4bb9e8caea515342ba98d3871da76cd4ec69916f chmalee Fri May 1 14:10:00 2026 -0700 Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users diff --git src/hg/hgTables/schema.c src/hg/hgTables/schema.c index cbb2b52c879..5930e7ccd86 100644 --- src/hg/hgTables/schema.c +++ src/hg/hgTables/schema.c @@ -1,833 +1,833 @@ /* schema - display info about database organization. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "memalloc.h" #include "obscure.h" #include "htmshell.h" #include "cheapcgi.h" #include "cart.h" #include "cartTrackDb.h" #include "jksql.h" #include "hdb.h" #include "web.h" #include "trackDb.h" #include "joiner.h" #include "tableDescriptions.h" #include "asParse.h" #include "customTrack.h" #include "bedCart.h" #include "hgMaf.h" #include "hgTables.h" #include "wikiTrack.h" -#include "makeItemsItem.h" +#include "myVariants.h" #include "bedDetail.h" #include "pgSnp.h" #include "barChartBed.h" #include "interact.h" #include "hubConnect.h" #include "trackHub.h" #include "errCatch.h" static char *nbForNothing(char *val) /* substitute for empty strings to keep table formating sane */ { char *s = skipLeadingSpaces(val); if ((s == NULL) || (s[0] == '\0')) return " "; else return val; } static char *abbreviateInPlace(char *val, int len) /* Abbreviate a string to len characters. */ { int vlen = strlen(val); if (vlen > len) strcpy(val+len-3, "..."); return val; } static char *cleanExample(char *val) /* Abbreviate example if necessary and add non-breaking space if need be */ { val = abbreviateInPlace(val, 30); val = nbForNothing(val); return val; } static struct slName *storeRow(struct sqlConnection *conn, char *query) /* Just save the results of a single row query in a string list. */ { struct sqlResult *sr = sqlGetResult(conn, query); char **row; struct slName *list = NULL, *el; int i, colCount = sqlCountColumns(sr); if ((row = sqlNextRow(sr)) != NULL) { for (i=0; i<colCount; ++i) { el = slNameNew(row[i]); slAddTail(&list, el); } } sqlFreeResult(&sr); return list; } void describeFields(char *db, char *table, struct asObject *asObj, struct sqlConnection *conn) /* Print out an HTML table showing table fields and types, and optionally * offering histograms for the text/enum fields. */ { struct sqlResult *sr; char **row; #define TOO_BIG_FOR_HISTO 500000 boolean tooBig = (sqlTableSize(conn, table) > TOO_BIG_FOR_HISTO); char query[256]; struct slName *exampleList, *example; boolean showItemRgb = FALSE; showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName)); // should we expect itemRgb instead of "reserved" sqlSafef(query, sizeof(query), "select * from %s limit 1", table); exampleList = storeRow(conn, query); sqlSafef(query, sizeof(query), "describe %s", table); sr = sqlGetResult(conn, query); hTableStart(); hPrintf("<TR><TH>field</TH>"); if (exampleList != NULL) hPrintf("<TH>example</TH>"); hPrintf("<TH>SQL type</TH> "); if (!tooBig) hPrintf("<TH>info</TH> "); if (asObj != NULL) hPrintf("<TH>description</TH> "); puts("</TR>\n"); example = exampleList; while ((row = sqlNextRow(sr)) != NULL) { if (showItemRgb && (sameWord(row[0],"reserved"))) hPrintf("<TR><TD><TT>itemRgb</TT></TD> "); else hPrintf("<TR><TD><TT>%s</TT></TD> ", row[0]); if (exampleList != NULL) { hPrintf("<TD>"); if (example != NULL) hPrintf("%s", cleanExample(example->name)); else hPrintf("n/a"); hPrintf("</TD>"); } // enums/sets with many items can make for painfully wide rows in the table -- // add spaces between quoted list values: if (stringIn("','", row[1])) { struct dyString *spaced = dyStringSub(row[1], "','", "', '"); hPrintf("<TD><TT>%s</TT></TD>", spaced->string); } else hPrintf("<TD><TT>%s</TT></TD>", row[1]); if (!tooBig) { hPrintf(" <TD>"); if ((isSqlStringType(row[1]) && !sameString(row[1], "longblob")) || isSqlEnumType(row[1]) || isSqlSetType(row[1])) { hPrintf("<A HREF=\"%s", getScriptName()); hPrintf("?