boolean wikiLinkEnabled()
/* Return TRUE if all wiki.* parameters are defined in hg.conf . */
{
return ((cfgOption(CFG_WIKI_HOST) != NULL) &&
(cfgOption(CFG_WIKI_USER_NAME_COOKIE) != NULL) &&
(cfgOption(CFG_WIKI_LOGGED_IN_COOKIE) != NULL));
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
void hgBotDelay()
/* High level bot delay call - looks up bottleneck server
* in hg.conf. */
{
char *host = cfgOption("bottleneck.host");
char *port = cfgOption("bottleneck.port");
if (host != NULL && port != NULL)
botDelayCgi(host, atoi(port));
}
static boolean canMakeImages()
/* Determine whether we have the necessary command line programs for
* creating images above. */
{
char *psxy = cfgOption("hgc.psxyPath");
char *ps2raster = cfgOption("hgc.ps2rasterPath");
char *ghostscript = cfgOption("hgc.ghostscriptPath");
if (isEmpty(psxy) || isEmpty(ps2raster) || isEmpty(ghostscript))
return FALSE;
if (!fileExists(psxy) || !fileExists(ps2raster) || !fileExists(ghostscript))
return FALSE;
return TRUE;
}
struct sqlConnection *dbConnect()
/* Get a connection do database specified in ~/.hg.conf */
{
struct sqlConnection *conn = NULL;
char *hdbHost = cfgOption("db.host");
char *hdbUser = cfgOption("db.user");
char *hdbPassword = cfgOption("db.password");
char *hdbDatabase = cfgOption("db.database");
if(hdbDatabase == NULL)
hdbDatabase = hDefaultDb();
if(hdbHost == NULL || hdbUser == NULL || hdbPassword == NULL)
errAbort("Cannot read in connection setting from configuration file.");
conn = sqlConnectRemote(hdbHost, hdbUser, hdbPassword, hdbDatabase);
return conn;
}
/***********************************************************************************************************************************
Process config protocol requests
***********************************************************************************************************************************/
bool
configProtocol(const String *command, const VariantList *paramList, ProtocolServer *server)
{
FUNCTION_LOG_BEGIN(logLevelDebug);
FUNCTION_LOG_PARAM(STRING, command);
FUNCTION_LOG_PARAM(VARIANT_LIST, paramList);
FUNCTION_LOG_PARAM(PROTOCOL_SERVER, server);
FUNCTION_LOG_END();
ASSERT(command != NULL);
// Attempt to satisfy the request -- we may get requests that are meant for other handlers
bool found = true;
MEM_CONTEXT_TEMP_BEGIN()
{
if (strEq(command, PROTOCOL_COMMAND_CONFIG_OPTION_STR))
{
VariantList *optionList = varLstNew();
for (unsigned int optionIdx = 0; optionIdx < varLstSize(paramList); optionIdx++)
varLstAdd(optionList, varDup(cfgOption(cfgOptionId(strPtr(varStr(varLstGet(paramList, optionIdx)))))));
protocolServerResponse(server, varNewVarLst(optionList));
}
else
found = false;
}
MEM_CONTEXT_TEMP_END();
FUNCTION_LOG_RETURN(BOOL, found);
}
void googleAnalytics()
/* check for analytics configuration item and output google hooks if OK */
{
static boolean done = FALSE;
if (done)
return;
done = TRUE; /* do not repeat this by mistake */
char *analyticsKey = cfgOption("analyticsKey");
/* if config is missing or empty, nothing happens here */
if (isEmpty(analyticsKey))
return;
hPrintf("\n<script type=\"text/javascript\">\n"
"var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");\n"
"document.write(unescape(\"%%3Cscript src='\" + gaJsHost + \"google-analytics.com/ga.js' type='text/javascript'%%3E%%3C/script%%3E\"));\n"
"</script>\n"
"<script type=\"text/javascript\">\n"
"var pageTracker = _gat._getTracker(\"%s\");\n"
"pageTracker._initData();\n"
"pageTracker._trackPageview();\n"
"</script>\n", analyticsKey);
}
void googleAnalytics()
/* check for analytics configuration item and output google hooks if OK */
{
static boolean done = FALSE;
if (done)
return;
done = TRUE; /* do not repeat this by mistake */
char *analyticsKey = cfgOption("analyticsKey");
/* if config is missing or empty, nothing happens here */
if (isEmpty(analyticsKey))
return;
/* updated to Universal Analytics code 2014-06-19 */
hPrintf("\n<script>\n"
" (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){\n"
" (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),\n"
" m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)\n"
" })(window,document,'script','//www.google-analytics.com/analytics.js','ga');\n"
" ga('require', 'displayfeatures');\n"
" ga('create', '%s', 'auto');\n"
" ga('send', 'pageview');\n"
"\n"
"</script>", analyticsKey);
}
int hgBotDelayTime()
/* Get suggested delay time from cgi. */
{
char *ip = getenv("REMOTE_ADDR");
char *host = cfgOption("bottleneck.host");
char *port = cfgOption("bottleneck.port");
int delay = 0;
if (host != NULL && port != NULL && ip != NULL)
{
char *botCheckString = getBotCheckString(ip);
delay = botDelayTime(host, atoi(port), botCheckString);
freeMem(botCheckString);
}
return delay;
}
boolean loginSystemEnabled()
/* Return TRUE if login.systemName parameter is defined in hg.conf . */
{
#ifdef USE_SSL
return (cfgOption(CFG_LOGIN_SYSTEM_NAME) != NULL);
#else
return FALSE;
#endif
}
char *wikiLinkHost()
/* Return the wiki host specified in hg.conf, or NULL. Allocd here.
* Returns hostname from http request if hg.conf entry is HTTPHOSTNAME.
