a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c
galt
Mon Jan 30 16:18:41 2017 -0800
Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c.
diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c
index d0b3ace..edd8f42 100644
--- src/hg/hgConvert/hgConvert.c
+++ src/hg/hgConvert/hgConvert.c
@@ -1,382 +1,382 @@
/* hgConvert - CGI-script to convert browser window coordinates
* using chain files */
/* Copyright (C) 2014 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#include "common.h"
#include "hash.h"
#include "errAbort.h"
#include "jksql.h"
#include "linefile.h"
#include "hCommon.h"
#include "fa.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "hdb.h"
#include "hui.h"
#include "cart.h"
#include "web.h"
#include "chain.h"
#include "liftOver.h"
#include "liftOverChain.h"
#include "chromInfo.h"
#include "net.h"
/* CGI Variables */
#define HGLFT_TOORG_VAR "hglft_toOrg" /* TO organism */
#define HGLFT_TODB_VAR "hglft_toDb" /* TO assembly */
#define HGLFT_DO_CONVERT "hglft_doConvert" /* Do the actual conversion */
/* Global Variables */
static struct cart *cart; /* CGI and other variables */
static struct hash *oldVars = NULL;
static char *organism = NULL;
static char *database = NULL;
/* Javascript to support New Assembly pulldown when New Genome changes. */
/* Copies selected values to a hidden form */
-char *onChangeToOrg = "onchange=\"document.mainForm.submit();\"";
+char *onChangeToOrg = "document.mainForm.submit();";
static struct dbDb *matchingDb(struct dbDb *list, char *name)
/* Find database of given name in list or die trying. */
{
struct dbDb *db;
for (db = list; db != NULL; db = db->next)
{
if (sameString(name, db->name))
return db;
}
errAbort("Can't find %s in matchingDb", name);
return NULL;
}
static void askForDestination(struct liftOverChain *liftOver, char *fromPos,
struct dbDb *fromDb, struct dbDb *toDb)
/* set up page for entering data */
{
struct dbDb *dbList;
cartWebStart(cart, database, "Convert %s to New Assembly", fromPos);
/* create HMTL form */
puts("<FORM ACTION=\"../cgi-bin/hgConvert\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
/* create HTML table for layout purposes */
puts("\n<TABLE WIDTH=\"100%%\">\n");
/* top row -- labels */
cgiSimpleTableRowStart();
cgiTableField("Old Genome: ");
cgiTableField("Old Assembly: ");
cgiTableField("New Genome: ");
cgiTableField("New Assembly: ");
cgiTableField(" ");
cgiTableRowEnd();
/* Next row -- data and controls */
cgiSimpleTableRowStart();
/* From organism and assembly. */
cgiTableField(fromDb->organism);
cgiTableField(fromDb->description);
/* Destination organism. */
cgiSimpleTableFieldStart();
dbList = hGetLiftOverToDatabases(liftOver->fromDb);
-printSomeGenomeListHtmlNamed(HGLFT_TOORG_VAR, liftOver->toDb, dbList, onChangeToOrg);
+printSomeGenomeListHtmlNamed(HGLFT_TOORG_VAR, liftOver->toDb, dbList, "change", onChangeToOrg);
cgiTableFieldEnd();
/* Destination assembly */
cgiSimpleTableFieldStart();
-printAllAssemblyListHtmlParm(liftOver->toDb, dbList, HGLFT_TODB_VAR, TRUE, "");
+printAllAssemblyListHtmlParm(liftOver->toDb, dbList, HGLFT_TODB_VAR, TRUE, NULL, NULL);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeButton(HGLFT_DO_CONVERT, "Submit");
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
puts("</FORM>\n");
cartWebEnd();
}
static double scoreLiftOverChain(struct liftOverChain *chain,
char *fromOrg, char *fromDb, char *toOrg, char *toDb, struct hash *dbRank )
/* Score the chain in terms of best match for cart settings */
{
double score = 0;
char *chainFromOrg = hOrganism(chain->fromDb);
char *chainToOrg = hOrganism(chain->toDb);
