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/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c
index 275ab9c..40a8a0d 100644
--- src/hg/hgTracks/hgTracks.c
+++ src/hg/hgTracks/hgTracks.c
@@ -132,31 +132,31 @@
char *protDbName; /* Name of proteome database for this genome. */
#define MAX_CONTROL_COLUMNS 6
#define LOW 1
#define MEDIUM 2
#define BRIGHT 3
#define MAXCHAINS 50000000
boolean hgDebug = FALSE; /* Activate debugging code. Set to true by hgDebug=on in command line*/
int imagePixelHeight = 0;
struct hash *oldVars = NULL;
struct jsonElement *jsonForClient = NULL;
boolean hideControls = FALSE; /* Hide all controls? */
boolean trackImgOnly = FALSE; /* caller wants just the track image and track table html */
boolean ideogramToo = FALSE; /* caller wants the ideoGram (when requesting just one track) */
-/* Structure returned from findGenomePos.
+/* Structure returned from resolvePosition.
* We use this to to expand any tracks to full
* that were found to contain the searched-upon
* position string */
struct hgPositions *hgp = NULL;
/* Other global variables. */
struct group *groupList = NULL; /* List of all tracks. */
char *browserName; /* Test, preview, or public browser */
char *organization; /* UCSC */
struct hash *trackHash = NULL; /* Hash of the tracks by their name. */
#ifdef DEBUG
void uglySnoopTrackList(int depth, struct track *trackList)
/* Print out some info on track list. */
@@ -8910,37 +8910,30 @@
"<A HREF=\"hgTracks?hgTracksConfigPage=configure\">image configuration menu</A>.");
printf("<LI>In the image configuration menu, change the size of the image,\n"
"to make it look more square.\n");
printf("</UL>\n");
printf("</div>\n");
}
else
printf("<BR><BR>PDF format not available");
printf("<a href='%s?%s=%s'><input type='button' VALUE='Return to Browser'></a>\n",
hgTracksName(), cartSessionVarName(), cartSessionId(cart));
}
-boolean isGenome(char *pos)
-/* Return TRUE if pos is genome. */
-{
-pos = trimSpaces(pos);
-return(sameWord(pos, "genome") || sameWord(pos, "hgBatch"));
-}
-
void setRulerMode()
/* Set the rulerMode variable from cart. */
{
char *s = cartUsualString(cart, RULER_TRACK_NAME, "dense");
if (sameWord(s, "full") || sameWord(s, "on"))
rulerMode = tvFull;
else if (sameWord(s, "dense"))
rulerMode = tvDense;
else
rulerMode = tvHide;
}
void setLayoutGlobals()
/* Figure out basic dimensions of display. */
{
@@ -8954,39 +8947,69 @@
withNextExonArrows = cartUsualBoolean(cart, "nextExonArrows", TRUE);
}
withExonNumbers = cartUsualBoolean(cart, "exonNumbers", TRUE);
emAltHighlight = cartUsualBoolean(cart, "emAltHighlight", FALSE);
if (!hIsGsidServer())
{
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
}
emPadding = cartUsualInt(cart, "emPadding", emPadding);
gmPadding = cartUsualInt(cart, "gmPadding", gmPadding);
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
fullInsideX = trackOffsetX();
fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX;
}
+static boolean resolvePosition(char **pPosition)
+/* Position may be an already-resolved chr:start-end, or a search term.
+ * If it is a search term:
+ * 1 match ==> set globals chromName, winStart, winEnd, return TRUE.
+ * 0 matches ==> switch back to lastPosition, hopefully get 1 match from that;
+ * set globals chromName, winStart, winEnd, return TRUE. If no lastPosition, try w/hDefaultPos().
+ * multiple matches ==> Display a page with links to match positions, return FALSE. */
+{
+boolean resolved = TRUE;
+struct dyString *dyWarn = dyStringNew(0);
+hgp = hgFindSearch(cart, pPosition, &chromName, &winStart, &winEnd, hgTracksName(), dyWarn);
+if (isNotEmpty(dyWarn->string))
+ warn("%s", dyWarn->string);
+if (hgp->singlePos)
+ {
+ createHgFindMatchHash();
+ }
+else
+ {
+ char *menuStr = menuBar(cart, database);
+ if (menuStr)
+ puts(menuStr);
+ hgPositionsHtml(database, hgp, hgTracksName(), cart);
+ resolved = FALSE;
+ }
+cartSetString(cart, "position", *pPosition);
+return resolved;
+}
+
void parseVirtPosition(char *position)
/* parse virtual position
* TODO this is just temporary */
{
if (!position)
{
errAbort("position NULL");
}
char *vPos = cloneString(position);
+stripChar(vPos, ',');
char *colon = strchr(vPos, ':');
if (!colon)
errAbort("position has no colon");
char *dash = strchr(vPos, '-');
if (!dash)
errAbort("position has no dash");
*colon = 0;
*dash = 0;
virtWinStart = atol(colon+1) - 1;
virtWinEnd = atol(dash+1);
}
void parseNonVirtPosition(char *position)
/* parse non-virtual position */
{
@@ -9064,94 +9087,63 @@
cartSetString(cart, "highlight", cartVar);
}
else
{
// erase the highlight cartvar if it has no overlap with the new virt chrom
cartRemove(cart, "highlight");
}
}
}
void tracksDisplay()
/* Put up main tracks display. This routine handles zooming and
* scrolling. */
{
-char *defaultPosition = hDefaultPos(database);
char titleVar[256];
char *oldPosition = cartUsualString(cart, "oldPosition", "");
boolean findNearest = cartUsualBoolean(cart, "findNearest", FALSE);
cartRemove(cart, "findNearest");
boolean positionIsVirt = FALSE;
position = getPositionFromCustomTracks();
if (NULL == position)
{
position = cartGetPosition(cart, database, &lastDbPosCart);
if (sameOk(cgiOptionalString("position"), "lastDbPos"))
{
restoreSavedVirtPosition();
}
if (startsWith("virt:", position))
{
position = stripCommas(position); // sometimes the position string arrives with commas in it.
positionIsVirt = TRUE;
}
}
if (sameString(position, ""))
{
hUserAbort("Please go back and enter a coordinate range or a search term in the \"search term\" field.<br>For example: chr22:20100000-20200000.\n");
}
if (!positionIsVirt)
{
- chromName = NULL;
- winStart = 0;
- if (isGenome(position) || NULL ==
- (hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart)))
- {
- if (winStart == 0) /* number of positions found */
- {
- freeMem(position);
- position = cloneString(cartUsualString(cart, "lastPosition", defaultPosition));
- hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd,cart);
- if (hgp != NULL && differentString(position, defaultPosition))
- cartSetString(cart, "position", position);
- }
- }
-
- /* After position is found set up hash of matches that should
- be drawn with names highlighted for easy identification. */
- createHgFindMatchHash();
-
- /* This means that no single result was found
- I.e., multiple results may have been found and are printed out prior to this code*/
- if (NULL == chromName)
- {
- // In case user manually edits the browser location as described in #13009,
- // revert the position. If they instead choose from the list as we expect,
- // that will set the position to their choice.
- // lastPosition gets set in cart.c
- char *lastPosition = cartUsualString(cart, "lastPosition", hDefaultPos(database));
- cartSetString(cart, "position", lastPosition);
+ if (! resolvePosition(&position))
return;
}
- }
-
virtMode = cartUsualBoolean(cart, "virtMode", FALSE);
/* Figure out basic dimensions of display. This
* needs to be done early for the sake of the
* zooming and dinking routines. */
setLayoutGlobals();
virtModeType = cartUsualString(cart, "virtModeType", virtModeType);
if (positionIsVirt && virtualSingleChrom())
{
// we need chromName to be set before initRegionList() gets called.
position = cartUsualString(cart, "nonVirtPosition", "");
if (!sameString(position,""))
parseNonVirtPosition(position);
@@ -9185,32 +9177,31 @@
if (nvh)
cartSetString(cart, "highlight", nvh);
if (!sameString(position,""))
parseNonVirtPosition(position);
}
if (initRegionList()) // initialize the region list, sets virtModeExtraState
{
break;
}
else
{ // virt mode failed, forced to return to default
virtModeType = "default";
cartSetString(cart, "virtModeType", virtModeType);
position = cloneString(hDefaultPos(database));
- hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart);
- cartSetString(cart, "position", position);
+ resolvePosition(&position);
positionIsVirt=FALSE;
virtMode=FALSE;
}
}
// PAD padding of exon regions is now being done inside the fetch/merge.
//if (emPadding > 0)
//padVirtRegions(emPadding); // this old routine does not handle multiple chroms yet
//testRegionList(); // check if it is ascending non-overlapping regions. (this is not the case with custom user-defined-regions)
makeVirtChrom();
//testVirtChromBinarySearch();
@@ -10243,31 +10234,31 @@
configPageSetTrackVis(-2);
}
else
{
tracksDisplay();
}
if (cartVarExists(cart, "hgt.convertChromToVirtChrom"))
{
cartRemove(cart, "hgt.convertChromToVirtChrom");
return;
}
jsonObjectAdd(jsonForClient, "measureTiming", newJsonBoolean(measureTiming));
// js code needs to know if a highlightRegion is defined for this db
-checkAddHighlight(); // call again in case tracksDisplay's call to findGenomePos changed vars
+checkAddHighlight(); // call again in case tracksDisplay's call to resolvePosition changed vars
char *highlightDef = cartOptionalString(cart, "highlight");
if (highlightDef && startsWith(database,highlightDef) && highlightDef[strlen(database)] == '.')
jsonObjectAdd(jsonForClient, "highlight", newJsonString(highlightDef));
jsonObjectAdd(jsonForClient, "enableHighlightingDialog",
newJsonBoolean(cartUsualBoolean(cart, "enableHighlightingDialog", TRUE)));
struct dyString *dy = dyStringNew(1024);
jsonDyStringPrint(dy, (struct jsonElement *) jsonForClient, "hgTracks", 0);
jsInline(dy->string);
dyStringFree(&dy);
if (measureTiming)
measureTime("Time at end of doMiddle, next up cart write");
if (cartOptionalString(cart, "udcTimeout"))