d1aafb0904765d2abfbb8b7eb92826460962b0ed angie Fri May 1 16:26:50 2015 -0700 Libifying hgTables' code that parses user's region input, so I can use it to add support for user regions to hgIntegrator. refs #14579 diff --git src/hg/hgTables/userRegions.c src/hg/hgTables/userRegions.c index f93c456..739244c 100644 --- src/hg/hgTables/userRegions.c +++ src/hg/hgTables/userRegions.c @@ -1,328 +1,225 @@ /* 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 "userRegions.h" #include "web.h" +static int maxRegions = 1000; +static int maxErrors = 100; -void doSetUserRegions(struct sqlConnection *conn) +void doSetUserRegionsAfterOpen(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()); +hPrintf("\n", getScriptName(), + cartUsualString(cart, "formMethod", "POST")); 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) - { - 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 +void doSetUserRegions(struct sqlConnection *conn) +/* Respond to set regions button. */ { - 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); +htmlOpen("Enter region definition\n"); +doSetUserRegionsAfterOpen(conn); } static char *limitText(char *text) -/* read text string and limit to 1000 actual data lines */ +/* read text string and limit to maxRegions 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)) +while (legitimateLineCount < maxRegions && 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); +if ((legitimateLineCount == maxRegions) && lineFileNext(lf, &lineStart, &lineLength)) + warn("WARNING: defined regions limit of %d definitions reached at line %d
\n", + maxRegions, lf->lineIx-1); lineFileClose(&lf); return (dyStringCannibalize(&limitedText)); } +static void cartRemoveUserRegions() +/* Remove all cart variables related to storage of user regions. */ +{ +cartRemove(cart, hgtaEnteredUserRegions); +cartRemove(cart, hgtaEnteredUserRegionFile); +cartRemove(cart, hgtaUserRegionsFile); +cartRemove(cart, hgtaUserRegionsDb); +cartRemove(cart, hgtaRegionType); +} + 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) +boolean success = TRUE; +if (isNotEmpty(idText)) { - 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 ) + int regionCount = 0; + char *warnText = NULL; + char *trashFileName = userRegionsParse(database, idText, maxRegions, maxErrors, + ®ionCount, &warnText); + if (isNotEmpty(warnText)) { - 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); + success = FALSE; + warn("%s", warnText); + } + if (regionCount == 0) + { + success = FALSE; + warn("No valid regions found in input; see below for formatting instructions"); } - carefulClose(&f); cartSetString(cart, hgtaUserRegionsDb, database); - cartSetString(cart, hgtaUserRegionsTable, curTable); - cartSetString(cart, hgtaUserRegionsFile, tn.forCgi); + cartSetString(cart, hgtaUserRegionsFile, trashFileName); cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions); if (strlen(idText) > 64 * 1024) cartRemove(cart, hgtaEnteredUserRegions); } else { - cartRemove(cart, hgtaUserRegionsFile); - cartRemove(cart, hgtaEnteredUserRegionFile); - cartRemove(cart, hgtaRegionType); + cartRemoveUserRegions(); } +if (success) mainPageAfterOpen(conn); +else + doSetUserRegionsAfterOpen(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); + cartRemoveUserRegions(); 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); +lineFileClose(&lf); 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); +cartRemoveUserRegions(); 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); +cartRemoveUserRegions(); mainPageAfterOpen(conn); htmlClose(); }