icsearch/dbsf.module File Reference

Detailed Description

Drupal Bioinformatic Server framework Module Developed by Alexie Papanicolaou and Ritika Chauhan. University of Exeter. Licensed under GPLv3

See also:: http://insectacentral.org

caution. Tabs needs the following settings to be set at /admin/settings/tabs due to tabs' bugs navigation buttons: enabled ; descriptive tab URLs: enabled. internet explorer 7 has a bug with double row tabs. use IE8

Definition in file dbsf.module.

Function Documentation

_dbsf_generate_options ( $ software_name )

Get software options, their values and the FAPI type

Parameters:

$software_name

Name of software to generate options for

Returns:: An 2D associative array. Primary key is option name and 2nd key is 'options' and 'type'. Content of options is a list array and type is a string.

Definition at line 1200 of file dbsf.module.

References dbsf_get_software_resources(), and icbasic_get_resource_cvterm_and_prop().

Referenced by dbsf_blast_form(), and dbsf_ssaha2_form().

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dbsf_admin_blast_page ( )

Create HTML for the administration BLAST page

Menu as admin/dbsf/blast

Definition at line 2202 of file dbsf.module.

References dbsf_admin_database_table(), and dbsf_check_software_active().

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dbsf_admin_database_files_table ( )

Builds a table with all files which could be added as datasets

Returns:: HTML of a table

Definition at line 1112 of file dbsf.module.

References dbsf_get_software(), and icbasic_get_add_resource().

Referenced by dbsf_admin_dataset_page().

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dbsf_admin_database_table ( $ software = NULL )

Builds a table containing all datasets that have been uploaded

Parameters:

$software

Optionally, software to create the table for. Defaults to NULL i.e. all

Returns:: HTML of a table

Definition at line 1024 of file dbsf.module.

References dbsf_get_resource_roles(), dbsf_get_software(), dbsf_get_software_resources(), icbasic_get_add_resource(), icbasic_get_linked_resources(), and icbasic_get_resource_cvterm_and_prop().

Referenced by dbsf_admin_blast_page(), dbsf_admin_dataset_page(), and dbsf_admin_ssaha2_page().

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dbsf_admin_dataset_page ( )

Produce HTML for the 'administrate dataset page'.

Menu admin/dbsf/dataset

Definition at line 210 of file dbsf.module.

References dbsf_admin_database_files_table(), and dbsf_admin_database_table().

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dbsf_admin_dataset_perms_form ( $ form_state )

Implements hook_form()

See also:: dbsf_admin_dataset_perms_form_validate()
dbsf_admin_dataset_perms_form_submit()

Parameters:

$form_state

hook_form data

Definition at line 924 of file dbsf.module.

References dbsf_get_role(), and icbasic_get_add_resource().

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dbsf_admin_dataset_perms_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_admin_dataset_perms_form()
dbsf_admin_dataset_perms_form_validate()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 974 of file dbsf.module.

References dbsf_link_unlink_resource_role().

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dbsf_admin_dataset_variables_form ( $ form_state )

Implements hook_form()

See also:: dbsf_admin_dataset_variables_form_validate()
dbsf_admin_dataset_variables_form_submit()

Parameters:

$form_state

hook_form data

Definition at line 412 of file dbsf.module.

dbsf_admin_dataset_variables_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_admin_dataset_variables_form_validate()
dbsf_admin_dataset_variables_form()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 496 of file dbsf.module.

References icbasic_get_add_resource().

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dbsf_admin_dataset_variables_form_validate	(	$	form,
		&$	form_state
	)

Implements hook_form_validate()

See also:: dbsf_admin_dataset_variables_form()
dbsf_admin_dataset_variables_form_submit()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 457 of file dbsf.module.

dbsf_admin_link_dataset_software_form	(	$	form_state,
		$	software = `NULL`
	)

Implements hook_form()

See also:: dbsf_admin_link_dataset_software_form_validate()
dbsf_admin_link_dataset_software_form_submit()

Parameters:

	$form_state	hook_form data
	$software	Which software to produce form for

Definition at line 761 of file dbsf.module.

