049e50b2293ce5e9102eef9177a7cb88b49d7a10 chmalee Wed Mar 4 14:14:03 2026 -0800 Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126 diff --git src/hg/inc/hgFind.h src/hg/inc/hgFind.h index e25cab9a6e2..74817ab4a2f 100644 --- src/hg/inc/hgFind.h +++ src/hg/inc/hgFind.h @@ -1,171 +1,177 @@ /* 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; }; boolean matchesHgvs(struct cart *cart, char *db, char *term, struct hgPositions *hgp, boolean measureTiming); /* Return TRUE if the search term looks like a variant encoded using the HGVS nomenclature * See http://varnomen.hgvs.org/ * If search term is a pseudo hgvs term like GeneName AminoAcidPosition (RUNX2 Arg155) and * matches more than one transcript, fill out the hgp with the potential matches so the user * can choose where to go, otherwise return a singlePos */ void fixSinglePos(struct hgPositions *hgp); /* Fill in posCount and if proper singlePos fields of hgp * by going through tables... */ +boolean parseAndResolvePosition(char **inpPos, char *db, struct hgPositions *inpHgPos, + int *relStart, int *relEnd, boolean *relativeFlag, boolean *singleBaseSpec); +/* If inpPos is a valid chromosome position string for db, fill out the associated + * hgPos, relative start and stop, and return TRUE. Otherwise return FALSE so our regular + * search code can deal with item name */ + 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, 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 */ 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 */