The JD2ResourceManagerJobInputter works with the JobDistributor to define the set of jobs that are to be executed. It reads the list of jobs and the set of resouces they require from one or more XML files. More...

#include <JD2ResourceManagerJobInputter.hh>

Public Member Functions
	JD2ResourceManagerJobInputter ()

virtual	~JD2ResourceManagerJobInputter ()

virtual void	pose_from_job (core::pose::Pose &pose, JobOP job)
	this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. More...

virtual void	fill_jobs (Jobs &jobs)
	this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must". More...

virtual JobInputterInputSource::Enum	input_source () const
	return the type of input source that the JobInputter is currently using More...

void	fill_jobs_from_stream (std::istream &instream, Jobs &jobs)

Public Member Functions inherited from protocols::jd2::JobInputter
virtual	~JobInputter ()

Private Member Functions
virtual void	cleanup_after_job_completion (std::string const &job_tag)
	Delete the Resources associated with a job. More...

void	parse_jobs_tags (utility::tag::TagCOP tag, Jobs &jobs)

void	parse_job_tag (utility::tag::TagCOP jobs_tags, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)

void	parse_jobs_table_tag (utility::tag::TagCOP tag, std::map< std::string, std::string > const &generic_resources_for_job, basic::resource_manager::JobOptions const &generic_job_options, Jobs &jobs)

void	record_job (std::string const &job_name, std::map< std::string, std::string > const &resources_for_job, basic::resource_manager::JobOptionsOP job_options, Jobs &jobs)

void	read_Option_subtag_for_job (utility::tag::TagCOP options_tag, basic::resource_manager::JobOptionsOP job_options)

void	parse_options_name_and_value (std::string const &optname, std::string const &value, basic::resource_manager::JobOptionsOP job_options)

void	read_BooleanOption_subtag_for_job (basic::options::BooleanOptionKey const &boolopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_FileOption_subtag_for_job (basic::options::FileOptionKey const &fileopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_IntegerOption_subtag_for_job (basic::options::IntegerOptionKey const &intopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_PathOption_subtag_for_job (basic::options::PathOptionKey const &pathopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_RealOption_subtag_for_job (basic::options::RealOptionKey const &realopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_StringOption_subtag_for_job (basic::options::StringOptionKey const &stringopt, std::string const &optname, std::string const &val, basic::resource_manager::JobOptionsOP job_options)

void	read_BooleanVectorOption_subtag_for_job (basic::options::BooleanVectorOptionKey const &boolvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_FileVectorOption_subtag_for_job (basic::options::FileVectorOptionKey const &filevectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_IntegerVectorOption_subtag_for_job (basic::options::IntegerVectorOptionKey const &intvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_PathVectorOption_subtag_for_job (basic::options::PathVectorOptionKey const &pathvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_RealVectorOption_subtag_for_job (basic::options::RealVectorOptionKey const &realvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_StringVectorOption_subtag_for_job (basic::options::StringVectorOptionKey const &strinvectopt, std::string const &optname, std::string const &val, utility::vector1< std::string > const &vals, basic::resource_manager::JobOptionsOP job_options)

void	read_Data_for_subtag (utility::tag::TagCOP options_tag, std::string const &jobname, std::string &input_tag, std::map< std::string, std::string > &resources_for_job)

void	read_ResidueType_for_subtag (utility::tag::TagCOP options_tag, std::map< std::string, std::string > &resources_for_job)

void	check_each_job_has_startstruct (Jobs const &jobs) const

Private Attributes
std::string	last_input_tag_
	save the last input tag so the resources loaded for it can be unloaded when we see a new input tag More...

Additional Inherited Members
Static Public Member Functions inherited from protocols::jd2::JobInputter
static std::string	job_inputter_input_source_to_string (JobInputterInputSource::Enum source)
	call this with input_source() to get the input source of a particular job inputter More...

Protected Member Functions inherited from protocols::jd2::JobInputter
void	load_pose_into_job (core::pose::Pose const &pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...

void	load_pose_into_job (core::pose::PoseCOP pose, JobOP job)
	this function modifies the InnerJob's pose. Access to that pose is via friendship. More...

virtual core::Size	get_nstruct () const
	this code is here to restrict the use of inner_job_nonconst (this class is a friend class and can do it) More...

Detailed Description

The JD2ResourceManagerJobInputter works with the JobDistributor to define the set of jobs that are to be executed. It reads the list of jobs and the set of resouces they require from one or more XML files.