int fromRank = hashIntValDefault(dbRank, chain->fromDb, 0);
int toRank = hashIntValDefault(dbRank, chain->toDb, 0);
int maxRank = hashIntVal(dbRank, "maxRank");
if (sameOk(fromOrg,chainFromOrg) &&
sameOk(fromDb,chain->fromDb) &&
sameOk(toOrg,chainToOrg) &&
sameOk(toDb,chain->toDb))
score += 10000000;
if (sameOk(fromOrg,chainFromOrg))
score += 2000000;
if (sameOk(fromDb,chain->fromDb))
score += 1000000;
if (sameOk(toOrg,chainToOrg))
score += 200000;
if (sameOk(toDb,chain->toDb))
score += 100000;
score += 10*(maxRank-fromRank);
score += (maxRank - toRank);
return score;
}
static struct liftOverChain *defaultChoices(struct liftOverChain *chainList, char *fromOrg, char *fromDb)
/* Out of a list of liftOverChains and a cart, choose a
* list to display. */
{
char *toOrg, *toDb;
struct liftOverChain *choice = NULL;
struct hash *dbRank = hGetDatabaseRank();
double bestScore = -1;
struct liftOverChain *this = NULL;
/* Get the initial values. */
toOrg = cartCgiUsualString(cart, HGLFT_TOORG_VAR, "0");
toDb = cartCgiUsualString(cart, HGLFT_TODB_VAR, "0");
if (sameWord(toOrg,"0"))
toOrg = NULL;
if (sameWord(toDb,"0"))
toDb = NULL;
for (this = chainList; this != NULL; this = this->next)
{
double score = scoreLiftOverChain(this, fromOrg, fromDb, toOrg, toDb, dbRank);
if (score > bestScore)
{
choice = this;
bestScore = score;
}
}
return choice;
}
static char *skipWord(char *s)
/* Skip word, and any leading spaces before next word. */
{
return skipLeadingSpaces(skipToSpaces(s));
}
static long chainTotalBlockSize(struct chain *chain)
/* Return sum of sizes of all blocks in chain */
{
struct cBlock *block;
long total = 0;
for (block = chain->blockList; block != NULL; block = block->next)
total += block->tEnd - block->tStart;
return total;
}
static struct chain *chainLoadIntersecting(char *fileName,
char *chrom, int start, int end)
/* Load the chains that intersect given region. */
{
struct lineFile *lf = netLineFileOpen(fileName);
char *line;
int chromNameSize = strlen(chrom);
struct chain *chainList = NULL, *chain;
#ifdef SOON /* Put in if we index. */
boolean gotChrom = FALSE;
#endif /* SOON */
int chainCount = 0;
while (lineFileNextReal(lf, &line))
{
if (startsWith("chain", line) && isspace(line[5]))
{
++chainCount;
line = skipWord(line); /* Skip over 'chain' */
line = skipWord(line); /* Skip over chain score */
if (startsWith(chrom, line) && isspace(line[chromNameSize]))
{
#ifdef SOON /* Put in if we index. */
gotChrom = TRUE;
#endif /* SOON */
lineFileReuse(lf);
chain = chainReadChainLine(lf);
if (rangeIntersection(chain->tStart, chain->tEnd, start, end) > 0)
{
chainReadBlocks(lf, chain);
slAddHead(&chainList, chain);
}
else
chainFree(&chain);
}
#ifdef SOON /* Put in if we index. */
else if (gotChrom)
break; /* We assume file is sorted by chromosome, so we're done. */
#endif /* SOON */
}
}
lineFileClose(&lf);
slReverse(&chainList);
return chainList;
}
static struct chain *chainLoadAndTrimIntersecting(char *fileName,
char *chrom, int start, int end)
/* Load the chains that intersect given region, and trim them
* to fit region. */
{
struct chain *rawList, *chainList = NULL, *chain, *next;
rawList = chainLoadIntersecting(fileName, chrom, start, end);
for (chain = rawList; chain != NULL; chain = next)
{
struct chain *subChain, *chainToFree;
next = chain->next;
chainSubsetOnT(chain, start, end, &subChain, &chainToFree);
if (subChain != NULL)
slAddHead(&chainList, subChain);
if (chainToFree != NULL)
chainFree(&chain);
}
slSort(&chainList, chainCmpScore);
return chainList;
}
static void doConvert(char *fromPos)
/* Actually do the conversion */
{
struct dbDb *fromDb = hDbDb(database), *toDb = hDbDb(cartString(cart, HGLFT_TODB_VAR));
