EnsEMBL::Web::SpeciesDefs

Location: /modules/EnsEMBL/Web/SpeciesDefs.pm
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Inherits from:

No subclasses

Overview

SpeciesDefs - Ensembl web configuration accessor This module provides programatic access to the web site configuration data stored in the $ENSEMBL_SERVERROOT/conf/*.ini (INI) files. See $ENSEMBL_SERVERROOT/conf/ini.README for details. Owing to the overhead implicit in parsing the INI files, two levels of caching (memory, filesystem) have been implemented. To update changes made to an INI file, the running process (e.g. httpd) must be halted, and the $ENSEMBL_SERVERROOT/conf/config.packed file removed. In the absence of a cache, the INI files are automatically parsed parsed at object instantiation. In the case of the Ensembl web site, this occurs at server startup via the $ENSEMBL_SERVERROOT/conf/perl.startup script. The filesystem cache is not enabled by default; the SpeciesDefs::store method is used to do this explicitly. Example usage: use SpeciesDefs; my $speciesdefs = SpeciesDefs->new; # List all configured species my @species = $speciesdefs->valid_species(); # Test to see whether a species is configured if( scalar( $species_defs->valid_species('Homo_sapiens') ){ } # Getting a setting (parameter value/section data) from the config my $sp_name = $speciesdefs->get_config('Homo_sapiens','SPECIES_COMMON_NAME'); # Alternative setting getter - uses autoloader my $sp_bio_name = $speciesdefs->SPECIE_%S_COMMON_NAME('Homo_sapiens'); # Can also use the ENSEMBL_SPECIES environment variable ENV{'ENSEMBL_SPECIES'} = 'Homo_sapiens'; my $sp_bio_name = $speciesdefs->SPECIES_COMMON_NAME; # Getting a parameter with multiple values my( @chromosomes ) = @{$speciesdefs->ENSEMBL_CHROMOSOMES};

Accessor

Constructor

Method

Unknown

  • DESTROY
  • _expand_database_templates
  • _info_line
  • _info_log
  • _merge_db_tree
  • _merge_in_dhtml
  • _munge_colours
  • _parse_referer (EnsEMBL::Web::Root)
  • _promote_general
  • _read_in_ini_file
  • compara_like_databases
  • dump
  • filters (EnsEMBL::Web::Root)
  • get_all_das
  • help_feedback (EnsEMBL::Web::Root)
  • is_available (EnsEMBL::Web::Root)
  • marts
  • multi_hash
  • multi_val
  • species_dropdown
  • species_label
  • table_info
  • table_info_other
  • timer_push
Documentation coverage: 65 %

Methods

    AUTOLOAD
    Accessor.
    View source

    _convert_date
    Converts a date from a species database into a human-friendly format for web display
    Argument date in format YYYY-MM with optional -string attached
    Returns: hash ref {'date' => 'Mmm YYYY', 'string' => 'xxxxx'}
    View source

    _format_error
    Format an error message by wrapping text to 120 columns
    Inherited from EnsEMBL::Web::Root
    View source

    _is_available_artefact
    Checks to see if a given artefact is available (or not available) in the stored configuration for a particular species
    Arguments species name (defaults to the current species), artefact to check for (string - artefact type and id, space separated)
    Returns: boolean
    View source

    _load_in_webtree
    Load in the contents of the web tree.... Check for cached value first....
    View source

    _parse
    Does the actual parsing of .ini files (1) Open up the DEFAULTS.ini file(s) Foreach species open up all {species}.ini file(s) merge in content of defaults load data from db.packed file make other manipulations as required Repeat for MULTI.iniReturns: boolean
    View source

    all_search_indexes
    Accessor.