* */
{
char *wikiHost = cfgOption(CFG_WIKI_HOST);
if ((wikiHost!=NULL) && sameString(wikiHost, "HTTPHOST"))
wikiHost = hHttpHost();
return cloneString(wikiHost);
}
char *getCfgOption(char *config, char *setting)
/* get setting for specified config */
{
char temp[256];
safef(temp, sizeof(temp), "%s.%s", config, setting);
char *value = cfgOption(temp);
if (!value)
errAbort("setting %s not found!",temp);
return value;
}
static char *getH1n1StructDir()
/* get location of h1n1 modeling directory */
{
static char *dir = NULL;
if (dir == NULL)
{
dir = cfgOption("gisaid.structDir");
if (dir == NULL)
errAbort("gisaid.structDir not set in hg.conf");
}
return dir;
}
static char *getH1n1StructUrl()
/* get URL of h1n1 modeling directory */
{
static char *url = NULL;
if (url == NULL)
{
url = cfgOption("gisaid.structUrl");
if (url == NULL)
errAbort("gisaid.structUrl not set in hg.conf");
}
return url;
}
boolean hIsGsidServer()
/* Is this the GSID-customized server? Change for config variable
* gsid.server=yes */
{
static boolean gsidHost = FALSE;
static boolean haveChecked = FALSE;
if (!haveChecked)
{
char *serverOpt = cfgOption("gsid.server");
gsidHost = (serverOpt != NULL) && sameString(serverOpt, "yes");
haveChecked = TRUE;
}
return gsidHost;
}
boolean hIsCgbServer()
/* Is this a cancer genome browser server? Change for config variable
* cgb.server=yes */
{
static boolean cgbHost = FALSE;
static boolean haveChecked = FALSE;
if (!haveChecked)
{
char *serverOpt = cfgOption("cgb.server");
cgbHost = (serverOpt != NULL) && sameString(serverOpt, "yes");
haveChecked = TRUE;
}
return cgbHost;
}
/** load the sage experiment data
*/
struct sageExp *loadSageExps(char *tableName, struct slName *nmList)
{
char *user = cfgOption("db.user");
char *password = cfgOption("db.password");
struct sqlConnection *sc = NULL;
char query[256];
struct sageExp *seList = NULL, *se=NULL;
char **row;
struct sqlResult *sr = NULL;
char *db = cgiUsualString("db", "hgFixed");
sc = sqlConnectRemote("localhost", user, password, db);
sqlSafef(query, sizeof query, "select * from sageExp order by num");
sr = sqlGetResult(sc,query);
while((row = sqlNextRow(sr)) != NULL)
{
se = sageExpLoad(row);
slAddHead(&seList,se);
}
sqlFreeResult(&sr);
sqlDisconnect(&sc);
slReverse(&seList);
return seList;
}
/** load the sage data by constructing a query based on the names in nmList
*/
struct sage *loadSageData(char *table, struct slName *nmList)
{
char *user = cfgOption("db.user");
char *password = cfgOption("db.password");
struct sqlConnection *sc = NULL;
struct dyString *query = newDyString(2048);
struct sage *sgList = NULL, *sg=NULL;
struct slName *nm =NULL;
char *db = cgiUsualString("db", "hgFixed");
char **row;
int count=0;
struct sqlResult *sr = NULL;
sc = sqlConnectRemote("localhost", user, password, db);
sqlDyStringPrintf(query, "select * from sage where ");
for(nm=nmList;nm!=NULL;nm=nm->next)
{
if (count++)
{
sqlDyStringPrintf(query," or uni=%s ", nm->name );
}
else
{
sqlDyStringPrintf(query," uni=%s ", nm->name);
}
}
sr = sqlGetResult(sc,query->string);
while((row = sqlNextRow(sr)) != NULL)
{
sg = sageLoad(row);
slAddHead(&sgList,sg);
}
sqlFreeResult(&sr);
sqlDisconnect(&sc);
slReverse(&sgList);
freeDyString(&query);
return sgList;
}
static void doMainPage()
/* Send HTML with javascript to bootstrap the user interface. */
{
// Start web page with new banner
char *db = NULL, *genome = NULL, *clade = NULL;
getDbGenomeClade(cart, &db, &genome, &clade, oldVars);
// If CGI has &lastDbPos=..., handle that here and save position to cart so it's in place for
// future cartJson calls.
char *position = cartGetPosition(cart, db, NULL);
cartSetString(cart, "position", position);
webStartJWest(cart, db, "Genome Browser Gateway");
if (cgiIsOnWeb())
checkForGeoMirrorRedirect(cart);
#define WARNING_BOX_START "<div id=\"previewWarningRow\" class=\"jwRow\">" \
"<div id=\"previewWarningBox\" class=\"jwWarningBox\">"
#define UNDER_DEV "Data and tools on this site are under development, have not been reviewed " \
"for quality, and are subject to change at any time. "
#define MAIN_SITE "The high-quality, reviewed public site of the UCSC Genome Browser is " \
"available for use at <a href=\"http://genome.ucsc.edu/\">http://genome.ucsc.edu/</a>."
#define WARNING_BOX_END "</div></div>"
if (hIsPreviewHost())
{
puts(WARNING_BOX_START
"WARNING: This is the UCSC Genome Browser preview site. "
"This website is a weekly mirror of our internal development server for public access. "
UNDER_DEV
"We provide this site for early access, with the warning that it is less available "
"and stable than our public site. "
MAIN_SITE
WARNING_BOX_END);
}
if (hIsPrivateHost() && !hHostHasPrefix("hgwdev-demo6"))
{
puts(WARNING_BOX_START
"WARNING: This is the UCSC Genome Browser development site. "
"This website is used for testing purposes only and is not intended for general public "
"use. "
UNDER_DEV
MAIN_SITE
WARNING_BOX_END);
}
// The visible page elements are all in ./hgGateway.html, which is transformed into a quoted .h
// file containing a string constant that we #include and print here (see makefile).
puts(
#include "hgGateway.html.h"
);
// Set global JS variables hgsid, activeGenomes, and survey* at page load time
// We can't just use "var hgsid = " or the other scripts won't see it -- it has to be
// "window.hgsid = ".
