4a030195664cbdd1d3c1a4b81b1ed41dbf6d9bc5
angie
Fri Feb 15 14:02:58 2019 -0800
Prevent hgFind lib (specifically genomePos -> hgPositionsHtml) from opening a web page; instead, pass up results and warning messages to the calling CGI so it can open the page its own way. refs #22945
hgTracks, hgTables and hgVai used to call findGenomePos{,Web} to resolve positions; hgTables and hgVai had to detect after the fact whether an HTML page had been started (with warnings and/or multiple results).
In fact, hgPositionsHtml called webEnd which could cause conflicts with what the CGI was doing afterwards.
Now, instead of findGenomePos{,Web} there is hgFindSearch which returns hgp and also warning messages, if any, via a dyString parameter.
The calling CGI decides how to open the page if necessary (for hgTracks, it's already open) and displays warnings/multiple results -- or just proceeds as usual with the single position result.
diff --git src/hg/lib/hgFind.c src/hg/lib/hgFind.c
index ac6219c..8d533c0 100644
--- src/hg/lib/hgFind.c
+++ src/hg/lib/hgFind.c
@@ -9,30 +9,31 @@
#include "portable.h"
#include "dystring.h"
#include "hash.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "web.h"
#include "jksql.h"
#include "hdb.h"
#include "hui.h"
#include "psl.h"
#include "genePred.h"
#include "genePredReader.h"
#include "bed.h"
#include "cytoBand.h"
#include "cart.h"
+#include "errCatch.h"
#include "hgFind.h"
#include "hgFindSpec.h"
#include "hgHgvs.h"
#include "snp.h"
#include "refLink.h"
#include "kgAlias.h"
#include "kgProtAlias.h"
#include "findKGAlias.h"
#include "findKGProtAlias.h"
#include "tigrCmrGene.h"
#include "minGeneInfo.h"
#include "pipeline.h"
#include "hgConfig.h"
#include "trix.h"
#include "trackHub.h"
@@ -96,58 +97,30 @@
static void hgPosTableFreeList(struct hgPosTable **pList)
/* Free a list of dynamically allocated hgPos's */
{
struct hgPosTable *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
hgPosTableFree(&el);
}
*pList = NULL;
}
-static void hgPositionsFree(struct hgPositions **pEl)
-/* Free up hgPositions. */
-{
-struct hgPositions *el;
-if ((el = *pEl) != NULL)
- {
- freeMem(el->query);
- freeMem(el->extraCgi);
- hgPosTableFreeList(&el->tableList);
- freez(pEl);
- }
-}
-
-#if 0 /* not used */
-static void hgPositionsFreeList(struct hgPositions **pList)
-/* Free a list of dynamically allocated hgPos's */
-{
-struct hgPositions *el, *next;
-
-for (el = *pList; el != NULL; el = next)
- {
- next = el->next;
- hgPositionsFree(&el);
- }
-*pList = NULL;
-}
-#endif
-
#define HGPOSRANGESIZE 64
static char *hgPosBrowserRange(struct hgPos *pos, char range[HGPOSRANGESIZE])
/* Convert pos to chrN:123-456 format. If range parameter is NULL it returns
* static buffer, otherwise writes and returns range. */
{
static char buf[HGPOSRANGESIZE];
if (range == NULL)
range = buf;
safef(range, HGPOSRANGESIZE, "%s:%d-%d",
pos->chrom, pos->chromStart+1, pos->chromEnd);
return range;
}
@@ -1583,144 +1556,162 @@
char query[256];
sqlSafef(query, sizeof(query),
"select count(*) from %s where qName = '%s'", table, acc);
return (sqlQuickNum(conn, query) > 0);
}
static int addMrnaPositionTable(char *db, struct hgPositions *hgp,
struct slName **pAccList,
struct hash *accOrgHash, struct cart *cart,
struct sqlConnection *conn, char *hgAppName,
boolean aligns, boolean isXeno)
/* Generate table of positions that match criteria.
