TaxonomyImporter Class Reference

Inheritance diagram for TaxonomyImporter:

Collaboration diagram for TaxonomyImporter:

Public Member Functions
	form ($form, &$form_state)
	formValidate ($form, &$form_state)
	run ()
Public Member Functions inherited from TripalImporter
	__construct (TripalJob $job=NULL)
	setJob (TripalJob $job)
	create ($run_args, $file_details=[])
	load ($import_id)
	submitJob ()
	prepareFiles ()
	cleanFile ()
	logMessage ($message, $variables=[], $severity=TRIPAL_INFO)
	formSubmit ($form, &$form_state)
	postRun ()
	getArguments ()

Static Public Attributes
static	$name = 'Chado NCBI Taxonomy Loader'
static	$machine_name = 'chado_taxonomy'
static	$description
static	$file_types = []
static	$upload_description = ''
static	$upload_title = 'File Upload'
static	$use_analysis = FALSE
static	$require_analysis = FALSE
static	$button_text = 'Import from NCBI Taxonomy'
static	$methods
static	$file_required = FALSE
static	$argument_list = []
static	$cardinality = 0
Static Public Attributes inherited from TripalImporter
static	$name = 'Tripal Loader'
static	$machine_name = 'tripal_loader'
static	$description = 'A base loader for all Tripal loaders'
static	$file_types = []
static	$upload_description = ''
static	$upload_title = 'File Upload'
static	$use_analysis = TRUE
static	$require_analysis = TRUE
static	$button_text = 'Import File'
static	$use_button = TRUE
static	$methods
static	$file_required = TRUE
static	$argument_list = []
static	$cardinality = 1
static	$menu_path = ''
static	$callback = ''
static	$callback_module = ''
static	$callback_path = ''

Additional Inherited Members
Static Public Member Functions inherited from TripalImporter
static	byID ($import_id)
Protected Member Functions inherited from TripalImporter
	setTotalItems ($total_items)
	addItemsHandled ($num_handled)
	setItemsHandled ($total_handled)
	setInterval ($interval)
Protected Attributes inherited from TripalImporter
	$job
	$arguments
	$import_id
	$is_prepared
	$reported = 0

Member Function Documentation

form()

TaxonomyImporter::form	(		$form,
		&	$form_state
	)

See also

TripalImporter::form()

Reimplemented from TripalImporter.

formValidate()

TaxonomyImporter::formValidate	(		$form,
		&	$form_state
	)

See also

TripalImporter::formValidate()

Reimplemented from TripalImporter.

run()

TaxonomyImporter::run

(

)

Performs the import.

Reimplemented from TripalImporter.

Member Data Documentation

$argument_list

TaxonomyImporter::$argument_list = []

static

The array of arguments used for this loader. Each argument should be a separate array containing a machine_name, name, and description keys. This information is used to build the help text for the loader.

$button_text

TaxonomyImporter::$button_text = 'Import from NCBI Taxonomy'

static

Text that should appear on the button at the bottom of the importer form.

$cardinality

TaxonomyImporter::$cardinality = 0

static

Indicates how many files are allowed to be uploaded. By default this is set to allow only one file. Change to any positive number. A value of zero indicates an unlimited number of uploaded files are allowed.

$description

TaxonomyImporter::$description

static

Initial value:

= 'Imports new organisms from NCBI using taxonomy IDs, ' .
                               'or loads taxonomic details about existing organisms.'

A brief description for this loader. This description will be presented to the site user.

$file_required

TaxonomyImporter::$file_required = FALSE

static

Indicates if the file must be provided. An example when it may not be necessary to require that the user provide a file for uploading if the loader keeps track of previous files and makes those available for selection.

$file_types

TaxonomyImporter::$file_types = []

static

An array containing the extensions of allowed file types.

$machine_name

TaxonomyImporter::$machine_name = 'chado_taxonomy'

static

The machine name for this loader. This name will be used to construct the URL for the loader.

$methods

TaxonomyImporter::$methods

static

Initial value:

= [
    
    'file_upload' => FALSE,
    
    'file_local' => FALSE,
    
    'file_remote' => FALSE,
  ]

Indicates the methods that the file uploader will support.

$name

TaxonomyImporter::$name = 'Chado NCBI Taxonomy Loader'

static

The name of this loader. This name will be presented to the site user.

$require_analysis

TaxonomyImporter::$require_analysis = FALSE

static

If the $use_analysis value is set above then this value indicates if the analysis should be required.

$upload_description

TaxonomyImporter::$upload_description = ''

static

Provides information to the user about the file upload. Typically this may include a description of the file types allowed.

$upload_title

TaxonomyImporter::$upload_title = 'File Upload'

static

The title that should appear above the upload button.

$use_analysis

TaxonomyImporter::$use_analysis = FALSE

static

If the loader should require an analysis record. To maintain provenance we should always indicate where the data we are uploading comes from. The method that Tripal attempts to use for this by associating upload files with an analysis record. The analysis record provides the details for how the file was created or obtained. Set this to FALSE if the loader should not require an analysis when loading. if $use_analysis is set to true then the form values will have an 'analysis_id' key in the $form_state array on submitted forms.

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

• tripal_chado/includes/TripalImporter/TaxonomyImporter.inc