puts("<script>");
printf("window.%s = '%s';\n", cartSessionVarName(), cartSessionId(cart));
puts("window.activeGenomes =");
printActiveGenomes();
puts(";");
char *surveyLink = cfgOption("survey");
if (isNotEmpty(surveyLink) && !sameWord(surveyLink, "off"))
{
printf("window.surveyLink=\"%s\";\n", jsonStringEscape(surveyLink));
char *surveyLabel = cfgOptionDefault("surveyLabel", "Please take our survey");
printf("window.surveyLabel=\"%s\";\n", jsonStringEscape(surveyLabel));
char *surveyLabelImage = cfgOption("surveyLabelImage");
if (isNotEmpty(surveyLabelImage))
printf("window.surveyLabelImage=\"%s\";\n", jsonStringEscape(surveyLabelImage));
else
puts("window.surveyLabelImage=null;");
}
else
{
puts("window.surveyLink=null;");
puts("window.surveyLabel=null;");
puts("window.surveyLabelImage=null;");
}
puts("</script>");
puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>");
puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>");
puts("<script src=\"../js/lodash.3.10.0.compat.min.js\"></script>");
puts("<script src=\"../js/cart.js\"></script>");
webIncludeResourceFile("jquery-ui.css");
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.watermarkinput.js", NULL);
jsIncludeFile("utils.js",NULL);
// Phylogenetic tree .js file, produced by dbDbTaxonomy.pl:
char *dbDbTree = cfgOptionDefault("hgGateway.dbDbTaxonomy", "../js/dbDbTaxonomy.js");
if (isNotEmpty(dbDbTree))
printf("<script src=\"%s\"></script>\n", dbDbTree);
// Main JS for hgGateway:
puts("<script src=\"../js/hgGateway.js\"></script>");
webIncludeFile("inc/jWestFooter.html");
cartFlushHubWarnings();
webEndJWest();
}
static char *wikiLinkLoggedInCookie()
/* Return the cookie name specified in hg.conf as the wiki logged-in cookie. */
{
return cfgOption(CFG_WIKI_LOGGED_IN_COOKIE);
}
static char *wikiLinkUserNameCookie()
/* Return the cookie name specified in hg.conf as the wiki user name cookie. */
{
return cfgOption(CFG_WIKI_USER_NAME_COOKIE);
}
/***********************************************************************************************************************************
Test run
***********************************************************************************************************************************/
void
testRun(void)
{
FUNCTION_HARNESS_VOID();
// Static tests against known values -- these may break as options change so will need to be kept up to date. The tests have
// generally been selected to favor values that are not expected to change but adjustments are welcome as long as the type of
// test is not drastically changed.
// *****************************************************************************************************************************
if (testBegin("check known values"))
{
TEST_ERROR(cfgCommandId(BOGUS_STR), AssertError, "invalid command 'BOGUS'");
TEST_RESULT_INT(cfgCommandId("archive-push"), cfgCmdArchivePush, "command id from name");
TEST_ERROR(
cfgCommandDefIdFromId(CFG_COMMAND_TOTAL), AssertError, "assertion 'commandId < cfgCmdNone' failed");
TEST_RESULT_INT(cfgCommandDefIdFromId(cfgCmdBackup), cfgDefCmdBackup, "command id to def id");
TEST_RESULT_STR(cfgCommandName(cfgCmdBackup), "backup", "command name from id");
TEST_RESULT_INT(cfgOptionDefIdFromId(cfgOptPgHost + 6), cfgDefOptPgHost, "option id to def id");
TEST_RESULT_INT(cfgOptionId("target"), cfgOptTarget, "option id from name");
TEST_RESULT_INT(cfgOptionId(BOGUS_STR), -1, "option id from invalid option name");
TEST_ERROR(
cfgOptionIdFromDefId(cfgDefOptionTotal(), 6), AssertError,
"assertion 'optionDefId < cfgDefOptionTotal()' failed");
TEST_ERROR(
cfgOptionIdFromDefId(0, 999999), AssertError,
"assertion 'index < cfgDefOptionIndexTotal(optionDefId)' failed");
TEST_RESULT_INT(cfgOptionIdFromDefId(cfgDefOptPgHost, 6), cfgOptPgHost + 6, "option def id to id");
TEST_ERROR(cfgOptionIndex(CFG_OPTION_TOTAL), AssertError, "assertion 'optionId < CFG_OPTION_TOTAL' failed");
TEST_RESULT_INT(cfgOptionIndex(cfgOptPgHostCmd + 6), 6, "option index");
TEST_RESULT_INT(cfgOptionIndex(cfgOptCompressLevel), 0, "option index");
TEST_RESULT_INT(cfgOptionIndexTotal(cfgOptPgPath), 8, "option index total");
TEST_RESULT_INT(cfgOptionIndexTotal(cfgOptLogLevelConsole), 1, "option index total");
TEST_RESULT_STR(cfgOptionName(cfgOptBackupStandby), "backup-standby", "option id from name");
}
// *****************************************************************************************************************************
if (testBegin("configuration"))
{
TEST_RESULT_VOID(cfgInit(), "config init");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_INT(cfgCommand(), cfgCmdNone, "command begins as none");
TEST_RESULT_VOID(cfgCommandSet(cfgCmdBackup), "command set to backup");
TEST_RESULT_INT(cfgCommand(), cfgCmdBackup, "command is backup");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_VOID(cfgCommandSet(cfgCmdBackup), "command set to backup");
TEST_RESULT_INT(cfgLogLevelDefault(), logLevelInfo, "default log level is info");
TEST_RESULT_BOOL(cfgLogFile(), true, "log file is on");
TEST_RESULT_BOOL(cfgLockRequired(), true, "lock is required");
TEST_RESULT_BOOL(cfgLockRemoteRequired(cfgCmdBackup), true, "remote lock is required");
TEST_RESULT_INT(cfgLockType(), lockTypeBackup, "lock is type backup");
TEST_RESULT_INT(cfgLockRemoteType(cfgCmdBackup), lockTypeBackup, "remote lock is type backup");