The JD2ResourceManagerJobInputter, in its fill_jobs() method, reads a set of XML files that are provided on the command line with the "jd2::resource_definition_files" flag. Multiple files can be given with this flag, and each will be read in the order that they are given. e.g. -jd2resource_definition_files file1.xml file2.xml

The XML file format for defining jobs is structured into blocks of declarations of objects of the same type. The blocks may be specified in any order and may be repeated as many times as is necessary. For example, it is useful to first declare a DatabaseConnection resource in a Resources block before then declaring a DatabaseResourceLocator object (which requires a database connection) in a ResourceLocators block, before then declaring resources in a second Resources block which may rely on the DatabaseResourceLocator for their creation. The key is that the data is processed in the order in which it is declared. If a Resource lists a ResourceLocator that isn't declared until later in the file, the JD2ResourceManagerJobInputter will exit with an error message; it will not wait until the entire file has been read to try and resolve whether the requested ResourceLocator will eventually be declared.

The structure of this XML file is given below.

/* (<--- please ignore this; it is merely an artifact of writing doxygen)

<JD2ResourceManager>
   <ResourceLocators>
      ... ResourceLocator definitions go in this block
   </ResourceLocators>
   <ResourceOptions>
      ... ResourceOption definitions go in this block
   </ResourceOptions>
   <Resources>
      ... Resource definitions go in this block
   </Resources>
   <Jobs>
      Job definitions go here.  Currently the structure is:
      List a) options and b) resources that are used by all jobs
      List c) individual jobs
         List options and resources for an individual job
      or,
      Provide d) a table of jobs and the resources that go with them
      from a database.

      a) Give a command line option that will apply to all jobs.
      <Option optionname=value/>
         Each option's name must be given with full namespacing.  (This hopefully will change)
         E.g.: if you want to set the -ex1 flag to true, you must pass it as
         "packing:ex1=1"
         with exactly one colon between the namespace (packing) and the flag (ex1).

         NOTE: Not all command line options are currently controlled by
         the ResourceManager.  Check first if the option you're interested
         in providing is controlled by the ResouceManager by looking...
         (APL note to self: figure out where someone should look to tell
         if an option is controlled by the ResourceManager)

      b) Give a resource that should be used by all jobs
      <Data desc=resource_description resource_tag=resource_name/>
         * where resource_description is the string that a protocol will use to find the desired resource
         e.g. "native", and
         * where resource_name is the string that was given as a name to some previously-declared
         resource.
      or
      <Data desc=startstruct pdb=pdbfilename/>
         * where pdbfilename is the string that identifies a particular pdb located on the file system
      or
      <Data desc=startstruct pdb=pdbidentifier locator=locator_tag/>
         * where pdbidentifier is a string that identifies a particular pdb, and
         * where locator_tag is a string that was given as a name to some previously-declared
         ResourceLocator.
         E.g., if the given locator_tag names a DatabaseResourceLocator, then the pdbidentifier
         will be used to construct an SQL query that rerieves a pdb-file string from a database.

      c) List individual jobs
      <Job name=jobname nstruct=number>
         * where name=jobname is optional and allows you to control the name given to a job
         and thus to the name of the output structures the job creates.  If no name is given
         then the name will be taken from the "startstruct" data for this job.
         And,
         * where nstruct=number is optional and allows you to control the number of times this
         job is to be performed.  If this is not provided, then the number of iterations is
         set to 1.  number should be an integer string, e.g. "nstruct=100"

         Note: All jobs must have a "startstruct" specified, either individually for the
         given job, or through the Data block above that applies to all jobs.  If the
         startstruct is given in the Data block above that applies to all jobs, then each
         individual job needs to be given a different jobname.

         provide options for this job
         <Option optionname=value/>
             * where the format for optionname and value are exactly as described above

         provide the resources for this job
         <Data desc=resource_description resource_tag=resource_name/> or
         <Data desc=startstruct pdb=pdfilename/> or
         <Data desc=startstruct pdb=pdbidentifier locator=locator_tag/>
             * where the formats for these three types of resource statements are
             exactly as described above
      </Job>

      d) Provide a table of jobs from a database
      <JobsTable sql_command=command database_resource=dbresource/>
          * where command is a string representing an SQL query, and
          * where dbresource is the name for a previously-declared database-connection resource
          connection resource.
          Each row of the jobs table should have one of the following formats
                job_name, 'Resource', desc, resource_tag
                job_name, 'Option', option_key, option_value
             * desc: A job-agnostic description for a resource like 'native' or 'symm_data'
               that can be referenced in the protocol.
             * resource_tag: The tag of a resource described in the <Resources/> block.
             * option_key: An optionally namespaced option key (string) for the options
               system like 'in:file:native'
             * option_value: A value or list of values that processed into the option system
   </Jobs>
</JD2ResourceManager>

See the documentation in the JD2ResourceManager for a description of the file format for the ResourceLocators block (JD2ResourceManager::read_resource_locators_tags), the ResourceOptions block (JD2ResourceManager::read_resource_options_tags) and the Resources block (JD2ResourceManager::read_resources_tags).