References dbsf_get_software(), and icbasic_get_add_resource().

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dbsf_admin_link_dataset_software_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_admin_link_dataset_software_form()
dbsf_admin_link_dataset_software_form_validate()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 887 of file dbsf.module.

References dbsf_link_unlink_software_resource().

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dbsf_admin_link_dataset_software_form_validate	(	$	form,
		&$	form_state
	)

Implements hook_form_validate()

See also:: dbsf_admin_link_dataset_software_form()
dbsf_admin_link_dataset_software_form_submit()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 826 of file dbsf.module.

References dbsf_get_dataset_path().

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dbsf_admin_newdataset_form ( $ form_state )

Implements hook_form()

See also:: dbsf_admin_newdataset_form_validate()
dbsf_admin_newdataset_form_submit()

Parameters:

$form_state

hook_form data

Definition at line 532 of file dbsf.module.

References icbasic_get_add_cv_withnames(), and icbasic_get_add_resource().

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dbsf_admin_newdataset_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_admin_newdataset_form()
dbsf_admin_newdataset_form_validate()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 703 of file dbsf.module.

References dbsf_link_unlink_resource_role(), icbasic_get_add_resource(), icbasic_link_unlink_resources(), and icbasic_populate_cvterms().

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dbsf_admin_newdataset_form_validate	(	$	form,
		&$	form_state
	)

Implements hook_form_validate()

See also:: dbsf_admin_newdataset_form()
dbsf_admin_newdataset_form_submit()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 614 of file dbsf.module.

References icbasic_get_add_resource().

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dbsf_admin_page ( )

Produce HTML for the 'administrate software page'.

Menu admin/settings/dbsf

Definition at line 166 of file dbsf.module.

dbsf_admin_software_page ( )

Produce HTML for the 'administrate software page'.

Menu admin/dbsf/software Grabs available plugins as well.

See also:: dbsf_software_form()
dbsf_software_blast_core_settings_form()

Definition at line 273 of file dbsf.module.

dbsf_batch_save_data	(	$	data = `NULL`,
		&$	context
	)

Save an array to be used for the batch API. see batch_set()

Parameters:

	$data	A variable to store to $context
	$context	The variable used by batch API to store data

Definition at line 1295 of file dbsf.module.

dbsf_batch_upload_fasta	(	$	batch_file_data,
		&$	context
	)

Upload FASTA as used in a batch operation.

Needed because we use the same create_fasta function more than once

See also:: icbasic_write_fastafile()
dbsf_formatdb_fastafile()

Parameters:

	$batch_file_data	Associative array with following keys. infile: all the infiles to be passed to icbasic_write_fastafile() outfile: likewise, all outfiles filetype: likewise all file types format: whether to run format this file via dbsf_formatdb_fastafile()
	$context	Array from batch_api

Returns:: It does not return anything, it updates $context instead by altering $context['finished']

Definition at line 1255 of file dbsf.module.

References dbsf_formatdb_fastafile(), and icbasic_write_fastafile().

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dbsf_blast_batch_finished	(	$	success,
		$	results,
		$	operations
	)

Implements hook_batch_finish

Handles the final operations of the BATCH API

Parameters:

	$success	See Drupal's BATCH API
	$results	See Drupal's BATCH API
	$operations	See Drupal's BATCH API

Returns:: FALSE on failure

Definition at line 2906 of file dbsf.module.

References dbsf_parameter_daemon().

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dbsf_blast_form	(	$	form_state,
		$	sample_data = `FALSE`
	)

Implements hook_form()

See also:: dbsf_blast_form_validate()
dbsf_blast_form_submit()

Parameters:

	$form_state	hook_form data
	$sample_data	Boolean, if TRUE then fill form with sample data

Definition at line 2334 of file dbsf.module.

References $user, _dbsf_generate_options(), and dbsf_get_user_datasets().

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dbsf_blast_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_blast_form()
dbsf_blast_form_validate()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 2701 of file dbsf.module.