TEST_RESULT_BOOL(cfgParameterAllowed(), false, "parameters not allowed");
TEST_RESULT_VOID(cfgCommandSet(cfgCmdInfo), "command set to info");
TEST_RESULT_INT(cfgLogLevelDefault(), logLevelDebug, "default log level is debug");
TEST_RESULT_INT(cfgLogLevelStdErrMax(), logLevelTrace, "max stderr log level is trace");
TEST_RESULT_BOOL(cfgLogFile(), false, "log file is off");
TEST_RESULT_BOOL(cfgLockRequired(), false, "lock is not required");
TEST_RESULT_BOOL(cfgLockRemoteRequired(cfgCmdInfo), false, "remote lock is not required");
TEST_RESULT_INT(cfgLockType(), lockTypeNone, "lock is type none");
TEST_RESULT_INT(cfgLockRemoteType(cfgCmdInfo), lockTypeNone, "remote lock is type none");
TEST_RESULT_VOID(cfgCommandSet(cfgCmdStanzaCreate), "command set to stanza-create");
TEST_RESULT_BOOL(cfgLockRequired(), true, "lock is required");
TEST_RESULT_INT(cfgLockType(), lockTypeAll, "lock is type all");
TEST_RESULT_VOID(cfgCommandSet(cfgCmdLocal), "command set to local");
TEST_RESULT_INT(cfgLogLevelStdErrMax(), logLevelError, "max stderr log level is error");
TEST_RESULT_BOOL(cfgLogFile(), true, "log file is on");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_BOOL(cfgCommandHelp(), false, "command help defaults to false");
TEST_RESULT_VOID(cfgCommandHelpSet(true), "set command help");
TEST_RESULT_BOOL(cfgCommandHelp(), true, "command help is set");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_INT(strLstSize(cfgCommandParam()), 0, "command param list defaults to empty");
TEST_RESULT_VOID(cfgCommandParamSet(strLstAddZ(strLstNew(), "param")), "set command param list");
TEST_RESULT_INT(strLstSize(cfgCommandParam()), 1, "command param list is set");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_PTR(cfgExe(), NULL, "exe defaults to null");
TEST_RESULT_VOID(cfgExeSet(strNew("/path/to/exe")), "set exe");
TEST_RESULT_STR(strPtr(cfgExe()), "/path/to/exe", "exe is set");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_BOOL(cfgOptionNegate(cfgOptConfig), false, "negate defaults to false");
TEST_RESULT_VOID(cfgOptionNegateSet(cfgOptConfig, true), "set negate");
TEST_RESULT_BOOL(cfgOptionNegate(cfgOptConfig), true, "negate is set");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_BOOL(cfgOptionReset(cfgOptConfig), false, "reset defaults to false");
TEST_RESULT_VOID(cfgOptionResetSet(cfgOptConfig, true), "set reset");
TEST_RESULT_BOOL(cfgOptionReset(cfgOptConfig), true, "reset is set");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_BOOL(cfgOptionValid(cfgOptConfig), false, "valid defaults to false");
TEST_RESULT_BOOL(cfgOptionTest(cfgOptConfig), false, "option not valid for the command");
TEST_RESULT_VOID(cfgOptionValidSet(cfgOptConfig, true), "set valid");
TEST_RESULT_BOOL(cfgOptionValid(cfgOptConfig), true, "valid is set");
TEST_RESULT_BOOL(cfgOptionTest(cfgOptConfig), false, "option valid but value is null");
TEST_RESULT_VOID(cfgOptionSet(cfgOptConfig, cfgSourceParam, varNewStrZ("cfg")), "set option config");
TEST_RESULT_BOOL(cfgOptionTest(cfgOptConfig), true, "option valid and value not null");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_PTR(cfgOption(cfgOptOnline), NULL, "online is null");
TEST_RESULT_VOID(cfgOptionSet(cfgOptOnline, cfgSourceParam, varNewBool(false)), "set online");
TEST_RESULT_BOOL(cfgOptionBool(cfgOptOnline), false, "online is set");
TEST_RESULT_VOID(cfgOptionSet(cfgOptOnline, cfgSourceParam, varNewStrZ("1")), "set online");
TEST_RESULT_BOOL(cfgOptionBool(cfgOptOnline), true, "online is set");
TEST_RESULT_INT(cfgOptionSource(cfgOptOnline), cfgSourceParam, "online source is set");
TEST_ERROR(
cfgOptionDbl(cfgOptOnline), AssertError,
"assertion 'varType(configOptionValue[optionId].value) == varTypeDouble' failed");
TEST_ERROR(
cfgOptionInt64(cfgOptOnline), AssertError,
"assertion 'varType(configOptionValue[optionId].value) == varTypeInt64' failed");
TEST_RESULT_VOID(cfgOptionSet(cfgOptCompressLevel, cfgSourceParam, varNewInt64(1)), "set compress-level");
TEST_RESULT_INT(cfgOptionInt(cfgOptCompressLevel), 1, "compress-level is set");
TEST_RESULT_VOID(cfgOptionSet(cfgOptCompressLevel, cfgSourceDefault, varNewStrZ("3")), "set compress-level");
TEST_RESULT_INT(cfgOptionUInt(cfgOptCompressLevel), 3, "compress-level is set");
TEST_RESULT_INT(cfgOptionSource(cfgOptCompressLevel), cfgSourceDefault, "compress source is set");
TEST_ERROR(
cfgOptionBool(cfgOptCompressLevel), AssertError,
"assertion 'varType(configOptionValue[optionId].value) == varTypeBool' failed");
TEST_RESULT_VOID(
cfgOptionSet(cfgOptArchivePushQueueMax, cfgSourceParam, varNewInt64(999999999999)), "set archive-push-queue-max");
TEST_RESULT_INT(cfgOptionInt64(cfgOptArchivePushQueueMax), 999999999999, "archive-push-queue-max is set");
TEST_RESULT_INT(cfgOptionUInt64(cfgOptArchivePushQueueMax), 999999999999, "archive-push-queue-max is set");
TEST_RESULT_VOID(cfgOptionSet(cfgOptProtocolTimeout, cfgSourceParam, varNewDbl(1.1)), "set protocol-timeout");
TEST_RESULT_DOUBLE(cfgOptionDbl(cfgOptProtocolTimeout), 1.1, "protocol-timeout is set");
TEST_RESULT_VOID(cfgOptionSet(cfgOptProtocolTimeout, cfgSourceConfig, varNewStrZ("3.3")), "set protocol-timeout");
TEST_RESULT_DOUBLE(cfgOptionDbl(cfgOptProtocolTimeout), 3.3, "protocol-timeout is set");
TEST_RESULT_INT(cfgOptionSource(cfgOptProtocolTimeout), cfgSourceConfig, "protocol-timeout source is set");
