e0db353cfefb9bde9cce31d6a2c2d2762dc1de4a kate Wed Sep 12 17:19:14 2018 -0700 IMplement fieldName> expansion in trackDb url setting. refs #22078 diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c index 01dd2ac..44f39b2 100644 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@ -1,217 +1,255 @@ /* Details page for interact type tracks */ /* Copyright (C) 2018 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "obscure.h" #include "hdb.h" +#include "jksql.h" #include "hgc.h" #include "interact.h" #include "interactUi.h" -static struct interact *getInteractsFromTable(struct trackDb *tdb, char *chrom, int start, int end, - char *foot) +struct interactPlusRow + { + /* Keep field values in string format, for url processing */ + struct interactPlusRow *next; + struct interact *interact; + char **row; + }; + +static struct interactPlusRow *getInteractsFromTable(struct trackDb *tdb, char *chrom, + int start, int end, char *foot) /* Retrieve interact items at this position from track table */ { struct sqlConnection *conn = NULL; struct customTrack *ct = lookupCt(tdb->track); char *table; if (ct != NULL) { conn = hAllocConn(CUSTOM_TRASH); table = ct->dbTableName; } else { conn = hAllocConnTrack(database, tdb); table = tdb->table; } if (conn == NULL) return NULL; -struct interact *inters = NULL, *inter = NULL; +struct interactPlusRow *iprs = NULL; char **row; int offset; struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset); +int fieldCount = 0; while ((row = sqlNextRow(sr)) != NULL) { - inter = interactLoadAndValidate(row+offset); + struct interact *inter = interactLoadAndValidate(row+offset); if (inter->chromStart != start || inter->chromEnd != end) continue; - slAddHead(&inters, inter); + + // got one, save object and row representation + struct interactPlusRow *ipr; + AllocVar(ipr); + ipr->interact = inter; + char **fieldVals; + if (fieldCount == 0) + fieldCount = sqlCountColumns(sr); + AllocArray(fieldVals, fieldCount); + int i; + for (i = 0; i < fieldCount; i++) + fieldVals[i] = cloneString(row[i]); + ipr->row = fieldVals; + slAddHead(&iprs, ipr); } sqlFreeResult(&sr); hFreeConn(&conn); -return inters; +return iprs; } -static struct interact *getInteractsFromFile(char *file, char *chrom, int start, int end, +static struct interactPlusRow *getInteractsFromFile(char *file, char *chrom, int start, int end, char *foot) /* Retrieve interact items at this position from big file */ { struct bbiFile *bbi = bigBedFileOpen(file); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); -struct interact *inters = NULL, *inter = NULL; +struct interactPlusRow *iprs = NULL; for (bb = bbList; bb != NULL; bb = bb->next) { char startBuf[16], endBuf[16]; - char *row[32]; - bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row)); - inter = interactLoadAndValidate(row); + int maxFields = 32; + char *row[maxFields]; // big enough ? + int fieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, maxFields); + struct interact *inter = interactLoadAndValidate(row); if (inter == NULL) continue; if (inter->chromStart != start || inter->chromEnd != end) continue; - slAddHead(&inters, inter); + + // got one, save object and row representation + struct interactPlusRow *ipr; + AllocVar(ipr); + ipr->interact = inter; + char **fieldVals; + AllocArray(fieldVals, fieldCount); + int i; + for (i = 0; i < fieldCount; i++) + fieldVals[i] = cloneString(row[i]); + ipr->row = fieldVals; + slAddHead(&iprs, ipr); } -return inters; +return iprs; } -static struct interact *getInteractions(struct trackDb *tdb, char *chrom, int start, int end, +static struct interactPlusRow *getInteractions(struct trackDb *tdb, char *chrom, int start, int end, char *foot) /* Retrieve interact items at this position. Also any others with the same endpoint, if endpoint clicked on*/ { -struct interact *inters = NULL; +struct interactPlusRow *iprs = NULL; char *file = trackDbSetting(tdb, "bigDataUrl"); if (file != NULL) - inters = getInteractsFromFile(file, chrom, start, end, foot); + iprs = getInteractsFromFile(file, chrom, start, end, foot); else - inters = getInteractsFromTable(tdb, chrom, start, end, foot); -slSort(&inters, bedCmpScore); -slReverse(&inters); -return inters; + iprs = getInteractsFromTable(tdb, chrom, start, end, foot); +// TODO: add sort on score in interacts in ipr +//slSort(&inters, bedCmpScore); +//slReverse(&inters); +return iprs; } void doInteractRegionDetails(struct trackDb *tdb, struct interact *inter) { /* print info for both regions */ /* Use