* Add to hgp if any found. Return number found */
{
struct hgPosTable *table = NULL;
-struct hgPos *pos = NULL;
struct slName *el = NULL;
struct slName *elToFree = NULL;
struct dyString *dy = newDyString(256);
-char query[512];
-char description[512];
-char product[256];
-char organism[128];
char *ui = getUiUrl(cart);
-char *acc = NULL;
int organismID = hOrganismID(hgp->database); /* id from mrna organism table */
int alignCount = 0;
char hgAppCombiner = (strchr(hgAppName, '?')) ? '&' : '?';
char *mrnaTable = isXeno ? "xenoMrna" : "all_mrna";
boolean mrnaTableExists = hTableExists(hgp->database, mrnaTable);
AllocVar(table);
/* Examine all accessions to see if they fit criteria for
* this table. Add all matching to the position list, and
* remove from the accession list */
for (el = *pAccList; el != NULL; el = el->next)
{
freez(&elToFree);
- acc = el->name;
+ char *acc = el->name;
/* check if item matches xeno criterion */
int itemOrganismID = hashIntVal(accOrgHash, acc);
if (isXeno == (itemOrganismID == organismID))
continue;
/* check if item matches alignment criterion */
if (aligns != (mrnaTableExists && mrnaAligns(conn, mrnaTable, acc)))
continue;
/* item fits criteria, so enter in table */
+ struct hgPos *pos = NULL;
AllocVar(pos);
slAddHead(&table->posList, pos);
pos->name = cloneString(acc);
pos->browserName = cloneString(acc);
dyStringClear(dy);
if (aligns)
{
dyStringPrintf(dy, "<A HREF=\"%s%cposition=%s",
hgAppName, hgAppCombiner, acc);
}
else
{
/* display mRNA details page -- need to add dummy CGI variables*/
dyStringPrintf(dy, "<A HREF=\"%s%cg=%s&i=%s&c=0&o=0&l=0&r=0",
hgcName(), hgAppCombiner, mrnaTable, acc);
}
if (ui != NULL)
dyStringPrintf(dy, "&%s", ui);
dyStringPrintf(dy, "%s\">",
hgp->extraCgi);
dyStringPrintf(dy, "%s</A>", acc);
/* print description for item, or lacking that, the product name */
+ char description[512];
safef(description, sizeof(description), "%s", "n/a");
+ char query[512];
sqlSafef(query, sizeof(query),
"select d.name from %s g,%s d"
" where g.acc = '%s' and g.description = d.id", gbCdnaInfoTable, descriptionTable, acc);
sqlQuickQuery(conn, query, description, sizeof(description));
if (sameString(description, "n/a"))
{
/* look for product name */
sqlSafef(query, sizeof(query),
"select p.name from %s g,%s p"
" where g.acc = '%s' and g.productName = p.id",
gbCdnaInfoTable, productNameTable, acc);
+ char product[256];
sqlQuickQuery(conn, query, product, sizeof(product));
if (!sameString(product, "n/a"))
{
/* get organism name */
sqlSafef(query, sizeof(query),
"select o.name from %s g,%s o"
" where g.acc = '%s' and g.organism = o.id", gbCdnaInfoTable, organismTable, acc);
+ char organism[128];
*organism = 0;
sqlQuickQuery(conn, query, organism, sizeof(organism));
safef(description, sizeof(description), "%s%s%s",
*organism ? organism : "",
*organism ? ", " : "",
product);
}
}
if (!sameString(description, "n/a"))
/* print description if it has been loaded */
dyStringPrintf(dy, " - %s", description);
dyStringPrintf(dy, "\n");
pos->description = cloneString(dy->string);
/* remove processed element from accession list */
slRemoveEl(pAccList, el);
elToFree = el;
}
/* fill in table and add to hgp only if it contains results */
alignCount = slCount(table->posList);
if (alignCount > 0)
{
char *organism = hOrganism(hgp->database); /* dbDb organism column */
+ if (alignCount == 1)
+ {
+ // So far we have not bothered to look up the coordinates because there are almost always
+ // multiple matches among which the user will have to choose. However, it is possible
+ // for there to be a unique match (hgwdev 19-02-15, hg38, "elmer" --> U01022). In that
+ // case we should look up the coordinates so the user doesn't have to click through a page
+ // with one match leading to another search.