TEST_ERROR(
cfgOptionKv(cfgOptProtocolTimeout), AssertError,
"assertion 'varType(configOptionValue[optionId].value) == varTypeKeyValue' failed");
TEST_RESULT_VOID(cfgOptionSet(cfgOptProtocolTimeout, cfgSourceConfig, NULL), "set protocol-timeout to NULL");
TEST_RESULT_PTR(cfgOption(cfgOptProtocolTimeout), NULL, "protocol-timeout is not set");
TEST_ERROR(
cfgOptionSet(cfgOptRecoveryOption, cfgSourceParam, varNewDbl(1.1)), AssertError,
"option 'recovery-option' must be set with KeyValue variant");
TEST_RESULT_VOID(cfgOptionSet(cfgOptRecoveryOption, cfgSourceConfig, varNewKv(kvNew())), "set recovery-option");
TEST_RESULT_INT(varLstSize(kvKeyList(cfgOptionKv(cfgOptRecoveryOption))), 0, "recovery-option is set");
TEST_ERROR(
cfgOptionLst(cfgOptRecoveryOption), AssertError,
"assertion 'configOptionValue[optionId].value == NULL"
" || varType(configOptionValue[optionId].value) == varTypeVariantList' failed");
TEST_RESULT_INT(varLstSize(cfgOptionLst(cfgOptDbInclude)), 0, "db-include defaults to empty");
TEST_ERROR(
cfgOptionSet(cfgOptDbInclude, cfgSourceParam, varNewDbl(1.1)), AssertError,
"option 'db-include' must be set with VariantList variant");
TEST_RESULT_VOID(cfgOptionSet(cfgOptDbInclude, cfgSourceConfig, varNewVarLst(varLstNew())), "set db-include");
TEST_RESULT_INT(varLstSize(cfgOptionLst(cfgOptDbInclude)), 0, "db-include is set");
TEST_ERROR(
cfgOptionStr(cfgOptDbInclude), AssertError,
"assertion 'configOptionValue[optionId].value == NULL"
" || varType(configOptionValue[optionId].value) == varTypeString' failed");
TEST_RESULT_PTR(cfgOptionStr(cfgOptStanza), NULL, "stanza defaults to null");
TEST_ERROR(
cfgOptionSet(cfgOptStanza, cfgSourceParam, varNewDbl(1.1)), AssertError,
"option 'stanza' must be set with String variant");
TEST_RESULT_VOID(cfgOptionSet(cfgOptStanza, cfgSourceConfig, varNewStrZ("db")), "set stanza");
TEST_RESULT_STR(strPtr(cfgOptionStr(cfgOptStanza)), "db", "stanza is set");
TEST_ERROR(
cfgOptionInt(cfgOptStanza), AssertError,
"assertion 'varType(configOptionValue[optionId].value) == varTypeInt64' failed");
// -------------------------------------------------------------------------------------------------------------------------
TEST_RESULT_VOID(cfgInit(), "config init resets value");
TEST_RESULT_INT(cfgCommand(), cfgCmdNone, "command begins as none");
}
// *****************************************************************************************************************************
if (testBegin("cfgOptionHostPort()"))
{
unsigned int port = 55555;
cfgInit();
cfgCommandSet(cfgCmdBackup);
cfgOptionValidSet(cfgOptRepoS3Host, true);
cfgOptionSet(cfgOptRepoS3Host, cfgSourceConfig, varNewStrZ("host.com")) ;
TEST_RESULT_STR(strPtr(cfgOptionHostPort(cfgOptRepoS3Host, &port)), "host.com", "check plain host");
TEST_RESULT_UINT(port, 55555, "check that port was not updated");
cfgOptionSet(cfgOptRepoS3Host, cfgSourceConfig, varNewStrZ("myhost.com:777")) ;
TEST_RESULT_STR(strPtr(cfgOptionHostPort(cfgOptRepoS3Host, &port)), "myhost.com", "check host with port");
TEST_RESULT_UINT(port, 777, "check that port was updated");
TEST_RESULT_STR(strPtr(cfgOptionHostPort(cfgOptRepoS3Endpoint, &port)), NULL, "check null host");
TEST_RESULT_UINT(port, 777, "check that port was not updated");
cfgOptionSet(cfgOptRepoS3Host, cfgSourceConfig, varNewStrZ("myhost.com:777:888")) ;
TEST_ERROR(
cfgOptionHostPort(cfgOptRepoS3Host, &port), OptionInvalidError,
"'myhost.com:777:888' is not valid for option 'repo1-s3-host'"
"\nHINT: is more than one port specified?");
TEST_RESULT_UINT(port, 777, "check that port was not updated");
cfgOptionValidSet(cfgOptRepoS3Endpoint, true);
cfgOptionSet(cfgOptRepoS3Endpoint, cfgSourceConfig, varNewStrZ("myendpoint.com:ZZZ")) ;
TEST_ERROR(
cfgOptionHostPort(cfgOptRepoS3Endpoint, &port), OptionInvalidError,
"'myendpoint.com:ZZZ' is not valid for option 'repo1-s3-endpoint'"
"\nHINT: port is not a positive integer.");
TEST_RESULT_UINT(port, 777, "check that port was not updated");
}
// *****************************************************************************************************************************
if (testBegin("cfgOptionDefault() and cfgOptionDefaultSet()"))
{
TEST_RESULT_VOID(cfgInit(), "config init");
TEST_RESULT_VOID(cfgCommandSet(cfgCmdBackup), "backup command");
TEST_RESULT_STR(strPtr(varStr(cfgOptionDefault(cfgOptType))), "incr", "backup type default");
TEST_RESULT_BOOL(varBool(cfgOptionDefault(cfgOptCompress)), "true", "backup compress default");
TEST_RESULT_DOUBLE(varDbl(cfgOptionDefault(cfgOptProtocolTimeout)), 1830, "backup protocol-timeout default");
TEST_RESULT_INT(varIntForce(cfgOptionDefault(cfgOptCompressLevel)), 6, "backup compress-level default");
TEST_RESULT_PTR(cfgOptionDefault(cfgOptDbInclude), NULL, "backup db-include default is null");
TEST_RESULT_VOID(cfgOptionSet(cfgOptPgHost, cfgSourceParam, varNewStrZ("backup")), "backup host set");
TEST_RESULT_VOID(cfgOptionDefaultSet(cfgOptPgHost, varNewStrZ("backup-default")), "backup host default");
TEST_RESULT_VOID(cfgOptionDefaultSet(cfgOptPgHost, varNewStrZ("backup-default2")), "reset backup host default");
TEST_RESULT_STR(strPtr(varStr(cfgOption(cfgOptPgHost))), "backup", "backup host value");
TEST_RESULT_STR(strPtr(varStr(cfgOptionDefault(cfgOptPgHost))), "backup-default2", "backup host default");