char *fileName = liftOverChainFile(fromDb->name, toDb->name);
fileName = hReplaceGbdbMustDownload(fileName);
char *chrom;
int start, end;
int origSize;
struct chain *chainList, *chain;
cartWebStart(cart, database, "%s %s %s to %s %s", fromDb->organism, fromDb->description,
fromPos, toDb->organism, toDb->description);
if (!hgParseChromRange(database, fromPos, &chrom, &start, &end))
errAbort("position %s is not in chrom:start-end format", fromPos);
origSize = end - start;
chainList = chainLoadAndTrimIntersecting(fileName, chrom, start, end);
if (chainList == NULL)
printf("Sorry this position couldn't be found in new assembly");
else
{
for (chain = chainList; chain != NULL; chain = chain->next)
{
int blockSize;
int qStart, qEnd;
if (chain->qStrand == '-')
{
qStart = chain->qSize - chain->qEnd;
qEnd = chain->qSize - chain->qStart;
}
else
{
qStart = chain->qStart;
qEnd = chain->qEnd;
}
blockSize = chainTotalBlockSize(chain);
/* Check if the toDb database exists and if the chromosome
sequence file (of the hgConvert result) exists in the location
specified in chromInfo for the toDb. */
boolean chromSeqExists = (sqlDatabaseExists(toDb->name) &&
chromSeqFileExists(toDb->name, chain->qName));
/* Check if the toDb has active set to 1 in dbDb if the toDb
database exists.
If these conditions are met then print position link to
browser for toDb, otherwise just print position without link. */
if (hDbIsActive(toDb->name) && chromSeqExists)
printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\">",
hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd);
printf("%s:%d-%d", chain->qName, qStart+1, qEnd);
if (hDbIsActive(toDb->name) && chromSeqExists)
printf("</A>");
printf(" (%3.1f%% of bases, %3.1f%% of span)<BR>\n",
100.0 * blockSize/origSize,
100.0 * (chain->tEnd - chain->tStart) / origSize);
}
}
cartWebEnd();
}
static struct liftOverChain *cleanLiftOverList(struct liftOverChain *list)
/* eliminate from the list where toDb doesn't exist in dbDb */
{
struct liftOverChain *cleanList = NULL;
struct hash *dbDbHash = hDbDbHash();
struct liftOverChain *this = NULL;
struct liftOverChain *next = NULL;
for (this = list; this != NULL; this = next)
{
next = this->next;
if (hashLookup(dbDbHash, this->toDb))
slAddHead(&cleanList, this);
else
liftOverChainFree(&this);
}
slReverse(&cleanList);
return cleanList;
}
static void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *fromPos = cartString(theCart, "position");
cart = theCart;
getDbAndGenome(cart, &database, &organism, oldVars);
// Try to deal with virt chrom position used by hgTracks.
if (startsWith("virt:", cartUsualString(cart, "position", "")))
cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", ""));
if (cartVarExists(cart, HGLFT_DO_CONVERT))
doConvert(fromPos);
else
{
struct liftOverChain *checkLiftOverList = liftOverChainListForDbFiltered(database);
struct liftOverChain *liftOverList = cleanLiftOverList(checkLiftOverList);
struct liftOverChain *choice = defaultChoices(liftOverList, organism, database);
if (choice == NULL)
errAbort("Sorry, no conversions available from this assembly.");
struct dbDb *dbList, *fromDb, *toDb;
dbList = hDbDbListMaybeCheck(FALSE);
fromDb = matchingDb(dbList, choice->fromDb);
toDb = matchingDb(dbList, choice->toDb);
askForDestination(choice, fromPos, fromDb, toDb);
liftOverChainFreeList(&liftOverList);
}
}
/* Null terminated list of CGI Variables we don't want to save
* permanently. */
char *excludeVars[] = { "submit", HGLFT_DO_CONVERT, NULL};
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
cgiExitTime("hgConvert", enteredMainTime);
return 0;
}