+ char shortLabel[256];
+ safef(shortLabel, sizeof shortLabel, "%s%s %sligned mRNAs",
+ isXeno ? "Non-" : "", organism,
+ aligns ? "A" : "Una");
+ char *acc = table->posList->name;
+ struct psl *pslList = getPslFromTable(conn, hgp->database, mrnaTable, acc);
+ addPslResultToHgp(hgp, hgp->database, mrnaTable, shortLabel, acc, pslList);
+ alignCount = slCount(hgp->tableList->posList);
+ }
+ else
+ {
char title[256];
slReverse(&table->posList);
safef(title, sizeof(title), "%s%s %sligned mRNA Search Results",
isXeno ? "Non-" : "", organism,
aligns ? "A" : "Una");
- freeMem(organism);
table->description = cloneString(title);
table->name = cloneString(mrnaTable);
table->htmlOnePos = mrnaKeysHtmlOnePos;
slAddHead(&hgp->tableList, table);
}
+ freeMem(organism);
+ }
freeDyString(&dy);
return alignCount;
}
static boolean findMrnaKeys(char *db, struct hgFindSpec *hfs,
char *keys, int limitResults, struct hgPositions *hgp)
/* Find mRNA that has keyword in one of its fields. */
{
int alignCount;
char *tables[] = {
productNameTable, geneNameTable,
authorTable, tissueTable, cellTable, descriptionTable, developmentTable,
};
struct hash *allKeysHash = NULL;
struct slName *allKeysList = NULL;
@@ -2369,70 +2360,67 @@
if ((row = sqlNextRow(sr)) != NULL)
dyStringPrintf(dy, "%s", row[0]);
sqlFreeResult(&sr);
}
if (dy->stringSize > 0)
pos->description = cloneString(dy->string);
dyStringFree(&dy);
}
found = TRUE;
}
}
hFreeConn(&conn);
return(found);
}
-static void hgPositionsHtml(char *db, struct hgPositions *hgp, FILE *f,
- boolean useWeb, char *hgAppName, struct cart *cart)
-/* Write out hgp table as HTML to file. */
+void hgPositionsHtml(char *db, struct hgPositions *hgp, char *hgAppName, struct cart *cart)
+/* Write multiple search results as HTML. */
{
struct hgPosTable *table;
struct hgPos *pos;
char *desc;
char range[HGPOSRANGESIZE];
char *ui = getUiUrl(cart);
char *extraCgi = hgp->extraCgi;
char hgAppCombiner = (strchr(hgAppName, '?')) ? '&' : '?';
boolean containerDivPrinted = FALSE;
struct trackDb *tdbList = NULL;
-
-if (useWeb)
- {
- webStart(cart, db, "Select Position");
- db = cartString(cart, "db");
- }
+// This used to be an argument, but only stdout was used:
+FILE *f = stdout;
for (table = hgp->tableList; table != NULL; table = table->next)
{
if (table->posList != NULL)
{
char *tableName = table->name;
if (startsWith("all_", tableName))
tableName += strlen("all_");
// clear the tdb cache if this track is a hub track
if (isHubTrack(tableName))
tdbList = NULL;
struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList);
if (!tdb)
errAbort("no track for table \"%s\" found via a findSpec", tableName);
char *trackName = tdb->track;
char *vis = hCarefulTrackOpenVis(db, trackName);
boolean excludeTable = FALSE;
if(!containerDivPrinted)
{
fprintf(f, "<div id='hgFindResults'>\n");
+ fprintf(f, "<p>Your search resulted in multiple matches. "
+ "Please select a position:</p>\n");
containerDivPrinted = TRUE;
}
if (table->htmlStart)
table->htmlStart(table, f);
else
fprintf(f, "<H2>%s</H2><PRE>\n", table->description);
for (pos = table->posList; pos != NULL; pos = pos->next)
{
if (table->htmlOnePos)
table->htmlOnePos(table, pos, f);
else
{
char *matches = excludeTable ? "" : pos->browserName;
char *encMatches = cgiEncode(matches);
hgPosBrowserRange(pos, range);
@@ -2478,135 +2466,193 @@
htmTextOut(f, desc);
}
fprintf(f, "\n");
freeMem(encMatches);
}
}
if (table->htmlEnd)
table->htmlEnd(table, f);
else
fprintf(f, "</PRE>\n");
}
}
if(containerDivPrinted)
fprintf(f, "</div>\n");
-
-if (useWeb)
- webEnd();
}
-
-static struct hgPositions *genomePos(char *db, char *spec, char **retChromName,
- int *retWinStart, int *retWinEnd, struct cart *cart, boolean showAlias,
- boolean useWeb, char *hgAppName)
-/* Search for positions in genome that match user query.