References dbsf_blastall_software_pars(), dbsf_get_dataset_path(), and icbasic_create_uid().

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dbsf_blast_form_validate	(	$	form,
		&$	form_state
	)

Implements hook_form_validate()

See also:: dbsf_blast_form()
dbsf_blast_form_submit()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 2626 of file dbsf.module.

References icbasic_validate_seq_dna(), and icbasic_validate_seq_protein().

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dbsf_blast_page ( $ sample_data = FALSE )

Creates HTML for the BLAST page

Menu as dbsf/blast

Parameters:

$sample_data

If true then the form will be prefilled with sample data

Returns:: HTML of BLAST page

Definition at line 2288 of file dbsf.module.

References dbsf_check_blast().

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dbsf_blast_result_form	(	$	form_state,
		$	uid,
		$	blastfile
	)

Implements hook_form()

Used to produce a table of results with checkboxes which we can then select for processing (e.g. downloading). This form is themed.

See also:: dbsf_theme_blast_result_form()
dbsf_blast_result_page()

Parameters:

	$form_state	Form API variable
	$uid	Unique Identifier of algorithm's BLAST search
	$blastfile	Full path to BLAST results as an XML file

Definition at line 3182 of file dbsf.module.

References dbsf_blast_result_xml().

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dbsf_blast_result_page ( $ submission_uid = NULL )

Produces HTML results for a BLAST

See also:: dbsf_blast_result_form()

Parameters:

$submission_uid

The UID relating to the submission. This is not the same as the individual BLAST algorithm UID as users can perform multiple algorithm searches from one form

Returns:: HTML of results, include a table and graph of hits.

Definition at line 3097 of file dbsf.module.

dbsf_blast_result_xml ( $ blastfile = NULL )

Parses a BLAST XML file.

Parameters:

$blastfile

Full path to BLAST XML file

Returns:: An associative array of the parsed XML, suitable for downstream processing

Definition at line 2962 of file dbsf.module.

Referenced by dbsf_blast_result_form().

dbsf_blastall_software_pars	(	$	data,
		$	algorithm
	)

Prepares the BLAST software cmdline parameters

They will then be return to a file for parsing by the daemon

See also:: dbsf_parameter_daemon Use this as a template for plugins

Parameters:

	$data	Associative array with BLAST option key/values for parsing into a parameter string
	$algorithm	The BLAST algorithm used TODO: Integrate it into $data

Returns:: A string with all the parameters, suitable to be used with cmdline interface. FALSE on failure.

Definition at line 2835 of file dbsf.module.

Referenced by dbsf_blast_form_submit().

dbsf_check_blast ( $ software )

Checks if BLAST is setup correctly

Use this function as a template for plugins.

Parameters:

$software

The name of software to check

Returns:

TRUE if software is correctly setup. Otherwise it return a string depending what is wrong:

variables: One of the variables such as execuutable path
datasets: Not enough datasets have been linked to the software
active: It has not been activated in the main settings page

Definition at line 2247 of file dbsf.module.

References dbsf_check_software_active(), and dbsf_get_softwareprop().

Referenced by dbsf_blast_page().

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dbsf_check_software_active ( $ software )

Helper function to check if a software is active

Parameters:

$software

ID or uniquename of software to check.

Returns:: TRUE if software is active, FALSE otherwise or on failure

Definition at line 185 of file dbsf.module.

Referenced by dbsf_admin_blast_page(), dbsf_admin_ssaha2_page(), dbsf_check_blast(), dbsf_check_ssaha2(), and dbsf_software_blast_core_settings_form().

dbsf_cron ( )

Implement hook_cron()

Finds temporary files

Definition at line 1577 of file dbsf.module.

dbsf_delete_temp ( $ file = NULL )

Delete a file if older than 7 days.

