The JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor. More...

#include <JD2ResourceManager.hh>

Public Member Functions
virtual void	clear ()

virtual	~JD2ResourceManager ()

basic::resource_manager::ResourceOP	get_resource (basic::resource_manager::ResourceDescription const &resource_description)

bool	has_resource_with_description (basic::resource_manager::ResourceDescription const &resource_description)

void	read_resource_locators_tags (utility::tag::TagCOP tags)
	Read the portion of an XML file that declares ResourceLocator objects. More...

void	read_resource_options_tags (utility::tag::TagCOP tags)
	For an example of a ResourceOptions object, see ImportPoseOptions. More...

void	read_resources_tags (utility::tag::TagCOP tags)

virtual bool	get_option (utility::options::BooleanOptionKey key) const

virtual utility::vector1< bool > const &	get_option (utility::options::BooleanVectorOptionKey key) const

virtual utility::file::FileName const &	get_option (utility::options::FileOptionKey key) const

virtual utility::vector1 < utility::file::FileName > const &	get_option (utility::options::FileVectorOptionKey key) const

virtual int	get_option (utility::options::IntegerOptionKey key) const

virtual utility::vector1< int > const &	get_option (utility::options::IntegerVectorOptionKey key) const

virtual utility::file::PathName const &	get_option (utility::options::PathOptionKey key) const

virtual utility::vector1 < utility::file::PathName > const &	get_option (utility::options::PathVectorOptionKey key) const

virtual platform::Real	get_option (utility::options::RealOptionKey key) const

virtual utility::vector1 < platform::Real > const &	get_option (utility::options::RealVectorOptionKey key) const

virtual std::string const &	get_option (utility::options::StringOptionKey key) const

virtual utility::vector1 < std::string > const &	get_option (utility::options::StringVectorOptionKey key) const

virtual bool	has_option (utility::options::BooleanOptionKey key) const

virtual bool	has_option (utility::options::BooleanVectorOptionKey key) const

virtual bool	has_option (utility::options::FileOptionKey key) const

virtual bool	has_option (utility::options::FileVectorOptionKey key) const

virtual bool	has_option (utility::options::IntegerOptionKey key) const

virtual bool	has_option (utility::options::IntegerVectorOptionKey key) const

virtual bool	has_option (utility::options::PathOptionKey key) const

virtual bool	has_option (utility::options::PathVectorOptionKey key) const

virtual bool	has_option (utility::options::RealOptionKey key) const

virtual bool	has_option (utility::options::RealVectorOptionKey key) const

virtual bool	has_option (utility::options::StringOptionKey key) const

virtual bool	has_option (utility::options::StringVectorOptionKey key) const

Public Member Functions inherited from basic::resource_manager::LazyResourceManager
virtual	~LazyResourceManager ()

virtual ResourceOP	create_resource_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag) const

virtual void	add_resource_tag_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag, ResourceTag const &resource_tag)

virtual bool	has_resource_tag_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag) const

virtual ResourceTag	find_resource_tag_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag) const

virtual ResourceOP	get_resource_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag)

virtual std::list< ResourceTag >	get_resource_tags_for_job_tag (JobTag const &job_tag) const

virtual platform::Size	get_count_of_jobs_associated_with_resource_tag (ResourceTag const &resource_tag) const

virtual void	mark_job_tag_as_complete (JobTag const &job_tag)

virtual void	free_resource_by_job_tag (ResourceDescription const &resource_description, JobTag const &job_tag)

virtual void	free_resource_by_tag (ResourceTag const &resource_tag)

virtual void	add_job_options (JobTag const &job_tag, JobOptionsOP job_options)

virtual bool	has_job_options (JobTag const &job_tag) const

virtual JobOptionsOP	get_job_options (JobTag const &job_tag) const

virtual void	add_resource_configuration (ResourceTag const &resource_tag, ResourceConfiguration const &resource_configuration)

virtual void	add_resource_locator (LocatorTag const &locator_tag, ResourceLocatorOP resource_locator)

virtual void	add_resource_options (ResourceOptionsTag const &resource_options_tag, ResourceOptionsOP resource_options)

virtual ResourceConfiguration const &	find_resource_configuration (ResourceTag const &resource_tag) const

