4dfb2a02da9b0a652a534911ebda73d3600872e2 galt Wed Apr 17 16:31:34 2013 -0700 Brian put setUdcCacheDir() earlier, but he should have cleaned the later ones out. diff --git src/hg/hgGenome/hgGenome.c src/hg/hgGenome/hgGenome.c index 0a78530..1ed3675 100644 --- src/hg/hgGenome/hgGenome.c +++ src/hg/hgGenome/hgGenome.c @@ -1,582 +1,581 @@ /* hgGenome is a CGI script that produces a web page containing * a graphic with all chromosomes in genome, and a graph or two * on top of them. This module just contains the main routine, * the routine that dispatches to various page handlers, and shared * utility functions. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "htmshell.h" #include "cart.h" #include "hui.h" #include "dbDb.h" #include "ra.h" #include "hdb.h" #include "web.h" #include "portable.h" #include "hgColors.h" #include "trackLayout.h" #include "chromInfo.h" #include "vGfx.h" #include "genoLay.h" #include "cytoBand.h" #include "hCytoBand.h" #include "errCatch.h" #include "chromGraph.h" #include "customTrack.h" #include "hCommon.h" #include "hPrint.h" #include "jsHelper.h" #include "hgGenome.h" /* ---- Global variables. ---- */ struct cart *cart; /* This holds cgi and other variables between clicks. */ struct hash *oldVars; /* Old cart hash. */ char *database; /* Name of genome database - hg15, mm3, or the like. */ char *genome; /* Name of genome - mouse, human, etc. */ struct trackLayout tl; /* Dimensions of things, fonts, etc. */ struct genoGraph *ggUserList; /* List of user graphs */ struct genoGraph *ggDbList; /* List of graphs in database. */ struct genoGraph *ggCompList; /* List of composite genome graphs (DB only). */ struct slRef *ggList; /* List of active genome graphs */ struct hash *ggHash; /* Hash of active genome graphs */ boolean withLabels; /* Draw labels? */ void usage() /* Explain usage and exit. */ { errAbort( "hgGenome - Full genome (as opposed to chromosome) view of data\n" "This is a cgi script, but it takes the following parameters:\n" " db=<genome database>\n" " hggt_table=on where table is name of chromGraph table\n" ); } /* ---- Get list of graphs. ---- */ struct genoGraph *getUserGraphs() /* Get list of all user graphs */ { struct genoGraph *list = NULL, *gg; struct customTrack *ct, *ctList = customTracksParseCart(database, cart, NULL, NULL); for (ct = ctList; ct != NULL; ct = ct->next) { struct trackDb *tdb = ct->tdb; if (sameString(tdb->type, "chromGraph")) { AllocVar(gg); gg->name = tdb->table; gg->shortLabel = tdb->shortLabel; gg->longLabel = tdb->longLabel; gg->binFileName = trackDbRequiredSetting(tdb, "binaryFile"); gg->settings = chromGraphSettingsGet(gg->name, NULL, tdb, cart); gg->isSubGraph = FALSE; gg->isComposite = FALSE; slAddHead(&list, gg); } } slReverse(&list); return list; } struct genoGraph *getCompGraphs(struct sqlConnection *conn) /* Get graphs defined in database that are part of a composite. */ { struct genoGraph *list = NULL, *gg; struct sqlConnection *conn2 = hAllocConn(database); struct slName *compositeGGList = NULL, *comp; /* Get initial information from metaChromGraph table */ if (sqlTableExists(conn, "metaChromGraph")) compositeGGList = sqlQuickList(conn, "select name from metaChromGraph where binaryFile='composite'"); /* Build a hash of genoGraphs out of composite trackDbs and fill in from cart. */ for (comp = compositeGGList; comp != NULL; comp = comp->next) { struct trackDb *tdb = hTrackDbForTrack(database, comp->name); if (tdb) { struct chromGraphSettings *cgs = chromGraphSettingsGet(comp->name, conn2, tdb, cart); AllocVar(gg); gg->name = cloneString(comp->name); gg->shortLabel = tdb->shortLabel; gg->longLabel = tdb->longLabel; gg->settings = cgs; gg->isSubGraph = FALSE; gg->isComposite = TRUE; slAddHead(&list, gg); } } hFreeConn(&conn2); slReverse(&list); return list; } struct genoGraph *getDbGraphs(struct sqlConnection *conn) /* Get graphs defined in database. Also use the composite settings if */ /* it's a subGraph. */ { struct genoGraph *list = NULL, *gg; struct sqlConnection *conn2 = hAllocConn(database); struct sqlResult *sr; char **row; /* Get initial information from metaChromGraph table */ if (sqlTableExists(conn, "metaChromGraph")) { sr = sqlGetResult(conn, "select name,binaryFile from metaChromGraph where binaryFile!