- * Return an hgp if the query results in a unique position.
- * Otherwise display list of positions, put # of positions in retWinStart,
- * and return NULL. */
+static struct hgPositions *hgPositionsSearch(char *db, char *spec,
+ char **retChromName, int *retWinStart, int *retWinEnd,
+ boolean *retIsMultiTerm, struct cart *cart,
+ char *hgAppName, char **retMultiChrom,
+ struct dyString *dyWarn)
+/* Search for positions that match spec (possibly ;-separated in which case *retIsMultiTerm is set).
+ * Return a container of tracks and positions (if any) that match term. If different components
+ * of a multi-term search land on different chromosomes then *retMultiChrom will be set. */
{
struct hgPositions *hgp = NULL;
-char *terms[16];
-int termCount = 0;
-int i = 0;
-boolean multiTerm = FALSE;
char *chrom = NULL;
int start = INT_MAX;
int end = 0;
-
-termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms));
-multiTerm = (termCount > 1);
-
+char *terms[16];
+int termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms));
+boolean multiTerm = (termCount > 1);
+if (retIsMultiTerm)
+ *retIsMultiTerm = multiTerm;
+if (retMultiChrom)
+ *retMultiChrom = NULL;
+int i;
for (i = 0; i < termCount; i++)
{
trimSpaces(terms[i]);
if (isEmpty(terms[i]))
continue;
+ // Append warning messages to dyWarn, but allow errAborts to continue
+ struct errCatch *errCatch = errCatchNew();
+ if (errCatchStart(errCatch))
hgp = hgPositionsFind(db, terms[i], "", hgAppName, cart, multiTerm);
- if (hgp == NULL || hgp->posCount == 0)
- {
- hgPositionsFree(&hgp);
- warn("Sorry, couldn't locate %s in %s %s\n", terms[i],
- trackHubSkipHubName(hOrganism(db)), hFreezeDate(db));
- if (multiTerm)
- hUserAbort("%s not uniquely determined -- "
- "can't do multi-position search.", terms[i]);
- *retWinStart = 0;
- return NULL;
- }
-
- if ((hgp->singlePos != NULL) && (!showAlias || !hgp->useAlias))
- {
- if (chrom != NULL && !sameString(chrom, hgp->singlePos->chrom))
- hUserAbort("Sites occur on different chromosomes: %s, %s.",
- chrom, hgp->singlePos->chrom);
+ errCatchEnd(errCatch);
+ if (errCatch->gotError)
+ errAbort("%s", errCatch->message->string);
+ else if (isNotEmpty(errCatch->message->string))
+ dyStringAppend(dyWarn, errCatch->message->string);
+ errCatchFree(&errCatch);
+ if (hgp->singlePos != NULL)
+ {
+ if (retMultiChrom && chrom != NULL && differentString(chrom, hgp->singlePos->chrom))
+ *retMultiChrom = cloneString(chrom);
chrom = hgp->singlePos->chrom;
if (hgp->singlePos->chromStart < start)
start = hgp->singlePos->chromStart;
if (hgp->singlePos->chromEnd > end)
end = hgp->singlePos->chromEnd;
}
- else
- {
- hgPositionsHtml(db, hgp, stdout, useWeb, hgAppName, cart);
- if (multiTerm && hgp->posCount != 1)
- hUserAbort("%s not uniquely determined (%d locations) -- "
- "can't do multi-position search.",
- terms[i], hgp->posCount);
- *retWinStart = hgp->posCount;
- hgp = NULL;
+ else if (hgp->posCount == 0 || (multiTerm && hgp->posCount > 1))
break;
}
- }
-if (hgp != NULL)
- {
+if (retChromName)
*retChromName = chrom;
+if (retWinStart)
*retWinStart = start;
+if (retWinEnd)
*retWinEnd = end;
- }
return hgp;
}