Used with cron

See also:: dbsf_cron()

Parameters:

$file

File to delete

Definition at line 1599 of file dbsf.module.

dbsf_form_clear	(	$	form,
		&$	form_state
	)

This submit button will clear any form which calls it, incl. storage and values

Used as a hook_form_validate

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 1009 of file dbsf.module.

dbsf_formatdb_fastafile	(	$	infile,
		$	file_type = `'protein'`
	)

Format a FASTA file for BLAST

Parameters:

	$infile	Full path to file to format.
	$file_type	Either 'protein' or 'nucleotide'

Returns:: Returns output of formatdb, or FALSE upon failure

Definition at line 1367 of file dbsf.module.

Referenced by dbsf_batch_upload_fasta().

dbsf_get_dataset_path ( $ dataset )

Get full path to a dataset

Parameters:

$dataset

Dataset to get path for

Returns:: Full path to directory.

Definition at line 2014 of file dbsf.module.

References $dir, and icbasic_get_linked_resources().

Referenced by dbsf_admin_link_dataset_software_form_validate(), dbsf_blast_form_submit(), and dbsf_ssaha2_form_submit().

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dbsf_get_resource_roles	(	$	resource,
		$	name_as_key = `NULL`
	)

Get roles linked to a specific resource

Parameters:

	$resource	id ID or uniquename of resource to get data for
	$name_as_key	If TRUE, return array is not indexed by id but by the name of roles

Returns:: An associative array with id and name of roles. The key is controlled by $name_as_key

Definition at line 1973 of file dbsf.module.

Referenced by dbsf_admin_database_table(), and dbsf_get_user_datasets().

dbsf_get_role ( $ limit = NULL )

Get drupal roles, optionally with a limit

Parameters:

$limit

Optionally add a limit. It can be a two element array with first element to act as the column name and second as the value. or it can be a string to be added after WHERE.

Returns:: FALSE on failure or an associative array of names with role.rid as key

Definition at line 1166 of file dbsf.module.

Referenced by dbsf_admin_dataset_perms_form().

dbsf_get_sequence	(	$	uid = `NULL`,
		$	database = `NULL`
	)

Retrieve the sequence from a formatdb-ed dataset

Used when retrieving hits of BLAST reports

Parameters:

	$uid	the UID of the BLAST report, used to grab the database
	$database	Explicitly set the database to get the sequence from. It can be a string or a list array.

Returns:: HTML text of sequences in FASTA format plus a link to download a text file

Definition at line 1468 of file dbsf.module.

dbsf_get_software	(	$	limit = `NULL`,
		$	name_as_key = `NULL`
	)

Get all software

Parameters:

	$limit	Optionally add a limit. It can be an assoc. array where key is column, value is constraint or a string to append with an AND
	$name_as_key	If TRUE then return array has uniquename as the key and id as the value.

Returns:: An associative array of data with ID as key unless $name_as_key is set. FALSE on failure

Definition at line 1919 of file dbsf.module.

Referenced by dbsf_admin_database_files_table(), dbsf_admin_database_table(), and dbsf_admin_link_dataset_software_form().

dbsf_get_software_resources	(	$	limit = `NULL`,
		$	name_as_key = `FALSE`
	)

Get all resources linked for a specific software

Parameters:

	$limit	Aptionally an array or string to add a constraint. NB: The software table is aliased as s; resource as r; software_resource as sr and cvterm (linked with resource) as rcvterm
	$name_as_key	A boolean, if TRUE then return array uses names instead of IDs

Returns:: An associative array where first keys is the software id/name, second key is the resource id/name. The value is the name of the resource type.

Definition at line 1857 of file dbsf.module.

Referenced by _dbsf_generate_options(), dbsf_admin_database_table(), and dbsf_get_user_datasets().

dbsf_get_softwareprop	(	$	limit = `NULL`,
		$	name_as_key = `FALSE`
	)

Get the properties from the softwareprop table

Parameters:

	$limit	Optionally add a limit. It can be a string to be added after WHERE or an array where they keys are the column names
	$name_as_key	If TRUE, set the return array to use the software uniquename as the key

Returns:: A 3D associative array. First key is ID or name (controlled by $name_as_key); second key is the type_name and third is the rank (an integer). The value of the property is the value of the array.

Definition at line 1812 of file dbsf.module.