virtual ResourceLocatorOP	find_resource_locator (LocatorTag const &locator_tag) const

virtual ResourceOptionsOP	find_resource_options (ResourceOptionsTag const &resource_options_tag) const

virtual bool	has_resource (ResourceTag const &resource_tag) const

virtual ResourceOP	find_resource (ResourceTag const &resource_tag)

virtual ResourceOP	create_resource (ResourceTag const &resource_tag) const

virtual void	create_resources (JobTag const &)

virtual void	show (std::ostream &out) const

bool	has_resource_configuration (ResourceTag const &resource_tag) const

bool	has_resource_locator (LocatorTag const &locator_tag) const

bool	has_resource_options (ResourceOptionsTag const &resource_options_tag) const

Static Public Member Functions
static JD2ResourceManager *	get_jd2_resource_manager_instance ()

Static Public Member Functions inherited from basic::resource_manager::LazyResourceManager
static ResourceManager *	get_instance ()

Protected Member Functions
	JD2ResourceManager ()

Protected Member Functions inherited from basic::resource_manager::LazyResourceManager
	LazyResourceManager ()

	ResourceManager ()

virtual void	add_resource (ResourceTag const &resource_tag, ResourceOP resource)

virtual void	free_resource (ResourceTag const &resource_tag)

Private Member Functions
void	read_resource_options_table_tag (utility::tag::TagCOP tag)

void	read_resource_option_item (utility::tag::TagCOP tag)

void	check_resource_loader_type (basic::resource_manager::LoaderType const &loader_type)

basic::resource_manager::ResourceTag	read_resource_tag_item (utility::tag::TagCOP tags, basic::resource_manager::LoaderType const &loader_type, basic::resource_manager::LocatorID const &locator_id)

void	read_resource_table_tag (utility::tag::TagCOP tags)

basic::resource_manager::LocatorTag	read_resource_locator_items (utility::tag::TagCOP tags, basic::resource_manager::LoaderType const &loader_type, basic::resource_manager::LocatorID &locator_id)
	find the LocatorTag item from the resource tag. Based on the LocatorTag fill the LocatorID. locator item (&string): FileSystemResourceLocator (default) More...

basic::resource_manager::ResourceOptionsTag	read_resource_options_tag_item (utility::tag::TagCOP tags, basic::resource_manager::LoaderType const &loader_type, basic::resource_manager::ResourceTag const &resource_tag)

basic::resource_manager::ResourceOP	create_resource_from_fallback (basic::resource_manager::FallbackConfigurationCOP fallback, basic::resource_manager::ResourceDescription const &resource_description)

Private Attributes
std::map< std::string, std::string >	fallback_resource_descriptions_created_

Friends
class	JD2ResourceManagerCreator

Detailed Description

The JD2ResourceManager is the ResourceManager that should be used when running protocols under the jd2 JobDistributor.

The purpose of the ResourceManager is to disentangle the process of feeding protocols with Resources they need from the job distribution system in which they run. When protocols request a resource under the ResourceManager, they do so without knowing what kind of ResourceManager they are communicating with. Protocols that are designed to run under JD2 could conceivably be run under any other job management scheme (e.g. a complicated MPI protocol). It's the job of the JD2ResourceManager to determine the right resource to deliver to a protocol, and the context that the JD2ResourceManager uses to make that decision is the job. E.g., when a protocol asks for the "native" (the Pose of the native structure), the JD2ResourceManager looks up what job is currently running and then delivers the (single) native Pose for that job.

The JD2ResourceManager is meant to work with the JD2ResourceManagerJobInputter. Jobs are defined in an input XML file and for each of the jobs that are defined, resources can be mapped to them. Resources are also declared in an XML file and may be declared in the same XML file as the Jobs or in a different XML file. The format of this XML file is specified in full between the documentation in the JD2ResourceManagerJobInputter class and three functions that are documented and implemented in this class.

The JD2ResourceManager keeps track of which resources are used by which jobs and keeps track of what jobs have completed. It allocates a Resource the first time that resource is requested by a protoocol, and it deallocates that Resource when all jobs that require that resource have finished. Thus a protocol that needs an expensive-to-create resource (e.g. a set of 9-mers) can load that resource once and then have that resource shared between all of the jobs that require that resource (e.g. 10K abinitio trajectories) without having to do any legwork itself. If you have 100K abinitio trajectories for 10 different targets, they could all be run in a single job. (Note: as of 9/2013, abinitio does not work with the jd2 or the ResourceManager but it should!)

