Library Configuration

Introduction

This chapter describes the run-time configuration parameters of the NCBI C++ Toolkit libraries. Such parameters change the default behavior of applications built using the Toolkit.

Configuration parameters can be set by environment variables, entered into a configuration file, defined by code, or any combination of those methods. Note: If a parameter is specified in both a configuration file and the environment, the environment takes precedence. The methods supported by each library and application are described below.

Chapter Outline

The following is an outline of the topics presented in this chapter:

• Defining and Using Parameters

  • CParam

  • Registry

  • Environment

• Non-Specific Parameters

  • Logging

  • Diagnostic Trace

  • Run-Time

  • Abnormal Program Termination

  • NCBI

• Library-Specific Parameters

  • Connection

  • CGI and FCGI

  • Serial

  • Objects, Object Manager, Object Tools

    • Objects library

    • Object Manager library

    • Genbank data loader and readers

    • PSG data loader

    • Object Tools library and other data loaders

    • psg_client library

  • cSRA

    • sraread library

    • ncbi_xloader_csra library

  • BAM

  • DBAPI

  • Eutils

• Distributed Computing (GRID) Specific Parameters

  • NetCache and NetSchedule

  • Worker Node

• Application-Specific Parameters

  • Seqfetch.cgi

Defining and Using Parameters

The following sections discuss the methods that libraries can use to define configuration parameters, and the corresponding methods that client applications can use to specify values for those parameters.

• CParam

• Registry

• Environment

CParam

Note: The preferred way for libraries to define their configuration parameters is with the macros in the CParam class (e.g. NCBI_PARAM_DECL). More details on the CParam class and its macros are presented in an earlier chapter. Libraries that use CParam can get configuration parameters using either the registry or the environment. Also, the CParam value can be stored and accessed on different levels: globally (application wide) and/or per-thread (TLS-like) and/or locally (cached within a CParam instance). Note that the name of an environment variable linked to a CParam can be customized or follow the default naming convention, so you have to look up the actual name used in the tables below before setting a configuration parameter using the environment.

Registry

If the CParam class cannot be used, the registry (configuration file) may be used to load, access, modify and store the values read from a configuration file. For libraries that use the registry, client applications can set the library configuration parameters using either the registry or the environment. In these cases the environment variable must follow the default naming convention.

These environment variables can be used to specify where to look for the registry.

Table 1. Registry configuration parameters

Purpose	Environment variable	Valid values
If this variable is defined, the value is an extra-high-priority configuration file whose entries override those from other configuration files.	NCBI_CONFIG_OVERRIDES	a valid path
If this variable is defined, use it exclusively as the registry search path.	NCBI_CONFIG_PATH	a valid path
If this variable is not defined, append the current directory and home directory to the registry search path (after NCBI_CONFIG_PATH).	NCBI_DONT_USE_LOCAL_CONFIG	anything
If this variable is defined, append the value to the registry search path (after the home directory).	NCBI	a valid path
For Windows: If this variable is defined, append the value to the registry search path (after NCBI). For non-Windows, this variable is not checked and /etc is appended to the registry search path (after NCBI).	SYSTEMROOT	a valid path
If this variable is not defined, attempt to load a low-priority system-wide registry (ncbi.ini on Windows; .ncbirc on non-Windows). Note: the system-wide registry will not be loaded if it contains the DONT_USE_NCBIRC entry in the NCBI section.	NCBI_DONT_USE_NCBIRC	anything

The registry is case-insensitive for section and entry names. More details on the registry are presented in an earlier chapter.

Environment

For configuration parameters defined by either CParam or the registry, there is an equivalent environment variable having the form NCBI_CONFIG__<section>__<name> (note the double-underscores preceding <section> and <name>). The equivalent form is all uppercase.

Note: Registry section and entry names may contain some characters that are difficult or impossible to use in environment variable names on some platforms. To obtain corresponding environment variable names, you can and should make some formal substitutions as detailed below. For example, the equivalent environment variable for [FastCGI]
WatchFile.Name is NCBI_CONFIG__FASTCGI__WATCHFILE_DOT_NAME.

Character	Substitution
'.' (dot, full stop, period)	_DOT_
'-' (hyphen, minus)	_HYPHEN_
'/' ([forward] slash, solidus)	_SLASH_
' ' (space)	_SPACE_

Note: Environment variables are case-sensitive on many platforms. Therefore, when setting a configuration parameter via the environment, be sure to use the case shown in the tables below.

Some configuration parameters can only be set with an environment variable - for example, DIAG_SILENT_ABORT. In such cases, there is no corresponding registry entry.

Non-Specific Parameters

The following sections discuss configuration parameters that are not library-specific.

• Logging

• Diagnostic Trace

• Run-Time

• Abnormal Program Termination

• NCBI

Logging

The application log consists of diagnostic messages. Some of them are available only in debug builds. Others - namely, those produced by the ERR_POST or LOG_POST macros - can be redirected into a file. Normally, the name and location of the application log is specified using the logfile command-line argument.

Log messages have different levels of severity. Setting the logging level is described in the next chapter Diagnostic Trace

These parameters tune the usage and behavior of the application log file.

Table 2. Log file configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If true, post log messages when configuration parameters are read by one of the ncbi::g_GetConfig*() functions. Messages include the parameter; the value; and whether the value came from the application registry, the environment, or a default value.	[N/A] N/A NCBI_CONFIG__NCBI__CONFIG_DUMP_VARIABLES	Boolean  b	(none)
Used by logging framework if the real client IP can not be obtained.	[LOG] Client_Ip NCBI_LOG_CLIENT_IP	a valid IPv4 or IPv6 address	””
Reset the log file to the specified file.	[LOG] File NCBI_CONFIG__LOG__FILE  c	a valid file name	””
Defines the default hit ID, which is used for application and for any request which has no explicit hit ID set.	[Log] Hit_Id NCBI_LOG_HIT_ID	any valid PHID string	””
Same as NCBI_LOG_HIT_ID, but passed through HTTP headers. Has priority over NCBI_LOG_HIT_ID.	[Log] Http_Hit_Id HTTP_NCBI_PHID	any valid PHID string	””
Same as NCBI_LOG_SESSION_ID, but passed through HTTP headers. Has priority over NCBI_LOG_SESSION_ID.	[Log] Http_Session_Id HTTP_NCBI_SID	any valid session ID string	“UNK_SESSION”
Specify when to use the File, NoCreate, Truncate, and TryRootLogFirst registry parameters shown in this table. Note: those parameters will only be used if the log file has not been set already or if IgnoreEnvArg is set to true.	[LOG] IgnoreEnvArg NCBI_CONFIG__LOG__IGNOREENVARG  c	Boolean  a	false
Specify the maximum number of sub-PHIDs that can be reported to the AppLog by a single request.	[Log] Issued_SubHit_Limit LOG_ISSUED_SUBHIT_LIMIT	unsigned integer	200
Log all app arguments before application run. The extra message starts with a “LogAppArguments=true” pair.	[LOG] LogAppArguments DIAG_LOG_APP_ARGUMENTS [sic]	Boolean  a	””
Log all environment variables as an ‘extra’ before application run. The extra message starts with a “LogAppEnvironment=true” pair.	[LOG] LogAppEnvironment DIAG_LOG_APP_ENVIRONMENT [sic]	Boolean  a	””
Log all environment variables as an ‘extra’ after application run. The extra message starts with a “LogAppEnvironment=true” pair.	[LOG] LogAppEnvironmentOnStop DIAG_LOG_APP_ENVIRONMENT_ON_STOP [sic]	Boolean  a	””
Log application executable path before application run. The extra message starts with a “LogAppPath=true” pair.	[LOG] LogAppPath DIAG_LOG_APP_PATH [sic]	Boolean  a	””
Log all registry variables as an ‘extra’ before application run. The extra message starts with a “LogAppRegistry=true” pair.	[LOG] LogAppRegistry DIAG_LOG_APP_REGISTRY [sic]	Boolean  a	””
Log all registry variables as an ‘extra’ after application run. The extra message starts with a “LogAppRegistry=true” pair.	[LOG] LogAppRegistryOnStop DIAG_LOG_APP_REGISTRY_ON_STOP [sic]	Boolean  a	””
Log memory and CPU consumed by application as an ‘extra’ after application run, just before stop. The extra message starts with a “LogAppResUsage=true” pair.	[LOG] LogAppResUsageOnStop DIAG_LOG_APP_RESUSAGE_ON_STOP [sic]	Boolean  a	””
Set [LOG]LogAppRegistry, [LOG]LogAppRegistryOnStop, [LOG]LogAppEnvironment, [LOG]LogAppEnvironmentOnStop, [LOG]LogAppArguments, [LOG]LogAppPath to the one specified value	[LOG] LogAppRunContext DIAG_LOG_APP_RUN_CONTEXT [sic]	Boolean  a	””
The listed environment variables will be logged as an ‘extra’ after each ‘request-start’ message. The extra message starts with a “LogEnvironment=true” pair.	[LOG] LogEnvironment DIAG_LOG_ENVIRONMENT [sic]	space separated list of environment variable names	””
The listed registry entries will be logged as an ‘extra’ after each ‘request-start’ message. The extra message starts with a “LogRegistry=true” pair.	[LOG] LogRegistry DIAG_LOG_REGISTRY [sic]	space separated list of registry section:name values	””
Space separated list of patterns. The patterns are matched against meta-data fields (e.g. HTTP headers), matching entries are logged as ‘extra’ messages.	NCBI_LOG_FIELDS	space separated list of patterns	””
Space separated list of patterns. Meta-data fields matching the patterns are logged on par with ‘NCBI_LOG_FIELDS’.	[LOG] Ncbi_Log_Fields_Custom NCBI_LOG_FIELDS_CUSTOM	space separated list of patterns	””
Do not create the log file if it does not exist already.	[Log] NoCreate NCBI_CONFIG__LOG__NOCREATE  c	Boolean  b	false
Specifies what to do if an invalid page hit ID is encountered. Valid PHIDs match the regex: [A-Za-z0-9:@_-]+(\.[0-9]+)*	[Log] On_Bad_Hit_Id LOG_ON_BAD_HIT_ID	“Allow”, “AllowAndReport”, “Ignore”, “IgnoreAndReport”, “Throw”	“AllowAndReport”
Specifies what to do if an invalid session ID is encountered. Valid session IDs match the format specified by LOG_SESSION_ID_FORMAT.	[Log] On_Bad_Session_Id LOG_ON_BAD_SESSION_ID	“Allow”, “AllowAndReport”, “Ignore”, “IgnoreAndReport”, “Throw”	“AllowAndReport”
Turn performance logging on or off (globally).	[Log] PerfLogging LOG_PerfLogging  c	Boolean  b	false
Defines the default session ID, which is used for any request which has no explicit session ID set.	[Log] Session_Id NCBI_LOG_SESSION_ID	any valid session ID string	“UNK_SESSION”
Specifies which format rule to check session IDs against: for “Ncbi” use ^[0-9]{16}_[0-9]{4,}SID$ for “Standard” use ^[A-Za-z0-9_.:@-]+$ for “Other” use ^.*$ (i.e. anything is valid).	[Log] Session_Id_Format LOG_SESSION_ID_FORMAT	“Ncbi”, “Standard”, “Other”	“Standard”
If this parameter is defined, use the CSysLog facility setting when posting.	[LOG] SysLogFacility NCBI_CONFIG__LOG__SYSLOGFACILITY  c	any non-empty string	(none)
Truncate the log file – i.e. discard the contents when opening an existing file.	[Log] Truncate LOG_TRUNCATE	Boolean  b	false
Specify whether to try creating the log file under /log before trying other locations (e.g. a location specified by the registry or by NCBI_CONFIG__LOG__FILE).	[LOG] TryRootLogFirst NCBI_CONFIG__LOG__TRYROOTLOGFIRST  c	Boolean  a	false
If true, default to logging warnings when unsafe static array types are copied.	[NCBI] STATIC_ARRAY_COPY_WARNING NCBI_STATIC_ARRAY_COPY_WARNING	Boolean  b	false
If true, log warnings for unsafe static array types.	[NCBI] STATIC_ARRAY_UNSAFE_TYPE_WARNING NCBI_STATIC_ARRAY_UNSAFE_TYPE_WARNING	Boolean  b	true

^a case-insensitive: true, t, yes, y, false, f, no, n

^b case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^c environment variable name formed from registry section and entry name

Diagnostic Trace

Severity level is the same for all macros (ERR_POST, LOG_POST, _TRACE). DIAG_TRACE enables _TRACE output regardless of the severity level. So, if your severity level is Warning and DIAG_TRACE is set, you will see Warnings (and above) and Traces but not Infos. This chapter tells more about logging severity: Setting Diagnostic Severity Levels

These parameters tune the visibility and contents of diagnostic messages produced by _TRACE, LOG_POST or ERR_POST macros.

See Table 3.

Table 3. Diagnostic trace configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Specify the severity level threshold for posting diagnostic messages – i.e. less severe messages will not be posted. Special case: Trace – print all messages and show Trace level messages. Note: If the parameter is set then the function ncbi::SetDiagPostLevel() is ignored - except for setting the level to eDiag_Trace, in which case Trace level messages will be shown anyway.	[DEBUG] DIAG_POST_LEVEL DIAG_POST_LEVEL	CI  b: Info, Warning, Error, Critical, Fatal, Trace	(none)
Messages with Trace level will be shown if this parameter is given any value.	[DEBUG] DIAG_TRACE DIAG_TRACE or NCBI_CONFIG__DEBUG__DIAG_TRACE  c	any non-empty string	(none)
Specify a file that stores a mapping of error codes to their descriptions.	[DEBUG] MessageFile NCBI_CONFIG__DEBUG__MESSAGEFILE  c	a valid file name	(none)
Specify the minimum severity that will result in the stack trace being added to diagnostic messages.	[DEBUG] Stack_Trace_Level DEBUG_STACK_TRACE_LEVEL	CI  b: Info, Warning, Error, Critical, Fatal, Trace	Fatal
Specify the maximum number of entries to be listed in a stack trace. All stack trace entries above the specified level are not printed.	[DEBUG] Stack_Trace_Max_Depth DEBUG_STACK_TRACE_MAX_DEPTH	a positive integer	200
Specify the maximum number of messages that can be posted to the AppLog within the AppLog period.	[Diag] AppLog_Rate_Limit DIAG_APPLOG_RATE_LIMIT	unsigned integer or OFF	50000
Specify the AppLog period in seconds.	[Diag] AppLog_Rate_Period DIAG_APPLOG_RATE_PERIOD	unsigned integer	10
Specify whether context properties should be automatically printed when set or changed.	[Diag] AutoWrite_Context DIAG_AUTOWRITE_CONTEXT	Boolean  a	false
Specify the maximum number of diagnostic messages to collect. Messages beyond the limit will result in erasing the oldest message.	[Diag] Collect_Limit DIAG_COLLECT_LIMIT	size_t	1000
Disable all Applog messages (start/stop, request start/stop, extra).	[Diag] Disable_AppLog_Messages DIAG_DISABLE_APPLOG_MESSAGES	Boolean  a	false
Specify the maximum number of messages that can be posted to the ErrLog within the ErrLog period.	[Diag] ErrLog_Rate_Limit DIAG_ERRLOG_RATE_LIMIT	unsigned integer or OFF	5000
Specify the ErrLog period in seconds.	[Diag] ErrLog_Rate_Period DIAG_ERRLOG_RATE_PERIOD	unsigned integer	1
Limit the log file size, and rotate the log when it reaches the limit.	[Diag] Log_Size_Limit DIAG_LOG_SIZE_LIMIT	non-negative long integer	0
Limit length of a single log line, truncate message if longer.	[Diag] Max_Line_Length DIAG_MAX_LINE_LENGTH	unsigned integer	0
If “On”, then replace newlines in diagnostic messages with a semicolon. N.B. Newlines are replaced in-place by “;” - they are not escaped.	[Diag] Merge_Lines DIAG_MERGE_LINES	“Default”, “Off”, or “On”	“Default” (which means “Off”)
Use the old output format if the flag is set.	[Diag] Old_Post_Format DIAG_OLD_POST_FORMAT	Boolean  a	true
Specify a diagnostics post filter string (see an earlier chapter for more detail on filtering).	[DIAG] POST_FILTER NCBI_CONFIG__DIAG__POST_FILTER  c	see the syntax rules	(none)
Print the system TID rather than CThread::GetSelf().	[Diag] Print_System_TID DIAG_PRINT_SYSTEM_TID	Boolean  a	false
Specify the minimum severity that will activate Tee_To_Stderr. See the Tee Output to STDERR section.	[Diag] Tee_Min_Severity DIAG_TEE_MIN_SEVERITY	CI  b: Info, Warning, Error, Critical, Fatal, Trace	Warning (debug); Error (release)
Duplicate messages to stderr. See the Tee Output to STDERR section.	[Diag] Tee_To_Stderr DIAG_TEE_TO_STDERR	Boolean  a	false
Specify a diagnostics trace filter string (see an earlier chapter for more detail on filtering).	[DIAG] TRACE_FILTER NCBI_CONFIG__DIAG__TRACE_FILTER  c	see the syntax rules	(none)
Specify the maximum number of messages that can be posted to the TraceLog within the TraceLog period.	[Diag] TraceLog_Rate_Limit DIAG_TRACELOG_RATE_LIMIT	unsigned integer or OFF	5000
Specify the TraceLog period in seconds.	[Diag] TraceLog_Rate_Period DIAG_TRACELOG_RATE_PERIOD	unsigned integer	1
If true and AppLog severity is not locked, print the current GMT time in diagnostic messages; otherwise print local time.	[Diag] UTC_Timestamp DIAG_UTC_TIMESTAMP	Boolean  a	false
Number of messages processed as a single batch by CAsyncDiagHandler.	[Diag] Async_Batch_Size DIAG_ASYNC_BATCH_SIZE	integer	10
Max size of CAsyncDiagHandler message buffer.	[Diag] Async_Buffer_Size DIAG_ASYNC_BUFFER_SIZE	unsigned integer	32768
Max number of lines in a single CAsyncDiagHandler message buffer.	[Diag] Async_Buffer_Max_Lines DIAG_ASYNC_BUFFER_MAX_LINES	unsigned integer	100
Max number of messages in the CAsyncDiagHandler queue.	[Diag] Max_Async_Queue_Size DIAG_MAX_ASYNC_QUEUE_SIZE	Uint4	10000

^a case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^b CI = case-insensitive

^c environment variable name formed from registry section and entry name

Run-Time

Run-time configuration parameters allow specifying memory size limit, CPU time limit, and memory allocation behavior. Note: not all operating systems support these parameters.

Table 4. Run-time configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Controls whether to enable libbackward’s support for printing stack traces on segmentation faults and the like; the default is based on the build-time flag --with-backward-cpp-sig. NB: Code bypassing CNcbiApplication but interested in this feature should explicitly call CStackTrace::s_HonorSignalHandlingConfiguration().	[Debug] Trace_Fatal_Signals DEBUG_TRACE_FATAL_SIGNALS	Boolean  a	varies by build-time configuration, but false for standard builds
Set a CPU time limit for the application in seconds.	[NCBI] CpuTimeLimit NCBI_CONFIG__NCBI__CPUTIMELIMIT  b	non-negative integer	0 (unlimited)
Set a memory size limit for the application. Setting the limit may not work on some systems, depends on OS, compilation options and etc. Some systems enforce memory limits, other didn’t. If the memory limit is reached, any subsequent memory allocations fails.	[NCBI] MemorySizeLimit NCBI_CONFIG__NCBI__MEMORYSIZELIMIT  b	A positive integer percent (e.g. “70%”) or an optionally suffixed non-negative real number (e.g. “123456789”, “100MiB”, or “1.25 G”). A percent limit is relative to the total system memory. No suffix means the given value is in MiB; a “B” suffix means the value is in bytes. If there is a suffix, there can be spaces between the number and the suffix. The default units are decimal (i.e. powers of 1000) - e.g. “MB”. The final “B” is optional for decimal units (e.g. “M”). You can use “i” to indicate binary units (i.e. powers of 1024) – e.g. “MiB”. Supported suffix characters are: “K”, “M”, “G”, “T”, “P”, and “E”. Suffixes are not case-sensitive.	0 (unlimited)
Specify the method for filling allocated memory.	[NCBI] MEMORY_FILL NCBI_MEMORY_FILL	CI  c: none, zero, pattern	pattern
Set stack size per thread.	[Thread] StackSize THREAD_STACK_SIZE	unsigned integer	2097152

^a case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^b environment variable name formed from registry section and entry name

^c CI = case-insensitive

Abnormal Program Termination

These parameters specify how to handle abnormal situations when executing a program.

Table 5. Abnormal program termination configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If this parameter is defined, abort the program if a CException is thrown.	[DEBUG] ABORT_ON_THROW NCBI_CONFIG__DEBUG__ABORT_ON_THROW  c	any non-empty string	(none)
Specify whether the NCBI application framework should catch exceptions that are not otherwise caught.	[Debug] Catch_Unhandled_Exceptions DEBUG_CATCH_UNHANDLED_EXCEPTIONS	Boolean  a	true
Specify whether ncbi::Abort() will call _ASSERT(false). Note: this only applies to MSVC.	[Diag] Assert_On_Abort DIAG_ASSERT_ON_ABORT	Boolean  a	false
If this parameter is true, abort the program if it detects CPU compatibility issues. In particular, program can check flags it compiled with current CPU possibilities.	[NCBI] TerminateOnCpuIncompatibility NCBI_CONFIG__TERMINATE_ON_CPU_INCOMPATIBILITY	Boolean  a	false
If this parameter is true, abort the program if a CObjectException is thrown.	[NCBI] ABORT_ON_COBJECT_THROW NCBI_ABORT_ON_COBJECT_THROW	Boolean  a	false
If this parameter is true, abort the program on an attempt to access or release a NULL pointer stored in a CRef object.	[NCBI] ABORT_ON_NULL NCBI_ABORT_ON_NULL	Boolean  a	false
Specify what to do when ncbi::Abort() is called. When the variable is set to a “yes” value, Abort() will call exit(255). When the variable is set to a “no” value, Abort() will call abort(). When the variable is not set, Abort() will call exit(255) for release builds and abort() for debug builds - unless compiled with MSVC and the DIAG_ASSERT_ON_ABORT parameter is true, in which case Abort() will call _ASSERT(false).	[N/A] N/A DIAG_SILENT_ABORT	Boolean  b	(none)

^a case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^b case-insensitive: y, 1, n, 0

^c environment variable name formed from registry section and entry name

NCBI

These parameters tune generic NCBI C++ Toolkit-wide behavior.

Table 6. NCBI C++ Toolkit-wide configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Specify whether throwing an exception of at least Critical severity will cause an immediate abort().	[EXCEPTION] Abort_If_Critical EXCEPTION_ABORT_IF_CRITICAL	Boolean  a	false
Specify the minimum severity that will result in the stack trace being added to exceptions.	[EXCEPTION] Stack_Trace_Level EXCEPTION_STACK_TRACE_LEVEL	CI  b: Trace, Info, Warning, Error, Critical, Fatal	Critical
A single path to check for common data files via g_FindDataFile(). Takes a lower precedence than paths in NCBI_DATA_PATH.	[NCBI] Data NCBI_CONFIG__NCBI__DATA  c	a valid path	””
A list of paths (delimited in the style of the OS) to check for common data files via g_FindDataFile().	[NCBI] DataPath NCBI_DATA_PATH	a delimited list of valid paths	””
Specify how read-only files are treated on Windows during a remove request.	[NCBI] DeleteReadOnlyFiles NCBI_CONFIG__DELETEREADONLYFILES	Boolean  a	false
Specify whether the API classes should have logging turned on.	[NCBI] FileAPILogging NCBI_CONFIG__FILEAPILOGGING	Boolean  a	DEFAULT_LOGGING_VALUE
Declare how umask settings on Unix affect creating files/directories in the File API.	[NCBI] FileAPIHonorUmask NCBI_CONFIG__FILEAPIHONORUMASK	Boolean  a	false
Specify whether to load plugins from DLLs.	[NCBI] Load_Plugins_From_DLLs NCBI_LOAD_PLUGINS_FROM_DLLS	Boolean  a	LOAD_PLUGINS_FROM_DLLS_BY_DEFAULT
Specify the directory to use for temporary files.	[NCBI] TmpDir NCBI_CONFIG__NCBI__TMPDIR  c	a valid path	””
Specify the file name of a Unicode-to-ASCII translation table.	[NCBI] UnicodeToAscii NCBI_CONFIG__NCBI__UNICODETOASCII  c	a valid path	””
Safety switch to turn async write off (making write blocking) for all CAsyncWriteCache instances.	[NCBI] cache_async_write NCBI_CONFIG__NCBI__CACHE_ASYNC_WRITE	Boolean  a	true
Enable CUrl class to parse input as ‘indexed’ query (RFC3875) when no ‘=’ is present.	[CUrl] enable_parsing_as_index NCBI_CONFIG__CURL__ENABLE_PARSING_AS_INDEX	Boolean  a	false

^a case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^b CI = case-insensitive

^c environment variable name formed from registry section and entry name

Library-Specific Parameters

The following sections discuss library-specific configuration parameters.

• Connection

• CGI and FCGI

• Serial

• Objects, Object Manager, Object Tools

• DBAPI

• Eutils

Connection

These parameters affect various aspects of internet connections established by the connection library. See the Networking and IPC chapter for a description of the corresponding network information structure.

Table 7. Connection library configuration parameters

Purpose	[Registry section] Registry name Environment variable (See Note 2)	Valid values	Default
Service-specific parameters follow this form. (See Note 1)	[<service>] CONN_<param_name> <service>_CONN_<param_name>
Global parameters follow this form. (See Note 1)	[CONN] <param_name> CONN_<param_name>
Specify arguments for the given service. (See Note 1)	[<service>] CONN_ARGS <service>_CONN_ARGS	(service-dependent)	””
Specify how much debug information will be output. (See Note 1)	[<service>] CONN_DEBUG_PRINTOUT <service>_CONN_DEBUG_PRINTOUT	CI  a: to get some: 1, on, yes, true, some to get all: data, all to get none: anything else	””
If this parameter is true, the network dispatcher will be disabled. (See Note 1)	[<service>] CONN_DISPD_DISABLE <service>_CONN_DISPD_DISABLE	Boolean  c	true
Sets the DTAB (delegation table) for routing via NAMERD. (See Note 1)	[<service>] CONN_DTAB <service>_CONN_DTAB	string	””
If this parameter is true, the Firewall mode will be enabled. (See Note 1)	[<service>] CONN_FIREWALL <service>_CONN_FIREWALL	Boolean  c	not set
Set the dispatcher host name. (See Note 1)	[<service>] CONN_HOST <service>_CONN_HOST	a valid host name	www.ncbi.nlm.nih.gov
Set the HTTP proxy server. (See Note 1)	[<service>] CONN_HTTP_PROXY_HOST <service>_CONN_HTTP_PROXY_HOST	a valid proxy host	””
Set the HTTP proxy server port number. This will be set to zero if <service>_CONN_HTTP_PROXY_HOST is not set. (See Note 1)	[<service>] CONN_HTTP_PROXY_PORT <service>_CONN_HTTP_PROXY_PORT	unsigned short	0
Set a custom user header. This is rarely used, and then typically for debugging purposes. (See Note 1)	[<service>] CONN_HTTP_USER_HEADER <service>_CONN_HTTP_USER_HEADER	a valid HTTP header	””
Prohibit the use of a local load balancer. Note: This parameter is discouraged for performance reasons - please use <service>_CONN_LBSMD_DISABLE instead. (See Note 1)	[<service>] CONN_LB_DISABLE <service>_CONN_LB_DISABLE	Boolean  c	false
Enable the use of LB-DNS for named services. (See Note 1)	[<service>] CONN_LBDNS_ENABLE <service>_CONN_LBDNS_ENABLE	Boolean  c	false
Prohibit the use of a local load balancer. This should be used instead of <service>_CONN_LB_DISABLE. (See Note 1)	[<service>] CONN_LBSMD_DISABLE <service>_CONN_LBSMD_DISABLE	Boolean  c	false
Enable linkerd-based service name resolution. (See Note 1) Note: Generally, you should also set <service>_CONN_LBSMD_DISABLE=1 for this to take effect. Note: If <service>_CONN_NAMERD_ENABLE is set then NAMERD would be attempted to use in order to figure out the service endpoint. If that failed (or the setting is not enabled) the service endpoint is synthetized.	[<service>] CONN_LINKERD_ENABLE <service>_CONN_LINKERD_ENABLE	Boolean  c	false
Enable the use of locally configured services. See <service>_CONN_LOCAL_SERVER_<n>. (See Note 1)	[<service>] CONN_LOCAL_ENABLE <service>_CONN_LOCAL_ENABLE	Boolean  c	false
Create a service entry for service, where n is a number from 0 to 100 (not necessarily sequential). The value must be a valid server descriptor, as it would be configured for the load balancing daemon (LBSMD). This is a quick way of configuring locally used services (usually, for the sole purposes of debugging / development) without the need to edit the actual LBSMD tables (which become visible for the whole NCBI). See <service>_CONN_LOCAL_ENABLE. Note: This parameter has no corresponding global parameter. (See Note 1)	[<service>] CONN_LOCAL_SERVER_<n> <service>_CONN_LOCAL_SERVER_<n>	any non-empty string	not set
Maximum number of attempts to establish connection. Zero means use the default. (See Note 1)	[<service>] CONN_MAX_TRY <service>_CONN_MAX_TRY	unsigned short	3
Enable namerd-based service name resolution. (See Note 1) (See Note 3) Note: Generally, you should also set <service>_CONN_LBSMD_DISABLE=1 for this to take effect.	[<service>] CONN_NAMERD_ENABLE <service>_CONN_NAMERD_ENABLE	Boolean  c	false
Specify a password for the connection (only used with <service>_CONN_USER). (See Note 1)	[<service>] CONN_PASS <service>_CONN_PASS	the user’s password	””
Set the path to the service. (See Note 1)	[<service>] CONN_PATH <service>_CONN_PATH	a valid service path	/Service/dispd.cgi
Set the dispatcher port number. (See Note 1)	[<service>] CONN_PORT <service>_CONN_PORT	unsigned short	0
Set the HTTP request method. (See Note 1)	[<service>] CONN_REQ_METHOD <service>_CONN_REQ_METHOD	CI a: any, get, post	ANY
Redirect connections to <service> to the specified alternative service. See Service Redirection. (See Note 1)	[<service>] CONN_SERVICE_NAME <service>_CONN_SERVICE_NAME	a replacement for the service name	(none)
Set to true if the client is stateless. (See Note 1)	[<service>] CONN_STATELESS <service>_CONN_STATELESS	Boolean  c	false
Zero means no waiting but polling (may not work well with all connections); “infinite” means no timeout (i.e. to wait for I/O indefinitely); other values are the maximum number of seconds to wait before failing. (See Note 1.)	[<service>] CONN_TIMEOUT <service>_CONN_TIMEOUT	floating point >= 0.0 (1 microsecond precision)  f or “infinite”	30.0
Specify a username for the connection (see <service>_CONN_PASS). Only necessary for connections requiring authentication. (See Note 1)	[<service>] CONN_USER <service>_CONN_USER	a username with access rights for the connection	(none)
Set the level of logging detail that TLS provider should produce about secure transactions. Generally, log levels greater than 7 also dump scrambled data.	[CONN] TLS_LOGLEVEL CONN_TLS_LOGLEVEL	0 to 10	0
A true value enables HTTP connections to dump headers of error server responses only (successful responses do not get logged).	[CONN] HTTP_ERROR_HEADER_ONLY CONN_HTTP_ERROR_HEADER_ONLY	Boolean  c	false
A true value enables HTTP connections to follow https to http transitions (http to https transitions are secure and therefore don’t need to be enabled).	[CONN] HTTP_UNSAFE_REDIRECTS CONN_HTTP_UNSAFE_REDIRECTS	Boolean  c	false
Set a default referer (applies to all HTTP connections).	[CONN] HTTP_REFERER CONN_HTTP_REFERER	a valid referer	(none)
A list of identifiers to be treated as local services defined in the registry / environment. This parameter is optional and is used only for reverse address-to-name lookups.	[CONN] LOCAL_SERVICES CONN_LOCAL_SERVICES	whitespace-delimited  d list of identifiers	(none)
Set the mail gateway host.	[CONN] MX_HOST CONN_MX_HOST	a valid host name	localhost on Unix platforms except Cygwin; mailgw on all other platforms
Set the mail gateway port.	[CONN] MX_PORT CONN_MX_PORT	1 to 65535	25 (SMTP)
Set the mail gateway communication timeout in seconds.	[CONN] MX_TIMEOUT CONN_MX_TIMEOUT	floating point >= 0.0 (zero means default)	120
Use poll(2) instead of select(2) to wait for available data for reading/writing. This is necessary if the number of open file descriptors exceeds 1024.	[CONN] PIPE_USE_POLL CONN_PIPE_USE_POLL	Boolean  c	false
Enable CServer to catch exceptions.	[server] Catch_Unhandled_Exceptions CSERVER_CATCH_UNHANDLED_EXCEPTIONS	Boolean  b	true
Enable CThreadInPool_ForServer to catch exceptions.	[ThreadPool] Catch_Unhandled_Exceptions NCBI_CONFIG__THREADPOOL__CATCH_UNHANDLED_EXCEPTIONS  e	Boolean  b	true
CUsageReportAPI - enable/disable.	[USAGE_REPORT] Enabled NCBI_USAGE_REPORT_ENABLED	Boolean  b	false
CUsageReportAPI - URL to report usage statistics.	[USAGE_REPORT] URL NCBI_USAGE_REPORT_URL	a valid URL	https://www.ncbi.nlm.nih.gov/stat
CUsageReportAPI - application name.	[USAGE_REPORT] AppName NCBI_USAGE_REPORT_APPNAME	string	(none)
CUsageReportAPI - application version.	[USAGE_REPORT] AppVersion NCBI_USAGE_REPORT_APPVERSION	string	(none)
CUsageReportAPI - maximum number of reporting jobs in the queue per reporter.	[USAGE_REPORT] MaxQueueSize NCBI_USAGE_REPORT_MAXQUEUESIZE	unsigned int	100

