MascotRemoteQuery Class Reference

Class which handles the communication between OpenMS and the Mascot server. More...

#include <OpenMS/FORMAT/MascotRemoteQuery.h>

Inheritance diagram for MascotRemoteQuery:

Collaboration diagram for MascotRemoteQuery:

Constructors and destructors
String	query_spectra_
std::string	mascot_xml_
std::string	mascot_decoy_xml_
String	error_message_
String	search_identifier_
String	server_path_
	Path on mascot server.
String	host_name_
	Hostname of the mascot server.
bool	requires_login_ = false
	Login required.
bool	use_ssl_ = false
	Use SSL connection.
String	boundary_
	boundary string that will be embedded into the HTTP requests
Int	to_ = 1500
	Timeout after these many seconds.
bool	export_decoys_ = false
	MascotRemoteQuery ()
	default constructor
MascotRemoteQuery &	operator= (const MascotRemoteQuery &rhs)=delete
	assignment operator
	MascotRemoteQuery (const MascotRemoteQuery &rhs)=delete
	copy constructor
	~MascotRemoteQuery () override
	destructor
void	setQuerySpectra (const String &exp)
	sets the query spectra, given in MGF file format
const std::string &	getMascotXMLResponse () const
	returns the Mascot XML response which contains the identifications
const std::string &	getMascotXMLDecoyResponse () const
	returns the Mascot XML response which contains the decoy identifications (note: setExportDecoys must be set to true, otherwise result will be empty)
bool	hasError () const
	predicate which returns true if an error occurred during the query
const String &	getErrorMessage () const
	returns the error message, if hasError can be used to check whether an error has occurred
String	getSearchIdentifier () const
	returns the search number
void	setExportDecoys (const bool b)
	request export of decoy summary and decoys (note: internal decoy search must be enabled in the MGF file passed to mascot)
void	run ()
	Execute the full Mascot workflow synchronously (login -> query -> export results).
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.
void	login (CURL *curl)
	login to Mascot server
void	execQuery (CURL *curl)
	execute query (upload file)
std::string	getResults (CURL *curl, const std::string &results_path)
	download result file and process response
std::string	httpGet (CURL *curl, const std::string &path)
	perform an HTTP GET and return the response body
std::string	httpPost (CURL *curl, const std::string &path, const std::string &body, const std::string &content_type)
	perform an HTTP POST with the given body and content type, return the response body
std::string	buildUrl (const std::string &path) const
	build full URL from a path
String	getSearchIdentifierFromFilePath (const String &path) const
	Extract search identifier from .dat file path.
std::string	removeHostName (const std::string &url) const
	Remove host name information from a url.

Additional Inherited Members
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const String &	getName () const
	Non-mutable access to the name.
void	setName (const String &name)
	Mutable access to the name.
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections.
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values.
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
String	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

Class which handles the communication between OpenMS and the Mascot server.

This class provides a communication interface which is able to query the Mascot server and reports the identifications provided be the Mascot server

Parameters of this class are:

Name	Type	Default	Restrictions	Description
hostname	string			Address of the host where Mascot listens, e.g. 'mascot-server' or '127.0.0.1'
host_port	int	80	min: 0	Port where the Mascot server listens, 80 should be a good guess
server_path	string	mascot		Path on the server where Mascot server listens, 'mascot' should be a good guess
timeout	int	1500	min: 0	Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps. Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!
boundary	string	GZWgAaYKjHFeUaLOLEIOMq		Boundary for the MIME section
use_proxy	string	false	true, false	Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'
proxy_host	string			Host where the proxy server runs on
proxy_port	int	0	min: 0	Port where the proxy server listens
proxy_username	string			Login name for the proxy server, if needed
proxy_password	string			Login password for the proxy server, if needed
login	string	false	true, false	Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then.
username	string			Name of the user if login is used (Mascot security must be enabled!)
password	string			Password of the user if login is used (Mascot security must be enabled!)
use_ssl	string	false	true, false	Flag indicating whether you want to send requests to an HTTPS server or not (HTTP). Requires OpenSSL to be installed (see openssl.org)
export_params	string	_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0		Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script). Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides.
skip_export	string	false	true, false	For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results. The output file produced by MascotAdapterOnline will contain only the Mascot search number.
batch_size	int	50000	min: 0	Number of spectra processed in one batch by Mascot (default 50000)

Note:

• If a section name is documented, the documentation is displayed as tooltip.
• Advanced parameter names are italic.

Constructor & Destructor Documentation

MascotRemoteQuery() [1/2]

MascotRemoteQuery

(

)

default constructor

MascotRemoteQuery() [2/2]

MascotRemoteQuery ( const MascotRemoteQuery &  rhs )

delete

copy constructor

~MascotRemoteQuery()

~MascotRemoteQuery ( )

override

destructor

Member Function Documentation

buildUrl()

std::string buildUrl ( const std::string &  path ) const

private

build full URL from a path

execQuery()

void execQuery ( CURL *  curl )

private

execute query (upload file)

getErrorMessage()

const String & getErrorMessage

(

)

const

returns the error message, if hasError can be used to check whether an error has occurred

getMascotXMLDecoyResponse()

const std::string & getMascotXMLDecoyResponse

(

)

const

returns the Mascot XML response which contains the decoy identifications (note: setExportDecoys must be set to true, otherwise result will be empty)

getMascotXMLResponse()

const std::string & getMascotXMLResponse

(

)

const

returns the Mascot XML response which contains the identifications

getResults()

std::string getResults ( CURL *  curl, const std::string &  results_path  )

private

download result file and process response

getSearchIdentifier()

String getSearchIdentifier

(

)

const

returns the search number

getSearchIdentifierFromFilePath()

String getSearchIdentifierFromFilePath ( const String &  path ) const

private

Extract search identifier from .dat file path.

hasError()

bool hasError

(

)

const

predicate which returns true if an error occurred during the query

httpGet()

std::string httpGet ( CURL *  curl, const std::string &  path  )

private

perform an HTTP GET and return the response body

httpPost()

std::string httpPost ( CURL *  curl, const std::string &  path, const std::string &  body, const std::string &  content_type  )

private

perform an HTTP POST with the given body and content type, return the response body

login()

void login ( CURL *  curl )

private

login to Mascot server

operator=()

MascotRemoteQuery & operator= ( const MascotRemoteQuery &  rhs )

delete

assignment operator

removeHostName()

std::string removeHostName ( const std::string &  url ) const

private

Remove host name information from a url.

run()

void run

(

)

Execute the full Mascot workflow synchronously (login -> query -> export results).

setExportDecoys()

void setExportDecoys

(

const bool

b

)

request export of decoy summary and decoys (note: internal decoy search must be enabled in the MGF file passed to mascot)

setQuerySpectra()

void setQuerySpectra

(

const String &

exp

)

sets the query spectra, given in MGF file format

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

boundary_

String boundary_

private

boundary string that will be embedded into the HTTP requests

error_message_

String error_message_

private

export_decoys_

bool export_decoys_ = false

private

host_name_

String host_name_

private

Hostname of the mascot server.

mascot_decoy_xml_

std::string mascot_decoy_xml_

private

mascot_xml_

std::string mascot_xml_

private

query_spectra_

String query_spectra_

private

requires_login_

bool requires_login_ = false

private

Login required.

search_identifier_

String search_identifier_

private

server_path_

String server_path_

private

Path on mascot server.

to_

Int to_ = 1500

private

Timeout after these many seconds.

use_ssl_

bool use_ssl_ = false

private

Use SSL connection.