Constructor & Destructor Documentation

protocols::jd2::JD2ResourceManagerJobInputter::JD2ResourceManagerJobInputter ( )

protocols::jd2::JD2ResourceManagerJobInputter::~JD2ResourceManagerJobInputter ( )

virtual

Member Function Documentation

void protocols::jd2::JD2ResourceManagerJobInputter::check_each_job_has_startstruct ( Jobs const & jobs ) const

private

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), and basic::resource_manager::LazyResourceManager::has_resource_tag_by_job_tag().

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion ( std::string const & job_tag )

privatevirtual

Delete the Resources associated with a job.

References basic::resource_manager::LazyResourceManager::find_resource(), basic::resource_manager::LazyResourceManager::free_resource_by_tag(), basic::resource_manager::LazyResourceManager::get_count_of_jobs_associated_with_resource_tag(), core::chemical::ChemicalManager::get_instance(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), basic::resource_manager::LazyResourceManager::get_resource_tags_for_job_tag(), basic::resource_manager::LazyResourceManager::mark_job_tag_as_complete(), residue_type_set, and protocols::jd2::tr.

Referenced by pose_from_job().

void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs ( Jobs & jobs )

virtual

this function determines what jobs exist. This function neither knows nor cares what jobs are already complete on disk/memory - it just figures out what ones should exist given the input. NOTE: your JobInputter should order Job objects in the Jobs vector to have as few "transitions" between inputs as possible (group all Jobs of the same input next to each other). This improves efficiency of the "FAIL_BAD_INPUT" functionality. Note I said "should", not "must".

Implements protocols::jd2::JobInputter.

References fill_jobs_from_stream(), basic::options::option, basic::options::OptionKeys::jd2::resource_definition_files, resource_definition_files, and protocols::jd2::tr.

void protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream	(	std::istream &	instream,
		Jobs &	jobs
	)

References utility::tag::Tag::create(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), parse_jobs_tags(), protocols::jd2::JD2ResourceManager::read_resource_locators_tags(), protocols::jd2::JD2ResourceManager::read_resource_options_tags(), and protocols::jd2::JD2ResourceManager::read_resources_tags().

Referenced by fill_jobs().

JobInputterInputSource::Enum protocols::jd2::JD2ResourceManagerJobInputter::input_source ( ) const

virtual

return the type of input source that the JobInputter is currently using

Implements protocols::jd2::JobInputter.

References protocols::jd2::JobInputterInputSource::RESOURCE_MANAGED_JOB.

void protocols::jd2::JD2ResourceManagerJobInputter::parse_job_tag	(	utility::tag::TagCOP	jobs_tags,
		std::map< std::string, std::string > const &	generic_resources_for_job,
		basic::resource_manager::JobOptions const &	generic_job_options,
		Jobs &	jobs
	)

private

References protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), basic::resource_manager::LazyResourceManager::has_resource_configuration(), jobname, parse_options_name_and_value(), read_Data_for_subtag(), read_Option_subtag_for_job(), read_ResidueType_for_subtag(), and record_job().

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_table_tag	(	utility::tag::TagCOP	tag,
		std::map< std::string, std::string > const &	generic_resources_for_job,
		basic::resource_manager::JobOptions const &	generic_job_options,
		Jobs &	jobs
	)

private

References check_statement_sanity(), key, parse_database_connection(), parse_options_name_and_value(), record_job(), safely_prepare_statement(), safely_read_from_database(), and protocols::jd2::tr.

Referenced by parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_jobs_tags	(	utility::tag::TagCOP	tag,
		Jobs &	jobs
	)

private

References check_each_job_has_startstruct(), parse_job_tag(), parse_jobs_table_tag(), read_Data_for_subtag(), and read_Option_subtag_for_job().

Referenced by fill_jobs_from_stream().

void protocols::jd2::JD2ResourceManagerJobInputter::parse_options_name_and_value	(	std::string const &	optname,
		std::string const &	value,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

void protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job	(	core::pose::Pose &	pose,
		JobOP	job
	)

virtual

this function is responsible for filling the pose reference with the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

Implements protocols::jd2::JobInputter.

