void doClearSubtrackMerge(struct sqlConnection *conn)
/* Respond to click on clear subtrack merge. */
{
cartRemovePrefix(cart, hgtaSubtrackMergePrefix);
cartRemovePrefix(cart, hgtaNextSubtrackMergePrefix);
doMainPage(conn);
}
void doAdvFilterClear(struct sqlConnection *conn, struct column *colList)
/* Clear variables in advanced filter page. */
{
cartRemovePrefix(cart, advFilterPrefix);
cartRemovePrefix(cart, advFilterPrefixI);
doAdvFilter(conn, colList);
}
void dispatch()
/* Set up a connection to database and dispatch control
* based on hgpDo type var. */
{
struct sqlConnection *conn = sqlConnect(visiDb);
if (cartVarExists(cart, hgpDoThumbnails))
doThumbnails(conn);
else if (cartVarExists(cart, hgpDoImage))
doImage(conn);
else if (cartVarExists(cart, hgpDoProbe))
doProbe(conn);
else if (cartVarExists(cart, hgpDoControls))
doControls(conn);
else if (cartVarExists(cart, hgpDoId))
doId(conn);
#ifdef SOON
else if (cartVarExists(cart, hgpDoConfig))
configPage(conn);
#endif /* SOON */
else if (cartVarExists(cart, hgpDoSearch))
doDefault(conn, TRUE);
else
{
char *oldListSpec = hashFindVal(oldCart, hgpListSpec);
char *newListSpec = cartOptionalString(cart, hgpListSpec);
boolean isNew = differentStringNullOk(oldListSpec, newListSpec);
doDefault(conn, isNew);
}
cartRemovePrefix(cart, hgpDoPrefix);
}
void doAdvFilterKeyPasted(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle submission in key-paste in form. */
{
char *pasteVarName = colVarName(col, keyWordPastedPrefix);
char *pasteVal = trimSpaces(cartString(cart, pasteVarName));
char *keyVarName = advFilterName(col, "keyFile");
if (pasteVal == NULL || pasteVal[0] == 0)
{
/* If string is empty then clear cart variable. */
cartRemove(cart, keyVarName);
}
else
{
/* Else write variable to temp file and save temp
* file name. */
struct tempName tn;
FILE *f;
makeTempName(&tn, "near", ".key");
f = mustOpen(tn.forCgi, "w");
mustWrite(f, pasteVal, strlen(pasteVal));
carefulClose(&f);
cartSetString(cart, keyVarName, tn.forCgi);
}
cartRemovePrefix(cart, keyWordPastedPrefix);
doAdvFilter(conn, colList);
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
cart = theCart;
/* Break out new block after have set cart */
{
int id = cartUsualInt(cart, hgbiId, 1);
struct sqlConnection *conn = sqlConnect("bioImage");
char *geneName = bioImageGeneName(conn, id);
if (cartVarExists(cart, hgbiDoFullSize))
{
htmStart(stdout, "BioImage Full Sized Image");
printf("<IMG SRC=\"/%s\"><BR>\n", bioImageFullSizePath(conn, id));
printCaption(conn, id, geneName);
htmlEnd();
}
else /* Default case - start fancy web page. */
{
mainPage(conn, id, geneName);
}
cartRemovePrefix(cart, hgbiDoPrefix);
sqlDisconnect(&conn);
}
}
void doAdvFilterKeyClear(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
cartRemovePrefix(cart, keyWordClearPrefix);
cartRemove(cart, advFilterName(col, "keyFile"));
doAdvFilter(conn, colList);
}
void doDefaultConfigure(struct sqlConnection *conn, struct column *colList)
/* Do configuration starting with defaults. */
{
struct column *col;
for (col=colList; col != NULL; col = col->next)
col->on = col->defaultOn;
cartRemovePrefix(cart, colConfigPrefix);
cartRemove(cart, colOrderVar);
//restoreDefaultOrder(&colList);
doConfigure(conn, colList); //, NULL);
}
void dispatchPage()
/* Look at command variables in cart and figure out which
* page to draw. */
{
struct sqlConnection *conn = hAllocConn(database);
if (checkAndClear(hggConfigure))
{
configurePage();
}
else if (checkAndClear(hggConfigureOne))
{
configureOnePage();
}
else if (checkAndClear(hggUpload))
{
uploadPage();
}
else if (checkAndClear(hggSubmitUpload))
{
submitUpload(conn);
}
else if (checkAndClear(hggImport))
{
importPage(conn);
}
else if (checkAndClear(hggSubmitImport))
{
submitImport();
}
else if (checkAndClear(hggCorrelate))
{
correlatePage(conn);
}
else if (checkAndClear(hggBrowse))
{
browseRegions(conn);
}
else if (checkAndClear(hggSort))
{
sortGenes(conn);
}
else
{
/* Default case - start fancy web page. */
if (cgiVarExists(hggPsOutput))
handlePostscript(conn);
else
mainPage(conn);
}
cartRemovePrefix(cart, hggDo);
}
void doAdvFilterKeyPaste(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordPastePrefix);
safef(buf, sizeof(buf), "Paste List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST>\n");
cartSaveSession(cart);
hPrintf("Paste in a list of items to match. ");
cgiMakeButton("submit", "submit");
hPrintf("<BR>\n");
varName = colVarName(col, keyWordPastedPrefix);
cgiMakeTextArea(varName, "", 10, 60);
hPrintf("</FORM>");
}
void doMiddle(struct cart *theCart)
/* Write the middle parts of the HTML page.
