af3a143571e5aa064eab75c34f9444b35413b562 chmalee Tue Nov 30 15:28:15 2021 -0800 Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results. diff --git src/hg/inc/hgFind.h src/hg/inc/hgFind.h index c433ec4..2352ea9 100644 --- src/hg/inc/hgFind.h +++ src/hg/inc/hgFind.h @@ -1,91 +1,144 @@ /* 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 *hgPositionsFind(char *db, char *query, char *extraCgi, - char *hgAppName, struct cart *cart, boolean multiTerm); -/* 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 */ 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); +/* 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 */ + +struct searchCategory *makeCategory(struct cart *cart, char *categName, struct searchableTrack *searchTrack, char *db, struct hash *trackHash, 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 *trackHash, struct hash *groupHash); +/* Return the default categories for all databases */ + +struct searchCategory *getCategsForDatabase(struct cart *cart, char *db, struct hash *trackHash, 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 *trackHash, 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. */ #endif /* HGFIND_H */