The main consequence of relying on the ResourceManager to hand resources to jobs is that jobs which require different resources (usually specified on the command line, and therefore requiring that each job run in a separate process) now can be run together in a single process. For MPI jobs, this is a major improvement, especially in constructing benchmarks, where many separate, (possibly short) jobs need to be run.

(Because Resources are not constructed until they are requested, resources can be declared and never used; you can give a resource file that describes every resource you use in every job, and a job declaration file that only uses one of those resources.)

Constructor & Destructor Documentation

protocols::jd2::JD2ResourceManager::JD2ResourceManager ( )

protected

protocols::jd2::JD2ResourceManager::~JD2ResourceManager ( )

virtual

Member Function Documentation

void protocols::jd2::JD2ResourceManager::check_resource_loader_type ( basic::resource_manager::LoaderType const & loader_type )

private

Check if the loader type is defined with the ResourceLoaderFactory

References basic::resource_manager::ResourceLoaderFactory::available_resource_loaders(), and basic::resource_manager::ResourceLoaderFactory::get_instance().

Referenced by read_resource_table_tag(), and read_resources_tags().

void protocols::jd2::JD2ResourceManager::clear ( )

virtual

Reimplemented from basic::resource_manager::LazyResourceManager.

References basic::resource_manager::LazyResourceManager::clear().

basic::resource_manager::ResourceOP protocols::jd2::JD2ResourceManager::create_resource_from_fallback	(	basic::resource_manager::FallbackConfigurationCOP	fallback,
		basic::resource_manager::ResourceDescription const &	resource_description
	)

private

References basic::resource_manager::LazyResourceManager::find_resource_locator(), and basic::resource_manager::ResourceLoaderFactory::get_instance().

Referenced by get_resource().

JD2ResourceManager * protocols::jd2::JD2ResourceManager::get_jd2_resource_manager_instance ( )

static

Referenced by protocols::jd2::JD2ResourceManagerJobInputter::check_each_job_has_startstruct(), protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion(), protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream(), protocols::jd2::JD2ResourceManagerJobInputter::parse_job_tag(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), protocols::jd2::JD2ResourceManagerJobInputter::read_Data_for_subtag(), and protocols::jd2::JD2ResourceManagerJobInputter::record_job().

bool protocols::jd2::JD2ResourceManager::get_option ( utility::options::BooleanOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< bool > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::BooleanVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::file::FileName const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::FileOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< utility::file::FileName > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::FileVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

int protocols::jd2::JD2ResourceManager::get_option ( utility::options::IntegerOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< int > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::IntegerVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::file::PathName const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::PathOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< utility::file::PathName > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::PathVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

platform::Real protocols::jd2::JD2ResourceManager::get_option ( utility::options::RealOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< platform::Real > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::RealVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

std::string const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::StringOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

utility::vector1< std::string > const & protocols::jd2::JD2ResourceManager::get_option ( utility::options::StringVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), protocols::jd2::Job::input_tag(), and basic::options::option.

ResourceOP protocols::jd2::JD2ResourceManager::get_resource ( basic::resource_manager::ResourceDescription const & resource_description )

virtual

Implements basic::resource_manager::LazyResourceManager.

References basic::resource_manager::LazyResourceManager::add_resource(), basic::resource_manager::LazyResourceManager::add_resource_configuration(), create_resource_from_fallback(), protocols::jd2::JobDistributor::current_job(), fallback_resource_descriptions_created_, basic::resource_manager::LazyResourceManager::find_resource(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_resource_by_job_tag(), basic::resource_manager::LazyResourceManager::has_resource_configuration(), basic::resource_manager::LazyResourceManager::has_resource_tag_by_job_tag(), protocols::jd2::Job::input_tag(), numeric::random::random_range(), basic::resource_manager::ResourceConfiguration::resource_tag, and utility::to_string().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::BooleanOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), and basic::resource_manager::LazyResourceManager::has_job_options().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::BooleanVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::FileOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::FileVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::IntegerOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::IntegerVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::PathOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::PathVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::RealOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::RealVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::StringOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_option ( utility::options::StringVectorOptionKey key ) const

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), basic::resource_manager::LazyResourceManager::get_job_options(), basic::resource_manager::LazyResourceManager::has_job_options(), and protocols::jd2::Job::input_tag().

bool protocols::jd2::JD2ResourceManager::has_resource_with_description ( basic::resource_manager::ResourceDescription const & resource_description )

virtual

Implements basic::resource_manager::LazyResourceManager.