different labels: 1) directional (source/target) 2) non-directional same chrom (lower/upper) 3) non-directional other chrom (this/other) */ char startBuf[1024], endBuf[1024], sizeBuf[1024]; printf("<b>Interaction region:</b> "); if (interactOtherChrom(inter)) printf("across chromosomes<br>"); else { sprintLongWithCommas(startBuf, inter->chromStart+1); sprintLongWithCommas(endBuf, inter->chromEnd); sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart); printf("<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>", inter->chrom, inter->chromStart, inter->chromEnd, inter->chrom, startBuf, endBuf); printf(" %s bp<br>\n", sizeBuf); } printf("<br>"); char *region1Label = "Source"; char *region1Chrom = inter->sourceChrom; int region1Start = inter->sourceStart; int region1End = inter->sourceEnd; char *region1Name = inter->sourceName; if (isEmptyTextField(inter->sourceName)) region1Name = ""; char *region2Label = "Target"; char *region2Chrom = inter->targetChrom; int region2Start = inter->targetStart; int region2End = inter->targetEnd; char *region2Name = inter->targetName; if (isEmptyTextField(inter->targetName)) region2Name = ""; if (!interactUiDirectional(tdb)) { if (interactOtherChrom(inter)) { region1Label = "This"; region2Label = "Other"; } else { region1Label = "Lower"; region2Label = "Upper"; } } // format and print sprintLongWithCommas(startBuf, region1Start + 1); sprintLongWithCommas(endBuf, region1End); sprintLongWithCommas(sizeBuf, region1End - region1Start); printf("<b>%s region:</b> %s " "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region1Label, region1Name, region1Chrom, region1Start+1, region1End, region1Chrom, startBuf, endBuf, inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand); printf(" %s bp<br>\n", sizeBuf); sprintLongWithCommas(startBuf, region2Start+1); sprintLongWithCommas(endBuf, region2End); sprintLongWithCommas(sizeBuf, region2End - region2Start); printf("<b>%s region:</b> %s " "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region2Label, region2Name, region2Chrom, region2Start+1, region2End, region2Chrom, startBuf, endBuf, inter->targetStrand[0] == '.' ? "" : inter->targetStrand); printf(" %s bp<br>\n", sizeBuf); int distance = interactRegionDistance(inter); if (distance > 0) { // same chrom sprintLongWithCommas(sizeBuf, distance); printf("<b>Distance between midpoints:</b> %s bp<br>\n", sizeBuf); } #ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/ double *scores; AllocArray(scores, count); #endif } -void doInteractItemDetails(struct trackDb *tdb, struct interact *inter, char *item, boolean isMultiple) +void doInteractItemDetails(struct trackDb *tdb, struct interactPlusRow *ipr, char *item, + boolean isMultiple) /* Details of interaction item */ { +struct interact *inter = ipr->interact; +struct slPair *fields = getFields(tdb, ipr->row); +printCustomUrlWithFields(tdb, item, item, TRUE, fields); if (!isEmptyTextField(inter->name)) - printf("<b>Interaction name:</b> %s<br>\n", inter->name); - - + printf("<b>Interaction:</b> %s<br>\n", inter->name); printf("<b>Score:</b> %d<br>\n", inter->score); printf("<b>Value:</b> %0.3f<br>\n", inter->value); if (!isEmptyTextField(inter->exp)) printf("<b>Experiment:</b> %s<br>\n", inter->exp); puts("<p>"); if (!isMultiple) doInteractRegionDetails(tdb, inter); } void doInteractDetails(struct trackDb *tdb, char *item) /* Details of interaction items */ { char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *foot = cartOptionalString(cart, "foot"); -struct interact *inter = NULL; -struct interact *inters = getInteractions(tdb, chrom, start, end, foot); -if (inters == NULL) +struct interactPlusRow *iprs = getInteractions(tdb, chrom, start, end, foot); +if (iprs == NULL) errAbort("Can't find interaction %s", item ? item : ""); -int count = slCount(inters); +int count = slCount(iprs); if (count > 1) { printf("<b>Interactions at this position:</b> %d<p>", count); - doInteractRegionDetails(tdb, inters); + doInteractRegionDetails(tdb, iprs->interact); printf("</p>"); } genericHeader(tdb, item); -for (inter = inters; inter; inter = inter->next) +static struct interactPlusRow *ipr = NULL; +for (ipr = iprs; ipr != NULL; ipr = ipr->next) { if (count > 1) printf("<hr>\n"); - doInteractItemDetails(tdb, inter, item, count > 1); - if (count > 1 && !isEmptyTextField(inter->name) && sameString(inter->name, item)) + doInteractItemDetails(tdb, ipr, item, count > 1); + if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item)) printf("<hr>\n"); } }