%s", cartSidUrlString(cart)); hPrintf("&%s=%s", hgtaDatabase, db); hPrintf("&%s=%s", hgtaHistoTable, table); hPrintf("&%s=%s", hgtaDoValueHistogram, row[0]); hPrintf("\">"); hPrintf("values"); hPrintf("</A>"); } else if (isSqlNumType(row[1])) { hPrintf("<A HREF=\"%s", getScriptName()); hPrintf("?%s", cartSidUrlString(cart)); hPrintf("&%s=%s", hgtaDatabase, db); hPrintf("&%s=%s", hgtaHistoTable, table); hPrintf("&%s=%s", hgtaDoValueRange, row[0]); hPrintf("\">"); hPrintf("range"); hPrintf("</A>"); } else { hPrintf(" "); } hPrintf("</TD>"); } if (asObj != NULL) { struct asColumn *asCol = asColumnFind(asObj, row[0]); hPrintf(" <TD>"); if (asCol != NULL) hPrintf("%s", asCol->comment); else { if (sameString("bin", row[0])) hPrintf("Indexing field to speed chromosome range queries."); else hPrintf(" "); } hPrintf("</TD>"); } puts("</TR>"); if (example != NULL) example = example->next; } hTableEnd(); sqlFreeResult(&sr); } void explainCoordSystem() /* Our coord system is counter-intuitive to users. Warn them in advance to * reduce the frequency with which they find this "bug" on their own and * we have to explain it on the genome list. */ { printf("<BR><I>Note: all start coordinates in our database are 0-based, not \n" "1-based. See explanation \n" "<A HREF=\"http%s://genome.ucsc.edu/FAQ/FAQtracks#tracks1\">" "here</A>.</I>", cgiAppendSForHttps()); } void printTableBrowserLink(struct trackDb *tdb, char* table) /* print link to table browser that opens this table */ { printf("<br>\nTo download this table in different text formats or to intersect or correlate it with other tables, use the " "<a href='hgTables?db=%s&hgta_group=%s&hgta_track=%s&hgta_table=%s'>Table Browser</a>.<br>", database, tdb->grp, tdb->track, table); } static void printSampleRows(int sampleCount, struct sqlConnection *conn, char *table) /* Put up sample values. */ { char query[256]; struct sqlResult *sr; char **row; int i, columnCount = 0; int itemRgbCol = -1; boolean showItemRgb = FALSE; showItemRgb=bedItemRgb(findTdbForTable(database, curTrack, table, ctLookupName)); // should we expect itemRgb instead of "reserved" /* Make table with header row containing name of fields. */ sqlSafef(query, sizeof(query), "describe %s", table); sr = sqlGetResult(conn, query); hTableStart(); hPrintf("<TR>"); while ((row = sqlNextRow(sr)) != NULL) { if (showItemRgb && sameWord(row[0],"reserved")) { hPrintf("<TH>itemRgb</TH>"); itemRgbCol = columnCount; } else hPrintf("<TH>%s</TH>", row[0]); ++columnCount; } hPrintf("</TR>"); sqlFreeResult(&sr); /* Get some sample fields. */ sqlSafef(query, sizeof(query), "select * from %s limit %d", table, sampleCount); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hPrintf("<TR>"); for (i=0; i<columnCount; ++i) { if (showItemRgb && (i == itemRgbCol)) { int rgb = atoi(row[i]); hPrintf("<TD>%d,%d,%d</TD>", (rgb & 0xff0000) >> 16, (rgb & 0xff00) >> 8, (rgb & 0xff)); } else { if (row[i] == NULL) { hPrintf("<TD></TD>"); } else { writeHtmlCell(row[i]); } } } hPrintf("</TR>\n"); } sqlFreeResult(&sr); hTableEnd(); explainCoordSystem(); } static int joinerPairCmpOnAandB (const void *va, const void *vb) /* Compare two joinerPair based on the a and b element of pair. */ { const struct joinerPair *jpA = *((struct joinerPair **)va); const struct joinerPair *jpB = *((struct joinerPair **)vb); struct joinerDtf *a1 = jpA->a; struct joinerDtf *a2 = jpA->b; struct joinerDtf *b1 = jpB->a; struct joinerDtf *b2 = jpB->b; int diff; diff = strcmp(a1->database, b1->database); if (diff == 0) { diff = strcmp(a1->table, b1->table); if (diff == 0) { diff = strcmp(a1->field, b1->field); if (diff == 0) { diff = strcmp(a2->database, b2->database); if (diff == 0) { diff = strcmp(a2->table, b2->table); if (diff == 0) diff = strcmp(a2->field, b2->field); } } } } return diff; } static boolean isViaIndex(struct joinerSet *jsPrimary, struct joinerDtf *dtf) /* Return's TRUE if dtf is part of identifier only by an array index. */ { struct joinerField *jf; struct slRef *chain, *link; struct joinerSet *js; boolean retVal = FALSE; boolean gotRetVal = FALSE; chain = joinerSetInheritanceChain(jsPrimary); for (link = chain; link != NULL; link = link->next) { js = link->val; for (jf = js->fieldList; jf != NULL; jf = jf->next) { if (sameString(jf->table, dtf->table)) if (sameString(jf->field, dtf->field)) if (slNameInList(jf->dbList, dtf->database)) { retVal = jf->indexOf; gotRetVal = TRUE; break; } } if (gotRetVal) break; } slFreeList(&chain); return retVal; } void printTrackHtml(struct trackDb *tdb) /* If trackDb has html for table, print it out in a new section. */ { if (tdb != NULL && isNotEmpty(tdb->html)) { webNewSection("%s (%s) Track Description", tdb->shortLabel, tdb->track); char *browserVersion; if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8') puts(tdb->html); else { // H2 (as in "<H2>Description</H2>") has a big top margin, which adds to // the 10px start-of-web-section <tr> (except for IE < 8, above). // Tim's trick for moving the text back up in this case, to look like more // like details pages in which HR's bottom margin melts into H2's top margin: char *s = skipLeadingSpaces(tdb->html); if (startsWith("<H2>", s) || startsWith("<h2>", s)) printf("<div style='position:relative; top:-1.2em; margin-bottom:0em;'>%s\n</div>", tdb->html); else puts(tdb->html); } } } static void addNotesForBbiTables(struct trackDb *tdb, struct sqlConnection *conn) /* single-row BBI file pointer tables are confusing, help the users a little here */ { if (tdb != NULL) { boolean isBig = printTypeHelpDesc(tdb->type); if (isBig) { char *fileName = trackDbSetting(tdb, "bigDataUrl"); if (!fileName) { char query[1024]; sqlSafef(query, sizeof query, "SELECT fileName from %s", tdb->table); char *bbiPath = sqlQuickString(conn, query); printf("The MySQL table contains only a single row with a pointer to the file.<BR>"); printf("You can download the binary file from our " "<a href=\"https://hgdownload.soe.ucsc.edu%s\">Download server</a>.<BR>", bbiPath); } } } } static void showSchemaDb(char *db, struct trackDb *tdb, char *table) /* Show schema to open html page. */ { struct trackDb *tdbForConn = tdb ? tdb : curTrack; struct sqlConnection *conn; if (tdbForConn == NULL) conn = hAllocConn(db); else conn = hAllocConnTrack(db, tdbForConn); struct joiner *joiner = allJoiner; struct joinerPair *jpList, *jp; struct asObject *asObj = asForTable(conn, table); char *splitTable = chromTable(conn, table); hPrintf("<B>Database:</B> %s", db); hPrintf(" <B>Primary Table:</B> %s", table); if (!sameString(splitTable, table)) hPrintf(" (%s)", splitTable); hPrintf(" <B>Row Count: </B> "); printLongWithCommas(stdout, sqlTableSize(conn, splitTable)); char *date = firstWordInLine(sqlTableUpdate(conn, splitTable)); if (date != NULL) printf("  <B> Data last updated: </B>%s<BR>\n", date); if (asObj != NULL) hPrintf("<B>Format description:</B> %s<BR>", asObj->comment); if (cartTrackDbIsNoGenome(db, table)) hPrintf(" Note: genome-wide queries are not available for this table."); else { hPrintf("<B>On download server: </B>"); hPrintf("<A HREF='https://hgdownload.soe.ucsc.edu/goldenPath/%s/database/'>MariaDB table dump directory</A><BR>", db); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (sameString(table, "knownGene") && bigDataUrl!=NULL) { hPrintf("This track is available both in ASCII MariaDB table dump format and bigGenePred (bigBed) format.