* This routine sets up some globals and then
* dispatches to the appropriate page-maker. */
{
cart = theCart;
if (hIsGisaidServer())
{
validateGisaidUser(cart);
}
if (cartVarExists(cart, confVarName))
doConfigure(conn, colList);
else if (cartVarExists(cart, defaultConfName))
doDefaultConfigure(conn, colList);
else if (cartVarExists(cart, hideAllConfName))
doConfigHideAll(conn, colList);
else if (cartVarExists(cart, showAllConfName))
doConfigShowAll(conn, colList);
else if (cartVarExists(cart, getSeqPageVarName))
doGetSeqPage(conn, colList);
else if (cartVarExists(cart, advFilterVarName))
doAdvFilter(conn, colList);
else if (cartVarExists(cart, advFilterClearVarName))
doAdvFilterClear(conn, colList);
else if ((col = advFilterKeyPastePressed(colList)) != NULL)
doAdvFilterKeyPaste(conn, colList, col);
else if ((col = advFilterKeyPastedPressed(colList)) != NULL)
doAdvFilterKeyPasted(conn, colList, col);
else if ((col = advFilterKeyUploadPressed(colList)) != NULL)
doAdvFilterKeyUpload(conn, colList, col);
else if ((col = advFilterKeyClearPressed(colList)) != NULL)
doAdvFilterKeyClear(conn, colList, col);
else
displayData(conn, colList);
cartRemovePrefix(cart, "gisaidTable.do.");
}
void doAdvFilterKeyUpload(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordUploadPrefix);
safef(buf, sizeof(buf), "Upload List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n");
cartSaveSession(cart);
hPrintf("Enter the name of a file from your computer that contains a list");
hPrintf("of items separated by a space, tab or line.<BR>");
varName = colVarName(col, keyWordPastedPrefix);
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", varName);
cgiMakeButton("submit", "submit");
hPrintf("</FORM>");
}
void doOutSelectedFields(char *table, struct sqlConnection *conn)
/* Put up select fields (for tab-separated output) page. */
{
if (anySubtrackMerge(database, curTable))
errAbort("Can't do selected fields output when subtrack merge is on. "
"Please go back and select another output type, or clear the subtrack merge.");
else if (anyIntersection())
errAbort("Can't do selected fields output when intersection is on. "
"Please go back and select another output type, or clear the intersection.");
else
{
char *fsTable = cartOptionalString(cart, hgtaFieldSelectTable);
char *dbTable = NULL;
table = connectingTableForTrack(table);
dbTable = getDbTable(database, table);
/* Remove cart state if table has been changed: */
if (fsTable && ! sameString(fsTable, dbTable))
{
cartRemovePrefix(cart, hgtaFieldSelectPrefix);
cartRemove(cart, hgtaFieldSelectTable);
}
doBigSelectPage(database, table);
}
}
static boolean allelesExists(struct section *section,
struct sqlConnection *conn, char *geneId)
// Return TRUE if common haplotype alleles exist.
{
// If there was a reset then clear out settings
if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
cartRemovePrefix(cart,HAPLO_TABLE "_" );
// Start with the default variables for haplotype retrieval
struct haploExtras *he = haplotypeExtrasDefault(database, 0);
section->extras = he;
// Need to get genePred struct from geneId
char where[128];
safef(where,sizeof(where),"name = '%s'",geneId);
struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
if (gp == NULL || gp->cdsStart == gp->cdsEnd) // Ain't interested in non-protein coding genes
{
haplotypeExtrasFree(&he);
return FALSE;
}
he->chrom = gp->chrom; // Probably not needed
he->justModel = lmCloneString(he->lm,geneId);
//he->growTree = FALSE; // Tree growing not needed here
// Need to determine the correct vcf file and open it
if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
struct vcfFile *vcff = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
if (vcff == NULL)
{
haplotypeExtrasFree(&he);
return FALSE;
}
vcfFileMakeReusePool(vcff,1024 * 1024);
// All or Limit to the 99%
boolean rareVars = cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
if (rareVars)
he->synonymous = TRUE;
else
he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
// Lets show the population distribution
he->populationsToo = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
if (he->populationsToo)
he->populationMinPct = 5;
else if (he->populationsMinor)
{
he->populationsMinor = FALSE;
cartRemove(cart, HAPLO_MINOR_DIST );
}
// Need to generate haplotypes
section->items = geneHapSetForOneModel(he,vcff,gp,TRUE);
return TRUE;// (section->items != NULL);
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
static void removeFilterVars()
/* Remove filter variables from cart. */
{
cartRemovePrefix(cart, hgtaFilterPrefix);
cartRemove(cart, hgtaFilterTable);
}