7df3ba2728fb2b20ac6159bb4935b9ccd829e695 galt Thu Feb 6 13:31:32 2025 -0800 squashed hgEncodeVocab-ra-danger-fix. fixes #287 diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index 7d754849564..d2b764c0745 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -18,30 +18,31 @@ #include "jksql.h" #include "obscure.h" #include "hCommon.h" #include "hdb.h" #include "web.h" #include "cart.h" #include "trackDb.h" #include "hui.h" #include "hgc.h" #include "encode/encodePeak.h" #include "expRecord.h" #include "bed6FloatScore.h" #include "ra.h" #include "jsHelper.h" #include "factorSource.h" +#include "cv.h" static void printClusterTableHeader(struct slName *otherCols, boolean withAbbreviation, boolean withDescription, boolean withSignal) /* Print out header fields table of tracks in cluster */ { webPrintLabelCell("#"); if (withSignal) webPrintLabelCell("signal"); if (withAbbreviation) webPrintLabelCell("abr"); struct slName *col; for (col = otherCols; col != NULL; col = col->next) webPrintLabelCell(col->name); if (withDescription) webPrintLabelCell("description"); @@ -73,38 +74,39 @@ 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. * If vocabFile is NULL, the vocabHash is not ENCODE, 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)) { // controlled vocabulary - link = wgEncodeVocabLink(vocabFile, "term", fieldVal, fieldVal, fieldVal, ""); + link = wgEncodeVocabLink("term", fieldVal, fieldVal, fieldVal, ""); } else if (!vocabFile && vocabHash != NULL) { // meta tables struct hash *fieldHash = hashFindVal(vocabHash, field->name); if (fieldHash != NULL) link = vocabLink(fieldHash, fieldVal, fieldVal); } webPrintLinkCell(link != NULL ? link : fieldVal); } } static void printMetadataForTable(char *table) /* If table exists, _and_ tdb associated with it exists, print out @@ -155,30 +157,33 @@ hashAdd(hash, "cellType", NULL); /* Will the kludge never end, no, never! */ return hash; } static void getVocab(struct trackDb *tdb, struct cart *cart, char **vocabFile, struct hash **vocabHash) /* Get vocabulary info from trackDb settings (CV or vocab tables) */ { char *file = NULL; struct hash *hash = NULL; char *vocab = trackDbSetting(tdb, "controlledVocabulary"); if (vocabSettingIsEncode(vocab)) { file = cloneFirstWord(vocab); + if (!sameString(file, "encode/cv.ra")) + errAbort("expected encode/cv.ra in trackDb settings for controlledVocabulary."); + file = (char *)cvFile(); // use the library location hash = getVocabHash(file); } else { hash = vocabBasicFromSetting(tdb, cart); } 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) @@ -208,50 +213,45 @@ if (signal == 0) continue; } printf("</TR><TR>\n"); webPrintIntCell(++displayNo); if (signal != 0) webPrintDoubleCell(signal); printControlledVocabFields(row+1, fieldCount, fieldList, vocabFile, vocabHash); printMetadataForTable(row[0]); } sqlFreeResult(&sr); freez(&vocabFile); dyStringFree(&query); } -static char *factorSourceVocabLink(char *vocabFile, char *fieldName, char *fieldVal) +static char *factorSourceVocabLink(char *fieldName, char *fieldVal) /* Add link to show controlled vocabulary entry for term. * Handles 'target' (factor) which is a special case, derived from Antibody entries */ { char *vocabType = (sameString(fieldName, "target") || sameString(fieldName, "factor")) ? "target" : "term"; -return wgEncodeVocabLink(vocabFile, vocabType, fieldVal, fieldVal, fieldVal, ""); +return wgEncodeVocabLink(vocabType, fieldVal, fieldVal, fieldVal, ""); } static void printFactorSourceTableHits(struct factorSource *cluster, struct sqlConnection *conn, char *sourceTable, char *inputTrackTable, struct slName *fieldList, boolean invert, char *vocab, struct hash *fieldToUrl) /* Put out a lines in an html table that shows assayed sources that have hits in this * cluster, or if invert is set, that have misses. */ { -char *vocabFile = NULL; -if (vocab) - { - vocabFile = cloneFirstWord(vocab); - } /* Make the monster SQL query to get all assays*/ struct dyString *query = dyStringNew(0); sqlDyStringPrintf(query, "select %s.id,%s.name,%s.tableName", sourceTable, sourceTable, inputTrackTable); struct slName *field; for (field = fieldList; field != NULL; field = field->next) sqlDyStringPrintf(query, ",%s.%s", inputTrackTable, field->name); sqlDyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable); sqlDyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable); sqlDyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable); boolean encodeStanford = FALSE; if (startsWith("enc", sourceTable)) encodeStanford = TRUE; @@ -280,31 +280,31 @@ printf("</TR><TR>\n"); webPrintIntCell(++displayNo); if (!invert) webPrintDoubleCell(signal); webPrintLinkCell(row[1]); int i = 0; // find position of CV metadata in field list int offset = 3; struct slName *field = fieldList; for (i=0; i<fieldCount && field != NULL; ++i, field = field->next) { char *fieldVal = row[i+offset]; char *link = NULL; if (vocab) { - link = cloneString(factorSourceVocabLink(vocabFile, field->name, fieldVal)); + link = cloneString(factorSourceVocabLink(field->name, fieldVal)); } else if (fieldToUrl != NULL) { // (outside) links on vocab items char *urlPattern = hashFindVal(fieldToUrl, field->name); if (urlPattern != NULL) { char *url = replaceInUrl(urlPattern, fieldVal, cart, database, seqName, winStart, winEnd, NULL, TRUE, NULL); if (url != NULL) { struct dyString *ds = dyStringCreate("<a target='_blank' href='%s'>%s</a>\n", url, fieldVal); link = dyStringCannibalize(&ds); } @@ -319,31 +319,30 @@ if (!file) webPrintLinkCell(table); else { webPrintLinkCellStart(); printf("<A target='_blank'" "href='https://www.encodeproject.org/files/%s'>%s</A>", file, file); webPrintLinkCellEnd(); } } else printMetadataForTable(table); } } sqlFreeResult(&sr); -freez(&vocabFile); dyStringFree(&query); } 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); @@ -512,33 +511,33 @@ char **row = sqlNextRow(sr); struct factorSource *cluster = NULL; if (row != NULL) cluster = factorSourceLoad(row + rowOffset); sqlFreeResult(&sr); if (cluster == NULL) errAbort("Error loading cluster from track %s", tdb->track); char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); char *factorLink = cluster->name; char *vocab = trackDbSetting(tdb, "controlledVocabulary"); if (vocab != NULL) { - char *file = cloneFirstWord(vocab); - factorLink = wgEncodeVocabLink(file, "term", factorLink, factorLink, factorLink, ""); + factorLink = wgEncodeVocabLink("term", factorLink, factorLink, factorLink, ""); } + printf("<B>Factor:</B> %s<BR>\n", factorLink); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, item); /* Get list of tracks we'll look through for input. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); char query[256]; sqlSafef(query, sizeof(query), "select tableName from %s where factor='%s' order by source", inputTrackTable, cluster->name); /* Next do the lists of hits and misses. We have the hits from the non-zero signals in * cluster->expScores. We need to figure out the sources actually assayed though * some other way. We'll do this by one of two techniques. */ char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");