fa9b1baf11ef0bda5abd10904cb385867db9a26b aamp Mon Apr 4 06:15:53 2011 -0700 Updated CGI to use new library function and deleted bits associated with having a variable data format. diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c index 733571e..464e008 100644 --- src/hg/hgLiftOver/hgLiftOver.c +++ src/hg/hgLiftOver/hgLiftOver.c @@ -10,73 +10,62 @@ #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "cart.h" #include "web.h" #include "hash.h" #include "liftOver.h" #include "liftOverChain.h" static char const rcsid[] = "$Id: hgLiftOver.c,v 1.62 2009/07/14 20:17:30 markd Exp $"; /* CGI Variables */ #define HGLFT_USERDATA_VAR "hglft_userData" /* typed/pasted in data */ #define HGLFT_DATAFILE_VAR "hglft_dataFile" /* file of data to convert */ -#define HGLFT_DATAFORMAT_VAR "hglft_dataFormat" /* format of data to convert */ #define HGLFT_FROMORG_VAR "hglft_fromOrg" /* FROM organism */ #define HGLFT_FROMDB_VAR "hglft_fromDb" /* FROM assembly */ #define HGLFT_TOORG_VAR "hglft_toOrg" /* TO organism */ #define HGLFT_TODB_VAR "hglft_toDb" /* TO assembly */ #define HGLFT_ERRORHELP_VAR "hglft_errorHelp" /* Print explanatory text */ #define HGLFT_REFRESHONLY_VAR "hglft_doRefreshOnly" /* Just refresh drop-down lists */ /* liftOver options: */ #define HGLFT_MINMATCH "hglft_minMatch" #define HGLFT_MINSIZEQ "hglft_minSizeQ" #define HGLFT_MINCHAINT "hglft_minChainT" #define HGLFT_MULTIPLE "hglft_multiple" #define HGLFT_MINBLOCKS "hglft_minBlocks" #define HGLFT_FUDGETHICK "hglft_fudgeThick" /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; -/* Data Formats */ -#define POSITION_FORMAT "Position" -#define BED_FORMAT "BED" -#define WIGGLE_FORMAT "Wiggle" - -char *formatList[] = - {BED_FORMAT, POSITION_FORMAT, 0}; - -#define DEFAULT_FORMAT "BED" - /* Filename prefix */ #define HGLFT "hglft" /* Javascript to support New Assembly pulldown when Orig Assembly changes */ /* Copies selected value from the Original Assembly pulldown to a hidden form */ char *onChange = "onchange=\"document.mainForm." HGLFT_REFRESHONLY_VAR ".value = 1;" "document.mainForm.submit();\""; -void webMain(struct liftOverChain *chain, char *dataFormat, boolean multiple) +void webMain(struct liftOverChain *chain, boolean multiple) /* set up page for entering data */ { struct dbDb *dbList; char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb); cgiParagraph( "This tool converts genome coordinates and genome annotation files " "between assemblies. " "The input data can be pasted into the text box, or uploaded from a file. " "If a pair of assemblies cannot be selected from the pull-down menus," " a direct lift between them is unavailable. " "However, a sequential lift may be possible. " "Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, " "Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9. " ""); @@ -176,43 +165,30 @@ cgiTableField("Min ratio of alignment blocks or exons that must map:"); cgiSimpleTableFieldStart(); cgiMakeDoubleVar(HGLFT_MINBLOCKS,chain->minBlocks,6); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:"); cgiSimpleTableFieldStart(); cgiMakeCheckBox(HGLFT_FUDGETHICK,(chain->fudgeThick[0]=='Y') ? TRUE : FALSE); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); -/* next row -- file format menu */ -cgiParagraph( - " For descriptions of the supported data formats, see the bottom of this page."); -cgiSimpleTableStart(); -cgiSimpleTableRowStart(); -cgiTableField("Data Format: "); -cgiSimpleTableFieldStart(); -cgiMakeDropList(HGLFT_DATAFORMAT_VAR, - formatList, sizeof(formatList)/sizeof (char*) - 1, dataFormat); -cgiTableFieldEnd(); -cgiTableRowEnd(); -cgiTableEnd(); - /* text box and two buttons (submit, reset) */ cgiParagraph(" Paste in data:\n"); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80); cgiTableFieldEnd(); /* right element of table is a nested table * with two buttons stacked on top of each other */ cgiSimpleTableFieldStart(); cgiSimpleTableStart(); cgiSimpleTableRowStart(); @@ -430,79 +406,77 @@ { choice = this; bestScore = score; } } return choice; } void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { /* struct liftOverChain *chainList = NULL, *chain; */ char *userData; /* char *dataFile; */ -char *dataFormat; char *organism; char *db; float minBlocks, minMatch; boolean multiple, fudgeThick; int minSizeQ, minChainT; boolean refreshOnly = FALSE; /* char *err = NULL; */ struct liftOverChain *chainList = NULL, *choice; cart = theCart; if (cgiOptionalString(HGLFT_ERRORHELP_VAR)) { puts("<PRE>"); puts(liftOverErrHelp()); //system("/usr/bin/cal"); puts("</PRE>"); return; } /* Get data to convert - from userData variable, or if * that is empty from a file. */ if (cartOptionalString(cart, "SubmitFile")) userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR); else userData = cartOptionalString(cart, HGLFT_USERDATA_VAR); -dataFormat = cartCgiUsualString(cart, HGLFT_DATAFORMAT_VAR, DEFAULT_FORMAT); cartWebStart(cart, NULL, "Lift Genome Annotations"); getDbAndGenome(cart, &db, &organism, oldVars); chainList = liftOverChainList(); choice = defaultChoices(chainList, db); if (choice == NULL) errAbort("Sorry, no conversions available from this assembly\n"); minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ); minChainT = cartCgiUsualInt(cart, HGLFT_MINCHAINT, choice->minChainT); minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks); minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch); fudgeThick = cartCgiUsualBoolean(cart, HGLFT_FUDGETHICK, (choice->fudgeThick[0]=='Y') ? TRUE : FALSE); multiple = cartCgiUsualBoolean(cart, HGLFT_MULTIPLE, (choice->multiple[0]=='Y') ? TRUE : FALSE); refreshOnly = cartCgiUsualInt(cart, HGLFT_REFRESHONLY_VAR, 0); -webMain(choice, dataFormat, multiple); +webMain(choice, multiple); liftOverChainFreeList(&chainList); if (!refreshOnly && userData != NULL && userData[0] != '\0') { struct hash *chainHash = newHash(0); char *chainFile; struct tempName oldTn, mappedTn, unmappedTn; FILE *old, *mapped, *unmapped; char *line; int lineSize; char *fromDb, *toDb; int ct = 0, errCt = 0; /* read in user data and save to file */ makeTempName(&oldTn, HGLFT, ".user"); @@ -516,85 +490,67 @@ * for lines that could not be mapped */ makeTempName(&mappedTn, HGLFT, ".bed"); makeTempName(&unmappedTn, HGLFT, ".err"); mapped = mustOpen(mappedTn.forCgi, "w"); chmod(mappedTn.forCgi, 0666); unmapped = mustOpen(unmappedTn.forCgi, "w"); chmod(unmappedTn.forCgi, 0666); fromDb = cgiString(HGLFT_FROMDB_VAR); toDb = cgiString(HGLFT_TODB_VAR); chainFile = liftOverChainFile(fromDb, toDb); if (chainFile == NULL) errAbort("ERROR: Can't convert from %s to %s: no chain file loaded", fromDb, toDb); readLiftOverMap(chainFile, chainHash); - if (sameString(dataFormat, WIGGLE_FORMAT)) - /* TODO: implement Wiggle */ - {} - else if (sameString(dataFormat, POSITION_FORMAT)) - { - ct = liftOverPositions(oldTn.forCgi, chainHash, - minMatch, minBlocks, 0, minSizeQ, - minChainT, 0, - fudgeThick, mapped, unmapped, FALSE, NULL, &errCt); - - - } - else if (sameString(dataFormat, BED_FORMAT)) - { - ct = liftOverBed(oldTn.forCgi, chainHash, + ct = liftOverBedOrPositions(oldTn.forCgi, chainHash, minMatch, minBlocks, 0, minSizeQ, minChainT, 0, fudgeThick, mapped, unmapped, multiple, NULL, &errCt); - } - else + if (ct == -1) /* programming error */ - errAbort("ERROR: Unsupported data format: %s\n", dataFormat); + errAbort("ERROR: Unsupported data format.\n"); webNewSection("Results"); - if (ct) + if (ct > 0) { /* some records succesfully converted */ cgiParagraph(""); printf("Successfully converted %d record", ct); printf("%s: ", ct > 1 ? "s" : ""); printf("<A HREF=%s TARGET=_blank>View Conversions</A>\n", mappedTn.forCgi); } if (errCt) { /* some records not converted */ cgiParagraph(""); printf("Conversion failed on %d record", errCt); printf("%s. ", errCt > 1 ? "s" : ""); printf("<A HREF=%s TARGET=_blank>Display failure file</A> \n", unmappedTn.forCgi); printf("<A HREF=\"../cgi-bin/hgLiftOver?%s=1\" TARGET=_blank>Explain failure messages</A>\n", HGLFT_ERRORHELP_VAR); puts("<P>Failed input regions:\n"); struct lineFile *errFile = lineFileOpen(unmappedTn.forCgi, TRUE); puts("<BLOCKQUOTE><PRE>\n"); while (lineFileNext(errFile, &line, &lineSize)) puts(line); lineFileClose(&errFile); puts("</PRE></BLOCKQUOTE>\n"); } - if (sameString(dataFormat, POSITION_FORMAT) && multiple) - { puts("<BLOCKQUOTE><PRE>\n"); - puts("Note: multiple checkbox ignored since it is not supported for position format."); + puts("Note: "multiple" option is not supported for position format."); puts("</PRE></BLOCKQUOTE>\n"); - } webParamsUsed(minMatch, multiple, minSizeQ, minChainT, minBlocks, fudgeThick); carefulClose(&unmapped); } webDataFormats(); webDownloads(); cartWebEnd(); } /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {"Submit", "submit", "SubmitFile", HGLFT_USERDATA_VAR, HGLFT_DATAFILE_VAR,