TEST_RESULT_VOID(cfgOptionSet(cfgOptPgSocketPath, cfgSourceDefault, NULL), "backup pg-socket-path set");
TEST_RESULT_VOID(cfgOptionDefaultSet(cfgOptPgSocketPath, varNewStrZ("/to/socket")), "backup pg-socket-path default");
TEST_RESULT_VOID(cfgOptionDefaultSet(cfgOptPgSocketPath, varNewStrZ("/to/socket2")), "reset backup pg-socket-path default");
TEST_RESULT_STR(strPtr(varStr(cfgOption(cfgOptPgSocketPath))), "/to/socket2", "backup pg-socket-path value");
TEST_RESULT_STR(strPtr(varStr(cfgOptionDefault(cfgOptPgSocketPath))), "/to/socket2", "backup pg-socket-path value default");
}
FUNCTION_HARNESS_RESULT_VOID();
}
void doBamDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a BAM file. */
{
if (item == NULL)
errAbort("doBamDetails: NULL item name");
int start = cartInt(cart, "o");
if (!tdb || !trackDbSetting(tdb, "bamSkipPrintQualScore"))
skipQualityScore = FALSE;
else
skipQualityScore = TRUE;
// TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
if (sameString(item, "zoom in"))
printf("Zoom in to a region with fewer items to enable 'detail page' links for individual items.<BR>");
char varName[1024];
safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->track);
boolean isPaired = cartUsualBoolean(cart, varName,
(trackDbSetting(tdb, "pairEndsByName") != NULL));
char position[512];
safef(position, sizeof(position), "%s:%d-%d", seqName, winStart, winEnd);
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
if (fileName == NULL)
{
if (isCustomTrack(tdb->table))
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tdb->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
fileName = hReplaceGbdb(bamFileNameFromTable(conn, tdb->table, seqName));
hFreeConn(&conn);
}
}
char *indexName = hReplaceGbdb(trackDbSetting(tdb, "bigDataIndex"));
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tdb, "refUrl");
bamAndIndexFetchPlus(fileName, indexName, position, oneBam, &btd, NULL, refUrl, cacheDir);
if (isPaired)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0 && hashNumEntries(pairHash) > 0)
{
// Repeat the search for item in a larger window:
struct hash *newPairHash = hashNew(0);
btd.pairHash = newPairHash;
safef(position, sizeof(position), "%s:%d-%d", seqName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetch(fileName, position, oneBam, &btd, NULL);
}
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
bam1_t *bam = hel->val;
const bam1_core_t *core = &bam->core;
if (! (core->flag & BAM_FMUNMAP))
printf("<B>Note: </B>unable to find paired end for %s "
"within +-%d bases of viewing window %s<BR>\n",
item, pairSearchRange, addCommasToPos(database, cartString(cart, "position")));
else
printf("<B>Paired read name:</B> %s<BR>\n", item);
singleBamDetails(bam);
}
}
}
char *customPpNext(struct customPp *cpp)
/* Return next line. */
{
/* Check first for line to reuse. */
struct slName *reused = cpp->reusedLines;
if (reused)
{
/* We need to keep line actually reusing in memory until next
* call to customPpNext, so we move it to inReuse rather than
* immediately freeing it. */
freeMem(cpp->inReuse);
cpp->reusedLines = reused->next;
cpp->inReuse = reused;
return reused->name;
}
/* Get next line from file on top of stack. If at EOF
* go to next file in stack. If get a http:// or https:// or ftp:// line
* open file this references and push it onto stack. Meanwhile
* squirrel away 'browser' lines. */
struct lineFile *lf;
while ((lf = cpp->fileStack) != NULL)
{
char *line;
if (lineFileNext(lf, &line, NULL))
{
// if user pastes just a URL, create a track line automatically
// also allow a filename from a local directory if it has been allowed via udc.localDir in hg.conf
bool isLocalFile = cfgOption("udc.localDir")!=NULL && startsWith(cfgOption("udc.localDir"), line);
if (startsWith("http://", line) || startsWith("https://", line) || startsWith("ftp://", line) ||
isLocalFile)
{
if (customTrackIsBigData(line))
line = bigUrlToTrackLine(line);
else
{
lf = netLineFileOpen(line);
slAddHead(&cpp->fileStack, lf);
#ifdef PROGRESS_METER
off_t remoteSize = 0;
remoteSize = remoteFileSize(line);
cpp->remoteFileSize = remoteSize;
#endif
continue;
}
}
else if (!cpp->ignoreBrowserLines && startsWith("browser", line))
{
char afterPattern = line[7];
if (isspace(afterPattern) || afterPattern == 0)
{
slNameAddTail(&cpp->browserLines, line);
continue;
}
}
return line;
}
else
{
cpp->fileStack = lf->next;
lineFileClose(&lf);
}
}
return NULL;
}
char *loginSystemName()
/* Return the wiki host specified in hg.conf, or NULL. Allocd here. */
{
return cloneString(cfgOption(CFG_LOGIN_SYSTEM_NAME));
}
/***********************************************************************************************************************************
Begin the command
***********************************************************************************************************************************/
void
cmdBegin(bool logOption)
{
FUNCTION_LOG_BEGIN(logLevelTrace);
FUNCTION_LOG_PARAM(BOOL, logOption);
FUNCTION_LOG_END();
ASSERT(cfgCommand() != cfgCmdNone);
// This is fairly expensive log message to generate so skip it if it won't be output
if (logWill(cfgLogLevelDefault()))
{
MEM_CONTEXT_TEMP_BEGIN()
{
// Basic info on command start
String *info = strNewFmt("%s command begin", cfgCommandName(cfgCommand()));
if (logOption)
{