='composite'"); while ((row = sqlNextRow(sr)) != NULL) { char *table = row[0], *binaryFile = row[1]; AllocVar(gg); gg->name = gg->shortLabel = gg->longLabel = cloneString(table); gg->binFileName = cloneString(binaryFile); slAddHead(&list, gg); } sqlFreeResult(&sr); } slReverse(&list); /* Where possible fill in additional info from trackDb. */ for (gg = list; gg != NULL; gg = gg->next) { struct trackDb *tdb = hTrackDbForTrack(database, gg->name); struct trackDb *compTdb = hCompositeTrackDbForSubtrack(database, tdb); gg->isSubGraph = (compTdb != NULL) ? TRUE : FALSE; gg->isComposite = FALSE; if (tdb != NULL) { struct chromGraphSettings *cgs = NULL; if (compTdb == NULL) cgs = chromGraphSettingsGet(gg->name, conn2, tdb, cart); else cgs = chromGraphSettingsGet(compTdb->table, conn2, compTdb, cart); gg->shortLabel = tdb->shortLabel; gg->longLabel = tdb->longLabel; gg->settings = cgs; } else { /* If we're here then there's an entry in metaChromGraph but not trackDb */ gg->settings = chromGraphSettingsGet(gg->name, NULL, NULL, NULL); } } hFreeConn(&conn2); slReverse(&list); return list; } void getGenoGraphs(struct sqlConnection *conn) /* Set up ggList and ggHash with all available genome graphs */ { struct genoGraph *userList = getUserGraphs(); struct genoGraph *compList = getCompGraphs(conn); struct genoGraph *dbList = getDbGraphs(conn); struct genoGraph *gg; struct slRef *ref, *refList = NULL; /* Buld up ggList from user and db lists. */ for (gg = compList; gg != NULL; gg = gg->next) refAdd(&refList, gg); for (gg = userList; gg != NULL; gg = gg->next) refAdd(&refList, gg); for (gg = dbList; gg != NULL; gg = gg->next) refAdd(&refList, gg); slReverse(&refList); ggList = refList; /* Buld up ggHash from ggList. */ ggHash = hashNew(0); for (ref = ggList; ref != NULL; ref = ref->next) { gg = ref->val; hashAdd(ggHash, gg->name, gg); } } void fakeEmptyLabels(struct chromGraphSettings *cgs) /* If no labels, fake them at 1/3 and 2/3 of the way through. */ { if (cgs->linesAtCount == 0) { cgs->linesAtCount = 2; AllocArray(cgs->linesAt, 2); double range = cgs->maxVal - cgs->minVal; cgs->linesAt[0] = cgs->minVal + range/3.0; cgs->linesAt[1] = cgs->minVal + 2.0*range/3.0; if (range >= 3) { cgs->linesAt[0] = round(cgs->linesAt[0]); cgs->linesAt[1] = round(cgs->linesAt[1]); } } } void ggRefineUsed(struct genoGraph *gg) /* Refine genoGraphs that are used. */ { if (!gg->didRefine) { struct chromGraphSettings *cgs = gg->settings; gg->cgb = chromGraphBinOpen(gg->binFileName); if (cgs->minVal >= cgs->maxVal) { cgs->minVal = gg->cgb->minVal; cgs->maxVal = gg->cgb->maxVal; } fakeEmptyLabels(gg->settings); gg->didRefine = TRUE; } } int ggLabelWidth(struct genoGraph *gg, MgFont *font) /* Return width used by graph labels. */ { struct chromGraphSettings *cgs = gg->settings; int i; int minLabelWidth = 0, labelWidth; char buf[24]; fakeEmptyLabels(cgs); for (i=0; i<cgs->linesAtCount; ++i) { safef(buf, sizeof(buf), "%g ", cgs->linesAt[i]); labelWidth = mgFontStringWidth(font, buf); if (labelWidth > minLabelWidth) minLabelWidth = labelWidth; } return minLabelWidth; } /* Routines to fetch cart variables. */ char *getThresholdName() /* Return threshold name. */ { static char buf[32]; safef(buf, sizeof(buf), "%s_%s", hggThreshold, database); return