+static struct hgPositions *revertPosition(struct cart *cart, char **pPosition,
+ char **retChrom, int *retStart, int *retEnd,
+ char *hgAppName, struct dyString *dyWarn)
+/* Revert *pPosition to lastPosition (or default position). Return a new hgp for the
+ * resolved position. Append warnings to dyWarn, errAbort if defaultPos doesn't work. */
+{
+struct hgPositions *hgp = NULL;
+boolean isMultiTerm = FALSE;
+char *multiDiffChrom = NULL;
+char *db = cartString(cart, "db");
+char *lastPosition = cartOptionalString(cart, "lastPosition");
+if (isNotEmpty(lastPosition) && !IS_CART_VAR_EMPTY(lastPosition))
+ {
+ if (startsWith("virt:", lastPosition))
+ {
+ lastPosition = cartUsualString(cart, "nonVirtPosition", hDefaultPos(db));
+ }
+ hgp = hgPositionsSearch(db, lastPosition, retChrom, retStart, retEnd, &isMultiTerm,
+ cart, hgAppName, &multiDiffChrom, dyWarn);
+ if (hgp->singlePos && !(isMultiTerm && isNotEmpty(multiDiffChrom)))
+ {
+ freez(pPosition);
+ *pPosition = cloneString(lastPosition);
+ return hgp;
+ }
+ else
+ dyStringPrintf(dyWarn, " Unable to resolve lastPosition '%s'; "
+ "reverting to default position.", lastPosition);
+ }
+char *defaultPosition = hDefaultPos(db);
+hgp = hgPositionsSearch(db, defaultPosition, retChrom, retStart, retEnd, &isMultiTerm,
+ cart, hgAppName, &multiDiffChrom, dyWarn);
+if (hgp->singlePos && !(isMultiTerm && isNotEmpty(multiDiffChrom)))
+ {
+ freez(pPosition);
+ *pPosition = cloneString(defaultPosition);
+ }
+else
+ errAbort("Unable to resolve default position '%s' for database '%s'.",
+ defaultPosition, db);
+return hgp;
+}
-struct hgPositions *findGenomePos(char *db, char *spec, char **retChromName,
- int *retWinStart, int *retWinEnd, struct cart *cart)
-/* Search for positions in genome that match user query.
- * Return an hgp if the query results in a unique position.
- * Otherwise display list of positions, put # of positions in retWinStart,
- * and return NULL. */
+static boolean posIsObsolete(char *pos)
+/* Return TRUE if pos is genome (or other obsolete keyword). Once upon a time position=genome
+ * was used to indicate genome-wide search, but now we have an independent option. */
{
-return genomePos(db, spec, retChromName, retWinStart, retWinEnd, cart, TRUE,
- FALSE, "hgTracks");
+pos = trimSpaces(pos);
+return(sameWord(pos, "genome") || sameWord(pos, "hgBatch"));
}
-struct hgPositions *findGenomePosWeb(char *db, char *spec, char **retChromName,
- int *retWinStart, int *retWinEnd, struct cart *cart,
- boolean useWeb, char *hgAppName)
-/* Search for positions in genome that match user query.
- * Use the web library to print out HTML headers if necessary, and use
- * hgAppName when forming URLs (instead of "hgTracks").
- * Return an hgp if the query results in a unique position.
- * Otherwise display list of positions, put # of positions in retWinStart,
- * and return NULL. */
+struct hgPositions *hgFindSearch(struct cart *cart, char **pPosition,
+ char **retChrom, int *retStart, int *retEnd,
+ char *hgAppName, struct dyString *dyWarn)
+/* If *pPosition is a search term, then try to resolve it to genomic position(s).
+ * If unable to find a unique position then revert pPosition to lastPosition (or default position).
