icsearch/icbasic.module File Reference

Go to the source code of this file.

Functions
	icbasic_init ()
	icbasic_encode ($variable)
	icbasic_decode ($encoded)
	icbasic_array2csv ($array=NULL, $quote=NULL, $separator= ',', $key=FALSE)
	icbasic_db_execute ($db=NULL, $function=NULL, $variables=NULL)
	icbasic_validate_ic_id ($accession=NULL)
	icbasic_validate_seq_dna ($seq=NULL)
	icbasic_validate_seq_protein ($seq=NULL)
	icbasic_chadoapi_get_single_table ($table=NULL, $field= 'uniquename', $value=NULL)
	icbasic_checkboxes_results2array ($results)
	icbasic_add_cv ($cv, $cvterm_array)
	icbasic_populate_prop ($table_type, $object_name, $cvterm_id, $property_array)
	icbasic_populate_cvterms ($table_type, $object_name, $cvname, $cvterm_array)
	icbasic_get_add_cv_withnames ($cv_name, $cvterm_name=NULL, $name_as_key=FALSE)
	icbasic_get_add_dbxref_withnames ($dbname, $accession)
	icbasic_clear_session ($var=NULL)
	icbasic_create_uid ($sessionid=NULL, $timestamp=NULL, $string=NULL)
	icbasic_get_resource_name_id ($resource, $name_as_key=FALSE)
	icbasic_get_add_resource ($type_name, $data=NULL, $add=FALSE, $name_as_key=FALSE)
	icbasic_get_resource_cvterm_and_prop ($resource)
	icbasic_link_unlink_resources ($subject, $rel, $object=NULL, $replace=FALSE)
	icbasic_get_linked_resources ($resource, $relationship_name=NULL, $name_as_key=FALSE, $limit=NULL)
	icbasic_write_fastafile ($infile=NULL, $outfile=NULL, $delete=NULL)

---

Detailed Description

Basic functions for InsectaCentral

Developed by Alexie Papanicolaou

See also:

http://insectacentral.org

TODO: List of things to do/consider

• convert resource uniquename to name; create uidx (name,type_id)
• consider some kind of write-protect in these get_add routines
• Add foreign keys like comca db_query('ALTER TABLE {ic_resource} ADD CONSTRAINT ic_resource_dbxref_id_fkey FOREIGN KEY (dbxref_id) REFERENCES {ic_dbxref} (dbxref_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED');

Definition in file icbasic.module.

---

Function Documentation

icbasic_add_cv	(	$	cv,
		$	cvterm_array
	)

Populate a CV table using a CV name and a list of CVTERMS

Parameters:

	$cv	Name of CV
	$cvterm_array	A list array of cvterm names to add

Returns:

FALSE on failure, the (int) cv_id on success

Definition at line 360 of file icbasic.module.

Referenced by dbsf_install(), and icbasic_populate_cvterms().

icbasic_array2csv	(	$	array = NULL,
		$	quote = NULL,
		$	separator = ',',
		$	key = FALSE
	)

Convert an array to a quoted string, suitable for SQL queries

Essentially implode() with bells and whistles

See also:

implode()

Parameters:

	$array	a list array of elements to ocnvert to a comma delimited string
	$quote	give TRUE to include quotes around element or pass any string to include left and right of element
	$separator	character to separate elements in list
	$key	Boolean, if true then return the keys of the $array.

Returns:

A String of comma delimited values, optionally quoted.

Definition at line 90 of file icbasic.module.

icbasic_chadoapi_get_single_table	(	$	table = NULL,
		$	field = 'uniquename',
		$	value = NULL
	)

Definition at line 313 of file icbasic.module.

icbasic_checkboxes_results2array

(

$

results

)

Cleans and decomposes a checkbox FAPI result array

Parameters:

$results

FAPI Checkboxes result as an associative array

Returns:

A list array of results

Definition at line 333 of file icbasic.module.

icbasic_clear_session

(

$

var = NULL

)

Clear all or part of $_SESSION

Parameters:

$var

A string or a list array of $_SESSION parameter names(s) to empty. If no $var is provided, then the whole of $_SESSION is emptied (use with care)

Definition at line 674 of file icbasic.module.

icbasic_create_uid	(	$	sessionid = NULL,
		$	timestamp = NULL,
		$	string = NULL
	)

Create a Unique Identifier using SESSIONID, time and, optionally, a string

Uses the md5 algorithm to generate a hexadecimal unique identifier.

