25 #include <QtCore/QString>
27 #include <QtCore/qcontainerfwd.h>
33 struct ParameterInformation;
69 BaseException(file, line, function,
"UnregisteredParameter", parameter)
81 BaseException(file, line, function,
"WrongParameterType", parameter)
93 BaseException(file, line, function,
"RequiredParameterNotGiven", parameter)
124 inline static const char* TAG_OUTPUT_FILE =
"output file";
125 inline static const char* TAG_INPUT_FILE =
"input file";
126 inline static const char* TAG_OUTPUT_DIR =
"output dir";
127 inline static const char* TAG_OUTPUT_PREFIX =
"output prefix";
128 inline static const char* TAG_ADVANCED =
"advanced";
129 inline static const char* TAG_REQUIRED =
"required";
148 EXTERNAL_PROGRAM_NOTFOUND
169 TOPPBase(
const String& name,
const String& description,
bool official =
true,
const std::vector<Citation>& citations = {},
bool toolhandler_test =
true);
398 return ini_location_;
613 Int default_value,
const String& description,
614 bool required =
true,
bool advanced =
false);
863 void writeLogInfo_(
const String& text)
const;
881 ExitCodes runExternalProcess_(
const QString& executable,
const QStringList& arguments,
const QString& workdir =
"")
const;
979 template <
typename Writer>
const char * tool_name
Definition: FLASHDeconvWizard.cpp:53
A container for consensus elements.
Definition: ConsensusMap.h:66
Description of the applied preprocessing steps.
Definition: DataProcessing.h:27
ProcessingAction
Definition: DataProcessing.h:33
Exception base class.
Definition: Exception.h:63
static GlobalExceptionHandler & getInstance()
The accessor for the singleton. It also serves as a replacement for the constructor.
Definition: GlobalExceptionHandler.h:62
static void setMessage(const std::string &message)
A required parameter was not given.
Definition: TOPPBase.h:90
RequiredParameterNotGiven(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:92
An unregistered parameter was accessed.
Definition: TOPPBase.h:66
UnregisteredParameter(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:68
A parameter was accessed with the wrong type.
Definition: TOPPBase.h:78
WrongParameterType(const char *file, int line, const char *function, const String ¶meter)
Definition: TOPPBase.h:80
A container for features.
Definition: FeatureMap.h:80
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
Class to hold strings, numeric values, vectors of strings and vectors of numeric values using the stl...
Definition: ParamValue.h:29
Management and storage of parameters / INI files.
Definition: Param.h:44
LogType
Possible log types.
Definition: ProgressLogger.h:43
A more convenient string class.
Definition: String.h:34
Base class for TOPP applications.
Definition: TOPPBase.h:122
Param param_inifile_
All parameters specified in the ini file.
Definition: TOPPBase.h:218
StringList getParamAsStringList_(const String &key, const StringList &default_value) const
Return the value of parameter key as a StringList or default_value if this value is not set.
String const ini_location_
Location in the ini file where to look for parameters.
Definition: TOPPBase.h:212
const ParamValue & getParam_(const String &key) const
Return the value key of parameters as DataValue. ParamValue::EMPTY indicates that a parameter was not...
TOPPBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)
Constructor.
void inputFileReadable_(const String &filename, const String ¶m_name) const
Checks if an input file exists, is readable and is not empty.
void registerInputFileList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
Registers a list of input files option.
String const tool_description_
Tool description. This is assigned once and for all in the constructor.
Definition: TOPPBase.h:206
void registerOutputFileList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)
Registers a list of output files option.
const String & getIniLocation_() const
Returns the location of the ini file where parameters are taken from. E.g. if the command line was TO...
Definition: TOPPBase.h:396
void addEmptyLine_()
Adds an empty line between registered variables in the documentation.