References protocols::nonlocal::current_job(), fallback_resource_descriptions_created_, protocols::jd2::JobDistributor::get_instance(), and basic::resource_manager::LazyResourceManager::has_resource_tag_by_job_tag().

LocatorTag protocols::jd2::JD2ResourceManager::read_resource_locator_items	(	utility::tag::TagCOP	tags,
		basic::resource_manager::LoaderType const &	loader_type,
		basic::resource_manager::LocatorID &	locator_id
	)

private

find the LocatorTag item from the resource tag. Based on the LocatorTag fill the LocatorID. locator item (&string): FileSystemResourceLocator (default)

file item is interchangable with the locatorID item locatorID item (&string):

Referenced by read_resources_tags().

*void protocols::jd2::JD2ResourceManager::read_resource_locators_tags ( utility::tag::TagCOP tags )

Read the portion of an XML file that declares ResourceLocator objects.

instantiate all the resource locators given in the input tags, and put them into the base class. Make sure no two resource locators share a common name.

The file format should be

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

The surrounding tag "ResourceLocators" will not be read by this function but
instead wil be read the by function that will call this function.  It is
listed here simply for context.
<ResourceLocators>

   declare one or more resource locators
   <LocatorType tag=name_for_this_instance >
      * where LocatorType is one of the several locator_types that have been
      implemented; the string must match the locator_type given by some
      ResourceLocatorCreator. E.g. "DatabaseResourceLocator". And,
      * where the "tag" (the name) for the declared instance must be unique
      among the set of all resource locators declared.
      <...\>
         provide any subtags that are required to instantiate a
         ResourceLocator of the indicated type
   <\LocatorType>

<\ResourceLocators>
/

Referenced by protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream().

void protocols::jd2::JD2ResourceManager::read_resource_option_item ( utility::tag::TagCOP tag )

private

Referenced by read_resource_options_table_tag(), and read_resource_options_tags().

void protocols::jd2::JD2ResourceManager::read_resource_options_table_tag ( utility::tag::TagCOP tag )

private

References check_statement_sanity(), key, parse_database_connection(), read_resource_option_item(), safely_prepare_statement(), safely_read_from_database(), t, tags, protocols::jd2::TR, and type.

Referenced by read_resource_options_tags().

ResourceOptionsTag protocols::jd2::JD2ResourceManager::read_resource_options_tag_item	(	utility::tag::TagCOP	tags,
		basic::resource_manager::LoaderType const &	loader_type,
		basic::resource_manager::ResourceTag const &	resource_tag
	)

private

Referenced by read_resources_tags().

*void protocols::jd2::JD2ResourceManager::read_resource_options_tags ( utility::tag::TagCOP tags )

For an example of a ResourceOptions object, see ImportPoseOptions.

instantiate all the resource options and put them in the base class. Make sure no two resource options are given the same name.

The file format should be

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

The surrounding tag "ResourceOptions" will not be read by this function but
instead wil be read the by function that will call this function.  It is
listed here simply for context.
<ResourceOptions>

   declare one or more resource options objects
   <OptionsType tag=name_for_this_instance >
      * where OptionsType is one of the several option_types that have been
      implemented; the string must match the option_type given by some
      ResourceOptionsCreator. E.g. "ImportPoseOptions". And,
      * where the "tag" (the name) for the declared instance must be unique
      among the set of all resource options declared.
      <...\>
         provide any subtags that are required to instantiate a
         ResourceOptions object of the indicated type
   <\OptionsType>

   or provide an SQL query to retrieve the ResourceOptions defined in
   a database
   <OptionsTable 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
      Each row of the resource options table should have the following format
          resource_options_tag, resource_options_type, resource_option_key, resource_option_value
       * The table should 'ORDER BY resource_options_tag', to have data for a
         specific resource-options object adjacent in the table
       * resource_option_{key, value}: Each resource options takes set of key value pairs (string -> string)
         for example, for PoseFromPDBOptions, has the key 'exit_if_missing_heavy_atoms' and takes '1' for true or '0' for false.;

<\ResourceOptions>

References utility::tag::Tag::getName(), read_resource_option_item(), and read_resource_options_table_tag().