+ * Return a container of matching tables and positions. Warnings/errors are appended to dyWarn. */
+{
+struct hgPositions *hgp = NULL;
+if (posIsObsolete(*pPosition))
{
-struct hgPositions *hgp;
-if (useWeb)
- webPushErrHandlersCartDb(cart, db);
-hgp = genomePos(db, spec, retChromName, retWinStart, retWinEnd, cart, TRUE,
- useWeb, hgAppName);
-if (useWeb)
- webPopErrHandlers();
+ hgp = revertPosition(cart, pPosition, retChrom, retStart, retEnd, hgAppName, dyWarn);
+ }
+else
+ {
+ boolean isMultiTerm = FALSE;
+ char *multiDiffChrom = NULL;
+ char *db = cartString(cart, "db");
+ hgp = hgPositionsSearch(db, *pPosition, retChrom, retStart, retEnd,
+ &isMultiTerm, cart, hgAppName, &multiDiffChrom, dyWarn);
+ if (isMultiTerm && isNotEmpty(multiDiffChrom))
+ {
+ dyStringPrintf(dyWarn, "Sites occur on different chromosomes: %s, %s.",
+ multiDiffChrom, hgp->singlePos->chrom);
+ hgp = revertPosition(cart, pPosition, retChrom, retStart, retEnd, hgAppName, dyWarn);
+ }
+ else if (hgp->posCount > 1 ||
+ // In weird cases it's possible to get a single result that does not have coords, but
+ // leads to another search a la multiple results! That happened with genbank keyword
+ // search ("elmer" in hg19, hg38 Feb. '19). I fixed it but there could be other cases.
+ (hgp->posCount == 1 && !hgp->singlePos))
+ {
+ if (isMultiTerm)
+ dyStringPrintf(dyWarn, "%s not uniquely determined (%d locations) -- "
+ "can't do multi-position search.",
+ hgp->query, hgp->posCount);
+ // Revert position in cart (#13009), but don't replace hgp -- hgPositionsHtml will need it.
+ revertPosition(cart, pPosition, retChrom, retStart, retEnd, hgAppName, dyWarn);
+ }
+ else if (hgp->posCount == 0)
+ {
+ dyStringPrintf(dyWarn, "Sorry, couldn't locate %s in %s %s", hgp->query,
+ trackHubSkipHubName(hOrganism(db)), hFreezeDate(db));
+ hgp = revertPosition(cart, pPosition, retChrom, retStart, retEnd, hgAppName, dyWarn);
+ }
+ if (hgp->singlePos && isEmpty(dyWarn->string))
+ {
+ char position[512];
+ safef(position, sizeof(position), "%s:%d-%d",
+ hgp->singlePos->chrom, hgp->singlePos->chromStart+1, hgp->singlePos->chromEnd);
+ *pPosition = cloneString(addCommasToPos(NULL, position));
+ }
+ }
return hgp;
}
#if 0 /* not used */
static void noRelative(boolean relativeFlag, int relStart, int relEnd,
char *table)
{
if (relativeFlag)
hUserAbort("Sorry, range spec (\":%d-%d\") is not supported for %s.",
relStart+1, relEnd, table);
}
#endif
static boolean isBigFileFind(struct hgFindSpec *hfs)
@@ -3104,31 +3150,31 @@
trackTable = "refGene";
singlePos(hgp, "HGVS", NULL, trackTable, term, "",
mapping->chrom, mapping->chromStart-padding, mapping->chromEnd+padding);
// highlight the mapped bases to distinguish from padding
hgp->tableList->posList->highlight = addHighlight(cart, db, mapping->chrom,
mapping->chromStart, mapping->chromEnd);
foundIt = TRUE;
}
dyStringFree(&dyWarn);
}
return foundIt;
}
struct hgPositions *hgPositionsFind(char *db, char *term, char *extraCgi,
char *hgAppNameIn, struct cart *cart, boolean multiTerm)
-/* Return table of positions that match term or NULL if none such. */
+/* Return container of tracks and positions (if any) that match term. */
{
struct hgPositions *hgp = NULL, *hgpItem = NULL;
regmatch_t substrs[4];
boolean canonicalSpec = FALSE;
boolean gbrowserSpec = FALSE;
boolean lengthSpec = FALSE;
boolean singleBaseSpec = FALSE;
boolean relativeFlag = FALSE;
int relStart = 0, relEnd = 0;
hgAppName = hgAppNameIn;
// Exhaustive searches can lead to timeouts on CGIs (#11626).
// However, hgGetAnn requires exhaustive searches (#11665).
// So... set a non-exhaustive search limit on all except hgGetAnn.