References core::chemical::ResidueTypeSet::add_residue_type(), cleanup_after_job_completion(), core::pose::Pose::clear(), basic::resource_manager::LazyResourceManager::find_resource_tag_by_job_tag(), core::chemical::ChemicalManager::get_instance(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), basic::resource_manager::LazyResourceManager::get_resource_by_job_tag(), basic::resource_manager::LazyResourceManager::has_resource_tag_by_job_tag(), protocols::jd2::Job::inner_job(), protocols::jd2::Job::input_tag(), last_input_tag_, protocols::jd2::JobInputter::load_pose_into_job(), core::chemical::ChemicalManager::nonconst_residue_type_set(), protocols::jd2::Job::nstruct_index(), core::chemical::ChemicalManager::residue_type_set(), and protocols::jd2::tr.

void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanOption_subtag_for_job	(	basic::options::BooleanOptionKey const &	boolopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_BooleanVectorOption_subtag_for_job	(	basic::options::BooleanVectorOptionKey const &	boolvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag	(	utility::tag::TagCOP	data_tag,
		std::string const &	jobname,
		std::string &	input_tag,
		std::map< std::string, std::string > &	resources_for_job
	)

private

Read the <Data> subtag of the <Job>

Form 1: <Data desc="resource_description" resource="resource_tag"> Precondition requirements: has_resource_configuration(resource_tag) Postcondition guarentees: resources_for_job["resource_description"] == "resource_tag"

References basic::resource_manager::LazyResourceManager::add_resource_configuration(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), basic::resource_manager::LazyResourceManager::has_resource_configuration(), basic::resource_manager::ResourceConfiguration::loader_type, basic::resource_manager::ResourceConfiguration::locator_id, basic::resource_manager::ResourceConfiguration::locator_tag, basic::resource_manager::ResourceConfiguration::resource_options_tag, basic::resource_manager::ResourceConfiguration::resource_tag, and protocols::jd2::tr.

Referenced by parse_job_tag(), and parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::read_FileOption_subtag_for_job	(	basic::options::FileOptionKey const &	fileopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_FileVectorOption_subtag_for_job	(	basic::options::FileVectorOptionKey const &	filevectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerOption_subtag_for_job	(	basic::options::IntegerOptionKey const &	intopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_IntegerVectorOption_subtag_for_job	(	basic::options::IntegerVectorOptionKey const &	intvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_Option_subtag_for_job	(	utility::tag::TagCOP	options_tag,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

References parse_options_name_and_value().

Referenced by parse_job_tag(), and parse_jobs_tags().

void protocols::jd2::JD2ResourceManagerJobInputter::read_PathOption_subtag_for_job	(	basic::options::PathOptionKey const &	pathopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_PathVectorOption_subtag_for_job	(	basic::options::PathVectorOptionKey const &	pathvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_RealOption_subtag_for_job	(	basic::options::RealOptionKey const &	realopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_RealVectorOption_subtag_for_job	(	basic::options::RealVectorOptionKey const &	realvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_ResidueType_for_subtag	(	utility::tag::TagCOP	options_tag,
		std::map< std::string, std::string > &	resources_for_job
	)

private

Referenced by parse_job_tag().

void protocols::jd2::JD2ResourceManagerJobInputter::read_StringOption_subtag_for_job	(	basic::options::StringOptionKey const &	stringopt,
		std::string const &	optname,
		std::string const &	val,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::read_StringVectorOption_subtag_for_job	(	basic::options::StringVectorOptionKey const &	strinvectopt,
		std::string const &	optname,
		std::string const &	val,
		utility::vector1< std::string > const &	vals,
		basic::resource_manager::JobOptionsOP	job_options
	)

private

Referenced by parse_options_name_and_value().

void protocols::jd2::JD2ResourceManagerJobInputter::record_job	(	std::string const &	job_name,
		std::map< std::string, std::string > const &	resources_for_job,
		basic::resource_manager::JobOptionsOP	job_options,
		Jobs &	jobs
	)

private

References basic::resource_manager::LazyResourceManager::add_job_options(), basic::resource_manager::LazyResourceManager::add_resource_tag_by_job_tag(), protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance(), and nstruct.

Referenced by parse_job_tag(), and parse_jobs_table_tag().

Member Data Documentation

std::string protocols::jd2::JD2ResourceManagerJobInputter::last_input_tag_

private

save the last input tag so the resources loaded for it can be unloaded when we see a new input tag

Referenced by pose_from_job().

The documentation for this class was generated from the following files:

symlinks/rosetta/src/protocols/jd2/JD2ResourceManagerJobInputter.hh
symlinks/rosetta/src/protocols/jd2/JD2ResourceManagerJobInputter.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation