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/inc/hgFind.h src/hg/inc/hgFind.h
index dfea4dd..f932597 100644
--- src/hg/inc/hgFind.h
+++ src/hg/inc/hgFind.h
@@ -1,88 +1,82 @@
/* hgFind.h - Find things in human genome annotations. */
/* Copyright (C) 2010 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#ifndef HGFIND_H
#define HGFIND_H
#ifndef CART_H
#include "cart.h"
#endif
#ifndef HGFINDSPEC_H
#include "hgFindSpec.h"
#endif
struct hgPositions *hgPositionsFind(char *db, char *query, char *extraCgi,
char *hgAppName, struct cart *cart, boolean multiTerm);
-/* Return table of positions that match query or NULL if none such. */
-
-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. */
-
-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. */
+/* Return container of tracks and positions (if any) that match term. */
+
+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. */
+
+void hgPositionsHtml(char *db, struct hgPositions *hgp, char *hgAppName, struct cart *cart);
+/* Write multiple search results as HTML. */
struct hgPositions
/* A bunch of positions in genome. */
{
struct hgPositions *next; /* Next in list. */
char *query; /* Query string that led to positions. */
char *database; /* Name of database. Not allocated here. */
struct hgPosTable *tableList; /* List of tables. */
int posCount; /* Number of positions in all tables. */
struct hgPos *singlePos; /* If resolves to a single position, reference to that here. */
char *extraCgi; /* Extra info to embed in CGI requests to browser. */
boolean useAlias; /* Set if an alias is used */
};
struct hgPosTable
/* A collection of position lists, one for each type of position. */
{
struct hgPosTable *next; /* Next table in list. */
char *name; /* Name of table. Not allocated here. */
char *description; /* Table description. No allocated here */
struct hgPos *posList; /* List of positions in this table. */
void (*htmlStart)(struct hgPosTable *table, FILE *f); /* Print preamble to positions. */
void (*htmlOnePos)(struct hgPosTable *table, struct hgPos *pos, FILE *f); /* Print one position. */
void (*htmlEnd)(struct hgPosTable *table, FILE *f); /* Print end. */
};
struct hgPos
/* A list of positions. */
{
struct hgPos *next; /* Next in list. */
char *chrom; /* Chromosome. Not allocated here. */
int chromStart; /* Start position in chromosome. */
int chromEnd; /* End position in chromosome. */
char *name; /* Name of position - one word. */
char *description; /* Position description - a sentence or so. */
char *browserName; /* name as in hgTracks tg->itemName(). */
bool canonical; /* The gene is the canonical version. */
struct tsrPos *tp; /* The trix search associated with the gene. */
char *highlight; /* If non-empty, new value for highlight cart variable */
};
void hgPositionsHelpHtml(char *organism, char *database);
/* Display contents of dbDb.htmlPath for database, or print an HTML comment
* explaining what's missing. */
char *hCarefulTrackOpenVis(char *db, char *trackName);
/* If track is already in full mode, return full; otherwise, return
* hTrackOpenVis. */
#endif /* HGFIND_H */