String getParamAsString_(const String &key, const String &default_value="") const
Return the value of parameter key as a string or default_value if this value is not set.
virtual Param getSubsectionDefaults_(const String §ion) const
This method should return the default parameters for subsections.
std::ofstream log_
Log file stream. Use the writeLog_() and writeDebug_() methods to access it.
Definition: TOPPBase.h:233
void registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
Registers an input file option.
Param const & getParam_() const
Return all parameters relevant to this TOPP tool.
void enableLogging_() const
Ensures that at least some default logging destination is opened for writing in append mode.
bool toolhandler_test_
Enable the ToolHandler tests.
Definition: TOPPBase.h:387
Int getParamAsInt_(const String &key, Int default_value=0) const
Return the value of parameter key as an integer or default_value if this value is not set.
Param param_
All parameters relevant to this invocation of the program.
Definition: TOPPBase.h:215
bool getFlag_(const String &name) const
Returns the value of a previously registered flag.
void writeDebug_(const String &text, UInt min_level) const
Writes a string to the log file and to OPENMS_LOG_DEBUG if the debug level is at least min_level.
std::vector< ParameterInformation > paramToParameterInformation_(const Param ¶m) const
Translates the given parameter object into a vector of ParameterInformation, that can be utilized for...
void registerStringList_(const String &name, const String &argument, const StringList &default_value, const String &description, bool required=true, bool advanced=false)
Registers a list of strings option.
ExitCodes runExternalProcess_(const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") const
static String topp_ini_file_
.TOPP.ini file for storing system default parameters
Definition: TOPPBase.h:996
std::vector< ParameterInformation > parameters_
Storage location for parameter information.
Definition: TOPPBase.h:246
Param parseCommandLine_(const int argc, const char **argv, const String &misc="misc", const String &unknown="unknown")
Parses command line arguments using parameter definitions from TOPPBase.
double getParamAsDouble_(const String &key, double default_value=0) const
Return the value of parameter key as a double or default_value if this value is not set.
String getParamArgument_(const Param::ParamEntry &entry) const
Utility function that determines a suitable argument value for the given Param::ParamEntry.
virtual ~TOPPBase()
Destructor.
void registerTOPPSubsection_(const String &name, const String &description)
Registers an allowed subsection in the INI file originating from the TOPP tool itself.
void printUsage_()
Prints the tool-specific command line options and appends the common options.
void registerIntList_(const String &name, const String &argument, const IntList &default_value, const String &description, bool required=true, bool advanced=false)
Registers a list of integers option.
String version_
Version string (if empty, the OpenMS/TOPP version is printed)
Definition: TOPPBase.h:375
void addDataProcessing_(FeatureMap &map, const DataProcessing &dp) const
Data processing setter for feature maps.
Param param_instance_
Parameters from instance section.
Definition: TOPPBase.h:224
Int const instance_number_
Instance number.
Definition: TOPPBase.h:209
void setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)
Sets the formats for a input/output file option or for all members of an input/output file lists.
void setMinInt_(const String &name, Int min)
Sets the minimum value for the integer parameter(can be a list of integers,too) name.
void registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)
Registers an integer option.
void setValidStrings_(const String &name, const std::string vstrings[], int count)
Sets the valid strings for a string option or a whole string list.
std::vector< Citation > citations_
Papers, specific for this tool (will be shown in '–help')
Definition: TOPPBase.h:384
DataProcessing getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const
Returns the data processing information.
ProgressLogger::LogType log_type_
Type of progress logging.
Definition: TOPPBase.h:949
void registerFlag_(const String &name, const String &description, bool advanced=false)
Registers a flag.
void setMaxInt_(const String &name, Int max)
Sets the maximum value for the integer parameter(can be a list of integers,too) name.
StringList getStringList_(const String &name) const
Returns the value of a previously registered StringList.
void addText_(const String &text)
String verboseVersion_
Version string including additional revision/date time information. Note: This differs from version_ ...
Definition: TOPPBase.h:378
Param getToolUserDefaults_(const String &tool_name) const
Returns the user defaults for the given tool, if any default parameters are stored in the users home.
void writeLogWarn_(const String &text) const
Writes a string to the log file and to OPENMS_LOG_WARN.
bool test_mode_
Test mode.
Definition: TOPPBase.h:993
void writeToolDescription_(Writer &writer, std::string write_type, std::string fileExtension)
Helper function avoiding repeated code between CTD, JSON and CWL.
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
String const tool_name_
Tool name. This is assigned once and for all in the constructor.
Definition: TOPPBase.h:203
void addDataProcessing_(PeakMap &map, const DataProcessing &dp) const
Data processing setter for peak maps.
TOPPBase()=delete
No default constructor.
String getStringOption_(const String &name) const
Returns the value of a previously registered string option (use getOutputDirOption() for output direc...
void writeDebug_(const String &text, const Param ¶m, UInt min_level) const
Writes a String followed by a Param to the log file and to OPENMS_LOG_DEBUG if the debug level is at ...
void setValidStrings_(const String &name, const std::vector< String > &strings)
Sets the valid strings for a string option or a whole string list.
std::map< String, String > subsections_TOPP_
Storage location and description for allowed subsections from TOPP tool's command-line parameters.
Definition: TOPPBase.h:272
void outputFileWritable_(const String &filename, const String ¶m_name) const
Checks if an output file is writable.
virtual void registerOptionsAndFlags_()=0
Sets the valid command line options (with argument) and flags (without argument).
static const Citation cite_openms
The latest and greatest OpenMS citation.
Definition: TOPPBase.h:199
DataProcessing getProcessingInfo_(DataProcessing::ProcessingAction action) const
Returns the data processing information.
Param param_common_tool_
Parameters from common section with tool name.
Definition: TOPPBase.h:227
IntList getIntList_(const String &name) const
Returns the value of a previously registered IntList.
Int debug_level_
Debug level set by -debug.
Definition: TOPPBase.h:999
String getOutputDirOption(const String &name) const
Returns the value of a previously registered output_dir option.
TOPPBase(const TOPPBase &)=delete
No default copy constructor.
IntList getParamAsIntList_(const String &key, const IntList &default_value) const
Return the value of parameter key as a IntList or default_value if this value is not set.
bool official_
Flag indicating if this an official TOPP tool.
Definition: TOPPBase.h:381
Param getDefaultParameters_() const
Returns the default parameters.
void registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
Registers an output file option.
void registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)
Registers a double option.
Param param_cmdline_
Parameters from command line.
Definition: TOPPBase.h:221
String getDocumentationURL() const
Returns a link to the documentation of the tool (accessible on our servers and only after inclusion i...
void registerDoubleList_(const String &name, const String &argument, const DoubleList &default_value, const String &description, bool required=true, bool advanced=false)
Registers a list of doubles option.
void setMaxFloat_(const String &name, double max)
Sets the maximum value for the floating point parameter(can be a list of floating points,...
void setMinFloat_(const String &name, double min)
Sets the minimum value for the floating point parameter(can be a list of floating points,...
static void setMaxNumberOfThreads(int num_threads)
Sets the maximal number of usable threads.
void registerParamSubsectionsAsTOPPSubsections_(const Param ¶m)
String getToolPrefix() const
Returns the prefix used to identify the tool.
ExitCodes
Exit codes.