Referenced by dbsf_check_blast(), and dbsf_check_ssaha2().

dbsf_get_user_datasets ( $ software_name )

Get software datasets available to visitor/user

Parameters:

$software_name

Name of software to get datasets for

Returns:: FALSE on failure and a 3D associative array if successful. The array structure is like so: [dbtype][dbgroup][id] = name

Definition at line 1402 of file dbsf.module.

References $user, dbsf_get_resource_roles(), dbsf_get_software_resources(), icbasic_get_linked_resources(), and icbasic_get_resource_cvterm_and_prop().

Referenced by dbsf_blast_form(), and dbsf_ssaha2_form().

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dbsf_init ( )

TODO Foreign Keys Implements hook_init().

Definition at line 28 of file dbsf.module.

dbsf_link_unlink_resource_role	(	$	resource,
		$	role,
		$	switch = `FALSE`
	)

Link a Drupal role with a resource

Parameters:

	$resource	The ID or uniquename of the resource to link
	$role	The ID or name of the Drupal role to link
	$switch	Boolean of whether to delete instead of linking an association. TRUE deletes. Also, TOGGLE links if unlinked and deletes if linked.

Returns:: FALSE on failure, GRANTED/REVOKED on success

Definition at line 1629 of file dbsf.module.

Referenced by dbsf_admin_dataset_perms_form_submit(), and dbsf_admin_newdataset_form_submit().

dbsf_link_unlink_software_resource	(	$	software,
		$	resource,
		$	switch = `FALSE`
	)

Link a software with a specific resource

Parameters:

	$software	The ID or uniquename of the software to link
	$resource	The id or name of the resource to link
	$switch	Boolean of whether to delete instead of linking an association. TRUE deletes. Also, TOGGLE links if unlinked and deletes if linked.

Returns:: FALSE on failure, GRANTED/REVOKED on success

Definition at line 1722 of file dbsf.module.

Referenced by dbsf_admin_link_dataset_software_form_submit().

dbsf_menu ( )

Implements hook_menu().

If it finds plugin files, it adds them too.

Definition at line 62 of file dbsf.module.

References dbsf_ssaha2_menu().

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dbsf_parameter_daemon	(	$	uid,
		$	dir,
		$	par,
		$	software = `'blastall'`,
		$	other_data = `NULL`
	)

Create parameter file for daemon

Parameters:

	$uid	A unique identifier
	$dir	Directory of where to create the file
	$par	Contents to print, such as the parameters to be used by the software
	$software	Name of software used
	$other_data	A string or array with any other data which should be written. If it is an associative array, the data are printed as $key : $value

Returns:: TRUE on success..

Definition at line 1317 of file dbsf.module.

References $dir.

Referenced by dbsf_blast_batch_finished().

dbsf_perm ( )

Implements hook_perm().

Definition at line 35 of file dbsf.module.

dbsf_software_blast_core_settings_form ( $ form_state )

Implements hook_form()

See also:: dbsf_software_blast_core_settings_form_validate()
dbsf_software_blast_core_settings_form_submit()

Parameters:

$form_state

hook_form data

Definition at line 2047 of file dbsf.module.

References dbsf_check_software_active().

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dbsf_software_blast_core_settings_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_software_blast_core_settings_form_validate()
dbsf_software_blast_core_settings_form()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 2160 of file dbsf.module.

dbsf_software_blast_core_settings_form_validate	(	$	form,
		&$	form_state
	)

Implements hook_form_validate()

See also:: dbsf_software_blast_core_settings_form()
dbsf_software_blast_core_settings_form_submit()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 2113 of file dbsf.module.

dbsf_software_form ( $ form_state )

Implements of hook_form()

Used when selecting which software to make available

See also:: dbsf_software_form_submit()

Parameters:

$form_state

hook_form data

Definition at line 336 of file dbsf.module.

dbsf_software_form_submit	(	$	form,
		&$	form_state
	)

Implements hook_form_submit()

See also:: dbsf_software_form()

Parameters:

	$form	hook_form data
	$form_state	hook_form data

Definition at line 385 of file dbsf.module.

dbsf_software_select_page ( )

Produce HTML for the 'select software page'.

