c6a3bbe14bed11668f0131bd1597c24f79d7f3dd angie Tue Oct 28 11:59:55 2014 -0700 Allow start==end in hgTables' user-defined regions BED (valid for insertions).fixes #14238 diff --git src/hg/hgTables/userRegions.c src/hg/hgTables/userRegions.c index dae9734..f93c456 100644 --- src/hg/hgTables/userRegions.c +++ src/hg/hgTables/userRegions.c @@ -1,328 +1,328 @@ /* identifiers - handle identifier lists: uploading, pasting, * and restricting to just things on the list. */ /* Copyright (C) 2011 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "cart.h" #include "jksql.h" #include "trackDb.h" #include "portable.h" #include "hgTables.h" #include "trashDir.h" #include "hui.h" #include "obscure.h" #include "web.h" void doSetUserRegions(struct sqlConnection *conn) /* Respond to set regions button. */ { char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, ""); char *db = cartOptionalString(cart, hgtaUserRegionsDb); if (db && !sameString(db, database)) oldPasted = ""; htmlOpen("Enter region definition\n"); hPrintf("
\n", getScriptName()); cartSaveSession(cart); hPrintf("
\n"); hPrintf("Paste regions:"); hPrintf(""); hPrintf("Or upload file:  
\n", hgtaEnteredUserRegionFile); hPrintf("
\n"); cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70); hPrintf("
\n"); cgiMakeButton(hgtaDoSubmitUserRegions, "submit"); hPrintf(" "); cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear"); hPrintf(" "); cgiMakeButton(hgtaDoMainPage, "cancel"); hPrintf("
"); hPrintf("

\n"); webIncludeHelpFile("hgTbUserRegionsHelp", FALSE); htmlClose(); } static boolean illegalCoordinate(char *chrom, int start, int end) /* verify start and end are legal for this chrom */ { int maxEnd = hChromSize(database, chrom); if (start < 0) { warn("chromStart (%d) less than zero", start); return TRUE; } if (end > maxEnd) { warn("chromEnd (%d) greater than chrom length (%s:%d)", end, chrom, maxEnd); return TRUE; } -if (start >= end) +if (start > end) { - warn("chromStart (%d) must be less than chromEnd (%s:%d)", start, chrom, end); + warn("chromStart (%d) greater than chromEnd (%s:%d)", start, chrom, end); return TRUE; } return FALSE; } static struct bed *parseRegionInput(char *inputString) /* scan the user region definition, turn into a bed list */ { int itemCount = 0; struct bed *bedList = NULL; struct bed *bedEl; int wordCount; char *words[5]; struct lineFile *lf; lf = lineFileOnString("userData", TRUE, inputString); while (0 != (wordCount = lineFileChopNext(lf, words, ArraySize(words)))) { char *chromName = NULL; int chromStart = 0; int chromEnd = 0; char *regionName = NULL; /* might be something of the form: chrom:start-end optionalRegionName */ if (((1 == wordCount) || (2 == wordCount)) && hgParseChromRange(NULL, words[0], &chromName, &chromStart, &chromEnd)) { if (2 == wordCount) regionName = cloneString(words[1]); } else if (!((3 == wordCount) || (4 == wordCount))) { int i; struct dyString *errMessage = dyStringNew(0); for (i = 0; i < wordCount; ++i) dyStringPrintf(errMessage, "%s ", words[i]); errAbort("line %d: '%s'
\n" "illegal bed size, expected 3 or 4 fields, found %d\n", lf->lineIx, dyStringCannibalize(&errMessage), wordCount); } else { chromName = hgOfficialChromName(database, words[0]); chromStart = sqlSigned(words[1]); chromEnd = sqlSigned(words[2]); if (wordCount > 3) regionName = cloneString(words[3]); } ++itemCount; if (itemCount > 1000) { warn("limit 1000 region definitions reached at line %d
\n", lf->lineIx); break; } AllocVar(bedEl); bedEl->chrom = chromName; if (NULL == bedEl->chrom) errAbort("at line %d, chrom name '%s' %s %s not recognized in this assembly %d", lf->lineIx, words[0], words[1], words[2], wordCount); bedEl->chromStart = chromStart; bedEl->chromEnd = chromEnd; if (illegalCoordinate(bedEl->chrom, bedEl->chromStart, bedEl->chromEnd)) errAbort("illegal input at line %d: %s %d %d", lf->lineIx, bedEl->chrom, bedEl->chromStart, bedEl->chromEnd); if (wordCount > 3) bedEl->name = regionName; else bedEl->name = NULL; /* if we wanted to give artifical names to each item */ #ifdef NOT { char name[128]; safef(name, ArraySize(name), "item_%04d", itemCount); bedEl->name = cloneString(name); } #endif slAddHead(&bedList, bedEl); } lineFileClose(&lf); // slSort(&bedList, bedCmp); /* this would do chrom,chromStart order */ slReverse(&bedList); /* with no sort, it is in order as user entered */ return (bedList); } static char *limitText(char *text) /* read text string and limit to 1000 actual data lines */ { struct dyString *limitedText = dyStringNew(0); /* yes, opening with FALSE so as not to destroy the original string */ struct lineFile *lf = lineFileOnString("limitText", FALSE, text); char *lineStart = NULL; int lineLength = 0; int legitimateLineCount = 0; while (legitimateLineCount < 1000 && lineFileNext(lf, &lineStart, &lineLength)) { char *s, c; s = skipLeadingSpaces(lineStart); c = s[0]; if (c != 0 && c != '#') ++legitimateLineCount; dyStringAppendN(limitedText, lineStart, lineLength); } if ((legitimateLineCount == 1000) && lineFileNext(lf, &lineStart, &lineLength)) warn("WARNING: defined regions limit of 1000 definitions reached at line %d
