0d1ffc7e1c162f115ffa1622a70535b99c465ee0 kate Tue Jan 20 18:12:40 2015 -0800 Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353 diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index 48e31e7..316375b 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -68,54 +68,55 @@ count += 1; sum += sqlDouble(row[signalCol]); } sqlFreeResult(&sr); hFreeConn(&conn); } if (count > 0) return sum/count; else return 0; } static void printControlledVocabFields(char **row, int fieldCount, struct slName *fieldList, char *vocabFile, struct hash *vocabHash) -/* Print out fields from row, linking them to controlled vocab if need be. */ +/* Print out fields from row, linking them to controlled vocab if need be. + * If vocabFile is NULL, the vocabHash is a metaHash, so links + mouseovers are + * generated differently */ { int i; struct slName *field; for (i=0, field = fieldList; i<fieldCount; ++i, field = field->next) { + char *link = NULL; char *fieldVal = row[i]; if (vocabFile && hashLookup(vocabHash, field->name)) { - char *link = controlledVocabLink(vocabFile, "term", - fieldVal, fieldVal, fieldVal, ""); - webPrintLinkCell(link); + // controlled vocabulary + link = controlledVocabLink(vocabFile, "term", fieldVal, fieldVal, fieldVal, ""); } - else - webPrintLinkCell(fieldVal); + else if (!vocabFile && vocabHash != NULL) + { + // meta tables + struct hash *fieldHash = hashFindVal(vocabHash, field->name); + if (fieldHash != NULL) + link = metaVocabLink(fieldHash, fieldVal, fieldVal); + } + webPrintLinkCell(link != NULL ? link : fieldVal); } - -struct hash *getVocabHash(char *fileName) -/* Get vocabulary term hash */ -{ -struct hash *hash = raTagVals(fileName, "type"); -hashAdd(hash, "cellType", NULL); /* Will the kludge never end, no, never! */ -return hash; } static void printMetadataForTable(char *table) /* If table exists, _and_ tdb associated with it exists, print out * a metadata link that expands on click. Otherwise print "unavailable" */ { webPrintLinkCellStart(); struct trackDb *tdb = hashFindVal(trackHash, table); if (tdb == NULL) printf("%s info n/a", table); else compositeMetadataToggle(database, tdb, "metadata", TRUE, FALSE); webPrintLinkCellEnd(); } @@ -123,49 +124,78 @@ struct slName *fieldList) /* Construct query in dyString to return contents of inputTrackTable ordered appropriately */ { struct dyString *fields = dyStringNew(0); struct slName *field; sqlDyStringPrintf(query, "select tableName "); for (field = fieldList; field != NULL; field = field->next) sqlDyStringPrintfFrag(fields, ",%s", field->name); sqlDyStringPrintf(query, "%-s from %s", fields->string, inputTrackTable); if (fieldList != NULL) // skip leading comma dyStringPrintf(query, " order by %s", fields->string+1); dyStringFree(&fields); } +static struct hash *getVocabHash(char *fileName) +/* Get vocabulary term hash */ +{ +struct hash *hash = raTagVals(fileName, "type"); +hashAdd(hash, "cellType", NULL); /* Will the kludge never end, no, never! */ +return hash; +} -static void printPeakClusterInfo(struct sqlConnection *conn, char *inputTrackTable, - struct slName *fieldList, char *vocab, struct bed *cluster) -/* Print an HTML table showing sources with hits in the cluster, along with signal. - If cluster is NULL, show all sources assayed */ +static void getVocab(struct trackDb *tdb, struct cart *cart, + char **vocabFile, struct hash **vocabHash) +/* Get vocabulary info from trackDb settings (CV or meta tables) */ { -char *vocabFile = NULL; -struct hash *vocabHash = NULL; + +char *file = NULL; +struct hash *hash = NULL; +char *vocab = trackDbSetting(tdb, "controlledVocabulary"); +struct hash *metaHash = metaBasicFromSetting(tdb, cart, "inputFieldMetaTables"); if (vocab) { - vocabFile = cloneFirstWord(vocab); - vocabHash = getVocabHash(vocabFile); + file = cloneFirstWord(vocab); + hash = getVocabHash(file); + } +else if (metaHash) + { + hash = metaHash; + } +if (vocabFile != NULL) + *vocabFile = file; +if (hash != NULL) + *vocabHash = hash; } +static void printPeakClusterInfo(struct trackDb *tdb, struct cart *cart, + struct sqlConnection *conn, char *inputTrackTable, + struct slName *fieldList, struct bed *cluster) +/* Print an HTML table showing sources with hits in the cluster, along with signal. + If cluster is NULL, show all sources assayed */ +{ + /* Make the SQL query to get the table and all other fields we want to show * from inputTrackTable. */ struct dyString *query = dyStringNew(0); queryInputTrackTable(query, inputTrackTable, fieldList); +char *vocabFile = NULL; +struct hash *vocabHash = NULL; +getVocab(tdb, cart, &vocabFile, &vocabHash); + int displayNo = 0; int fieldCount = slCount(fieldList); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { double signal = 0; if (cluster != NULL) { char *table = row[0]; signal = getSignalAt(table, cluster); if (signal == 0) continue; } printf("</TR><TR>\n"); @@ -262,33 +292,32 @@ } void doPeakClusterListItemsAssayed() /* Put up a page that shows all experiments associated with a cluster track. */ { struct trackDb *clusterTdb = tdbForTableArg(); cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); struct sqlConnection *conn = hAllocConn(database); char *inputTableFieldDisplay = trackDbSetting(clusterTdb, "inputTableFieldDisplay"); webPrintLinkTableStart(); if (inputTableFieldDisplay) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); printClusterTableHeader(fieldList, FALSE, FALSE, FALSE); - char *vocab = trackDbSetting(clusterTdb, "controlledVocabulary"); char *inputTrackTable = trackDbRequiredSetting(clusterTdb, "inputTrackTable"); - printPeakClusterInfo(conn, inputTrackTable, fieldList, vocab, NULL); + printPeakClusterInfo(clusterTdb, cart, conn, inputTrackTable, fieldList, NULL); //http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_table=uwEnc2DnasePeaksWgEncodeEH000507 } else errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay", clusterTdb->track); webPrintLinkTableEnd(); hFreeConn(&conn); } void doPeakClusters(struct trackDb *tdb, char *item) /* Display detailed info about a cluster of DNase peaks from other tracks. */ { int start = cartInt(cart, "o"); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); @@ -303,44 +332,43 @@ "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) cluster = bedLoadN(row+rowOffset, 5); sqlFreeResult(&sr); if (cluster != NULL) { /* Get list of subgroups to display */ char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); - char *vocab = trackDbSetting(tdb, "controlledVocabulary"); char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); /* Print out some information about the cluster overall. */ printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, sqlRowCount(conn, sqlCheckIdentifier(inputTrackTable))); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); /* In a new section put up list of hits. */ webNewSection("List of Items in Cluster"); webPrintLinkTableStart(); printClusterTableHeader(fieldList, FALSE, FALSE, TRUE); - printPeakClusterInfo(conn, inputTrackTable, fieldList, vocab, cluster); + printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster); } else errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay", tdb->track); webPrintLinkTableEnd(); } printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(), tdb->track); printf("List all items assayed"); printf("</A><BR>\n"); webNewSection("Track Description"); printTrackHtml(tdb); hFreeConn(&conn); }