Menu dbsf/software

Definition at line 136 of file dbsf.module.

dbsf_theme ( )

Implement hook_theme()

Definition at line 47 of file dbsf.module.

dbsf_theme_blast_result_form ( $ form )

Themes BLAST result form

See also:: dbsf_blast_result_form()

Parameters:

$form

Form API form variable which will be themed.

Returns:: String with HTML of themed form.

Definition at line 3283 of file dbsf.module.


Functions
	dbsf_init ()
	dbsf_perm ()
	dbsf_theme ()
	dbsf_menu ()
	dbsf_software_select_page ()
	dbsf_admin_page ()
	dbsf_check_software_active ($software)
	dbsf_admin_dataset_page ()
	dbsf_admin_software_page ()
	dbsf_software_form ($form_state)
	dbsf_software_form_submit ($form, &$form_state)
	dbsf_admin_dataset_variables_form ($form_state)
	dbsf_admin_dataset_variables_form_validate ($form, &$form_state)
	dbsf_admin_dataset_variables_form_submit ($form, &$form_state)
	dbsf_admin_newdataset_form ($form_state)
	dbsf_admin_newdataset_form_validate ($form, &$form_state)
	dbsf_admin_newdataset_form_submit ($form, &$form_state)
	dbsf_admin_link_dataset_software_form ($form_state, $software=NULL)
	dbsf_admin_link_dataset_software_form_validate ($form, &$form_state)
	dbsf_admin_link_dataset_software_form_submit ($form, &$form_state)
	dbsf_admin_dataset_perms_form ($form_state)
	dbsf_admin_dataset_perms_form_submit ($form, &$form_state)
	dbsf_form_clear ($form, &$form_state)
	dbsf_admin_database_table ($software=NULL)
	dbsf_admin_database_files_table ()
	dbsf_get_role ($limit=NULL)
	_dbsf_generate_options ($software_name)
	dbsf_batch_upload_fasta ($batch_file_data, &$context)
	dbsf_batch_save_data ($data=NULL, &$context)
	dbsf_parameter_daemon ($uid, $dir, $par, $software= 'blastall', $other_data=NULL)
	dbsf_formatdb_fastafile ($infile, $file_type= 'protein')
	dbsf_get_user_datasets ($software_name)
	dbsf_get_sequence ($uid=NULL, $database=NULL)
	dbsf_cron ()
	dbsf_delete_temp ($file=NULL)
	dbsf_link_unlink_resource_role ($resource, $role, $switch=FALSE)
	dbsf_link_unlink_software_resource ($software, $resource, $switch=FALSE)
	dbsf_get_softwareprop ($limit=NULL, $name_as_key=FALSE)
	dbsf_get_software_resources ($limit=NULL, $name_as_key=FALSE)
	dbsf_get_software ($limit=NULL, $name_as_key=NULL)
	dbsf_get_resource_roles ($resource, $name_as_key=NULL)
	dbsf_get_dataset_path ($dataset)
	dbsf_software_blast_core_settings_form ($form_state)
	dbsf_software_blast_core_settings_form_validate ($form, &$form_state)
	dbsf_software_blast_core_settings_form_submit ($form, &$form_state)
	dbsf_admin_blast_page ()
	dbsf_check_blast ($software)
	dbsf_blast_page ($sample_data=FALSE)
	dbsf_blast_form ($form_state, $sample_data=FALSE)
	dbsf_blast_form_validate ($form, &$form_state)
	dbsf_blast_form_submit ($form, &$form_state)
	dbsf_blastall_software_pars ($data, $algorithm)
	dbsf_blast_batch_finished ($success, $results, $operations)
	dbsf_blast_result_xml ($blastfile=NULL)
	dbsf_blast_result_page ($submission_uid=NULL)
	dbsf_blast_result_form ($form_state, $uid, $blastfile)
	dbsf_theme_blast_result_form ($form)

icsearch/dbsf.module File Reference

Functions

Detailed Description

Function Documentation