL) hPrintf("%s (%s)", sr->matchingId, sr->shortLabel); else hPrintf("%s", sr->shortLabel); hPrintf("</A> - %s<BR>\n", sr->longLabel); } } } } static char *transcriptToCanonical(struct sqlConnection *conn, char *transcript) /* Translate transcript to canonical ID if possible, otherwise just return * a copy of transcript. */ { struct dyString *dy = newDyString(1024); char *cannon = genomeSetting("canonicalTable"); char *isoform = genomeSetting("isoformTable"); char buf[128]; char *result = NULL; sqlDyStringPrintf(dy, "select %s.transcript from %s,%s where %s.transcript = '%s'", cannon, isoform, cannon, isoform, transcript); sqlDyStringPrintf(dy, " and %s.clusterId = %s.clusterId", isoform, cannon); result = sqlQuickQuery(conn, dy->string, buf, sizeof(buf)); if (result != NULL) return(cloneString(result)); else return(cloneString(transcript)); } static struct genePos *findKnownAccessions(struct sqlConnection *conn, char *search) /* Return list of known accessions. */ { search = transcriptToCanonical(conn, search); return findGenePredPos(conn, genomeSetting("geneTable"), search); } void doSearch(struct sqlConnection *conn, struct column *colList) /* Search. If result is unambiguous call displayData, otherwise * put up a page of choices. */ { char *search = cartString(cart, searchVarName); char *escSearch = makeEscapedString(trimSpaces(search), '\''); struct genePos *accList; accList = findKnownAccessions(conn, escSearch); if (accList != NULL) { if (slCount(accList) == 1 || !sameString(groupOn, "position")) displayData(conn, colList, accList); else { struct genePos *acc; hPrintf("%s maps to %d positions, please pick one below:<BR>\n", search, slCount(accList)); for (acc = accList; acc != NULL; acc = acc->next) { hPrintf(" "); selfAnchorSearch(acc); hPrintf("%s:%d-%d</A><BR>\n", acc->chrom, acc->start+1, acc->end); } } } else { searchAllColumns(conn, colList, escSearch); } freez(&escSearch); }