buf; } double getThreshold() /* Return user-set threshold */ { return cartUsualDouble(cart, getThresholdName(), defaultThreshold); } boolean getYellowMissing() /* Return draw background in yellow for missing data flag. */ { return cartUsualBoolean(cart, hggYellowMissing, FALSE); } int graphHeight() /* Return height of graph. */ { return cartUsualIntClipped(cart, hggGraphHeight, 27, 5, 200); } int regionPad() /* Number of bases to pad regions by. */ { return cartUsualIntClipped(cart, hggRegionPad, hggRegionPadDefault, 0, 10000000); } int graphsPerLine() /* Return number of graphs to draw per line. */ { return cartUsualIntClipped(cart, hggGraphsPerLine, defaultGraphsPerLine, minGraphsPerLine, maxGraphsPerLine); } int linesOfGraphs() /* Return number of lines of graphs */ { return cartUsualIntClipped(cart, hggLinesOfGraphs, defaultLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs); } char *chromLayout() /* Return one of above strings specifying layout. */ { return cartUsualString(cart, hggChromLayout, layTwoPerLine); } char *graphVarName(int row, int col) /* Get graph data source variable for given row and column. Returns * static buffer. */ { static char buf[32]; safef(buf, sizeof(buf), "%s_%s_%d_%d", hggGraphPrefix, database, row+1, col+1); return buf; } char *graphColorVarName(int row, int col) /* Get graph color variable for givein row and column. Returns * static buffer. */ { static char buf[32]; safef(buf, sizeof(buf), "%s_%s_%d_%d", hggGraphColorPrefix, database, row+1, col+1); return buf; } char *graphSourceAt(int row, int col) /* Return graph source at given row/column, NULL if none. */ { char *varName = graphVarName(row, col); char *source = NULL; if (cartVarExists(cart, varName)) { source = skipLeadingSpaces(cartString(cart, varName)); if (source[0] == 0) source = NULL; } return source; } struct genoGraph *ggAt(int row, int col) /* Return genoGraph at given position or NULL */ { char *source = graphSourceAt(row, col); if (source != NULL) return hashFindVal(ggHash, source); return NULL; } struct genoGraph *ggFirstVisible() /* Return first visible graph, or NULL if none. */ { int graphRows = linesOfGraphs(); int graphCols = graphsPerLine(); struct genoGraph *gg = NULL; int i,j; for (i=0; i<graphRows; ++i) for (j=0; j<graphCols; ++j) if ((gg = ggAt(i,j)) != NULL) return gg; return NULL; } struct slRef *ggAllVisible() /* Return list of references to all visible graphs */ { struct slRef *list = NULL; int graphRows = linesOfGraphs(); int graphCols = graphsPerLine(); struct genoGraph *gg = NULL; int i,j; for (i=0; i<graphRows; ++i) for (j=0; j<graphCols; ++j) if ((gg = ggAt(i,j)) != NULL) refAddUnique(&list, gg); slReverse(&list); return list; } struct genoLay *ggLayout(struct sqlConnection *conn, int graphRows, int graphCols) /* Figure out how to lay out image. */ { int i,j; struct genoLayChrom *chromList; int oneRowHeight; int minLeftLabelWidth = 0, minRightLabelWidth = 0; /* Figure out basic dimensions of image. */ trackLayoutInit(&tl, cart); tl.picWidth = cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth); /* Refine all graphs actually used, and calculate label * widths if need be. */ for (i=0; i<graphRows; ++i) { for (j=0; j<graphCols; ++j) { char *source = graphSourceAt(i,j); if (source != NULL) { struct genoGraph *gg = hashFindVal(ggHash, source); if (gg != NULL) { ggRefineUsed(gg); if (withLabels) { int labelWidth; labelWidth = ggLabelWidth(gg, tl.font); if (j == 0 && labelWidth > minLeftLabelWidth) minLeftLabelWidth = labelWidth; if (j == 1 && labelWidth > minRightLabelWidth) minRightLabelWidth = labelWidth; } } } } } /* Get list of chromosomes and lay them out. */ chromList = genoLayDbChroms(conn, FALSE); oneRowHeight = graphHeight()+betweenRowPad; return genoLayNew(chromList, tl.font, tl.picWidth, graphRows*oneRowHeight, minLeftLabelWidth, minRightLabelWidth, chromLayout()); } static void addPadToBed3(struct bed3 *bedList, int atStart, int atEnd) /* Add padding to bed3 list */ { struct bed3 *bed; for (bed = bedList; bed != NULL; bed = bed->next) { int start = bed->chromStart + atStart; if (start < 0) start = 0; int end = bed->chromEnd + atEnd; int chromEnd = hChromSize(database, bed->chrom); if (end > chromEnd) end = chromEnd; bed->chromStart = start; bed->chromEnd = end; } } struct bed3 *regionsOverThreshold(struct genoGraph *gg) /* Get list of regions over threshold */ { /* Get list of regions. */ if (gg == NULL) errAbort("Please go back and select a graph."); double threshold = getThreshold(); struct bed3 *bedList = chromGraphBinToBed3(gg->binFileName, threshold); if (bedList == NULL) errAbort("No regions over %g, please go back and set a lower threshold", threshold); int pad = regionPad(); addPadToBed3(bedList, -pad, pad); return bedList; } boolean checkAndClear(char *cartVar) /* If cart var exists, clear it and return TRUE */ { if (cartVarExists(cart, cartVar)) { cartRemove(cart, cartVar); /* in case of errAbort */ return TRUE; } return FALSE; } void dispatchPage() /* Look at command variables in cart and figure out which * page to draw. */ { struct sqlConnection *conn = hAllocConn(database); if (checkAndClear(hggConfigure)) { configurePage(); } else if (checkAndClear(hggConfigureOne)) { configureOnePage(); } else if (checkAndClear(hggUpload)) { uploadPage(); } else if (checkAndClear(hggSubmitUpload)) { submitUpload(conn); } else if (checkAndClear(hggImport)) { importPage(conn); } else if (checkAndClear(hggSubmitImport)) { submitImport(); } else if (checkAndClear(hggCorrelate)) { correlatePage(conn); } else if (checkAndClear(hggBrowse)) { browseRegions(conn); } else if (checkAndClear(hggSort)) { sortGenes(conn); } else { /* Default case - start fancy web page. */ if (cgiVarExists(hggPsOutput)) handlePostscript(conn); else mainPage(conn); } cartRemovePrefix(cart, hggDo); } void hggDoUsualHttp() /* Wrap html page dispatcher with code that writes out * HTTP header and write cart back to database. */ { cartWriteCookie(cart, hUserCookie()); printf("Content-Type:text/html\r\n\r\n"); /* Dispatch other pages, that actually want to write HTML. */ cartWarnCatcher(dispatchPage, cart, cartEarlyWarningHandler); cartCheckout(&cart); } void dispatchLocation() /* When this is called no output has been written at all. We * look at command variables in cart and figure out if we just * are going write an HTTP location line, which happens when we * want to invoke say the genome browser or gene sorter without * another intermediate page. If we need to do more than that * then we call hggDoUsualHttp. */ { struct sqlConnection *conn = NULL; getDbAndGenome(cart, &database, &genome, oldVars); -setUdcCacheDir(); cartSetString(cart, "db", database); /* Some custom tracks code needs this */ withLabels = cartUsualBoolean(cart, hggLabels, TRUE); conn = hAllocConn(database); getGenoGraphs(conn); /* Handle cases that just want a HTTP Location line: */ if (cartVarExists(cart, hggClickX)) { clickOnImage(conn); return; } hFreeConn(&conn); /* For other cases we want to print out some of the usual HTTP * lines including content-type */ hggDoUsualHttp(); } char *excludeVars[] = {"Submit", "submit", NULL}; int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); htmlPushEarlyHandlers(); cgiSpoof(&argc, argv); // htmlSetStyle(htmlStyleUndecoratedLink); if (argc != 1) usage(); setUdcCacheDir(); oldVars = hashNew(12); cart = cartForSession(hUserCookie(), excludeVars, oldVars); dispatchLocation(); cgiExitTime("hgGenome", enteredMainTime); return 0; }