Definition: TOPPBase.h:133
@ INPUT_FILE_EMPTY
Definition: TOPPBase.h:138
@ INPUT_FILE_CORRUPT
Definition: TOPPBase.h:137
@ ILLEGAL_PARAMETERS
Definition: TOPPBase.h:140
@ MISSING_PARAMETERS
Definition: TOPPBase.h:141
@ EXTERNAL_PROGRAM_ERROR
Definition: TOPPBase.h:143
@ INCOMPATIBLE_INPUT_DATA
Definition: TOPPBase.h:145
@ UNKNOWN_ERROR
Definition: TOPPBase.h:142
@ EXECUTION_OK
Definition: TOPPBase.h:134
@ INTERNAL_ERROR
Definition: TOPPBase.h:146
@ INPUT_FILE_NOT_FOUND
Definition: TOPPBase.h:135
@ INPUT_FILE_NOT_READABLE
Definition: TOPPBase.h:136
@ CANNOT_WRITE_OUTPUT_FILE
Definition: TOPPBase.h:139
@ PARSE_ERROR
Definition: TOPPBase.h:144
@ UNEXPECTED_RESULT
Definition: TOPPBase.h:147
bool parseRange_(const String &text, Int &low, Int &high) const
Parses a range string ([a]:[b]) into two variables (integers)
void registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
Registers a string option.
virtual ExitCodes main_(int argc, const char **argv)=0
The actual "main" method. main_() is invoked by main().
const ParameterInformation & findEntry_(const String &name) const
Finds the entry in the parameters_ array that has the name name.
std::map< String, String > subsections_
Storage location and description for allowed subsections.
Definition: TOPPBase.h:269
void fileParamValidityCheck_(String ¶m_value, const String ¶m_name, const ParameterInformation &p) const
checks if an input file exists (respecting the flags)
double getDoubleOption_(const String &name) const
Returns the value of a previously registered double option.
bool parseRange_(const String &text, double &low, double &high) const
Parses a range string ([a]:[b]) into two variables (doubles)
void checkIfIniParametersAreApplicable_(const Param &ini_params)
Checks if the parameters of the provided ini file are applicable to this tool.
String getSubsection_(const String &name) const
Get the part of a parameter name that makes up the subsection.
void checkParam_(const Param ¶m, const String &filename, const String &location) const
Checks top-level entries of param according to the information during registration.
void addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const
Data processing setter for consensus maps.
Param getSubsectionDefaults_() const
Returns a single Param object containing all subsection parameters.
const String & toolName_() const
Returns the tool name.
void registerOutputPrefix_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
Registers an output file prefix used for tools with multiple file output.
void writeLogError_(const String &text) const
Writes a string to the log file and to OPENMS_LOG_ERROR.
void registerSubsection_(const String &name, const String &description)
Registers an allowed subsection in the INI file (usually from OpenMS algorithms).
ParameterInformation paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const
Transforms a ParamEntry object to command line parameter (ParameterInformation).
DoubleList getParamAsDoubleList_(const String &key, const DoubleList &default_value) const
Return the value of parameter key as a DoubleList or default_value if this value is not set.
void registerFullParam_(const Param ¶m)
Register command line parameters for all entries in a Param object.
void fileParamValidityCheck_(const StringList ¶m_value, const String ¶m_name, const ParameterInformation &p) const
checks if files of an input file list exist
ParameterInformation & getParameterByName_(const String &name)
Returns the parameter identified by the given name.
Param param_common_
Parameters from common section without tool name.
Definition: TOPPBase.h:230
Int getIntOption_(const String &name) const
Returns the value of a previously registered integer option.
bool getParamAsBool_(const String &key) const
Return the value of flag parameter key as bool.
void registerOutputDir_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
Registers an output directory used for tools with multiple output files which are not an output file ...
DoubleList getDoubleList_(const String &name) const
Returns the value of a previously registered DoubleList.
int Int
Signed integer type.
Definition: Types.h:72
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:29
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:36
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:48
std::string toString() const
mangle members to string
Definition: TOPPBase.h:55
std::string when_where
suggested format: journal. year; volume, issue: pages
Definition: TOPPBase.h:51
std::string authors
list of authors in AMA style, i.e. "surname initials", ...
Definition: TOPPBase.h:49
std::string title
title of article
Definition: TOPPBase.h:50
std::string doi
plain DOI (no urls), e.g. 10.1021/pr100177k
Definition: TOPPBase.h:52
Parameter entry used to store the actual information inside of a Param entry.
Definition: Param.h:49