^a CI = case-insensitive

^b case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^c case-insensitive: true values are { 1, on, yes, true }; false is anything else

^d whitespace can be any number of spaces and/or tabs

^e environment variable name formed from registry section and entry name

^f although very precise values may be specified, practical host limitations my result in less precise effective values

Note 1: All service-specific parameters shown in Table 7 (except one) have corresponding global parameters - i.e. parameters that apply to all services. For these global parameters, the registry section name is CONN; the registry entry name doesn’t have the CONN_ prefix; and the environment variable doesn’t have the <service>_ prefix. For example, the service-specific parameter specified by the CONN_ARGS entry in a given [<service>] section of the registry (or by the <service>_CONN_ARGS environment variable) corresponds to the global parameter specified by the ARGS entry in the [CONN] section of the registry (or by the CONN_ARGS environment variable). When both a service-specific parameter and its corresponding global parameter are set, the service-specific parameter takes precedence.

Note 2: Environment variable names for service-specific parameters are formed by capitalizing the service name.

Note 3: See Dispatching with namerd and Linkerd for additional namerd-related configuration parameters not typically needed by end users.

CGI and FCGI

The folowing sections show parameters that tune CGI and FCGI applications and CGI load balancing.

• CGI

• FCGI

• CGI Load Balancing

CGI

These parameters tune the behavior of CGI applications.

Table 8. CGI-related configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Set to the user agent string you would like to be used by the web server.	[N/A] N/A HTTP_USER_AGENT	A valid user agent string.	(none)
Allow SIGPIPE in a plain (non-FastCGI) C++ Toolkit CGI (i.e. CCgiApplication-derived).	[CGI] Allow_Sigpipe CGI_ALLOW_SIGPIPE	Boolean  c	false
Add to the user agent list of bot names. This parameter affect only CCgiUserAgent::IsBot().	[CGI] Bots NCBI_CONFIG__CGI__BOTS  f	Delimited list  b of bot names, e.g. “Googlebot Scooter WebCrawler Slurp”.	(none)
When true (and when using HTTP/1.1), produce the CGI response in chunks, with the size set by [CGI].ChunkSize.	[CGI] ChunkedTransfer CGI_CHUNKED_TRANSFER	“Disable” or “Enable”	“Disable”
Set the size of the chunks when producing chunked CGI responses per [CGI].ChunkedTransfer.	[CGI] ChunkSize CGI_CHUNK_SIZE	positive integer	4096
According to RFC-2109, cookies should not be encoded. Instead, they should be just quoted. However, for backward compatibility with code that decodes incoming cookies, both quoted cookies and encoded cookies can be parsed. This setting controls which method of encoding/decoding is used.	[CGI] Cookie_Encoding CGI_COOKIE_ENCODING	“Url”, “Quote”	“Url”
Specifies a cookie name to get an authorization token from (for the ‘auth_token’ property of the request context).	[CGI] cookie_auth_token NCBI_CONFIG__CGI__COOKIE_AUTH_TOKEN	string	“WebCubbyUser”
Severity level for cookie-related error messages.	[CGI] Cookie_Error_Severity CGI_Cookie_Error_Severity	CI  e: Info, Warning, Error, Critical, Fatal, Trace	Error
Defines which characters cannot be used in cookie names.	[CGI] Cookie_Name_Banned_Symbols CGI_Cookie_Name_Banned_Symbols	A string of banned characters.	”  ,;=”
See CGI_CORS_Enable. Specify the value of the Access-Control-Allow-Credentials header, which indicates whether or not the response to the request can be exposed when the credentials flag is true.  g	[CGI] CORS_Allow_Credentials CGI_CORS_ALLOW_CREDENTIALS	either do not set, or use the string “true”	(not set)
See CGI_CORS_Enable. Specify the value of the Access-Control-Allow-Headers header, which is used in response to a preflight request to indicate which HTTP headers can be used when making the actual request.  g	[CGI] CORS_Allow_Headers CGI_CORS_ALLOW_HEADERS	string	“X-Requested-With”
See CGI_CORS_Enable. Specify the value of the Access-Control-Allow-Methods header, which specifies the method or methods allowed when accessing the resource (in response to a preflight request).  g	[CGI] CORS_Allow_Methods CGI_CORS_ALLOW_METHODS	string	“GET, POST, OPTIONS”
See CGI_CORS_Enable. Specify the value of the Access-Control-Allow-Origin header. Should be a space-separated list of domain suffixes (e.g. ‘foo.com bar.org’) that are permitted to access the resource. The Origin header sent by the client is matched against the list. If there’s no match, CORS is not enabled. If matched, the client provided Origin is copied to the outgoing Access-Control-Allow-Origin. To allow any origin set the value to ‘*’ (this should be a single character, not part of the list).	[CGI] CORS_Allow_Origin CGI_CORS_ALLOW_ORIGIN	string - either “*” or a valid origin	“ncbi.nlm.nih.gov”
Set to true to enable Cross-Origin Resource Sharing (CORS), and use non-empty parameters for given headers (e.g. CORS_Allow_Origin etc) to set the value for those headers. If false or not set, cross-origin request headers will cause an error.	[CGI] CORS_Enable CGI_CORS_Enable	Boolean  c	false
See CGI_CORS_Enable. Specify the value of the Access-Control-Expose-Headers header, which lets a server whitelist headers that browsers are allowed to access.  g	[CGI] CORS_Expose_Headers CGI_CORS_EXPOSE_HEADERS	string	””
See CGI_CORS_Enable. Param to enable JQuery JSONP hack to allow Cross-Origin Resource Sharing for browsers that don’t support CORS (e.g. IE versions earlier than 11). If it is set to true and the HTTP request contains entry “callback” whose value starts with “JQuery_” (case-insensitive, configurable - see CGI_CORS_JQUERY_CALLBACK_PREFIX), then: 1. Set the response Content-Type to “text/javascript”; and 2. Wrap the response content into: “JQuery_foobar(original_content)”	[CGI] CORS_JQuery_Callback_Enable CGI_CORS_JQUERY_CALLBACK_ENABLE	Boolean  c	false
See CGI_CORS_Enable. Specify a prefix other than “JQuery_” for the JQuery JSONP callback name (see CGI_CORS_JQUERY_CALLBACK_ENABLE). Use the symbol ‘*’ if any name is good.	[CGI] CORS_JQuery_Callback_Prefix CGI_CORS_JQUERY_CALLBACK_PREFIX	string	”*”
See CGI_CORS_Enable. Specify the value of the Access-Control-Max-Age header, which indicates how long the results of a preflight request can be cached.  g	[CGI] CORS_Max_Age CGI_CORS_MAX_AGE	string (seconds)	””
Enable CSRF token validation in CCgiApplication.	[CGI] ValidateCSRFToken CGI_VALIDATE_CSRF_TOKEN	Boolean	false
Set to true to make the application count the amount of data read/sent. The numbers are then printed in request stop log messages.	[CGI] Count_Transfered CGI_COUNT_TRANSFERED	Boolean  c	true
Set the name of an environment variable, which in turn specifies a prefix that will be added to all diagnostic messages issued during HTTP request processing.	[CGI] DiagPrefixEnv NCBI_CONFIG__CGI__DIAGPREFIXENV  f	a valid environment variable name	(none)
When true, discard the session tracking ID if it’s set to “UNK_SESSION”. For example, if “UNK_SESSION” is set through HTTP_NCBI_SID (which would generally be a bad practice), this will result in it being replaced with a valid SID.	[CGI] Discard_UNK_SESSION NCBI_CGI_DISCARD_UNK_SESSION	Boolean c	false
When true, and when the request method is GET and the ncbi_help[=format] URL parameter is passed, return a help message to the CGI client. The following sources are checked in the given order for the help message content (all sources except the last are files located with the CGI): • <cginame>.help.<format> • help.<format> • <cginame>.help.<accept_hdr_subtype><accept_hdr_mediarangeparams> • help.<accept_hdr_subtype><accept_hdr_mediarangeparams> • <cginame>.help.html • <cginame>.help.xml • <cginame>.help.json • help.html • help.xml • help.json • an XML representation of the result of GetArgDescriptions()	[CGI] EnableHelpRequest CGI_ENABLE_HELP_REQUEST	Boolean  c	true
When the request method is “GET” and the [CGI].EnableVersionRequest configuration parameter is true and the ncbi_version URL parameter is supplied and empty or “short” or “full”, then the CGI application version is returned to the CGI client. Alternatively, the [CGI].EnableVersionRequest configuration parameter can name a URL parameter that will substitute for ncbi_version. In both cases, the short version is returned unless “full” is specified. By default, the version is returned as content type “text/plain”, but this can be overridden by supplying either “xml” or “json” as the subtype in an Accept header. A non-empty ncbi_version (or overridden URL parameter) with a value other than “short” or “full” will result in an error, as will an Accept header subtype other than “xml” or “json”.	[CGI] EnableVersionRequest CGI_ENABLE_VERSION_REQUEST	either Boolean c or the name of a URL parameter	false
This parameter applies only to HEAD requests: If false, no exception is thrown and the application continues to run, but the output stream is blocked so that no more data can be sent to the client. If any attempts are made to write response content after the headers have been written, then an error will be posted to the log (but only the first time). If true, the CGI application framework will throw CCgiHeadException after writing the headers. Note: This exception must percolate up to CCgiApplication::Run() for this option to work correctly, typically by catching and rethrowing it in ProcessRequest(). In this case the application will exit immediately after writing the headers with HTTP status code 200.	[CGI] ExceptionAfterHEAD NCBI_CONFIG__CGI__EXCEPTIONAFTERHEAD  f	Boolean  c	false
Set to true to disable the creation of a tracking cookie during session initialization.	[CGI] DisableTrackingCookie NCBI_CONFIG__CGI__DISABLETRACKINGCOOKIE  f	Boolean  c	false
Set to true to enable logging.	[CGI] Log NCBI_CONFIG__CGI__LOG  f	CI  e: On => enabled; True => enabled; OnError => enabled for errors; OnDebug => enabled (debug builds only)	disabled
An ampersand-delimited string of GET and/or POST arguments to exclude from the log (helps limit the size of the log file)	[CGI] LOG_EXCLUDE_ARGS CGI_LOG_EXCLUDE_ARGS	valid format: arg1&arg2…	(none)
Allows specifying limits for multiple GET and/or POST arguments in one parameter string.	[CGI] LOG_LIMIT_ARGS CGI_LOG_LIMIT_ARGS	valid format: arg1:size1&arg2:size2…&*:size special argument: * means all unspecified arguments; special limits: -2 means exclude; -1 means no limit	*:1000000
Enable logging of CGI request parameters. Only the specified parameters will be logged.	[CGI] LogArgs NCBI_CONFIG__CGI__LOGARGS  f	Delimited list  a of environment variables (optionally aliased on output for shortening logs, e.g. envvar=1).	(none)
Set to true to merge log lines.	[CGI] Merge_Log_Lines CGI_MERGE_LOG_LINES	Boolean  c	true
Specify additional mobile device names. This parameter affect only CCgiUserAgent::IsMobileDevice().	[CGI] MobileDevices NCBI_CONFIG__CGI__MobileDevices  f	Delimited list  b of additional device names.	(none)
Add to the user agent list of names that aren’t bots. This parameter affect only CCgiUserAgent::IsBot().	[CGI] NotBots NCBI_CONFIG__CGI__NotBots  f	Delimited list  b of names that aren’t bots.	(none)
Add to the user agent list of names that aren’t mobile devices. This parameter affect only CCgiUserAgent::IsMobileDevice().	[CGI] NotMobileDevices NCBI_CONFIG__CGI__NotMobileDevices  f	Delimited list  b of names that aren’t mobile devices.	(none)
Add to the user agent list of names that aren’t phone devices. This parameter affect only CCgiUserAgent::IsPhoneDevice().	[CGI] NotPhoneDevices NCBI_CONFIG__CGI__NotPhoneDevices  f	Delimited list  b of names that aren’t phone devices.	(none)
Add to the user agent list of names that aren’t tablet devices. This parameter affect only CCgiUserAgent::IsTabletDevice().	[CGI] NotTabletDevices NCBI_CONFIG__CGI__NotTabletDevices  f	Delimited list  b of names that aren’t tablet devices.	(none)
Control error handling of incoming cookies (doesn’t affect outgoing cookies set by application).	[CGI] On_Bad_Cookie CGI_ON_BAD_COOKIE	CI  e: Throw, SkipAndError, Skip, StoreAndError, Store	Store
Specify additional phone device names. This parameter affect only CCgiUserAgent::IsPhoneDevice().	[CGI] PhoneDevices NCBI_CONFIG__CGI__PhoneDevices  f	Delimited list  b of additional device names.	(none)
Specifies whether to print the referer during LogRequest().	[CGI] Print_Http_Referer CGI_PRINT_HTTP_REFERER	Boolean  c	true
Specifies whether to print the URL during LogRequest().	[CGI] Print_Self_Url CGI_PRINT_SELF_URL	Boolean  c	true
Specifies whether to print the user agent during LogRequest().	[CGI] Print_User_Agent CGI_PRINT_USER_AGENT	Boolean  c	true
Specifies whether to print the request method during LogRequest().	[CGI] Print_Request_Method CGI_PRINT_REQUEST_METHOD	Boolean  c	true
Set the size of CGI request buffer that is printed when the request cannot be parsed.	[CGI] RequestErrBufSize NCBI_CONFIG__CGI__REQUESTERRBUFSIZE  f	buffer size in bytes	256
Specify the registry section name for the result cache.	[CGI] ResultCacheSectionName NCBI_CONFIG__CGI__RESULTCACHESECTIONNAME  f	valid section name	result_cache
Enable statistics logging.	[CGI] StatLog NCBI_CONFIG__CGI__STATLOG  f	Boolean  d	false
Specify additional tablet device names. This parameter affect only CCgiUserAgent::IsTabletDevice().	[CGI] TabletDevices NCBI_CONFIG__CGI__TabletDevices  f	Delimited list  b of additional device names.	(none)
Controls whether the output stream will throw for bad states.	[CGI] ThrowOnBadOutput NCBI_CONFIG__CGI__THROWONBADOUTPUT  f	Boolean  c	true
Log start time, end time, and elapsed time.	[CGI] TimeStamp NCBI_CONFIG__CGI__TIMESTAMP  f	Boolean  d	false
Disable statistics logging if the CGI request took less than the specified number of seconds.	[CGI] TimeStatCutOff NCBI_CONFIG__CGI__TIMESTATCUTOFF  f	non-negative integer (zero enables logging)	0
Specify the domain for the tracking cookie.	[CGI] TrackingCookieDomain NCBI_CONFIG__CGI__TRACKINGCOOKIEDOMAIN  f	valid domain	.nih.gov
Specify the tracking cookie name.	[CGI] TrackingCookieName NCBI_CONFIG__CGI__TRACKINGCOOKIENAME  f	valid cookie name	ncbi_sid
Specify the path for the tracking cookie.	[CGI] TrackingCookiePath NCBI_CONFIG__CGI__TRACKINGCOOKIEPATH  f	valid path	/
Defines the name of the NCBI tracking cookie (session ID cookie).	[CGI] TrackingTagName CGI_TrackingTagName	Any valid cookie name.	“NCBI-SID”
Specify a set of fields (e.g. HTTP headers when the protocol is HTTP) to be taken from incoming requests and passed to outgoing requests. For more details, see the NCBI Context Fields Confluence page.	[Context] Fields NCBI_CONTEXT_FIELDS	A space-delimited, case-insensitive list of glob patterns.	””
If configured, replaces messages of any exceptions from user code (e.g. from ProcessRequest) with a configured one.	[CGI] Exception_Message NCBI_CONFIG__CGI__EXCEPTION_MESSAGE  f	string	””