<br>"); printDownloadLink("bigBed", tdb, bigDataUrl); } } describeFields(db, splitTable, asObj, conn); if (tdbForConn && sameString(tdbForConn->track, table)) { struct trackDb *childTdb = tdbForTrack(db, table, NULL); addNotesForBbiTables(childTdb, conn); printTableBrowserLink(tdbForConn, table); } jpList = joinerRelate(joiner, db, table, NULL); /* sort and unique list */ slUniqify(&jpList, joinerPairCmpOnAandB, joinerPairFree); if (jpList != NULL) { webNewSection("Connected Tables and Joining Fields"); for (jp = jpList; jp != NULL; jp = jp->next) { if (cartTrackDbIsAccessDenied(jp->b->database, jp->b->table)) continue; struct joinerSet *js = jp->identifier; boolean aViaIndex, bViaIndex; hPrintSpaces(6); hPrintf("%s.", jp->b->database); hPrintf("<A HREF=\"%s?", cgiScriptName()); hPrintf("%s&", cartSidUrlString(cart)); hPrintf("%s=%s&", hgtaDoSchemaDb, jp->b->database); hPrintf("%s=%s", hgtaDoSchemaTable, jp->b->table); hPrintf("\">"); hPrintf("%s", jp->b->table); hPrintf("</A>"); aViaIndex = isViaIndex(js, jp->a); bViaIndex = isViaIndex(js, jp->b); hPrintf(".%s ", jp->b->field); if (aViaIndex && bViaIndex) { hPrintf("(%s.%s and %s.%s are arrays sharing an index)", jp->a->table, jp->a->field, jp->b->table, jp->b->field); } else if (aViaIndex) { hPrintf("(which is an array index into %s.%s)", jp->a->table, jp->a->field); } else if (bViaIndex) { hPrintf("(%s.%s is an array index into %s.%s)", jp->a->table, jp->a->field, jp->b->table, jp->b->field); } else { hPrintf("(via %s.%s)", jp->a->table, jp->a->field); } if (cartTrackDbIsNoGenome(jp->b->database, jp->b->table)) hPrintf(" Note: genome-wide queries are not available for this table."); hPrintf("<BR>\n"); } } webNewSection("Sample Rows"); printSampleRows(10, conn, splitTable); printTrackHtml(tdb); hFreeConn(&conn); } static void showSchemaCtWiggle(char *table, struct customTrack *ct) /* Show schema on wiggle format custom track. */ { hPrintf("<B>Wiggle Custom Track ID:</B> %s<BR>\n", table); hPrintf("Wiggle custom tracks are stored in a dense binary format."); printTrackHtml(ct->tdb); } static void showSchemaCtChromGraph(char *table, struct customTrack *ct) /* Show schema on wiggle format custom track. */ { hPrintf("<B>ChromGraph Custom Track ID:</B> %s<BR>\n", table); hPrintf("ChromGraph custom tracks are stored in a dense binary format."); printTrackHtml(ct->tdb); } static void showSchemaCtMaf(char *table, struct customTrack *ct) /* Show schema on maf format custom track. */ { hPrintf("<B>MAF Custom Track ID:</B> %s<BR>\n", table); hPrintf("For formatting information see: "); hPrintf("<A HREF=\"../FAQ/FAQformat.html#format5\">MAF</A> "); hPrintf("format."); struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); webNewSection("Sample Rows"); printSampleRows(10, conn, ct->dbTableName); printTrackHtml(ct->tdb); hFreeConn(&conn); } static void showSchemaCtBed(char *table, struct customTrack *ct) /* Show schema on bed format custom track. */ { struct bed *bed; int count = 0; boolean showItemRgb = FALSE; showItemRgb=bedItemRgb(ct->tdb); /* should we expect itemRgb */ /* instead of "reserved" */ /* Find named custom track. */ hPrintf("<B>Custom Track ID:</B> %s ", table); hPrintf("<B>Field Count:</B> %d<BR>", ct->fieldCount); hPrintf("For formatting information see: "); hPrintf("<A HREF=\"../FAQ/FAQformat.html#format1\">BED</A> "); hPrintf("format."); if (ct->dbTrack) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); webNewSection("Sample Rows"); printSampleRows(10, conn, ct->dbTableName); printTrackHtml(ct->tdb); hFreeConn(&conn); } else { webNewSection("Sample Rows"); hPrintf("<TT><PRE>"); if (showItemRgb) { for(bed = ct->bedList;bed != NULL && count < 10;bed = bed->next,++count) bedTabOutNitemRgb(bed, ct->fieldCount, stdout); } else { for(bed = ct->bedList;bed != NULL && count < 10;bed = bed->next,++count) bedTabOutN(bed, ct->fieldCount, stdout); } hPrintf("</PRE></TT>\n"); } } static