strCatFmt(info, " %s:", PROJECT_VERSION);
// Add command parameters if they exist
const StringList *commandParamList = cfgCommandParam();
if (strLstSize(commandParamList) != 0)
{
strCatFmt(info, " [");
for (unsigned int commandParamIdx = 0; commandParamIdx < strLstSize(commandParamList); commandParamIdx++)
{
const String *commandParam = strLstGet(commandParamList, commandParamIdx);
if (commandParamIdx != 0)
strCatFmt(info, ", ");
if (strchr(strPtr(commandParam), ' ') != NULL)
commandParam = strNewFmt("\"%s\"", strPtr(commandParam));
strCat(info, strPtr(commandParam));
}
strCatFmt(info, "]");
}
// Loop though options and add the ones that are interesting
for (ConfigOption optionId = 0; optionId < CFG_OPTION_TOTAL; optionId++)
{
// Skip the option if it is not valid
if (!cfgOptionValid(optionId))
continue;
// If option was negated
if (cfgOptionNegate(optionId))
strCatFmt(info, " --no-%s", cfgOptionName(optionId));
// If option was reset
else if (cfgOptionReset(optionId))
strCatFmt(info, " --reset-%s", cfgOptionName(optionId));
// Else set and not default
else if (cfgOptionSource(optionId) != cfgSourceDefault && cfgOptionTest(optionId))
{
ConfigDefineOption optionDefId = cfgOptionDefIdFromId(optionId);
// Don't show redacted options
if (cfgDefOptionSecure(optionDefId))
strCatFmt(info, " --%s=<redacted>", cfgOptionName(optionId));
// Output boolean option
else if (cfgDefOptionType(optionDefId) == cfgDefOptTypeBoolean)
strCatFmt(info, " --%s", cfgOptionName(optionId));
// Output other options
else
{
StringList *valueList = NULL;
// Generate the values of hash options
if (cfgDefOptionType(optionDefId) == cfgDefOptTypeHash)
{
valueList = strLstNew();
const KeyValue *optionKv = cfgOptionKv(optionId);
const VariantList *keyList = kvKeyList(optionKv);
for (unsigned int keyIdx = 0; keyIdx < varLstSize(keyList); keyIdx++)
{
strLstAdd(
valueList,
strNewFmt(
"%s=%s", strPtr(varStr(varLstGet(keyList, keyIdx))),
strPtr(varStrForce(kvGet(optionKv, varLstGet(keyList, keyIdx))))));
}
}
// Generate values for list options
else if (cfgDefOptionType(optionDefId) == cfgDefOptTypeList)
{
valueList = strLstNewVarLst(cfgOptionLst(optionId));
}
// Else only one value
else
{
valueList = strLstNew();
strLstAdd(valueList, varStrForce(cfgOption(optionId)));
}
// Output options and values
for (unsigned int valueListIdx = 0; valueListIdx < strLstSize(valueList); valueListIdx++)
{
const String *value = strLstGet(valueList, valueListIdx);
strCatFmt(info, " --%s", cfgOptionName(optionId));
if (strchr(strPtr(value), ' ') != NULL)
value = strNewFmt("\"%s\"", strPtr(value));
strCatFmt(info, "=%s", strPtr(value));
}
}
}
}
}
LOG(cfgLogLevelDefault(), 0, strPtr(info));
}
MEM_CONTEXT_TEMP_END();
}
FUNCTION_LOG_RETURN_VOID();
}
/***********************************************************************************************************************************
Build JSON output from options
***********************************************************************************************************************************/
String *
perlOptionJson(void)
{
FUNCTION_TEST_VOID();
String *result = NULL;
MEM_CONTEXT_TEMP_BEGIN()
{
KeyValue *configKv = kvNew();
for (ConfigOption optionId = 0; optionId < CFG_OPTION_TOTAL; optionId++)
{
// Skip if not valid
if (!cfgOptionValid(optionId))
continue;
Variant *optionVar = varNewKv(kvNew());
// Add valid
kvPut(varKv(optionVar), VARSTRDEF("valid"), BOOL_TRUE_VAR);
// Add source
const Variant *source = NULL;
switch (cfgOptionSource(optionId))
{
case cfgSourceParam:
{
source = VARSTRDEF("param");
break;
}
case cfgSourceConfig:
{
source = VARSTRDEF("config");
break;
}
case cfgSourceDefault:
{
source = VARSTRDEF("default");
break;
}
}
kvPut(varKv(optionVar), VARSTRDEF("source"), source);
// Add negate and reset
kvPut(varKv(optionVar), VARSTRDEF("negate"), VARBOOL(cfgOptionNegate(optionId)));
kvPut(varKv(optionVar), VARSTRDEF("reset"), VARBOOL(cfgOptionReset(optionId)));
// Add value if it is set
if (cfgOptionTest(optionId))
{
const Variant *valueVar = NULL;
switch (cfgDefOptionType(cfgOptionDefIdFromId(optionId)))
{
case cfgDefOptTypeBoolean:
case cfgDefOptTypeFloat:
case cfgDefOptTypeInteger:
case cfgDefOptTypePath:
case cfgDefOptTypeSize:
case cfgDefOptTypeString:
{
valueVar = cfgOption(optionId);
break;
}
case cfgDefOptTypeHash:
{
valueVar = varNewKv(kvNew());
const KeyValue *valueKv = cfgOptionKv(optionId);
const VariantList *keyList = kvKeyList(valueKv);
for (unsigned int listIdx = 0; listIdx < varLstSize(keyList); listIdx++)
kvPut(varKv(valueVar), varLstGet(keyList, listIdx), kvGet(valueKv, varLstGet(keyList, listIdx)));
break;
}
case cfgDefOptTypeList:
{
valueVar = varNewKv(kvNew());
const VariantList *valueList = cfgOptionLst(optionId);
for (unsigned int listIdx = 0; listIdx < varLstSize(valueList); listIdx++)
kvPut(varKv(valueVar), varLstGet(valueList, listIdx), BOOL_TRUE_VAR);
break;
}
}
kvPut(varKv(optionVar), VARSTRDEF("value"), valueVar);
}
kvPut(configKv, VARSTRZ(cfgOptionName(optionId)), optionVar);
}
memContextSwitch(MEM_CONTEXT_OLD());
result = jsonFromKv(configKv, 0);
memContextSwitch(MEM_CONTEXT_TEMP());
}
MEM_CONTEXT_TEMP_END();
FUNCTION_TEST_RETURN(result);
}
char *webTimeStampedLinkToResource(char *fileName, boolean wrapInHtml)
// If wrapInHtml
// returns versioned link embedded in style or script html (free after use).
