748b06ac95ff2a3957be3845bd3594984e3cc3cf chmalee Wed Aug 17 19:21:48 2022 -0700 Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind diff --git src/hg/hubApi/dataApi.h src/hg/hubApi/dataApi.h index 6077f3e..27bb057 100644 --- src/hg/hubApi/dataApi.h +++ src/hg/hubApi/dataApi.h @@ -1,241 +1,250 @@ /* dataApi.h - functions for API access to UCSC data resources */ #ifndef DATAAPH_H #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "hui.h" #include "udc.h" #include "knetUdc.h" #include "genbank.h" #include "trackHub.h" #include "hgConfig.h" #include "hCommon.h" #include "hPrint.h" #include "bigWig.h" #include "hubConnect.h" #include "obscure.h" #include "errCatch.h" #include "vcf.h" #include "bedTabix.h" #include "bamFile.h" #include "jsonParse.h" #include "jsonWrite.h" #include "chromInfo.h" #include "wiggle.h" #include "hubPublic.h" #ifdef USE_HAL #include "halBlockViz.h" #endif /* reference for these error codes: * https://www.restapitutorial.com/httpstatuscodes.html */ /* error return codes */ #define err206 206 #define err206Msg "Partial Content" #define err301 301 #define err301Msg "Moved Permanently" #define err400 400 #define err400Msg "Bad Request" #define err403 403 #define err403Msg "Forbidden" #define err404 404 #define err404Msg "Not Found" #define err415 415 #define err415Msg "Unsupported track type" #define err429 429 #define err429Msg "Too Many Requests" #define err500 500 #define err500Msg "Internal Server Error" /* list of all potential arguments */ #define argHubUrl "hubUrl" #define argGenome "genome" #define argTrackLeavesOnly "trackLeavesOnly" #define argTrack "track" #define argChrom "chrom" #define argStart "start" #define argEnd "end" #define argMaxItemsOutput "maxItemsOutput" #define argJsonOutputArrays "jsonOutputArrays" +#define argCategories "categories" +#define argSearchTerm "search" /* valid argument listings to verify extraneous arguments * initialized in hubApi.c */ extern char *argListPublicHubs[]; extern char *argListUcscGenomes[]; extern char *argListHubGenomes[]; extern char *argListTracks[]; extern char *argListChromosomes[]; extern char *argListSchema[]; extern char *argGetDataTrack[]; extern char *argGetDataSequence[]; +extern char *argSearch[]; /* maximum number of words expected in PATH_INFO parsing * so far only using 2 */ #define MAX_PATH_INFO 32 /* maximum amount of DNA allowed in a get sequence request */ #define MAX_DNA_LENGTH 499999999 /* this size is directly related to the max limit in needMem used in * jsonWriteString */ extern long enteredMainTime; /* will become = clock1000() on entry */ /* limit amount of output to a maximum to avoid overload */ extern int maxItemsOutput; /* can be set in URL maxItemsOutput=N */ extern long long itemsReturned; /* for getData functions, number of items returned */ extern boolean reachedMaxItems; /* during getData, signal to return */ /* downloadUrl for use in error exits when reachedMaxItems */ extern struct dyString *downloadUrl; /* supportedTypes will be initialized to a known supported set */ extern struct slName *supportedTypes; /* for debugging purpose, current bot delay value */ extern int botDelay; extern boolean debug; /* can be set in URL debug=1, to turn off: debug=0 */ /* default is to list all trackDb entries, composite containers too. * This option will limit to only the actual track entries with data */ extern boolean trackLeavesOnly; /* set by CGI parameter 'trackLeavesOnly' */ /* this selects output type 'arrays', where the default type is: objects */ extern boolean jsonOutputArrays; /* set by CGI parameter 'jsonOutputArrays' */ extern boolean measureTiming; /* set by CGI parameters */ /* functions in hubApi.c */ struct hubPublic *hubPublicDbLoadAll(); struct dbDb *ucscDbDb(); /* return the dbDb table as an slList */ char *verifyLegalArgs(char *validArgList[]); /* validArgList is an array of strings for valid arguments * returning string of any other arguments not on that list found in * cgiVarList(), NULL when none found. */ /* ######################################################################### */ /* functions in apiUtils.c */ void startProcessTiming(); /* for measureTiming, beginning processing */ void apiFinishOutput(int errorCode, char *errorString, struct jsonWrite *jw); /* finish json output, potential output an error code other than 200 */ void apiErrAbort(int errorCode, char *errString, char *format, ...); /* Issue an error message in json format, and exit(0) */ struct jsonWrite *apiStartOutput(); /* begin json output with standard header information for all requests */ extern char *jsonTypeStrings[]; #define JSON_STRING 0 // "string", /* type 0 */ #define JSON_NUMBER 1 // "number", /* type 1 */ #define JSON_OBJECT 2 // "object", /* type 2 */ #define JSON_ARRAY 3 // "array", /* type 3 */ #define JSON_BOOLEAN 4 // "boolean", /* type 4 */ #define JSON_NULL 5 // "null" /* type 5 */ #define JSON_DOUBLE 6 // UCSC json type double /* type 6 */ int autoSqlToJsonType(char *asType); /* convert an autoSql field type to a Json type */ int tableColumns(struct sqlConnection *conn, char *table, char ***nameReturn, char ***typeReturn, int **jsonTypes); /* return the column names, the MySQL data type, and json data type * for the given table return number of columns (aka 'fields') */ struct trackHub *errCatchTrackHubOpen(char *hubUrl); /* use errCatch around a trackHub open in case it fails */ struct trackDb *obtainTdb(struct trackHubGenome *genome, char *db); /* return a full trackDb fiven the hub genome pointer, or ucsc database name */ struct trackDb *findTrackDb(char *track, struct trackDb *tdb); /* search tdb structure for specific track, recursion on subtracks */ struct bbiFile *bigFileOpen(char *trackType, char *bigDataUrl); /* open bigDataUrl for correct trackType and error catch if failure */ int chromInfoCmp(const void *va, const void *vb); /* Compare to sort based on size */ boolean allowedBigBedType(char *type); /* return TRUE if the big* type is to be supported * add to this list as the big* supported types are expanded */ /* temporarily from table browser until proven works, then move to library */ struct asObject *asForTable(struct sqlConnection *conn, char *table, struct trackDb *tdb); /* Get autoSQL description if any associated with table. */ /* Wrap some error catching around asForTable. */ struct trackHubGenome *findHubGenome(struct trackHub *hub, char *genome, char *endpoint, char *hubUrl); /* given open 'hub', find the specified 'genome' called from 'endpoint' */ struct dbDb *ucscDbDb(); /* return the dbDb table as an slList */ boolean isSupportedType(char *type); /* is given type in the supportedTypes list ? */ void wigColumnTypes(struct jsonWrite *jw); /* output column headers for a wiggle data output schema */ void outputSchema(struct trackDb *tdb, struct jsonWrite *jw, char *columnNames[], char *columnTypes[], int jsonTypes[], struct hTableInfo *hti, int columnCount, int asColumnCount, struct asColumn *columnEl); /* print out the SQL schema for this trackDb */ void bigColumnTypes(struct jsonWrite *jw, struct sqlFieldType *fiList, struct asObject *as); /* show the column types from a big file autoSql definitions */ boolean trackHasData(struct trackDb *tdb); /* check if this is actually a data track: * TRUE when has data, FALSE if has no data * When NO trackDb, can't tell at this point, will check that later */ #define trackHasNoData(tdb) (!trackHasData(tdb)) boolean protectedTrack(struct trackDb *tdb, char *trackName); /* determine if track is off-limits protected data */ boolean isWiggleDataTable(char *type); /* is this a wiggle data track table */ /* ######################################################################### */ /* functions in getData.c */ void apiGetData(char *words[MAX_PATH_INFO]); /* 'getData' function, words[1] is the subCommand */ /* ######################################################################### */ /* functions in list.c */ void apiList(char *words[MAX_PATH_INFO]); /* 'list' function words[1] is the subCommand */ +/* ######################################################################### */ +/* functions in search.c */ + +void apiSearch(char *words[MAX_PATH_INFO]); +/* search function */ + #endif /* DATAAPH_H */