\n", lf->lineIx-1); lineFileClose(&lf); return (dyStringCannibalize(&limitedText)); } void doSubmitUserRegions(struct sqlConnection *conn) /* Process submit in set regions page. */ { char *idText = trimSpaces(cartString(cart, hgtaEnteredUserRegions)); char *userRegionFile = trimSpaces(cartString(cart, hgtaEnteredUserRegionFile)); boolean hasData = (idText != NULL && idText[0] != 0) || (userRegionFile != NULL && userRegionFile[0] != 0); /* beware, the string pointers from cartString() point to strings in the * cart hash. If they are manipulated and changed, they will get saved * back to the cart in their changed form. You don't want to be * altering them like that. Thus, the idText is duplicated below with * the cloneString(idText) */ htmlOpen("Table Browser (Region definitions)"); /* presence of fileName text overrides previously existing text area * contents */ if (userRegionFile != NULL && userRegionFile[0] != 0) { idText = cloneString(userRegionFile); cartRemove(cart, hgtaEnteredUserRegions); cartRemove(cart, hgtaUserRegionsFile); cartSetString(cart, hgtaEnteredUserRegions, idText); } else idText = cloneString(idText); char *lineLimitText = limitText(idText); if ( (strlen(lineLimitText) > 0) && (strlen(lineLimitText) != strlen(idText)) ) { freeMem(idText); idText = lineLimitText; cartSetString(cart, hgtaEnteredUserRegions, lineLimitText); } else freeMem(lineLimitText); if (hasData) { struct tempName tn; FILE *f; struct bed *bedEl; struct bed *bedList = parseRegionInput(idText); if (NULL == bedList) errAbort("no valid data points found in input"); trashDirFile(&tn, "hgtData", "user", ".region"); f = mustOpen(tn.forCgi, "w"); for (bedEl = bedList; bedEl; bedEl = bedEl->next ) { if (bedEl->name) fprintf(f, "%s\t%d\t%d\t%s\n", bedEl->chrom, bedEl->chromStart, bedEl->chromEnd, bedEl->name); else fprintf(f, "%s\t%d\t%d\n", bedEl->chrom, bedEl->chromStart, bedEl->chromEnd); } carefulClose(&f); cartSetString(cart, hgtaUserRegionsDb, database); cartSetString(cart, hgtaUserRegionsTable, curTable); cartSetString(cart, hgtaUserRegionsFile, tn.forCgi); cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions); if (strlen(idText) > 64 * 1024) cartRemove(cart, hgtaEnteredUserRegions); } else { cartRemove(cart, hgtaUserRegionsFile); cartRemove(cart, hgtaEnteredUserRegionFile); cartRemove(cart, hgtaRegionType); } mainPageAfterOpen(conn); htmlClose(); } char *userRegionsFileName() /* File name defined regions are in, or NULL if no such file. */ { char *fileName = cartOptionalString(cart, hgtaUserRegionsFile); char *db = cartOptionalString(cart, hgtaUserRegionsDb); if (db && !sameString(database, db)) return NULL; if (fileName == NULL) return NULL; if (fileExists(fileName)) return fileName; else { cartRemove(cart, hgtaUserRegionsFile); cartRemove(cart, hgtaRegionType); return NULL; } } struct region *getUserRegions(char *fileName) /* Get user defined regions from fileName. */ { struct region *list = NULL, *region; struct lineFile *lf; char *words[4]; int wordCount; lf = lineFileOpen(fileName, TRUE); /* TRUE == replace CR with 0 */ while (0 != (wordCount = lineFileChopNext(lf, words, ArraySize(words)))) { AllocVar(region); region->chrom = cloneString(words[0]); region->start = atoi(words[1]); region->end = atoi(words[2]); if (wordCount > 3) region->name = cloneString(words[3]); else region->name = NULL; slAddHead(&list, region); } slReverse(&list); return list; } void doClearSetUserRegionsText(struct sqlConnection *conn) /* Respond to clear within user regions enter page. */ { char *fileName = userRegionsFileName(); if (fileName != NULL) remove(fileName); cartRemove(cart, hgtaEnteredUserRegions); cartRemove(cart, hgtaEnteredUserRegionFile); cartRemove(cart, hgtaUserRegionsFile); cartRemove(cart, hgtaRegionType); doSetUserRegions(conn); } void doClearUserRegions(struct sqlConnection *conn) /* Respond to clear user regions button. */ { char *fileName = userRegionsFileName(); htmlOpen("Table Browser (Cleared Region List)"); if (fileName != NULL) remove(fileName); cartRemove(cart, hgtaEnteredUserRegions); cartRemove(cart, hgtaEnteredUserRegionFile); cartRemove(cart, hgtaUserRegionsFile); cartRemove(cart, hgtaRegionType); mainPageAfterOpen(conn); htmlClose(); }