774479fda06428280150d609bdf4052f5f35d571 hiram Wed Feb 13 14:17:16 2019 -0800 list functions moved to list.c refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index cb478e5..850fb5f 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,161 +1,101 @@ /* hubApi - access mechanism to hub data resources. */ #include "dataApi.h" -#ifdef NOT -#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" - -#ifdef USE_HAL -#include "halBlockViz.h" -#endif - -#endif /* +------------------+------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +------------------+------------------+------+-----+---------+-------+ | hubUrl | longblob | NO | PRI | NULL | | | shortLabel | varchar(255) | NO | | NULL | | | longLabel | varchar(255) | NO | | NULL | | | registrationTime | varchar(255) | NO | | NULL | | | dbCount | int(10) unsigned | NO | | NULL | | | dbList | blob | YES | | NULL | | | descriptionUrl | longblob | YES | | NULL | | +------------------+------------------+------+-----+---------+-------+ */ +#ifdef NOT +/*this definition should be over in hg/inc/hubPublic.h but that does not exist*/ struct hubPublic /* Table of public track data hub connections. */ { struct hubPublic *next; /* Next in singly linked list. */ char *hubUrl; /* URL to hub.ra file */ char *shortLabel; /* Hub short label. */ char *longLabel; /* Hub long label. */ char *registrationTime; /* Time first registered */ unsigned dbCount; /* Number of databases hub has data for. */ char *dbList; /* Comma separated list of databases. */ char *descriptionUrl; /* URL to description HTML */ }; +#endif /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static struct hash *trackCounter = NULL; static long totalTracks = 0; static boolean measureTiming = FALSE; /* set by CGI parameters */ static boolean allTrackSettings = FALSE; /* checkbox setting */ static char **shortLabels = NULL; /* public hub short labels in array */ // struct hubPublic *publicHubList = NULL; static int publicHubCount = 0; static char *defaultHub = "Plants"; static char *defaultDb = "ce11"; static long enteredMainTime = 0; /* will become = clock1000() on entry */ /* to allow calculation of when to bail out, taking too long */ static long timeOutSeconds = 100; static boolean timedOut = FALSE; #ifdef NOT -/* ######################################################################### */ -static struct jsonWrite *jsonStartOutput() -/* begin json output with standard header information for all requests */ -{ -time_t timeNow = time(NULL); -// struct tm tm; -// gmtime_r(&timeNow, &tm); -struct jsonWrite *jw = jsonWriteNew(); -jsonWriteObjectStart(jw, NULL); -jsonWriteString(jw, "apiVersion", "0.1"); -jsonWriteString(jw, "source", "UCSantaCruz"); -jsonWriteDateFromUnix(jw, "downloadTime", (long long) timeNow); -jsonWriteNumber(jw, "downloadTimeStamp", (long long) timeNow); -return jw; -} - -static void jsonErrAbort(char *format, ...) -/* Issue an error message in json format, and exit(0) */ -{ -char errMsg[2048]; -va_list args; -va_start(args, format); -vsnprintf(errMsg, sizeof(errMsg), format, args); -struct jsonWrite *jw = jsonStartOutput(); -jsonWriteString(jw, "error", errMsg); -jsonWriteObjectEnd(jw); -fputs(jw->dy->string,stdout); -exit(0); -} -#endif - static void hubPublicJsonData(struct jsonWrite *jw, struct hubPublic *el) /* Print array data for one row from hubPublic table, order here * must be same as was stated in the columnName header element * TODO: need to figure out how to use the order of the columns as * they are in the 'desc' request */ { jsonWriteListStart(jw, NULL); jsonWriteString(jw, NULL, el->hubUrl); jsonWriteString(jw, NULL, el->shortLabel); jsonWriteString(jw, NULL, el->longLabel); jsonWriteString(jw, NULL, el->registrationTime); jsonWriteNumber(jw, NULL, (long long)el->dbCount); jsonWriteString(jw, NULL, el->dbList); jsonWriteString(jw, NULL, el->descriptionUrl); jsonWriteListEnd(jw); } -int trackDbTrackCmp(const void *va, const void *vb) +static int trackDbTrackCmp(const void *va, const void *vb) /* Compare to sort based on 'track' name; use shortLabel as secondary sort key. * Note: parallel code to hgTracks.c:tgCmpPriority */ { const struct trackDb *a = *((struct trackDb **)va); const struct trackDb *b = *((struct trackDb **)vb); int dif = strcmp(a->track, b->track); if (dif < 0) return -1; else if (dif == 0.0) return strcasecmp(a->shortLabel, b->shortLabel); else return 1; } +#endif + static int publicHubCmpCase(const void *va, const void *vb) /* Compare two slNames, ignore case. */ { const struct hubPublic *a = *((struct hubPublic **)va); const