ff3dcac9269104df22c3b06fe44556f71bcae0c3
gperez2
Thu Jun 20 17:30:01 2024 -0700
Switching the Advanced track search page, View chromosomes page, hgConvert, hgCustom, hgGateway, hgLiftOver, hgPcr, hgSession, hgTracks, and hgCustom labels/buttons to sentence case, refs #25787
diff --git src/hg/hgConvert/hgConvert.c src/hg/hgConvert/hgConvert.c
index 95e09ca..197cf20 100644
--- src/hg/hgConvert/hgConvert.c
+++ src/hg/hgConvert/hgConvert.c
@@ -1,444 +1,444 @@
/* hgConvert - CGI-script to convert browser window coordinates
* using chain files */
/* Copyright (C) 2014 The Regents of the University of California
* See kent/LICENSE or http://genome.ucsc.edu/license/ 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"
#include "genark.h"
#include "trackHub.h"
#include "quickLift.h"
#include "exportedDataHubs.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 = "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;
boolean askAboutQuickLift = FALSE;
if (exportedDataHubsEnabled())
askAboutQuickLift = TRUE;
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("Old genome: ");
+cgiTableField("Old assembly: ");
+cgiTableField("New genome: ");
+cgiTableField("New assembly: ");
if (askAboutQuickLift)
- cgiTableField("QuickLift Tracks: ");
+ cgiTableField("QuickLift tracks: ");
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, "change", onChangeToOrg);
cgiTableFieldEnd();
/* Destination assembly */
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(liftOver->toDb, dbList, HGLFT_TODB_VAR, TRUE, NULL, NULL);
cgiTableFieldEnd();
if (askAboutQuickLift)
{
cgiSimpleTableFieldStart();
boolean quickLift = cartUsualBoolean(cart, "doQuickLift", FALSE);
cgiMakeCheckBoxWithId("doQuickLift", quickLift, "doQuickLift");
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;
if (toRank == 0) // chains to db's that are not active shouldn't be considered
return 0;
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(trackHubSkipHubName(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;
struct dyString *visDy = NULL;
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;
boolean doQuickLift = cartUsualBoolean(cart, "doQuickLift", FALSE);
unsigned quickChain = 0;
unsigned quickHub = 0;
if (doQuickLift)
{
quickChain = quickLiftGetChain(fromDb->name, toDb->name);
if (quickChain == 0)
errAbort("can't find quickChain from %s to %s", fromDb->name, toDb->name);
visDy = newDyString(1024);
char *newHub = trackHubBuild(fromDb->name, cart, visDy);
if ((quickHub = registerExportedDataHub(fromDb->name, newHub)) == 0)
errAbort("can't register exportedDataHub %s\n", newHub);
}
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. */
boolean startedAnchor = FALSE;
if ((hDbIsActive(toDb->name) && chromSeqExists) || startsWith("hub:",toDb->nibPath))
{
if (quickChain)
printf("<A HREF=\"%s?db=%s&position=%s:%d-%d&quickLift.%d.%s=%d&hideTracks=1%s\">",
hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain, visDy->string);
else
printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\">",
hgTracksName(), toDb->name, chain->qName, qStart+1, qEnd);
startedAnchor = TRUE;
}
else if (sameString(toDb->nibPath, "genark"))
{
char *hubUrl = genarkUrl(toDb->name);
if (hubUrl)
{
startedAnchor = TRUE;
if (quickChain)
printf("<A HREF=\"%s?genome=%s&hubUrl=%s&position=%s:%d-%d&quickLift.%d.%s=%d\">",
hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd, quickHub, toDb->name, quickChain);
else
printf("<A HREF=\"%s?genome=%s&hubUrl=%s&position=%s:%d-%d\">",
hgTracksName(), toDb->name, hubUrl, chain->qName, qStart+1, qEnd);
}
}
printf("%s:%d-%d", chain->qName, qStart+1, qEnd);
if (startedAnchor)
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( MULTI_REGION_CHROM, cartUsualString(cart, "position", ""))
|| startsWith(OLD_MULTI_REGION_CHROM, cartUsualString(cart, "position", "")))
cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", ""));
if (cartVarExists(cart, HGLFT_DO_CONVERT))
doConvert(fromPos);
else
{
struct liftOverChain *checkLiftOverList = liftOverChainListForDbFiltered(trackHubSkipHubName(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;
}