    View source

    anyother_species
    DEPRECATED - use get_config instead
    View source

    colour
    Accessor. return the colour associated with the $key of $set colour set (or the whole hash associated reference);
    View source

    de_romanize
    Converts a number from roman (IV...) format to number...
    Inherited from EnsEMBL::Web::Root
    View source

    dynamic_use
    Equivalent of USE - but used at runtime
    Inherited from EnsEMBL::Web::Root
    View source

    dynamic_use_failure
    Return error message cached if use previously failed!
    Inherited from EnsEMBL::Web::Root
    View source

    evaluate_bp
    Reverse of round BP - takes a value with a K/M/G at the end and converts to integer value...
    Inherited from EnsEMBL::Web::Root
    View source

    get_config
    Arguments species name(string), parameter name (string)
    Returns: parameter value (any type), or undef on failure
    View source

    get_table_size
    Accessor function for table size,
    Arguments hashref: {-db => 'database' (e.g. 'DATABASE_CORE'), -table =>'table name' (e.g. 'feature' ) } species name (string)
    Returns: Number of rows in the table
    View source

    is_valid_module_name
    returns true if valid module name...
    Inherited from EnsEMBL::Web::Root
    View source

    make_directory
    Creates a writeable directory - making sure all parents exist!
    Inherited from EnsEMBL::Web::Root
    View source

    multi
    Accessor.
    Arguments configuration type (string), species name (string)

    View source

    multiX
    Accessor.
    Arguments configuration type (string)

    View source

    multidb
    Accessor.
    View source

    name
    Accessor. returns the name of the current species
    View source

    neat_sr_name
    Returns seq-region name formatted neatly...
    Inherited from EnsEMBL::Web::Root
    View source

    new
    Constructor.
    View source

    new
    Constructor. Constructs the class - as its a base class contains nothing.!
    Inherited from EnsEMBL::Web::Root
    View source

    not_allowed
    Loops through array of filters and returns the first one that fails
    Inherited from EnsEMBL::Web::Root
    View source

    other_species
    DEPRECATED - use get_config instead
    View source

    parse
    Retrieves a stored configuration or creates a new one Caller: $self->new when filesystem and memory caches are emptyReturns: boolean
    View source

    pretty_date
    Converts a MySQL datetime field into something human-readable
    Inherited from EnsEMBL::Web::Root
    View source

    retrieve
    Retrieves stored configuration from disk
    Exceptions The filesystem-cache file cannot be opened
    Returns: boolean
    View source

    round_bp
    Returns #bp formatted neatly as either m/k
    Inherited from EnsEMBL::Web::Root
    View source

    seq_region_sort
    Used to sort chromosomes into a sensible order!
    Inherited from EnsEMBL::Web::Root
    View source

    set_config
    Overrides the config value for a given species and a given config key (use with care!)
    Arguments species name (string), parameter name (string), parameter value (any)
    Returns: boolean
    View source

    set_write_access
    sets a given database adaptor to write access instead of read-only
    Arguments database type (e.g. 'core'), species name (string)
    Returns: none
    View source

    species_full_name
    Accessor. returns full species name from the short name
    View source

    store
    Creates filesystem-cache by storing config to disk.
    Caller perl.startup, on first (validation) pass of httpd.conf
    Returns: boolean
    View source

    temp_file_create
    Creates a temporary file name and makes sure its parent directory exists
    Inherited from EnsEMBL::Web::Root
    View source

    temp_file_name
    Creates a random filename
    Inherited from EnsEMBL::Web::Root
    View source

    templatize
    Takes a string, and a template pattern and returns the string with "/" from the template inserted...
    Inherited from EnsEMBL::Web::Root
    View source

    thousandify
    Retuns comma separated version of number...
    Inherited from EnsEMBL::Web::Root
    View source

    ticket
    Returns a random ticket string
    Inherited from EnsEMBL::Web::Root
    View source

    timer
    Provides easy-access to the ENSEMBL_WEB_REGISTRY's timer
    View source

    translate
    Dictionary functionality (not currently used)
    Arguments word to be translated (string)
    Returns: translated word (string) or original word if not found
    View source

    url
    Assembles a valid URL, adding the site's base URL and CGI-escaping any parametersreturns a URL string
    Inherited from EnsEMBL::Web::Root
    View source

    valid_species
    Filters the list of species to those configured in the object. If an empty list is passes, returns a list of all configured speciesReturns: array of configured species names
    View source


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