c6ce277e36a537437a04146c8fa7adebb40428ff chmalee Wed May 15 12:10:42 2024 -0700 Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731 diff --git src/hg/inc/hgFind.h src/hg/inc/hgFind.h index ab5072a..20ed351 100644 --- src/hg/inc/hgFind.h +++ src/hg/inc/hgFind.h @@ -1,158 +1,160 @@ /* hgFind.h - Find things in human genome annotations. */ /* Copyright (C) 2010 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ 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 /* 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 */ boolean shortCircuited; /* Is this a result of a short circuit? */ }; 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. */ long searchTime; /* How long did this search take */ }; 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 */ }; struct searchCategory /* struct searchCategory: a model for the category/filter selection in the UI */ { struct searchCategory *next; char *id; // The id in the tree of the hgFindSpec to query, should be a valid hgFindSpec or trix name char *name; // the label in the tree hfs to query char *searchString; struct trix *trix; // the associated trix file if any char *label; // the label for this search, probably from hgFindSpec/trackDb char *description; // the description for this search, probably from hgFindSpec/trackDb char visibility; // whether this track is currently on char *groupName; // the group name this track belongs to if it's a track float priority; // the priority level from trackDb, used for sorting later struct slName *parents; // the parents of this track in order from nearest to furthest struct slName *errors; // Any error messages we received trying to construct the filter struct trackDb *tdb; // Save the trackDb here for easier conversion back to a trackDb list }; /* struct searchableTrack: essentially a few fields from a struct trackDb that we need to form the * searchCategory */ struct searchableTrack { struct searchableTrack *next; char *track; char *shortLabel; char *longLabel; char *description; unsigned char visibility; float priority; char *grp; }; struct hgPositions *hgPositionsFind(char *db, char *query, char *extraCgi, char *hgAppName, struct cart *cart, boolean multiTerm, boolean measureTiming, struct searchCategory *categories); /* 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); + char *hgAppName, struct dyString *dyWarn, struct searchCategory *categories); /* 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. */ void hgPosFree(struct hgPos **pEl); /* Free up hgPos. */ void searchCategoryFree(struct searchCategory **el); /* Free a searchCategory */ #define hgFixedTrix "/gbdb/hgFixed/search/" #define publicHubsTrix "hubSearchTextRows" #define helpDocsTrix "searchableDocs" int cmpCategories(const void *a, const void *b); /* Compare two categories for uniquifying */ struct trix *openStaticTrix(char *trixName); /* Open up a trix file in hgFixed */ -/* Caches used by various searching routines */ -extern struct hash *hgFindTrackHash; -extern struct hash *hgFindGroupHash; struct searchCategory *makeCategory(struct cart *cart, char *categName, struct searchableTrack *searchTrack, char *db, struct hash *groupHash); /* Make a single searchCategory, unless the requested categName is a container * track or track group (for example all phenotype tracks), in which case we make * categories for each subtrack */ struct searchCategory *getCategsForNonDb(struct cart *cart, char *db, struct hash *groupHash); /* Return the default categories for all databases */ struct searchCategory *getCategsForDatabase(struct cart *cart, char *db, struct hash *groupHash); /* Get the default categories to search if user has not selected any before. * By default we search for gene loci (knownGene), track names, and track items */ struct searchCategory *getAllCategories(struct cart *cart, char *db, struct hash *groupHash); /* If we have saved categories for this database from the last search, return those, * otherwise return the default selection */ void hgPositionsHelpHtmlCart(struct cart *cart, char *organism, char *database); /* Display contents of dbDb.htmlPath for database, or print an HTML comment * explaining what's missing. */ #define hgPositionsHelpHtml(o, d) hgPositionsHelpHtmlCart(cart, o, d) char *hCarefulTrackOpenVisCart(struct cart *cart, char *db, char *trackName); /* If track is already in full mode, return full; otherwise, return * hTrackOpenVis. */ #define hCarefulTrackOpenVis(d, t) hCarefulTrackOpenVisCart(cart, d, t) char *addHighlight(char *db, char *chrom, unsigned start, unsigned end); /* Return a string that can be assigned to the cart var addHighlight, to add a yellow highlight * at db.chrom:start+1-end for search results. */ +void hashTracksAndGroups(struct cart *cart, char *db); +/* get the list of tracks available for this assembly, along with their group names + * and visibility-ness. Note that this implicitly makes connected hubs show up + * in the trackList struct, which means we get item search for connected + * hubs for free */ #endif /* HGFIND_H */