struct hubPublic *b = *((struct hubPublic **)vb); return strcasecmp(a->shortLabel, b->shortLabel); } static void publicHubSortCase(struct hubPublic **pList) /* Sort slName list, ignore case. */ { slSort(pList, publicHubCmpCase); } static struct hubPublic *hubPublicLoad(char **row) @@ -166,31 +106,31 @@ AllocVar(ret); ret->hubUrl = cloneString(row[0]); ret->shortLabel = cloneString(row[1]); ret->longLabel = cloneString(row[2]); ret->registrationTime = cloneString(row[3]); ret->dbCount = sqlUnsigned(row[4]); ret->dbList = cloneString(row[5]); // if (row[6]) ret->descriptionUrl = cloneString(row[6]); // else // ret->descriptionUrl = cloneString(""); return ret; } -static struct hubPublic *hubPublicLoadAll() +struct hubPublic *hubPublicLoadAll() { char query[1024]; struct hubPublic *list = NULL; struct sqlConnection *conn = hConnectCentral(); sqlSafef(query, sizeof(query), "select * from %s", hubPublicTableName()); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct hubPublic *el = hubPublicLoad(row); slAddHead(&list, el); } sqlFreeResult(&sr); hDisconnectCentral(&conn); publicHubSortCase(&list); @@ -446,31 +386,31 @@ { hPrintf(" <li>%s : %s</li>\n", hel->name, (char *)hel->val); if (sameWord("trackDb", hel->name)) /* examine the trackDb structure */ { struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome); retTbd = tdb; hubTrackList(tdb, genome); } if (timeOutReached()) break; } hPrintf(" </ul>\n"); return retTbd; } -static struct slName *genomeList(struct trackHub *hubTop, struct trackDb **dbTrackList, char *selectGenome) +struct slName *genomeList(struct trackHub *hubTop, struct trackDb **dbTrackList, char *selectGenome) /* follow the pointers from the trackHub to trackHubGenome and around * in a circle from one to the other to find all hub resources * return slName list of the genomes in this track hub * optionally, return the trackList from this hub for the specified genome */ { struct slName *retList = NULL; long totalAssemblyCount = 0; struct trackHubGenome *genome = hubTop->genomeList; hPrintf("<h4>genome sequences (and tracks) present in this track hub</h4>\n"); hPrintf("<ul>\n"); long lastTime = clock1000(); for ( ; genome; genome = genome->next ) @@ -526,55 +466,57 @@ * and then get the shortLabel */ { char hubUrl[1024]; char query[1024]; struct sqlConnection *conn = hConnectCentral(); // Build a query to select the hubUrl for the given shortLabel sqlSafef(query, sizeof(query), "select hubUrl from %s where shortLabel='%s'", hubPublicTableName(), shortLabel); if (! sqlQuickQuery(conn, query, hubUrl, sizeof(hubUrl))) hubUrl[0] = 0; hDisconnectCentral(&conn); return cloneString(hubUrl); } +#ifdef NOT static void dbDbJsonData(struct jsonWrite *jw, struct dbDb *el) /* Print out dbDb table element in JSON format. * must be same as was stated in the columnName header element * TODO: need to figure out how to use the order of the columns as * they are in the 'desc' request */ { jsonWriteListStart(jw, NULL); jsonWriteString(jw, NULL, el->name); jsonWriteString(jw, NULL, el->description); jsonWriteString(jw, NULL, el->nibPath); jsonWriteString(jw, NULL, el->organism); jsonWriteString(jw, NULL, el->defaultPos); jsonWriteNumber(jw, NULL, (long long)el->active); jsonWriteNumber(jw, NULL, (long long)el->orderKey); jsonWriteString(jw, NULL, el->genome); jsonWriteString(jw, NULL, el->scientificName); jsonWriteString(jw, NULL, el->htmlPath); jsonWriteNumber(jw, NULL, (long long)el->hgNearOk); jsonWriteNumber(jw, NULL, (long long)el->hgPbOk); jsonWriteString(jw, NULL, el->sourceName); jsonWriteNumber(jw, NULL, (long long)el->taxId); jsonWriteListEnd(jw); } + static boolean tableColumns(struct jsonWrite *jw, char *table) /* output the column names for the given table * return: TRUE on error, FALSE on success */ { jsonWriteListStart(jw, "columnNames"); char query[1024]; struct sqlConnection *conn = hConnectCentral(); sqlSafef(query, sizeof(query), "desc %s", table); struct sqlResult *sr = sqlGetResult(conn, query); char **row; row = sqlNextRow(sr); if (NULL == row) { jsonErrAbort("ERROR: can not 'desc' table '%s'", table); @@ -600,59 +542,61 @@ struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteString(jw, "tableName", hubPublicTableName()); tableColumns(jw, hubPublicTableName()); jsonWriteListStart(jw, "publicHubData"); for ( ; el != NULL; el = el->next ) { hubPublicJsonData(jw, el); } jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } +#endif static int dbDbCmpName(const void *va, const void *vb) /* Compare two dbDb elements: name, ignore case. */ { const struct dbDb *a = *((struct dbDb **)va); const struct dbDb *b = *((struct dbDb **)vb); return strcasecmp(a->name, b->name); } -static struct dbDb *ucscDbDb() +struct dbDb *ucscDbDb() /* return the dbDb table as an slList */ { char query[1024]; struct sqlConnection *conn = hConnectCentral(); sqlSafef(query, sizeof(query), "select * from dbDb"); struct dbDb *dbList = NULL, *el = NULL; struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { el = dbDbLoad(row); slAddHead(&dbList, el); } sqlFreeResult(&sr); hDisconnectCentral(&conn); slSort(&dbList, dbDbCmpName); return dbList; } +#ifdef NOT static void jsonDbDb() /* output the dbDb SQL table */ { struct sqlConnection *conn = hConnectCentral(); char *dataTime = sqlTableUpdate(conn, "dbDb"); hDisconnectCentral(&conn); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); struct dbDb *dbList = ucscDbDb(); struct dbDb *el; struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteString(jw, "tableName", "dbDb"); @@ -771,92 +715,30 @@ char *dataTime = sqlTableUpdate(conn, "trackDb"); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); hFreeConn(&conn); struct trackDb *tdbList = hTrackDb(db); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "db", db); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); recursiveTrackList(jw, tdbList, "tracks"); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } /* static void trackDbJsonOutput(char *db, FILE *f) */ -#ifdef NOT -static void getTrackData() -{ -} - -static void getSequenceData() -/* given at least a db=name and chrom=chr, optionally start and end */ -{ -char *db = cgiOptionalString("db"); -char *chrom = cgiOptionalString("chrom"); -char *start = cgiOptionalString("start"); -char *end = cgiOptionalString("end"); - -if (isEmpty(db)) - jsonErrAbort("missing URL db=<ucscDb> name for endpoint '/getData/sequence"); -if (isEmpty(chrom)) - jsonErrAbort("missing URL chrom=<name> for endpoint '/getData/sequence?db=%s", db); -if (chromSeqFileExists(db, chrom)) - { - struct chromInfo *ci = hGetChromInfo(db, chrom); - struct dnaSeq *seq = NULL; - if (isEmpty(start) || isEmpty(end)) - seq = hChromSeqMixed(db, chrom, 0, 0); - else - seq = hChromSeqMixed(db, chrom, sqlSigned(start), sqlSigned(end)); - if (NULL == seq) - jsonErrAbort("can not find sequence for chrom=%s for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom); - struct jsonWrite *jw = jsonStartOutput(); - jsonWriteString(jw, "db", db); - jsonWriteString(jw, "chrom", chrom); - if (isEmpty(start) || isEmpty(end)) - { - jsonWriteNumber(jw, "start", (long long)0); - jsonWriteNumber(jw, "end", (long long)ci->size); - } - else - { - jsonWriteNumber(jw, "start", (long long)sqlSigned(start)); - jsonWriteNumber(jw, "end", (long long)sqlSigned(end)); - } - jsonWriteString(jw, "dna", seq->dna); - jsonWriteObjectEnd(jw); - fputs(jw->dy->string,stdout); - freeDnaSeq(&seq); - } -else - jsonErrAbort("can not find specified chrom=%s in sequence for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom); -} -#endif - -#define MAX_PATH_INFO 32 -static void apiGetData(char *words[MAX_PATH_INFO]) -/* 'getData' function, words[1] is the subCommand */ -{ -if (sameWord("track", words[1])) - getTrackData(); -else if (sameWord("sequence", words[1])) - getSequenceData(); -else - jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); -} - static void apiList(char *words[MAX_PATH_INFO]) /* 'list' function words[1] is the subCommand */ { if (sameWord("publicHubs", words[1])) jsonPublicHubs(); else if (sameWord("ucscGenomes", words[1])) jsonDbDb(); else if (sameWord("hubGenomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); if (isEmpty(hubUrl)) jsonErrAbort("must supply hubUrl='http:...' some URL to a hub for /list/hubGenomes"); struct trackHub *hub = NULL; struct errCatch *errCatch = errCatchNew(); @@ -925,30 +807,31 @@ char *hubUrl = cgiOptionalString("hubUrl"); // char *genome = cgiOptionalString("genome"); char *db = cgiOptionalString("db"); if (isEmpty(hubUrl) && isEmpty(db)) jsonErrAbort("ERROR: must supply hubUrl or db name to return chromosome list"); if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { chromInfoJsonOutput(stdout, db); return; } } else jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); } +#endif static struct hash *apiFunctionHash = NULL; static void setupFunctionHash() /* initialize the apiFunctionHash */ { if (apiFunctionHash) return; /* already done */ apiFunctionHash = hashNew(0); hashAdd(apiFunctionHash, "list", &apiList); hashAdd(apiFunctionHash, "getData", &apiGetData); } static void apiFunctionSwitch(char *pathInfo)