void showSchemaCtArray(char *table, struct customTrack *ct) /* Show schema on bed format custom track. */ { struct bed *bed; int count = 0; /* Find named custom track. */ hPrintf("<B>Custom Track ID:</B> %s ", table); hPrintf("<B>Field Count:</B> %d<BR>", ct->fieldCount); hPrintf("For formatting information see: "); hPrintf("<A HREF=\"../FAQ/FAQformat.html#format6.5\">Microarray</A> "); hPrintf("format."); if (ct->dbTrack) { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); webNewSection("Sample Rows"); printSampleRows(10, conn, ct->dbTableName); printTrackHtml(ct->tdb); hFreeConn(&conn); } else { webNewSection("Sample Rows"); hPrintf("<TT><PRE>"); for(bed = ct->bedList;bed != NULL && count < 10;bed = bed->next,++count) bedTabOutN(bed, ct->fieldCount, stdout); hPrintf("</PRE></TT>\n"); } } static void showSchemaWithAsObj(char *db, char *trackId, struct customTrack *ct, struct asObject *asObj) /* Show schema on custom track using autoSqlString defined for this track type. */ { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); char *table = ct->dbTableName; hPrintf("<B>Genome Database:</B> %s ", db); hPrintf("<B>Track ID:</B> %s ", trackId); hPrintf("<B>MySQL table:</B> %s", table); hPrintf(" <B>Row Count:</B> "); printLongWithCommas(stdout, sqlTableSize(conn, table)); hPrintf("<BR>\n"); if (asObj != NULL) hPrintf("<B>Format description:</B> %s<BR>", asObj->comment); describeFields(CUSTOM_TRASH, table, asObj, conn); webNewSection("Sample Rows"); printSampleRows(10, conn, ct->dbTableName); printTrackHtml(ct->tdb); hFreeConn(&conn); } static void showSchemaCt(char *db, char *table) /* Show schema on custom track. */ { struct customTrack *ct = ctLookupName(table); char *type = ct->tdb->type; if (startsWithWord("wig", type) || startsWithWord("bigWig", type)) showSchemaCtWiggle(table, ct); else if (startsWithWord("chromGraph", type)) showSchemaCtChromGraph(table, ct); else if (startsWithWord("bed", type) || startsWithWord("bedGraph", type)) showSchemaCtBed(table, ct); else if (startsWithWord("bedMethyl", type)) showSchemaCtBed(table, ct); else if (startsWithWord("maf", type)) showSchemaCtMaf(table, ct); else if (startsWithWord("array", type)) showSchemaCtArray(table, ct); -else if (startsWithWord("makeItems", type)) +else if (startsWithWord("myVariants", type)) { - struct asObject *asObj = makeItemsItemAsObj(); + struct asObject *asObj = myVariantsAsObj(); showSchemaWithAsObj(db, table, ct, asObj); asObjectFree(&asObj); } else if (sameWord("bedDetail", type)) { struct asObject *asObj = bedDetailAsObj(); showSchemaWithAsObj(db, table, ct, asObj); asObjectFree(&asObj); } else if (sameWord("pgSnp", type)) { struct asObject *asObj = pgSnpAsObj(); showSchemaWithAsObj(db, table, ct, asObj); asObjectFree(&asObj); } else if (sameWord("barChart", type)) { struct asObject *asObj = barChartAsObj(); showSchemaWithAsObj(db, table, ct, asObj); asObjectFree(&asObj); } else if (sameWord("interact", type)) { struct asObject *asObj = interactAsObj(); showSchemaWithAsObj(db, table, ct, asObj); asObjectFree(&asObj); } else errAbort("Unrecognized customTrack type %s", type); } static void showSchemaHub(char *db, char *table) /* Show schema on a hub track. */ { struct trackDb *tdb = hashMustFindVal(fullTableToTdbHash, table); hubConnectAddDescription(db, tdb); char *type = cloneFirstWord(tdb->type); if (tdbIsBigBed(tdb)) showSchemaBigBed(table, tdb); else if (sameString(type, "longTabix")) showSchemaLongTabix(table, tdb); else if (sameString(type, "bam")) showSchemaBam(table, tdb); else if (sameString(type, "vcfTabix")) showSchemaVcf(table, tdb, TRUE); else if (sameString(type, "hic")) showSchemaHic(table, tdb); else { hPrintf("Binary file of type %s stored at %s<BR>\n", type, trackDbSetting(tdb, "bigDataUrl")); printTrackHtml(tdb); } } static void showSchemaWiki(struct trackDb *tdb, char *table) /* Show schema for the wikiTrack. */ { hPrintf("<B>User annotations to UCSC genes or genome regions</B><BR>\n"); showSchemaDb(wikiDbName(), tdb, table); printTrackHtml(tdb); } static void showSchema(char *db, struct trackDb *tdb, char *table) /* Show schema to open html page. */ { boolean isTabix = FALSE; if (isHubTrack(table)) showSchemaHub(db, table); else if (isBigBed(database, table, curTrack, ctLookupName)) showSchemaBigBed(table, tdb); else if (isLongTabixTable(table)) showSchemaLongTabix(table, tdb); else if (isBamTable(table)) showSchemaBam(table, tdb); else if (isVcfTable(table, &isTabix)) showSchemaVcf(table, tdb, isTabix); else if (isHicTable(table)) showSchemaHic(table, tdb); else if (isCustomTrack(table)) showSchemaCt(db, table); else if (sameWord(table, WIKI_TRACK_TABLE)) showSchemaWiki(tdb, table); else if (isBigWig(database, table, curTrack, ctLookupName) && !hTableExists(db, table)) showSchemaBigWigNoTable(db, table, tdb); else if (tdb && sameString(tdb->type, "lorax")) showSchemaBigBed(table, tdb); else showSchemaDb(db, tdb, table); } void doTableSchema(char *db, char *table, struct sqlConnection *conn) /* Show schema around table (which is not described by curTrack). */ { struct trackDb *tdb = NULL; char parseBuf[256]; dbOverrideFromTable(parseBuf, &db, &table); htmlOpen("Schema for %s", table); tdb = hTrackDbForTrack(database, table); showSchema(db, tdb, table); htmlClose(); } static boolean curTrackDescribesCurTable() /* Return TRUE if curTable is curTrack or its subtrack. */ { if (curTrack == NULL) return FALSE; if (sameString(curTrack->table, curTable)) return TRUE; else if (startsWith("wigMaf", curTrack->type)) { struct consWiggle *wig, *wiggles = wigMafWiggles(database, curTrack); for (wig = wiggles; wig != NULL; wig = wig->next) if (sameString(curTable, wig->table)) return TRUE; } else if (curTrack->subtracks != NULL) { struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *sTdb = tdbRef->val; if (sameString(sTdb->table, curTable)) return TRUE; } } return FALSE; } void doSchema(struct sqlConnection *conn) /* Show schema around current track. */ { if (curTrackDescribesCurTable()) { char *table = connectingTableForTrack(curTable); if (!isCustomTrack(table) && !hashFindVal(fullTableToTdbHash, table)) hashAdd(fullTableToTdbHash, table, curTrack); htmlOpen("Schema for %s - %s", curTrack->shortLabel, curTrack->longLabel); showSchema(trackHubSkipHubName(database), curTrack, table); htmlClose(); } else doTableSchema(trackHubSkipHubName(database), curTable, conn); } struct asObject *asForTableNoTdb(struct sqlConnection *conn, char *table) /* Get autoSQL description if any associated with table. Don't try tdb */ { // Some cases are for tables with no tdb! struct asObject *asObj = NULL; if (sqlTableExists(conn, "tableDescriptions")) { struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { char query[256]; sqlSafef(query, sizeof(query), "select autoSqlDef from tableDescriptions where tableName='%s'", table); char *asText = asText = sqlQuickString(conn, query); // If no result try split table. (not likely) if (asText == NULL) { sqlSafef(query, sizeof(query), "select autoSqlDef from tableDescriptions where tableName='chrN_%s'", table); asText = sqlQuickString(conn, query); } if (asText != NULL && asText[0] != 0) { asObj = asParseText(asText); } freez(&asText); } errCatchEnd(errCatch); errCatchFree(&errCatch); } return asObj; } struct asObject *asForTable(struct sqlConnection *conn, char *table) /* Get autoSQL description if any associated with table. */ /* Wrap some error catching around asForTable. */ { struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table); if (tdb != NULL) return asForTdb(conn,tdb); return asForTableNoTdb(conn, table); }