// else
// returns full path of a versioned path to the requested resource file (js, or css).
// NOTE: png, jpg and gif should also be supported but are untested.
//
// In production sites we use a versioned softlink that includes the CGI version. This has the following benefits:
// a) flushes user's web browser cache when the user visits a GB site whose version has changed since their last visit;
// b) enforces the requirement that static files are the same version as the CGIs (something that often fails to happen in mirrors).
// (see notes in redmine #3170).
//
// In dev trees we use mtime to create a pseudo-version; this forces web browsers to reload css/js file when it changes,
// so we don't get odd behavior that can be caused by caching of mis-matched javascript and style files in dev trees.
//
// In either case, the actual file has to have been previously created by running make in the appropriate directory (kent/src/hg/js
// or kent/src/hg/htdocs/style).
{
char baseName[PATH_LEN];
char extension[FILEEXT_LEN];
splitPath(fileName, NULL, baseName, extension);
boolean js = sameString(".js",extension);
boolean style = !js && sameString(".css",extension);
boolean image = !js
&& !style
&& ( sameString(".png",extension)
|| sameString(".jpg",extension)
|| sameString(".gif",extension));
if (!js && !style) // && !image) NOTE: This code has not been tested on images but should work.
errAbort("webTimeStampedLinkToResource: unknown resource type for %s.\n", fileName);
// Build and verify directory
char *dirName = "";
if (js)
dirName = cfgOptionDefault("browser.javaScriptDir", "js");
else if (style)
dirName = cfgOptionDefault("browser.styleDir","style");
else if (image)
dirName = cfgOptionDefault("browser.styleImagesDir","style/images");
struct dyString *fullDirName = NULL;
char *docRoot = hDocumentRoot();
if (docRoot != NULL)
fullDirName = dyStringCreate("%s/%s", docRoot, dirName);
else
// tolerate missing docRoot (i.e. when running from command line)
fullDirName = dyStringCreate("%s", dirName);
if (!fileExists(dyStringContents(fullDirName)))
errAbort("webTimeStampedLinkToResource: dir: %s doesn't exist.\n",
dyStringContents(fullDirName));
// build and verify real path to file
struct dyString *realFileName = dyStringCreate("%s/%s", dyStringContents(fullDirName), fileName);
if (!fileExists(dyStringContents(realFileName)))
errAbort("webTimeStampedLinkToResource: file: %s doesn't exist.\n",
dyStringContents(realFileName));
// build and verify link path including timestamp in the form of dir/baseName + timeStamp or CGI Version + ext
long mtime = fileModTime(dyStringContents(realFileName));
struct dyString *linkWithTimestamp;
char *scriptName = cgiScriptName();
if (scriptName == NULL)
scriptName = cloneString("");
boolean nonVersionedLinks = FALSE;
if (endsWith(scriptName, "qaPushQ"))
nonVersionedLinks = TRUE;
if (nonVersionedLinks)
linkWithTimestamp = dyStringCreate("%s/%s%s", dyStringContents(fullDirName), baseName, extension);
else if ((cfgOption("versionStamped") == NULL) && (hIsPreviewHost() || hIsPrivateHost()))
linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), baseName, mtime, extension);
else
linkWithTimestamp = dyStringCreate("%s/%s-v%s%s", dyStringContents(fullDirName), baseName, CGI_VERSION, extension);
if (!fileExists(dyStringContents(linkWithTimestamp)))
errAbort("Cannot find correct version of file '%s'; this is due to an installation error\n\nError details: %s does not exist",
fileName, dyStringContents(linkWithTimestamp));
// Free up all that extra memory
dyStringFree(&realFileName);
dyStringFree(&fullDirName);
char *linkFull = dyStringCannibalize(&linkWithTimestamp);
char *link = linkFull;
if (docRoot != NULL)
{
link = cloneString(linkFull + strlen(docRoot) + 1);
freeMem(linkFull);
}
if (wrapInHtml) // wrapped for christmas
{
struct dyString *wrapped = dyStringNew(0);
if (js)
dyStringPrintf(wrapped,"<script type='text/javascript' SRC='/%s'></script>\n", link);
else if (style)
dyStringPrintf(wrapped,"<LINK rel='STYLESHEET' href='/%s' TYPE='text/css' />\n", link);
else // Will be image, since these are the only three choices allowed
dyStringPrintf(wrapped,"<IMG src='/%s' />\n", link);
freeMem(link);
link = dyStringCannibalize(&wrapped);
}
return link;
}
void bamLoadItemsCore(struct track *tg, boolean isPaired)
/* Load BAM data into tg->items item list, unless zoomed out so far
* that the data would just end up in dense mode and be super-slow. */
{
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
int minAliQual = atoi(cartOrTdbString(cart, tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
if (fileName == NULL)
{
if (tg->customPt)
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileName = bamFileNameFromTable(conn, tg->table, chromName);
hFreeConn(&conn);
}
}
char *fileName2 = hReplaceGbdb(fileName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tg->tdb, "refUrl");
if (!isPaired)
bamFetchPlus(fileName2, posForBam, addBam, &btd, NULL, refUrl, cacheDir);
else
{
char *setting = trackDbSettingClosestToHomeOrDefault(tg->tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0)
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetchPlus(fileName2, posForBam, addBamPaired, &btd, NULL, refUrl, cacheDir);
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct linkedFeatures *lf = hel->val;
if (lf->start < winEnd && lf->end > winStart)
slAddHead(&(tg->items), lfsFromLf(lf));
}
}
freez(&fileName2);
if (tg->visibility != tvDense)
{
slReverse(&(tg->items));
if (isPaired)
slSort(&(tg->items), linkedFeaturesSeriesCmp);
else if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
slSort(&(tg->items), linkedFeaturesCmpOri);
else if (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_ALI_QUAL))
slSort(&(tg->items), linkedFeaturesCmpScore);
else
slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
{
// flag drawItems to make a mapBox for the whole track
tg->customInt = 1;
tg->mapItem = dontMapItem;
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
char *wikiLinkHost()
/* Return the wiki host specified in hg.conf, or NULL. Allocd here. */
{
return cloneString(cfgOption(CFG_WIKI_HOST));
}