Referenced by protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream().

void protocols::jd2::JD2ResourceManager::read_resource_table_tag ( utility::tag::TagCOP tags )

private

References check_resource_loader_type(), check_statement_sanity(), basic::resource_manager::ResourceConfiguration::loader_type, basic::resource_manager::ResourceConfiguration::locator_id, basic::resource_manager::ResourceConfiguration::locator_tag, parse_database_connection(), basic::resource_manager::ResourceConfiguration::resource_options_tag, basic::resource_manager::ResourceConfiguration::resource_tag, safely_prepare_statement(), safely_read_from_database(), and protocols::jd2::TR.

Referenced by read_resources_tags().

ResourceTag protocols::jd2::JD2ResourceManager::read_resource_tag_item	(	utility::tag::TagCOP	tags,
		basic::resource_manager::LoaderType const &	loader_type,
		basic::resource_manager::LocatorID const &	locator_id
	)

private

make sure the resource object has been given a tag and that no other resource object has been delecared with the same name.

Referenced by read_resources_tags().

*void protocols::jd2::JD2ResourceManager::read_resources_tags ( utility::tag::TagCOP tags )

read through all the resources, and put them into the base class for later instantiation. Make sure each resource is named, that it is the only resource that has been declared with that name.

The file format should be

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

The surrounding tag "Resources" will not be read by this function but
instead wil be read the by function that will call this function.  It is
listed here simply for context.
<Resources>

   declare one or more resource objects
   <ResourceLoaderType tag=name_for_this_instance locator=locatorname locatorID=locid options=optname \>
      * where ResourceLoaderType is one of the several loader_types that have been
      implemented; the string must match the loader_type given by some
      ResourceLoaderCreator. E.g. "LoopsFile" which is given by the
      LoopsFileLoaderCreator. And,
      * where the (required) "name_for_this_instance" (the tag) for the declared instance
      must be unique among the set of all resources declared,
      * where the (optional) "locatorname" must refer to a previously-declared resource locator,
      if a locator is not given, the FileSystemResourceLocator is used
      * where the (required) "locid" provides the locatorID that the resource locator uses
      to create the input stream needed to read in the resource (e.g. the file name), and
      * where the (optional) "optname" string refers to a previously-declared ResourceOptions object
      that will be used by the indicated ResourceLoader (if not given, then the ResourceLoader
      will use the default ResourceOptions object).
   <\ResourceLoaderType>
   or
   <ResourceLoaderType tag=name_for_this_instance file=filename locator=locatorname options=optname >
      * where ResourceLoaderType is the same as above,
      * where the (required) "name_for_this_instance" is the same as above,
      * where the (optional) "locatorname" must refer to a previously defined FileSystemResourceLocator
      * where the (required) "filename" is the path to the file used to create the resource
      * where the (optional) "optsname" is the same as above
   <\ResourceLoaderType>
   or provide an SQL query to retrieve the Resources defined in a database
   <ResourceTable 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
      The ResourceTable tag requires a 'sql_command' tag that
      is an SQL SELECT statement that returns the following columns:
         resource_tag
         locator_tag
         locator_id
         loader_type
         resource_options_tag

<\Resources>

References check_resource_loader_type(), basic::resource_manager::ResourceConfiguration::loader_type, basic::resource_manager::ResourceConfiguration::locator_id, basic::resource_manager::ResourceConfiguration::locator_tag, read_resource_locator_items(), read_resource_options_tag_item(), read_resource_table_tag(), read_resource_tag_item(), basic::resource_manager::ResourceConfiguration::resource_options_tag, and basic::resource_manager::ResourceConfiguration::resource_tag.

Referenced by protocols::jd2::JD2ResourceManagerJobInputter::fill_jobs_from_stream().