^a List may be delimited by semicolon, space, tab, or comma.

^b List may be delimited by newlines or any of the special characters: semicolon, space, tab, vertical bar, or tilde. If the list contains one or more newlines then only newlines will be used as delimiters and the values in the list will be the content of the lines including any special characters. If the list does not contain any newline characters then all special characters will act as independent delimiters. Therefore, if any value in the list needs to include any of the special characters, then newlines must be used as the delimiter.

^c case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^d case-insensitive: true, t, yes, y, false, f, no, n

^e CI = case-insensitive

^f environment variable name formed from registry section and entry name

^g some information from HTTP access control (CORS) by Mozilla Contributors, adapted under CC-BY-SA

FCGI

These parameters tune the behavior of FCGI applications.

Table 9. FCGI-related configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
A true value enables logging of current iteration, max iterations, and process ID during the FastCGI run.	[FastCGI] Debug NCBI_CONFIG__FASTCGI__DEBUG  b	Boolean  a	false
A true value enables termination of a FastCGI application by the presence of the request entry “exitfastcgi”.	[FastCGI] HonorExitRequest NCBI_CONFIG__FASTCGI__HONOREXITREQUEST  b	Boolean  a	false
Specify the number of requests that the FCGI application will process before exiting.	[FastCGI] Iterations NCBI_CONFIG__FASTCGI__ITERATIONS  b	positive integer	10
Make the FastCGI application run as a stand-alone server on a local port. The value is a Unix domain socket or a MS Windows named pipe, or a colon followed by a port number	[FastCGI] StandaloneServer FCGI_STANDALONE_SERVER	valid local port or named socket	(none)
Make the FastCGI application stop if an error is encountered.	[FastCGI] StopIfFailed NCBI_CONFIG__FASTCGI__STOPIFFAILED  b	Boolean  a	false
Make the FastCGI application stop if the memory limit is exceeded.	[FastCGI] TotalMemoryLimit NCBI_CONFIG__FASTCGI__TOTALMEMORYLIMIT	An optionally suffixed non-negative real number (e.g. “123456789”, “100MiB”, or “1.25 G”). No suffix (or a “B” suffix) means the given value is in bytes. If there is a suffix, there can be spaces between the number and the suffix. The default units are decimal (i.e. powers of 1000) - e.g. “MB”. The final “B” is optional for decimal units (e.g. “M”). You can use “i” to indicate binary units (i.e. powers of 1024) – e.g. “MiB”. Valid suffix characters are: “K”, “M”, “G”, “T”, “P”, and “E”. Suffixes are not case-sensitive.	0 (unlimited)
Make the FastCGI application exit if the named file changes.	[FastCGI] WatchFile.Name NCBI_CONFIG__FASTCGI__WATCHFILE_DOT_NAME  b	valid file name	(none)
The number of bytes to read from the watch file to see if it has changed.	[FastCGI] WatchFile.Limit NCBI_CONFIG__FASTCGI__WATCHFILE_DOT_LIMIT  b	positive integer (non-positives trigger default)	1024
The period in seconds between checking the watch file for changes.	[FastCGI] WatchFile.Timeout NCBI_CONFIG__FASTCGI__WATCHFILE_DOT_TIMEOUT  b	positive integer (non-positives trigger default, which is to disable the watch file checking)	0
Maximum number of request processing threads.	[FastCGI] MaxThreads NCBI_CONFIG__FASTCGI__MAXTHREADS  b	positive integer or 0 for the default value	8

^a case-insensitive: true, t, yes, y, false, f, no, n

^b environment variable name formed from registry section and entry name

CGI Load Balancing

These parameters tune the CGI load balancer.

Table 10. CGI load balancing configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Specify the internet domain.	[CGI-LB] Domain NCBI_CONFIG__CGI-LB__DOMAIN  b	a valid domain	.ncbi.nlm.nih.gov
Specify the host IP address.	[CGI-LB] Host NCBI_CONFIG__CGI-LB__HOST  b	a valid host IP	(none)
Specify the cookie expiration period in seconds.	[CGI-LB] LifeSpan NCBI_CONFIG__CGI-LB__LIFESPAN  b	integer	0
Specify the name of the load balancing cookie in the HTTP response.	[CGI-LB] Name NCBI_CONFIG__CGI-LB__NAME  b	a valid cookie name	(none)
Specify the cookie path.	[CGI-LB] Path NCBI_CONFIG__CGI-LB__PATH  b	a valid path	(none)
Specify the cookie security mode.	[CGI-LB] Secure NCBI_CONFIG__CGI-LB__SECURE  b	Boolean  a	false

^a case-insensitive: true, t, yes, y, false, f, no, n

^b environment variable name formed from registry section and entry name

Serial

These parameters tune the behavior of the Serial library.

Table 11. Serial library configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Skip unknown data members in the input stream, or throw an exception.	[N/A] N/A SERIAL_SKIP_UNKNOWN_MEMBERS	CI  a: yes, no, never, always	no (throw)
If true, causes CObjectOStream::WriteDouble() to use fast conversion.	[SERIAL] FastWriteDouble NCBI_CONFIG__SERIAL__FastWriteDouble  b	Boolean  c	true
While reading binary ASN.1 data allow VisibleString tag where UTF-8 string tag is expected by specification.	[SERIAL] READ_ANY_UTF8STRING_TAG SERIAL_READ_ANY_UTF8STRING_TAG	Boolean  c	true
While reading binary ASN.1 data allow UTF-8 string tag where VisibleString tag is expected by specification.	[SERIAL] READ_ANY_VISIBLESTRING_TAG SERIAL_READ_ANY_VISIBLESTRING_TAG	0 (disallow, throws an exception); 1 (allow, but warn once); 2 (allow without warning)	1
If true, use memory-mapped file access, which associates a file’s content with a portion of the virtual address space of a process. This can result in a modest performance increase (probably < 15%).	[SERIAL] READ_MMAPBYTESOURCE SERIAL_READ_MMAPBYTESOURCE	Boolean  c	false
Specify how to handle unknown variants when reading Object streams.	[SERIAL] SKIP_UNKNOWN_MEMBERS NCBI_CONFIG__SERIAL__SKIP_UNKNOWN_MEMBERS  b	CI  a: no (throw an exception), never (even if set to skip later), yes (skip), always (even if set to not skip later)	no
Specify how to handle unknown variants when reading Object streams.	[SERIAL] SKIP_UNKNOWN_VARIANTS NCBI_CONFIG__SERIAL__SKIP_UNKNOWN_VARIANTS  b	CI  a: no (throw an exception), never (even if set to skip later), yes (skip), always (even if set to not skip later)	no
Throw an exception on an attempt to access an uninitialized data member.	[SERIAL] VERIFY_DATA_GET SERIAL_VERIFY_DATA_GET	CI  a: yes, no, never, always, defvalue, defvalue_always	yes
Throw an exception if a mandatory data member is missing in the input stream.	[SERIAL] VERIFY_DATA_READ SERIAL_VERIFY_DATA_READ	CI  a: yes, no, never, always, defvalue, defvalue_always	yes
Throw an exception on an attempt to write an uninitialized data member.	[SERIAL] VERIFY_DATA_WRITE SERIAL_VERIFY_DATA_WRITE	CI  a: yes, no, never, always, defvalue, defvalue_always	yes
While writing binary ASN.1 data issue UTF8 string tag as determined by specification, otherwise issue plain string tag.	[SERIAL] WRITE_UTF8STRING_TAG SERIAL_WRITE_UTF8STRING_TAG	Boolean  c	false
Specifies what to do if an invalid character is read.	[SERIAL] WRONG_CHARS_READ NCBI_CONFIG__SERIAL__WRONG_CHARS_READ  b	“ALLOW”, “REPLACE”, “REPLACE_AND_WARN”, “THROW”, “ABORT”	“REPLACE_AND_WARN”
Specifies what to do if an invalid character is written.	[SERIAL] WRONG_CHARS_WRITE NCBI_CONFIG__SERIAL__WRONG_CHARS_WRITE  b	“ALLOW”, “REPLACE”, “REPLACE_AND_WARN”, “THROW”, “ABORT”	“REPLACE_AND_WARN”
Specifies number of attempts to send request to the service.	[<SERVICE_NAME>.rpc_client] max_try <SERVICE_NAME>__RPC_CLIENT__MAX_TRY	int a positive integer or zero to use the default number	3
Specifies delay in seconds between attempts to send request to the service.	[<SERVICE_NAME>.rpc_client] retry_delay <SERVICE_NAME>__RPC_CLIENT__RETRY_DELAY	double delay in seconds	0

^a CI = case-insensitive

^b environment variable name formed from registry section and entry name

^c case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

Objects, Object Manager, Object Tools

Objects library

These parameters tune the behavior of the Objects library.

Table 13.1. Objects-related configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If non-zero, reserve Dense-seg vectors using predefined pre-read hook.	[OBJECTS] DENSE_SEG_RESERVE OBJECTS_DENSE_SEG_RESERVE	Boolean  a	true
Specify whether Seq-id general trees are packed.	[OBJECTS] PACK_GENERAL OBJECTS_PACK_GENERAL	Boolean  a	true
Specify whether Seq-id text-seq trees are packed.	[OBJECTS] PACK_TEXTID OBJECTS_PACK_TEXTID	Boolean  a	true
Specify whether empty Seq-descr’s will be allowed (or throw if not).	[OBJECTS] SEQ_DESCR_ALLOW_EMPTY OBJECTS_SEQ_DESCR_ALLOW_EMPTY	Boolean  a	false
If non-zero, reserve Seq-graph vectors using predefined pre-read hook.	[OBJECTS] SEQ_GRAPH_RESERVE OBJECTS_SEQ_GRAPH_RESERVE	Boolean  a	true
If non-zero, reserve Seq-table vectors using predefined pre-read hook.	[OBJECTS] SEQ_TABLE_RESERVE OBJECTS_SEQ_TABLE_RESERVE	Boolean  a	true
If true, try to avoid GIs where possible, even if there’s no accessions to prefer.	[SeqId] AvoidGi SEQ_ID_AVOID_GI	Boolean  a	false
If true, give GIs worse (higher) score to prefer accessions in CSeq_id ranking methods.	[SeqId] PreferAccessionOverGi SEQ_ID_PREFER_ACCESSION_OVER_GI	Boolean  a	false
If true, replace ranges that cannot be mapped with a NULL location instead of using the neighbor’s fuzz.	[Mapper] NonMapping_As_Null MAPPER_NONMAPPING_AS_NULL	Boolean a	false
SNP PTIS GRPC server, if not set then GRPC_PROXY environment variable is used.	[ID2SNP] PTIS_NAME NCBI_CONFIG__ID2SNP__PTIS_NAME	“host:port”	“linderd:4142”
SNP PTIS client debug level.	[ID2SNP] PTIS_DEBUG NCBI_CONFIG__ID2SNP__PTIS_DEBUG	int: if >= 5 dbsnp requests and replies are logged	1
SNP PTIS client number of retries.	[ID2SNP] RETRY NCBI_CONFIG__ID2SNP__RETRY	int	5
The TIMEOUT* parameters describe the timeout for opening a SNP PTIS connection.	[ID2SNP] TIMEOUT NCBI_CONFIG__ID2SNP__TIMEOUT	any floating point value >= 0.0	1 second
TIMEOUT_MULTIPLIER and TIMEOUT_INCREMENT specify the way the open timeout is increased if no response is received (next_open_timeout = prev_open_timeout * multiplier + increment).	[ID2SNP] TIMEOUT_INCREMENT NCBI_CONFIG__ID2SNP__TIMEOUT_INCREMENT	any floating point value >= 0.0	0 seconds
The limit of increasing the open timeout using TIMEOUT_MULTIPLIER and TIMEOUT_INCREMENT.	[ID2SNP] TIMEOUT_MAX NCBI_CONFIG__ID2SNP__TIMEOUT_MAX	floating point >= 0.0	10 seconds
See TIMEOUT_INCREMENT	[ID2SNP] TIMEOUT_MULTIPLIER NCBI_CONFIG__ID2SNP__TIMEOUT_MULTIPLIER	floating point >= 0.0	1.5
The WAIT_TIME* parameters describe the wait time before opening new connections in case of communication errors. WAIT_TIME is the initial wait after the first error.	[ID2SNP] WAIT_TIME NCBI_CONFIG__ID2SNP__WAIT_TIME	floating point >= 0.0	0.5 seconds
WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT specify the way wait time is increased if errors continue to happen (next_wait_time = prev_wait_time * multiplier + increment).	[ID2SNP] WAIT_TIME_INCREMENT NCBI_CONFIG__ID2SNP__WAIT_TIME_INCREMENT	any floating point value >= 0.0	0 second
The limit of increasing wait time using WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT.	[ID2SNP] WAIT_TIME_MAX NCBI_CONFIG__ID2SNP__WAIT_TIME_MAX	floating point >= 0.0	10 seconds
See WAIT_TIME_INCREMENT	[ID2SNP] WAIT_TIME_MULTIPLIER NCBI_CONFIG__ID2SNP__WAIT_TIME_MULTIPLIER	any floating point value >= 0.0	1.5

Object Manager library

These parameters tune the behavior of the Object Manager library.

Table 13.2. Object Manager configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Default adaptive depth heuristic will include adaptive depth by named annot accession: if only named annot accessions are requested in SAnnotSelector then iterator stops at level where all requested names are seen.	[OBJMGR] ADAPTIVE_DEPTH_BY_NAMED_ACC NCBI_CONFIG__OBJMGR__ADAPTIVE_DEPTH_BY_NAMED_ACC	Boolean a	true
Sets the maximum number of master TSE blobs that will be cached.	[OBJMGR] BLOB_CACHE OBJMGR_BLOB_CACHE	unsigned int	10
Data source uses bulk chunk requests to load blobs.	[OBJMGR] BULK_CHUNKS OBJMGR_BULK_CHUNKS	Boolean a	true
CObjectManager reports scope register/revoke operations. Checked only in debug builds.	[OBJMGR] DEBUG_SCOPE NCBI_CONFIG__OBJMGR__DEBUG_SCOPE	Boolean a	false
Keep external annotations (SNP, CDD, etc.) visible on edited sequences. Potentially slow due to size of SNP data.	[OBJMGR] KEEP_EXTERNAL_FOR_EDIT NCBI_CONFIG__OBJMGR__KEEP_EXTERNAL_FOR_EDIT	Boolean a	false
Specify whether the scope can be auto-released.	[OBJMGR] SCOPE_AUTORELEASE OBJMGR_SCOPE_AUTORELEASE	Boolean  a	true
Specify the size of the scope auto-release.	[OBJMGR] SCOPE_AUTORELEASE_SIZE OBJMGR_SCOPE_AUTORELEASE_SIZE	unsigned int	10
Controls MT optimization of object deletion in CScope. If the value is not zero CScope deletes unused entries outside of its mutex, avoiding MT-bottleneck.	[OBJMGR] SCOPE_POSTPONE_DELETE OBJMGR_SCOPE_POSTPONE_DELETE	int	1

Genbank data loader and readers

These parameters tune the behavior of the Genbank data loader. More details about Genbank loader and readers cofniguration can be found here.

Table 13.3a. Genbank data loader configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
The Object Manager will attach WGS master descriptors to Bioseq data by default. Setting this parameter to false will disable this behavior.	[GENBANK] ADD_WGS_MASTER NCBI_CONFIG__GENBANK__ADD_WGS_MASTER	Boolean  a	true
Allow GenBank loader readers to process loader commands partially, in hope that missing data will be loaded later.	[GENBANK] ALLOW_INCOMPLETE_COMMANDS GENBANK_ALLOW_INCOMPLETE_COMMANDS	Boolean a	false
Load external annotations for other loaders.	[GENBANK] ALWAYS_LOAD_EXTERNAL NCBI_CONFIG__GENBANK__ALWAYS_LOAD_EXTERNAL	Boolean a	false
Load NANNOT annotations for other loaders.	[GENBANK] ALWAYS_LOAD_NAMED_ACC NCBI_CONFIG__GENBANK__ALWAYS_LOAD_NAMED_ACC	Boolean a	true
A non-zero value turns on debugging messages about GenBank loader’s interaction with cache.	[GENBANK] CACHE_DEBUG GENBANK_CACHE_DEBUG	>=0, currently only zero and non-zero are distinguished	0
Specify whether an attempt should be made to recompress the cache.	[GENBANK] CACHE_RECOMPRESS GENBANK_CACHE_RECOMPRESS	Boolean  a	true
A non-zero value turns on debugging messages about opening/closing connections to ID1/ID2 services.	[GENBANK] CONN_DEBUG GENBANK_CONN_DEBUG	>=0, currently only zero and non-zero are distinguished	0
Offset all GIs loaded by GenBank loader by a 64-bit value. Use this option only to test your code for 64-bit GI compatibility, the data from GenBank loader will be modified!	[GENBANK] GI_OFFSET GENBANK_GI_OFFSET	64-bit int	0
Expiration timeout of id resolution information in seconds (must be > 0).	[GENBANK] ID_EXPIRATION_TIMEOUT NCBI_CONFIG__GENBANK__ID_EXPIRATION_TIMEOUT	positive integer	7200 (2hr)
Size of id resolution GC queues.	[GENBANK] ID_GC_SIZE NCBI_CONFIG__GENBANK__ID_GC_SIZE	unsigned int	10000
Set the severity level for ID1 debug tracing.	[GENBANK] ID1_DEBUG GENBANK_ID1_DEBUG	int: 0 = none, 1 = error, 2 = open, 4 = conn, 5 = asn, 8 = asn data	0
Specify the ID1 reader service name. Note: The services can be redirected using generic Service Redirection technique. Has precedence over [NCBI].SERVICE_NAME_ID1	[GENBANK] ID1_SERVICE_NAME GENBANK_ID1_SERVICE_NAME	a valid reader service name	ID1 (see API)
Set the severity level for ID2 debug tracing.	[GENBANK] ID2_DEBUG GENBANK_ID2_DEBUG	int: 0 = none, 1 = error, 2 = open, 4 = conn, 5 = asn, 8 = blob, 9 = blob data	debug: none release: error (see API)
Number of chunks allowed in a single request.	[GENBANK] ID2_MAX_CHUNKS_REQUEST_SIZE GENBANK_ID2_MAX_CHUNKS_REQUEST_SIZE	int: 0 = unlimited request size; 1 = do not use packets or get-chunks requests	100
Specify the ID2 reader service name. Note: The services can be redirected using generic Service Redirection technique. Has precedence over [GENBANK].ID2_SERVICE_NAME	[GENBANK] ID2_CGI_NAME GENBANK_ID2_CGI_NAME	a valid reader service name	ID2 (see API)
Maximum number of requests packed in a single ID2 packet.	[GENBANK] ID2_MAX_IDS_REQUEST_SIZE GENBANK_ID2_MAX_IDS_REQUEST_SIZE	>=0	100
Plug-in libraries with CID2Processor implementation. Useful for development of alternative data sources.	[GENBANK] ID2_PROCESSOR GENBANK_ID2_PROCESSOR	comma-separated list of names of id2proc interface plug-ins	””
Specify the ID2 reader service name. Note: The services can be redirected using generic Service Redirection technique. Has precedence over [NCBI].SERVICE_NAME_ID2	[GENBANK] ID2_SERVICE_NAME GENBANK_ID2_SERVICE_NAME	a valid reader service name	ID2 (see API)
Prioritized list of drivers to try for the reader or writer. Less precedence than [GENBANK].READER_NAME or [GENBANK].WRITER_NAME.	[GENBANK] LOADER_METHOD GENBANK_LOADER_METHOD	list items are semicolon-delimited; each item is a colon-delimited list of drivers. valid drivers: id1, id2, cache, pubseqos “psg” can be used to enable PSG loader (no other readers are allowed with “psg”)	#if defined(HAVE_PUBSEQ_OS) “ID2:PUBSEQOS:ID1” else “ID2:ID1” #endif (see API)
Flag switching CGBDataLoader to PSG mode. If set to true, PSG data loader is used to process requests instead of the normal Genbank loader.	[GENBANK] LOADER_PSG GENBANK_LOADER_PSG	Boolean a	false
Whether to open first connection immediately or not. Has precedence over any reader-specific PREOPEN parameters.	[GENBANK] PREOPEN NCBI_CONFIG__GENBANK__PREOPEN  b	Boolean  a	true
How GBLoader should react on PTIS failure.	[GENBANK] PTIS_ERROR_ACTION NCBI_CONFIG__GENBANK__PTIS_ERROR_ACTION	“ignore”, “report” or “throw”	“report”
Turns on different levels of debug messages in PubSeqOS reader. A value >=2 means debug opening connections while >=5 means debug results of Seq-id resolution requests. Note: only applies to debug builds.	[GENBANK] PUBSEQOS_DEBUG GENBANK_PUBSEQOS_DEBUG	int	0
Prioritized list of drivers to try for the reader. Can be overridden by [GENBANK].READERNAME. Has precedence over [GENBANK].LOADER_METHOD.	[GENBANK] READER_NAME GENBANK_READER_NAME	See [GENBANK].LOADER_METHOD.	See [GENBANK].LOADER_METHOD.
Prioritized list of drivers to try for the reader. Has precedence over [GENBANK].READER_NAME and [GENBANK].LOADER_METHOD.	[GENBANK] READERNAME GENBANK_READERNAME	See [GENBANK].LOADER_METHOD.	See [GENBANK].LOADER_METHOD.
Specify the level of reader statistics to collect.	[GENBANK] READER_STATS GENBANK_READER_STATS	int: 0 = none, 1 = verbose	0
Specify whether the reader manager should automatically register ID1, ID2, and cache.	[GENBANK] REGISTER_READERS GENBANK_REGISTER_READERS	Boolean  a	true
On some platforms, equal strings can share their character data, reducing the required memory. Set this parameter to true to have the GenBank loader try to use this feature if it is available.	[GENBANK] SNP_PACK_STRINGS GENBANK_SNP_PACK_STRINGS	Boolean  a	true
In ID1/PubSeqOS readers present SNP data as ID2-split entries to reduce memory usage.	[GENBANK] SNP_SPLIT GENBANK_SNP_SPLIT	Boolean  a	true
Storing all the SNPs as plain ASN.1 objects would require a huge amount of memory. The SNP table is a compact way of storing SNPs to reduce memory consumption. Set this parameter to true to have the object manager try to use the SNP table.	[GENBANK] SNP_TABLE GENBANK_SNP_TABLE	Boolean  a	true
Set to a positive integer to enable dumping (to stderr in text ASN.1 form) all the SNPs that don’t fit into the SNP table. Note: this is only available in debug mode.	[GENBANK] SNP_TABLE_DUMP GENBANK_SNP_TABLE_DUMP	Boolean  a	false
Set this parameter to true to dump (to stdout) some statistics on the process of storing SNPs into the SNP table. This option may help determine why not all the SNPs could fit in the table.	[GENBANK] SNP_TABLE_STAT GENBANK_SNP_TABLE_STAT	Boolean  a	false
Verbosity level of loading information in GenBank loader.	[GENBANK] TRACE_LOAD GENBANK_TRACE_LOAD	int	0
Specify whether to use a memory pool.	[GENBANK] USE_MEMORY_POOL GENBANK_USE_MEMORY_POOL	Boolean  a	true
Enable version 2 (from MongoDB… despite “VDB” in the name) source of CDD annotations on os_gateway ID2 server with GenBank ID2 reader.	[GENBANK] VDB_CDD GENBANK_VDB_CDD	Boolean a	false
Enable version 2 (from VDB) source of SNP annotations on os_gateway ID2 server with GenBank ID2 reader.	[GENBANK] VDB_SNP GENBANK_VDB_SNP	Boolean a	false
Enable VDB source of WGS sequences on os_gateway ID2 server with GenBank ID2 reader.	[GENBANK] VDB_WGS GENBANK_VDB_WGS	Boolean a	true
Prioritized list of drivers to try for the writer. Can be overridden by [GENBANK].WRITERNAME. Has precedence over [GENBANK].LOADER_METHOD.	[GENBANK] WRITER_NAME GENBANK_WRITER_NAME	See [GENBANK].LOADER_METHOD.	See [GENBANK].LOADER_METHOD.
Prioritized list of drivers to try for the writer. Has precedence over [GENBANK].WRITER_NAME and [GENBANK].LOADER_METHOD.	[GENBANK] WRITERNAME GENBANK_WRITERNAME	See [GENBANK].LOADER_METHOD.	See [GENBANK].LOADER_METHOD.
Specify the ID1 reader service name. Note: The services can be redirected using generic Service Redirection technique. Less precedence than [GENBANK].ID1_SERVICE_NAME.	[NCBI] SERVICE_NAME_ID1 GENBANK_SERVICE_NAME_ID1	a valid reader service name	ID1 (see API)
Specify the ID2 reader service name. Note: The services can be redirected using generic Service Redirection technique. Less precedence than [GENBANK].ID2_SERVICE_NAME.	[NCBI] SERVICE_NAME_ID2 GENBANK_SERVICE_NAME_ID2	a valid reader service name	ID2 (see API)

These parameters tune the behavior of the Genbank readers. Each parameter is checked in the [GENBANK/<reader_name>] section first, then if the section does not exist, [<reader_name>] is checked as well.

Table 13.3b. Genbank readers configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
The maximum number of connections the reader can establish to the data source. This is run-time limited to 1 for single threaded clients and for all clients using the cache or gi reader, and to 5 for multi-threaded clients using the ID1, ID2, PubSeqOS, and PubSeqOS2 readers.	[GENBANK/<reader_name>] or [<reader_name>] MAX_NUMBER_OF_CONNECTIONS or NO_CONN	int	3 for ID1 and ID2; 2 for PubSeqOS and PubSeqOS2
The OPEN_TIMEOUT* parameters describe the timeout for opening a GenBank connection (ID1, ID2 and PubSeqOS2 readers). The timeout allows the server a reasonable time to respond while providing a means to quickly abandon unresponsive servers.	[GENBANK/<reader_name>] or [<reader_name>] OPEN_TIMEOUT	any floating point value >= 0.0	5 seconds
OPEN_TIMEOUT_MULTIPLIER and OPEN_TIMEOUT_INCREMENT (ID1 and ID2 readers) specify the way the open timeout is increased if no response is received (next_open_timeout = prev_open_timeout * multiplier + increment).	[GENBANK/<reader_name>] or [<reader_name>] OPEN_TIMEOUT_INCREMENT or OPEN_INCREMENT	any floating point value >= 0.0	0 seconds
The limit of increasing the open timeout using OPEN_TIMEOUT_MULTIPLIER and OPEN_TIMEOUT_INCREMENT (ID1 and ID2 readers).	[GENBANK/<reader_name>] or [<reader_name>] OPEN_TIMEOUT_MAX or OPEN_MAX	floating point >= 0.0	30 seconds
See OPEN_TIMEOUT_INCREMENT	[GENBANK/<reader_name>] or [GENBANK/<reader_name>] OPEN_TIMEOUT_MULTIPLIER or OPEN_MULTIPLIER	floating point >= 0.0	1.5
Whether to open first connection immediately or not. Can be overriden by [GENBANK].PREOPEN.	[GENBANK/<reader_name>] or [<reader_name>] PREOPEN	Boolean a	false
Number of retries on errors.	[GENBANK/<reader_name>] or [<reader_name>] RETRY	int	5
Timeout of network connections in seconds (ID1, ID2 and PubSeqOS2 readers).	[GENBANK/<reader_name>] or [<reader_name>] TIMEOUT	integer	20 seconds
The WAIT_TIME* parameters describe the wait time before opening new GenBank connections in case of communication errors. The wait time is necessary to allow network and/or GenBank servers to recover. WAIT_TIME is the initial wait after the first error.	[GENBANK/<reader_name>] or [<reader_name>] WAIT_TIME	floating point >= 0.0	1 second
Specifies for how many sequential communication errors the response should be to use wait time, before trying to open a new connection instead.	[GENBANK/<reader_name>] or [<reader_name>] WAIT_TIME_ERRORS	int	2 errors
WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT specify the way wait time is increased if errors continue to happen (next_wait_time = prev_wait_time * multiplier + increment).	[GENBANK/<reader_name>] or [<reader_name>] WAIT_TIME_INCREMENT	any floating point value >= 0.0	1 second
The limit of increasing wait time using WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT.	[GENBANK/<reader_name>] or [<reader_name>] WAIT_TIME_MAX	floating point >= 0.0	30 seconds
See WAIT_TIME_INCREMENT	[GENBANK/<reader_name>] or [<reader_name>] WAIT_TIME_MULTIPLIER	any floating point value >= 0.0	1.5
ID1 and ID2 reader service name. Overrides [GENBANK].ID*_SERVICE_NAME and [NCBI].SERVICE_NAME_ID*.	[GENBANK/<reader_name>] SERVICE	a valid reader service name	ID1 or ID2
Prioritized list of DBAPI drivers for PubSeqOS/PubSeqOS2 readers.	[GENBANK/<reader_name>] or [<reader_name>] DRIVER	semicolon-delimited list of driver names	“ftds;ctlib”
Disable attaching WGS master descriptors when retrieving ASN.1 blobs using the PubSeqOS/PubSeqOS2 readers.	[GENBANK/<reader_name>] or [<reader_name>] EXCLUDE_WGS_MASTER	Boolean  a	true for PubSeqOS false for PubSeqOS2
Password for PubSeqOS/PubSeqOS2 database.	[GENBANK/<reader_name>] or [<reader_name>] PASSWORD	string	“allowed”
Server name for PubSeqOS/PubSeqOS2 database.	[GENBANK/<reader_name>] or [<reader_name>] SERVER	string	“PUBSEQ_OS_PUBLIC_GI64”
Fetch user name from MyNCBI and put the value into cubby_user variable for PubSeqOS/PubSeqOS2 database.	[GENBANK/<reader_name>] or [<reader_name>] SET_CUBBY_USER	Boolean  a	false
User name for PubSeqOS/PubSeqOS2 database.	[GENBANK/<reader_name>] or [<reader_name>] USER	string	“anyone”
Allow gzip compression of PubSeqOS data.	[GENBANK/pubseqos] or [pubseqos] GZIP	Boolean  a	true
Path to the gicache index files.	[GENBANK/gicache] or [gicache] PATH	valid path	”//panfs/pan1.be-md.ncbi.nlm.nih.gov/id_dumps/gi_cache”
ICache driver or a list of drivers for cache reader and writer. For more details about cache configuration see GenBank data loader configuration.	[GENBANK/cache/<cache_type>] or [cache/<cache_type>] DRIVER	semicolon-delimited list of driver names (“bdb” and “netcache”)	“bdb”
ID2 reader SNP scale limit.	[GENBANK] ID2SNP_SCALE_LIMIT GENBANK_ID2SNP_SCALE_LIMIT	“Chromosome”, “Supercontig”, “Contig”, “Unit”, or empty string to use server default	empty string

PSG data loader

These parameters tune the behavior of the PSG data loader.

Table 13.4. PSG data loader configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
The Object Manager will attach WGS master descriptors to Bioseq data by default. Setting this parameter to false will disable this behavior.	[PSG_LOADER] ADD_WGS_MASTER NCBI_CONFIG__PSG_LOADER__ADD_WGS_MASTER	Boolean  a	true
Number of retries when fetching bulk data.	[PSG_LOADER] BULK_RETRY_COUNT PSG_LOADER_BULK_RETRY_COUNT	unsigned int	8
Set the severity level for PSG debug tracing.	[PSG_LOADER] DEBUG PSG_LOADER_DEBUG	int: <5 = none 5..8 = different details of loading data	1
Expiration timeout of in-memory caches in seconds (must be > 0).	[PSG_LOADER] ID_EXPIRATION_TIMEOUT NCBI_CONFIG__PSG_LOADER__ID_EXPIRATION_TIMEOUT	positive unsigned integer	7200 (2hr)
Size of in-memory caches.	[PSG_LOADER] ID_GC_SIZE NCBI_CONFIG__PSG_LOADER__ID_GC_SIZE	unsigned int	10000
Number of threads in the thread pool used by PSG loader.	[PSG_LOADER] MAX_POOL_THREADS PSG_LOADER_MAX_POOL_THREADS	unsigned int	10
By default PSG loader prefers loading split data. If this parameter is set to true the loader will request original non-split data instead.	[PSG_LOADER] NO_SPLIT NCBI_CONFIG__PSG_LOADER__NO_SPLIT	Boolean  a	false
Prefetch information about bioseqs having no CDD annotations to avoid sending unnecessary CDD requests.	[PSG_LOADER] PREFETCH_CDD PSG_LOADER_PREFETCH_CDD	Boolean  a	false
Number of retries when fetching data (non-bulk).	[PSG_LOADER] RETRY_COUNT PSG_LOADER_RETRY_COUNT	unsigned int	4
PSG loader service name.	[PSG_LOADER] SERVICE_NAME PSG_LOADER_SERVICE_NAME	a valid service name	“PSG2”
SNP scale limit.	[PSG_LOADER] SNP_SCALE_LIMIT PSG_LOADER_SNP_SCALE_LIMIT	“Chromosome”, “Supercontig”, “Contig”, “Unit”, or empty string to use server default	empty string
The WAIT_TIME* parameters describe the wait time before opening new PSG connections in case of communication errors. The wait time is necessary to allow network and/or PSG servers to recover. WAIT_TIME is the initial wait after the first error.	[PSG_LOADER] WAIT_TIME	floating point >= 0.0	1 second
WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT specify the way wait time is increased if errors continue to happen (next_wait_time = prev_wait_time * multiplier + increment).	[PSG_LOADER] WAIT_TIME_INCREMENT	any floating point value >= 0.0	1 second
The limit of increasing wait time using WAIT_TIME_MULTIPLIER and WAIT_TIME_INCREMENT.	[PSG_LOADER] WAIT_TIME_MAX	floating point >= 0.0	30 seconds
See WAIT_TIME_INCREMENT	[PSG_LOADER] WAIT_TIME_MULTIPLIER	any floating point value >= 0.0	1.5
If this parameter is set to true the loader will request whole TSEs instead of split ones. If [PSG_LOADER].NO_SPLIT is set to true this parameter is ignored and original TSEs are requested.	[PSG_LOADER] WHOLE_TSE PSG_LOADER_WHOLE_TSE	Boolean  a	false
If this parameter is set to false the loader will request split TSEs instead of whole ones in bulk mode. If [PSG_LOADER].NO_SPLIT is set to true this parameter is ignored and original TSEs are requested.	[PSG_LOADER] WHOLE_TSE_BULK PSG_LOADER_WHOLE_TSE_BULK	Boolean  a	true

Object Tools library and other data loaders

These parameters tune the behavior of the Object Tools library and data loaders implemented in other parts of the C++ Toolkit.

Table 13.5. Object Tools configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Specify whether the blob stream processor should try to use string packing.	[N/A] N/A NCBI_SERIAL_PACK_STRINGS	Boolean  c	true
Database lock control. By default LDS2 databases are read-only, so they are cached in memory. If an explicit mode is set in the code, this config parameter is ignored. Note: To set locks the database must be writable.	[LDS2] DataLoader_Lock LDS2_DATALOADER_LOCK	“lock”, “nolock”, or “cache”	“cache”
Max number of data files allowed to be kept open by LDS2 file handler.	[LDS2] MAX_CACHED_STREAMS LDS2_MAX_CACHED_STREAMS	unsigned integer	3
Data format to be used by CDD client.	[CDD] data_format NCBI_CONFIG__CDD__DATA_FORMAT	“JSON”, “semi-binary”, or “binary”	“binary”
CDD client timeout.	[CDD] client_timeout NCBI_CONFIG__CDD__CLIENT_TIMEOUT	floating point > 0.0	none - use the default connection timeout
Specify whether the new FASTA implementation will be used.	[READ_FASTA] USE_NEW_IMPLEMENTATION NCBI_CONFIG__READ_FASTA__USE_NEW_IMPLEMENTATION  b	Boolean  a	true
SNP data loader scale limit.	[SNP_LOADER] SCALE_LIMIT SNP_LOADER_SCALE_LIMIT	“Chromosome”, “Supercontig”, “Contig”, “Unit”, or empty string to use default value (“Chromosome”)	empty string

^a case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^b environment variable name formed from registry section and entry name

^c case-insensitive: true values are { yes | 1 }; anything else is false

psg_client library

These parameters tune the behavior of the psg_client library.

Table 13.6. psg_client library configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Either a name of service (which can be resolved into a set of PSG servers) or a single fixed PSG server (in format “host:port”).	[PSG] service NCBI_PSG_SERVICE	string	“PSG2”
How often to query LBSM, in seconds. Less or equal to zero means no rebalance based on time	[PSG] rebalance_time NCBI_CONFIG__PSG__REBALANCE_TIMEa	double	10.0
How often to query LBSM while no servers discovered, in seconds. Less or equal to zero means rebalance_time is used instead	[PSG] no_servers_retry_delay NCBI_CONFIG__PSG__NO_SERVERS_RETRY_DELAYa	double	1.0
Number of internal I/O threads.	[PSG] num_io NCBI_CONFIG__PSG__NUM_IOa	integer	6
Max number of sessions (TCP connections) per server per I/O thread. Each thread has one session per server at start. New sessions are added dynamically (up to the limit) if all existing ones are full.	[PSG] max_sessions NCBI_CONFIG__PSG__MAX_SESSIONSa	integer	40
Maximum number of concurrent streams per session (TCP connection)	[PSG] max_concurrent_streams NCBI_CONFIG__PSG__MAX_CONCURRENT_STREAMSa	integer	100
Maximum number of concurrent submits per “on queue” callback. Essentially, maximum number of requests to be sent per one I/O operation.	[PSG] max_concurrent_submits NCBI_CONFIG__PSG__MAX_CONCURRENT_SUBMITSa	integer	150
Maximum number of concurrent requests per server.	[PSG] max_concurrent_requests_per_server NCBI_CONFIG__PSG__MAX_CONCURRENT_REQUESTS_PER_SERVERa	integer	500
Number of requests to submit consecutively per I/O thread	[PSG] requests_per_io NCBI_CONFIG__PSG__REQUESTS_PER_IOa	integer	1
Timeout on blob stream reading, in seconds	[PSG] reader_timeout NCBI_CONFIG__PSG__READER_TIMEOUTa	integer	12
Logging of debug printout of PSG protocol. Setting to ‘some’ will output everything except blob data.	[PSG] debug_printout NCBI_CONFIG__PSG__DEBUG_PRINTOUTa	none, some, allb	none
Instructing server as whether to use LMDB cache. Setting to ‘default’ will let servers use their own parameters on using LMDB cache	[PSG] use_cache NCBI_CONFIG__PSG__USE_CACHEa	no, yes, defaultb	default
I/O timer period, in seconds. Defines accuracy and precision for ‘competitive_after’ and ‘request_timeout’.	[PSG] io_timer_period NCBI_CONFIG__PSG__IO_TIMER_PERIODa	double	0.4
Number of seconds after a competitive hit is started for a request not yet received a reply.	[PSG] competitive_after NCBI_CONFIG__PSG__COMPETITIVE_AFTERa	double	2.0
Number of retries after any failure before giving up on a request	[PSG] request_retries NCBI_CONFIG__PSG__REQUEST_RETRIESa	integer	2
Number of retries after REFUSED_STREAM failure before giving up on a request.	[PSG] refused_stream_retries NCBI_CONFIG__PSG__REFUSED_STREAM_RETRIESa	integer	2
Timeout on request, in seconds	[PSG] request_timeout NCBI_CONFIG__PSG__REQUEST_TIMEOUTa	double	10.0
Arbitrary URL arguments to add to every request	[PSG] request_user_args NCBI_CONFIG__PSG__REQUEST_USER_ARGSa	string	””
Enables using user contexts as request IDs. If enabled, user contexts are internally cast to strings and, if successful, then used in logging of debug printout (see above).	[PSG] user_request_ids NCBI_CONFIG__PSG__USER_REQUEST_IDSa	Boolean c	false
Whether to throw an exception on retrieving an unknown reply item type (or, if set false, to log an error instead, once per process)	[PSG] fail_on_unknown_items NCBI_CONFIG__PSG__FAIL_ON_UNKNOWN_ITEMSa	Boolean c	false
Whether to fail an item/reply on receiving an unknown chunk type. If enabled, such items/replies will then get the error status and a corresponding message. The error message is logged (once per process) regardless	[PSG] fail_on_unknown_chunks NCBI_CONFIG__PSG__FAIL_ON_UNKNOWN_CHUNKSa	Boolean c	false
Localhost preference multiplier	[PSG] localhost_preference NCBI_CONFIG__PSG__LOCALHOST_PREFERENCEa	integer	1
Whether to use HTTPS	[PSG] https NCBI_CONFIG__PSG__HTTPSa	Boolean c	false
Enables reporting of PSG client API stats. If enabled, the stats are reported using ERR_POST(Note)	[PSG] stats NCBI_CONFIG__PSG__STATSa	Boolean c	false
Defines how often to report PSG client API stats, in seconds. Less or equal to zero means the stats are only reported on exit	[PSG] stats_period NCBI_CONFIG__PSG__STATS_PERIODa	double	0.0
Specifies a cookie name for any authorization token (from the ‘auth_token’ property of the request context).	[PSG] auth_token_name NCBI_PSG_AUTH_TOKEN_NAME	string	“WebCubbyUser”
Sets/overrides a cookie value for any authorization token (from the ‘auth_token’ property of the request context).	[PSG] auth_token NCBI_PSG_AUTH_TOKEN	string	”” (ignored)
Specifies a cookie name for admin authorization token.	[PSG] admin_auth_token_name NCBI_PSG_ADMIN_AUTH_TOKEN_NAME	string	“AdminAuthToken”
Sets/overrides a cookie value for admin authorization token.	[PSG] admin_auth_token NCBI_PSG_ADMIN_AUTH_TOKEN	string	”” (ignored)
Indicates whether throttling is enabled and, if so, when server throttling is released, in seconds	[PSG] throttle_relaxation_period NCBI_CONFIG__PSG__THROTTLE_RELAXATION_PERIODa	integer	0 (throttling is disabled)
This is one condition that will trigger server throttling and is defined as a string having the form “A / B” where A and B are integers. Throttling will be triggered if there are A failures in the last B operations	[PSG] throttle_by_connection_error_rate NCBI_CONFIG__PSG__THROTTLE_BY_CONNECTION_ERROR_RATEa	a string having the form “A / B” where A and B are integers	”” (ignored)
This is another condition that will trigger server throttling and is defined as follows. Server throttling will be triggered if this number of consecutive connection failures happens	[PSG] throttle_by_consecutive_connection_failures NCBI_CONFIG__PSG__THROTTLE_BY_CONSECUTIVE_CONNECTION_FAILURESa	integer	0 (ignored)
Do not release server throttling until the server appears in LBSMD	[PSG] throttle_hold_until_active_in_lb NCBI_CONFIG__PSG__THROTTLE_HOLD_UNTIL_ACTIVE_IN_LBa	Boolean c	false

^a environment variable name formed from registry section and entry name

^b case-insensitive

^c case-insensitive: true, t, yes, y, false, f, no, n

cSRA

sraread library

Note: This section applies only inside NCBI.

The following parameters tune the behavior of the sraread library:

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If true, will add CIGAR info to Seq-align’s returned by cSRA iterators.	[csra] cigar_in_align_ext CSRA_CIGAR_IN_ALIGN_EXT	Boolean	true
If true, will clip the read ranges returned by cSRA short read iterators according to quality.	[csra] clip_by_quality CSRA_CLIP_BY_QUALITY	Boolean	true
If true, will add mate info to Seq-align’s returned by cSRA iterators.	[csra] explicit_mate_info CSRA_EXPLICIT_MATE_INFO	Boolean	false
If true, cSRA short read iterators will also include technical reads.	[csra] include_technical_reads CSRA_INCLUDE_TECHNICAL_READS	Boolean	true

ncbi_xloader_csra library

Note: This section applies only inside NCBI.

The following parameters tune the behavior of the ncbi_xloader_csra library:

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If >= 9, log alignment chunks. If >= 5, log major function calls. If >= 2, log refseq stats. If >= 1, log summary data.	[csra_loader] debug CSRA_LOADER_DEBUG	int	0
The max number of SRR files to keep open.	[csra_loader] gc_size CSRA_LOADER_GC_SIZE	size_t	10
If > 0, defines the max number of separate spot groups.	[csra_loader] max_separate_spot_groups CSRA_LOADER_MAX_SEPARATE_SPOT_GROUPS	int	0
If > 0, defines the minimum quality threshold for loading alignment and pileup chunks.	[csra_loader] pileup_graphs CSRA_LOADER_PILEUP_GRAPHS	int	0
If true, fetch quality graphs along with short reads.	[csra_loader] quality_graphs CSRA_LOADER_QUALITY_GRAPHS	Boolean	false

BAM

bamread library

Purpose	[Registry section] Registry name	Valid values	Default
Specifies directory where BAM and BAM index files are looked for.	[bam] dir_path	Directory name
Specifies BAM file name. If dir_path is also specified, then the file name is relative to the dir_path.	[bam] bam_name	File Name
Specifies BAM index file name. If dir_path is also specified, then the file name is relative to the dir_path. If index_name is not set then index file name is derived form BAM file name by adding “.bai” extension.	[bam] index_name	File Name
Enables CIGAR string in Seq-align Traceback ext object	[bam] cigar_in_align_ext	Boolean	true
Enables skipping of CIGAR string with ambiguous match	[bam] omit_ambiguous_match_cigar	Boolean	false
Enables 2nd generation of BAM parsing code	[bam] use_raw_index	Boolean	false

ncbi_xloader_bam library

Purpose	[Registry section] Registry name	Valid values	Default
Enables debugging log messages (if not zero), the higher the number, the more messages are logged.	[bam_loader] debug	Number (0-3)	0
Specified file name for CIdMapperConfig used to map BAM sequence ids into CSeq_id.	[bam_loader] mapper_file	File Name
Use specified context as an argument to the CIdMapperConfig.	[bam_loader] mapper_context	String
Generate pileup graphs for alignments	[bam_loader] pileup_graphs	Boolean	true
Do not create pileup graphs from the set (ACGT,match,insert) if the graph is completely zero.	[bam_loader] skip_empty_pileup_graphs	Boolean	true
Use fast estimation for coverage graph if possible.	[bam_loader] estimated_coverage_graph	Boolean	true
Set alignment visibility MAPQ threshold.	[bam_loader] min_map_quality	Integer	1
Do not open BAM files at time of loader registration, open them only when alignments or graphs are requested.	[bam_loader] preopen	Boolean	false

DBAPI

These parameters tune the behavior of the DBAPI library.

Table 14. DBAPI configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
If RESET_SYBASE is true, the Sybase client path will be set to the value in the SYBASE variable.	[N/A] N/A RESET_SYBASE	Boolean  a	(none)
If RESET_SYBASE is true, the Sybase client path will be set to the value in the SYBASE variable.	[N/A] N/A SYBASE	a path containing a Sybase client	(none)
The version of the TDS protocol to use with the CTLIB driver.	[CTLIB] TDS_VERSION CTLIB_TDS_VERSION	an installed TDS version	125 (see API)
The version of the TDS protocol to use with the FTDS driver.	[FTDS] TDS_VERSION FTDS_TDS_VERSION	0 (auto-detect), 50 (Sybase or Open Server), 70 (SQL Server)	0
Whether connecting with Kerberos authentication is supported. If true, and the username and password are empty strings, then DBAPI will attempt to use Kerberos to connect to the database. The user must ensure that the database will allow them to connect via Kerberos and that their Kerberos ticket is not expired.	[dbapi] can_use_kerberos NCBI_CONFIG__DBAPI__CAN_USE_KERBEROS  c	Boolean  b	false
Whether to encrypt login data.	[dbapi] conn_use_encrypt_data NCBI_CONFIG__DBAPI__CONN_USE_ENCRYPT_DATA  c	Boolean  b	false
The maximum number of simultaneously open connections to database servers.	[dbapi] max_connection NCBI_CONFIG__DBAPI__MAX_CONNECTION  c	unsigned int	100
The maximum number of connection attempts that will be made for any server.	[DB_CONNECTION_FACTORY] MAX_CONN_ATTEMPTS NCBI_CONFIG__DB_CONNECTION_FACTORY__MAX_CONN_ATTEMPTS  c	unsigned int	1
The maximum number of validation attempts that will be made for each connection.	[DB_CONNECTION_FACTORY] MAX_VALIDATION_ATTEMPTS NCBI_CONFIG__DB_CONNECTION_FACTORY__MAX_VALIDATION_ATTEMPTS  c	unsigned int	1
The maximum number of servers to try to connect to for each service name (this is only meaningful if the number of servers running this service exceeds this value).	[DB_CONNECTION_FACTORY] MAX_SERVER_ALTERNATIVES NCBI_CONFIG__DB_CONNECTION_FACTORY__MAX_SERVER_ALTERNATIVES  c	unsigned int	32
The maximum number of connections to be made to one particular server (when several connections to the same service name are requested) before an attempt to connect to another server will be made. A value of 0 means connect to the same server indefinitely.	[DB_CONNECTION_FACTORY] MAX_DISPATCHES NCBI_CONFIG__DB_CONNECTION_FACTORY__MAX_DISPATCHES  c	unsigned int	0
The timeout, in seconds, to be used for all connection attempts (0 means to use either the default value or a value set specifically for the driver context).	[DB_CONNECTION_FACTORY] CONNECTION_TIMEOUT NCBI_CONFIG__DB_CONNECTION_FACTORY__CONNECTION_TIMEOUT  c	unsigned int	30
The timeout, in seconds, to be used while logging into the server for all connection attempts (0 means to use either the default value or a value set specifically for the driver context).	[DB_CONNECTION_FACTORY] LOGIN_TIMEOUT NCBI_CONFIG__DB_CONNECTION_FACTORY__LOGIN_TIMEOUT  c	unsigned int	30
If DBAPI resolved the passed name as a service name and then couldn’t connect to any server associated with that service name, then this parameter determines whether DBAPI should also try to resolve the passed name as a server name (a database alias from “interfaces” file or a DNS name). See also: database load balancing.	[DB_CONNECTION_FACTORY] TRY_SERVER_AFTER_SERVICE NCBI_CONFIG__DB_CONNECTION_FACTORY__TRY_SERVER_AFTER_SERVICE  c	Boolean  a	false
See ‘PRAGMA cache_size’ in the SQLite documentation.	[LDS2] SQLiteCacheSize LDS2_SQLITE_CACHE_SIZE	any valid cache size for an SQLite database	2000
The parameter tells if the SET XACT_ABORT ON option should be sent to the server as the first thing when a new connection is created. The parameter is applicable for the MS SQL servers only. The Sybase servers do not support this option and DBAPI will not try to send it regardless of the parameter value. See more on MS SQL server documentation.	[dbapi] set_xact_abort NCBI_CONFIG__DBAPI__SET_XACT_ABORT c	Boolean b	true
DBAPI parameter value length cutoff (in bytes) to impose when reporting DBAPI exceptions or logging debug messages. Longer values will be truncated so as to accommodate a trailing ellipsis (“...”) within the cutoff.	[dbapi] max_logged_param_length NCBI_CONFIG__DBAPI__MAX_LOGGED_PARAM_LENGTH c	unsigned int	255

^a case-insensitive: true, t, yes, y, false, f, no, n

^b case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^c environment variable name formed from registry section and entry name

Eutils

These parameters tune the behavior of the Eutils library.

Table 15. eutils library configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Specify the base URL for Eutils requests.	[Eutils] Base_URL EUTILS_BASE_URL	a valid URL	The host returned by resolving “eutils_lb” service or “eutils.ncbi.nlm.nih.gov” by default, with “/entrez/eutils/” path appended (“https://eutils.ncbi.nlm.nih.gov/entrez/eutils/”).

Distributed Computing (GRID) Specific Parameters

The following sections discuss configuration parameters that are specific to NCBI Distributed Computing (GRID).

Note: This section only applies within NCBI.

• NetCache and NetSchedule

• Worker Node

NetCache and NetSchedule

Table 16 describes configuration parameters that are common to both NetCache and NetSchedule client APIs. These parameters are found in the netservice_api registry section.

Table 16. Common NetCache and NetSchedule client API configuration parameters (netservice_api)

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Fail the request if the network I/O is inactive (blocked waiting for the communication channel to become readable or writable) for more than the specified timeout in seconds. Applies to all socket operations after the initial connection is established (see NCBI_CONFIG__NETSERVICE_API__CONNECTION_TIMEOUT). Can be overridden by NCBI_CONFIG__NETCACHE_API__COMMUNICATION_TIMEOUT or NCBI_CONFIG__NETSCHEDULE_API__COMMUNICATION_TIMEOUT.	[netservice_api] communication_timeout NCBI_CONFIG__NETSERVICE_API__COMMUNICATION_TIMEOUT  a	floating point >= 0.0 (zero means default)	12.0 (see API for up-to-date default)
Turn on socket-specific logging, such as status and transferred data.	[netservice_api] connection_data_logging NCBI_CONFIG__NETSERVICE_API__CONNECTION_DATA_LOGGING  a	Boolean  b	false
The maximum number of times the API will retry a communication command on a socket. Setting connection_max_retries to zero will prevent NetCache API from retrying the connection and command execution.	[netservice_api] connection_max_retries NCBI_CONFIG__NETSERVICE_API__CONNECTION_MAX_RETRIES  a	unsigned int	4
The timeout in seconds for establishing a new connection to a server. Can be overridden by NCBI_CONFIG__NETCACHE_API__CONNECTION_TIMEOUT or NCBI_CONFIG__NETSCHEDULE_API__CONNECTION_TIMEOUT.	[netservice_api] connection_timeout N/A	floating point > 0.0, millisecond precision, minimum 0.001 (1 millisecond)	2.0 (see API for up-to-date default)
The number of connections to keep in the local connection pool. If zero, the server will grow the connection pool as necessary to accomodate new connections. Otherwise, when all connections in the pool are used, new connections will be created and destroyed.	[netservice_api] max_connection_pool_size NCBI_CONFIG__NETSERVICE_API__MAX_CONNECTION_POOL_SIZE  a	non-negative int	0 (meaning unlimited)
The maximum number of attempts to resolve the LBSMD service name. If not resolved within this limit an exception is thrown.	[netservice_api] max_find_lbname_retries NCBI_CONFIG__NETSERVICE_API__MAX_FIND_LBNAME_RETRIES  a	positive int	3
The delay in seconds between retrying a command; the total time should not exceed NCBI_CONFIG__NETCACHE_API__MAX_CONNECTION_TIME.	[netservice_api] retry_delay NCBI_CONFIG__NETSERVICE_API__RETRY_DELAY  a	floating point >= 0.0	1.0 (see API for up-to-date default)
Close connections with zero timeout to prevent sockets in TIME_WAIT on the client side. By default, the Linux kernel delays releasing ports for a certain period after close() because there might be a delayed arrival of packets. Setting this parameter to true disables that behavior and therefore allows faster recycling of ports. This is important when the server is handling a large number of connections due to the limited number of ports available.	[netservice_api] use_linger2 NCBI_CONFIG__NETSERVICE_API__USE_LINGER2  a	Boolean  b	false
Enables a warning action on unexpected server reply (not started with either ‘OK:’ or ‘ERR:’). If enabled, the actual warning action is either a calling of a warning handler (if the latter is set for an API instance) or simply a logging of a corresponding warning message (otherwise).	[netservice_api] warn_on_unexpected_reply NCBI_CONFIG__NETSERVICE_API__WARN_ON_UNEXPECTED_REPLY  a	Boolean  b	false
Enables an error action on unexpected server reply (not started with either ‘OK:’ or ‘ERR:’). If enabled, the actual error action is either a calling of an error handler (if the latter is set for an API instance) or simply a throwing of a corresponding exception (otherwise).	[netservice_api] error_on_unexpected_reply NCBI_CONFIG__NETSERVICE_API__ERROR_ON_UNEXPECTED_REPLY  a	Boolean  b	false

^a environment variable name formed from registry section and entry name

^b case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

Table 17 describes configuration parameters for NetCache client applications. These parameters are found in the netcache_api registry section. Note: The netcache_api registry section was formerly called netcache_client.

Table 17. NetCache client API configuration parameters (netcache_api)

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Enable input caching (provides for slow blob retrieval).	[netcache_api] cache_input N/A	Boolean  b	false
Only applies when using CNetICacheClient. Provides a “namespace” for blobs. Thus, blobs are uniquely identified by the { key, version, subkey, cache_name } combination.	[netcache_api] cache_name N/A	up to 36 characters (case-sensitive and no spaces)	(none)
Enable output caching (provides for saving a blob with pauses more than “communication_timeout”).	[netcache_api] cache_output N/A	Boolean  b	false
The name of your application, as identified to NetCache.	[netcache_api] client N/A	your application’s name	(none)
Synonym for [netcache_api]/client, which is preferred.	[netcache_api] client_name N/A
Can be used to override NCBI_CONFIG__NETSERVICE_API__COMMUNICATION_TIMEOUT. Please see that entry for details.	[netcache_api] communication_timeout N/A	floating point >= 0.0 (zero means use the default from NCBI_CONFIG__NETSERVICE_API__COMMUNICATION_TIMEOUT)	(none)
Can be used to override [netservice_api]/connection_timeout. Please see that entry for details.	[netcache_api] connection_timeout N/A	floating point >= 0.0, minimum 0.001 (zero means use the default from [netservice_api]/connection_timeout)	(none)
Depending on the value, enables mirroring: if true, mirroring is unconditionally enabled, if false, it is disabled completely. The special value “if_key_mirrored” is used to enable mirroring for the blobs that already have mirroring extensions in their keys.	[netcache_api] enable_mirroring N/A	Boolean  c, or “if_key_mirrored”	“if_key_mirrored”
The host:port address for the NetCache server that will be used for blob creation if none of the servers configured via LBSM were able to create the blob. This is only for new blob requests.	[netcache_api] fallback_server NCBI_CONFIG__NETCACHE_API__FALLBACK_SERVER  a	a valid server	””
Sets a communication timeout (in seconds) for accessing the first server in a service while submitting a job. If the first server does not reply within the specified amount of time, the next server will be tried, but the second and all subsequent servers will be given the full communication_timeout to reply. If LBSM services are not used or there’s only one server in the service, this parameter does not apply.	[netcache_api] first_server_timeout NCBI_CONFIG__NETCACHE_API__FIRST_SERVER_TIMEOUT  a	floating point >= 0.0 (zero means use default)	[netschedule_api]/communication_timeout if defined, or 300ms
In conjunction with [netcache_api]/port, a synonym for [netcache_api]/service_name, which is preferred.	[netcache_api] host N/A
Max total time for each NetCache transaction.	[netcache_api] max_connection_time N/A	floating point >= 0.0 (zero means to ignore)	0.0
In conjunction with [netcache_api]/host, a synonym for [netcache_api]/service_name, which is preferred.	[netcache_api] port N/A
A trigger for LBSM query (query LBSM once per the specified number of NetCache operations).	[netcache_api] rebalance_requests N/A	integer >= 0 (zero means to not rebalance based on requests)	5000 requests
Another trigger for LBSM query (query LBSM at least once per the specified number of seconds)	[netcache_api] rebalance_time N/A	floating point >= 0.0 (zero means to not rebalance based on time)	10.0 seconds
Synonym for [netcache_api]/host, which is preferred.	[netcache_api] server N/A
Synonym for [netcache_api]/service_name.	[netcache_api] service N/A
The LBSM name that specifies which servers to use. The service name is only used when creating blobs.	[netcache_api] service_name N/A	any registered LBSM service	(none)
This is one condition that will trigger server throttling and is defined as a string having the form “A / B” where A and B are integers. Throttling will be triggered if there are A failures in the last B operations.	[netcache_api] throttle_by_connection_error_rate N/A	a string having the form “A / B” where A and B are integers	“0 / 0” (ignored)
This is another condition that will trigger server throttling and is defined as follows. Server throttling will be triggered if this number of consecutive connection failures happens.	[netcache_api] throttle_by_consecutive_connection_failures N/A	integer	0 (ignored)
Do not release server throttling until the server appears in LBSMD.	[netcache_api] throttle_hold_until_active_in_lb N/A	Boolean  c	false
Indicates when server throttling will be released.	[netcache_api] throttle_relaxation_period N/A	integer time period in seconds	0 (throttling is disabled)
Where to save blob caches.	[netcache_api] tmp_dir N/A	a valid directory	(none)
Synonym for [netcache_api]/tmp_dir.	[netcache_api] tmp_path N/A
A true value enables an alternative method for checking if a blob exists. Note: This option is available only for backward compatibility and should not be used.	[netcache_api] use_hasb_fallback NCBI_CONFIG__NETCACHE_API__USE_HASB_FALLBACK  a	Boolean  b	false
Defines LBSM affinity name to use for floor assignment, etc.	[netcache_api] use_lbsm_affinity N/A	a valid affinity	(none)
If this parameter is set to true, blob key contains service name and server (listed in the blob key) is not present in that service, then do not try to connect to that server. If set to ‘auto’ and key has a “Check-Server” hint set to NO, then assume ‘server_check = no’; otherwise, assume ‘server_check = yes’. Otherwise, unconditionally try to connect to the server.	[netcache_api] server_check	true/false/auto	auto
This is a hint for the blob readers that use ‘server_check = auto’. If set to true, blob readers are advised to pre-check the server which is listed in the blob key.	[netcache_api] server_check_hint	true/false	true
If set, restricts NetCache API to specified services (unless [netcache_api] server_check is explicitly set to false). It is highly recommended to also set [netcache_api] server_check to true to prevent circumventing this check by using blob keys containing explicit instructions to turn server check off.	[netcache_api] allowed_services	comma/space separated list	””

^a environment variable name formed from registry section and entry name

^b case-insensitive: true, t, yes, y, 1, false, f, no, n, 0

^c case-insensitive: true, t, yes, y, false, f, no, n

Table 18 describes configuration parameters for NetSchedule client applications. These parameters are found in the netschedule_api registry section.

Table 18. NetSchedule client API configuration parameters (netschedule_api)

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Name of the queue (DO NOT use default queue for your application).	[netschedule_api] queue_name N/A	your application’s queue name	(none)
The name of your application, as identified to NetSchedule.	[netschedule_api] client_name N/A	your application’s name	(none)
Can be used to override NCBI_CONFIG__NETSERVICE_API__COMMUNICATION_TIMEOUT. Please see that entry for details.	[netschedule_api] communication_timeout N/A	floating point >= 0.0 (zero means use the default from NCBI_CONFIG__NETSERVICE_API__COMMUNICATION_TIMEOUT)	12.0 seconds
Can be used to override [netservice_api]/connection_timeout. Please see that entry for details.	[netschedule_api] connection_timeout N/A	floating point >= 0.0 (zero means use the default from [netservice_api]/connection_timeout)	2.0 seconds
Use affinity information when requesting jobs.	[netschedule_api] use_affinities	true/false	false
Initial set of preferred affinities. Initial (comma/space separated) list of preferred affinities. Example: job_type_a, job_type_b	[netschedule_api] affinity_list	comma/space separated list	””
A prioritized lists of affinities, which overrides the default job processing order. Cannot be used with affinity_list. Example: high_priority_job, mid_priority_job, low_priority_job	[netschedule_api] affinity_ladder	comma/space separated list	””
Use affinity information and accept new affinities automatically. Cannot be used with affinity_ladder.	[netschedule_api] claim_new_affinities	true/false	false
Allow the worker node to process jobs without affinities as well as jobs with “non-preferred” affinities. Cannot be used in combination with ‘claim_new_affinities’.	[netschedule_api] process_any_job	true/false	false

Worker Node

Table 19 describes configuration parameters for Worker Nodes.

Table 19. Worker Node configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Deprecated.	[server] allow_implicit_job_return NCBI_CONFIG__SERVER__ALLOW_IMPLICIT_JOB_RETURN  e	Boolean  b	false
Maximum time worker nodes are allowed to live without a single NetSchedule server.	[server] max_wait_for_servers NCBI_CONFIG__SERVER__MAX_WAIT_FOR_SERVERS  e	unsigned int	24 * 60 * 60 seconds
Causes the worker node to shut down if any jobs fail.	[server] stop_on_job_errors NCBI_CONFIG__SERVER__STOP_ON_JOB_ERRORS  e	Boolean  b	true
Maximum number of jobs(threads) can be served simultaneously. This parameter defines job parallelism. For computationally intensive algorithms this value should not be more than number of CPUs if set to ‘auto’, the node will determine the number of CPUs on the system and use this number.	[server] max_threads		auto
Initial number of threads created for incoming jobs	[server] init_threads		1
TCP/IP and UDP port number for control messages (like shutdown, version) and job notifications. It runs special control thread for incoming administrative requests (from netschedule_control and netschedule_admin) Can take a ports range (ex. 9300-9310). In this case the system will try to find an available port in the given range	[server] control_port
Server side logging. A worker node can ask its context if this flag is set to true	[server] log
Internal. Delay in seconds node task dispatcher waits for free space in the job queue. Lower value usually gives better response to shutdown command (CPU traded off)	[server] thread_pool_timeout
Time worker node spends waiting for new jobs without connecting to the netschedule server queue. Server sends UPD requests to wake the node up. Bigger values of this parameter reduces the netschedule server load in expense of job delivery latency (because of potential loss of UDP packages)	[server] job_wait_timeout
The max total number of jobs after which the node will shutdown itself. Restarting the node periodically is useful due to accumulating heap fragmentation possible leaks etc.	[server] max_total_jobs		0 - means unlimited number of jobs.
The max number of failed jobs after which the node will shutdown itself.	[server] max_failed_jobs		0 - means unlimited number of failed jobs.
When true, server transforms into a daemon, detached from the current program group (for UNIX only)	[server] daemon
The list of worker nodes which this node will check before attempting to retrieve a job from the NetSchedule queue. If at least one of these worker nodes has an ideal thread, this node will not connect to the queue for a job. This node and all nodes from the given list must be connected to the same NetSchedule service, the same queue and must run the same job. If the list is empty (defult) then this node is a master.	[server] master_nodes		empty - this node is a master.
List of network hosts which are allowed admin access to the worker node if this worker node is controled by grid_node_watcher.sh don’t forget to to add “localhost” to this list.	[server] admin_hosts
Time delay (in seconds) between the node enters an idle mode (all jobs are done and there are no new jobs in the queue) and the idle task gets executed. Can not be less then 1 sec.	[server] idle_run_delay		30
The node will automatically shut itself down if it is idle for a continuous period of time longer than this (in seconds):	[server] auto_shutdown_if_idle		0 - means never auto shutdown
Specifies if the framework should reuse an instance of the job class. Setting this parameter to true means that only one instance of the job class will be create per each execution thread. False means that an instance of job class will be created per each incoming job.	[server] reuse_job_object		false
Allows the node to detect infinite loops in job execution. If a job is being executed for more then the specified time, it is assumed to be stuck in an infinite loop. It this happens, the node enters shutdown mode, and when all other jobs, which may be running on this node, are done, the node terminates.	[server] infinite_loop_time		0, which means that the node will not detect infinite loops.
Time in seconds. Specifies how often the node should check states of jobs it is processing. It is used as a feedback from the client to see if it wants to cancel the job execution	[server] check_status_period
Sets the maximum limit for total memory consumption by this worker node. When this limit is reached, the worker node shuts down.	[server] total_memory_limit
Sets the maximum limit for total runtime of this worker node (in seconds). When this limit is reached, the worker node shuts down.	[server] total_time_limit		0, which means there is no limit.
Default timeout before the job is terminated in case of pullback. This value can be overridden by the ‘–timeout’ option specified with ‘grid_cli suspend –pullback’.	[server] default_pullback_timeout
Sets the maximum number of jobs with the same client IP address running in parallel. While this limit is being reached for a client IP address, the worker node immediately returns all new jobs with the same client IP address back to the queue also blacklisting them. Blacklisted jobs will not be given again to the same worker node for some time (server configured).	[server] max_jobs_per_client_ip	unsigned	0 - unlimited
Sets the maximum number of jobs with the same session ID running in parallel. While this limit is being reached for a session ID, the worker node immediately returns all new jobs with the same session ID back to the queue also blacklisting them. Blacklisted jobs will not be given again to the same worker node for some time (server configured).	[server] max_jobs_per_session_id	unsigned	0 - unlimited
Specifies how often (in seconds) the worker node retries to commit a job after communication errors. The worker node gives up retrying either after it takes more than queue timeout (server configured) or if server successfully receives corresponding commit request but responds with an error.	[server] commit_job_interval	unsigned > 0	2
If set to true, the worker node forks at start. Parent process is only used to clear the node on servers on exit and child process does everything else. Thus, the node is realiably cleared even if child process crashes/is killed (for UNIX only).	[server] reliable_cleanup	Boolean  b	false

See the Distributed Computing chapter for more information on NetCache and NetSchedule.

Configuration parameters for NetCache daemons are described in the file:

https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c++/src/app/netcache/netcached.ini?view=log

Application-Specific Parameters

The following sections discuss configuration parameters that are specific to selected applications.

• Seqfetch.cgi

Seqfetch.cgi

Note: This applies only inside NCBI.

These parameters tune the behavior of the seqfetch.cgi application.

Table 19. seqfetch.cgi application configuration parameters

Purpose	[Registry section] Registry name Environment variable	Valid values	Default
Point to the current script.	[SeqFetch] Viewer_fcgi_path SEQFETCH_VIEWER_FCGI_PATH	a valid path	/sviewer/viewer.fcgi
Name the current load-balanced proxy.	[SeqFetch] Viewer_fcgi_proxy SEQFETCH_VIEWER_FCGI_PROXY	a valid proxy name	sviewer_lb

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