See also:

session_id()

time()

md5()

Parameters:

	$sessionid	the session id to include in the calculation. If empty, it is retrieved.
	$timestamp	Unix timestamp (integer) to include in md5 calculation. If empty, it's retrieved.
	$string	Optionally, add a string to the md5 calculation. This allows you to generate multiple UIDs with the same timestamp.

Returns:

A 32 letter long hexadecimal string. e.g. d0bfa38422474be81a716e3dbe7ad21e

Definition at line 712 of file icbasic.module.

Referenced by dbsf_blast_form_submit(), and dbsf_ssaha2_form_submit().

icbasic_db_execute	(	$	db = NULL,
		$	function = NULL,
		$	variables = NULL
	)

Seamlessly execute a connection to an non-drupal database

Parameters:

	$db	Name of database to connect to as in settings.php
	$function	Function to execute to $db
	$variables	variables to pass to above function

Returns:

array of results or if none expected FALSE/TRUE on failure/success respectively

Definition at line 137 of file icbasic.module.

icbasic_decode

(

$

encoded

)

Decodes icbasic_encode function

See also:

icbasic_encode()

Parameters:

$encoded

Variable to be decoded

Returns:

Decoded and unserialized variable

Definition at line 64 of file icbasic.module.

icbasic_encode

(

$

variable

)

Encodes a variable using base64,serialize and gzcompress

Allows encoding of more than 2000 characters (IE6 problem)

See also:

icbasic_decode()

Parameters:

$variable

Variable to be encoded

Returns:

Encoded variable as a serialized string

Definition at line 46 of file icbasic.module.

icbasic_get_add_cv_withnames	(	$	cv_name,
		$	cvterm_name = NULL,
		$	name_as_key = FALSE
	)

Get cvterm_id for a CV, add it first if it does not exist.

Also if cvterm_name is not given, it will return all cvterm_id/cvterm_names for the CV. $name_as_key controls the return array

Parameters:

	$cv_name	The name of the CV to which the cvterm belong.
	$cvterm_name	The name of the cvterm to look for or add. Not needed if just want to retrieve all cvterms
	$name_as_key	TRUE, FALSE or BOTH. False gives cvterm_id as key to return array; TRUE gives name with ID as value; BOTH gives name both as key and value (useful for FAPI)

Returns:

FALSE on failure. If cvterm has been provided, then an integer of the cvterm_id is returned. If no cvterm, then return is an associative array where keys are controlled by $name_as_key.

Definition at line 543 of file icbasic.module.

Referenced by dbsf_add_software_blast(), dbsf_add_software_ssaha2(), dbsf_admin_newdataset_form(), icbasic_get_add_resource(), icbasic_get_linked_resources(), and icbasic_link_unlink_resources().

icbasic_get_add_dbxref_withnames	(	$	dbname,
		$	accession
	)

Get dbxref_id for a dbxref; add it first if it doesn't exist

Parameters:

	$dbname	Name of db to link dbxref
	$accession	Accession/uniquename for dbxref to get and/or add.

Returns:

FALSE on failure or an integer with the dbxref_id on success.

Definition at line 623 of file icbasic.module.

Referenced by dbsf_add_software_blast(), dbsf_add_software_ssaha2(), and icbasic_get_add_resource().

icbasic_get_add_resource	(	$	type_name,
		$	data = NULL,
		$	add = FALSE,
		$	name_as_key = FALSE
	)

Get a list of resources, replace or add a new one

Parameters:

	$type_name	Name of the cvterm which defines the resource type
	$data	(optional) An assoc. array to limit SELECT queries: the keys are used as column and values as the condition. Further, when adding/replacing, $data has to contain keys with 'uniquename' and 'dbxref_name'
	$add	Switch which can be FALSE/NULL, ADD, DELETE or REPLACE
	$name_as_key	A boolean. If TRUE the return array has uniquename as keys and resource_id as values.

Returns:

An associative array with resource_id as the keys and uniquename as values. Or FALSE on failure.

Definition at line 778 of file icbasic.module.

References icbasic_get_add_cv_withnames(), and icbasic_get_add_dbxref_withnames().

Referenced by dbsf_admin_database_files_table(), dbsf_admin_database_table(), dbsf_admin_dataset_perms_form(), dbsf_admin_dataset_variables_form_submit(), dbsf_admin_link_dataset_software_form(), dbsf_admin_newdataset_form(), dbsf_admin_newdataset_form_submit(), and dbsf_admin_newdataset_form_validate().

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icbasic_get_linked_resources	(	$	resource,
		$	relationship_name = NULL,
		$	name_as_key = FALSE,
		$	limit = NULL
	)

Get all object resources stored in the resource_resource table

Parameters:

	$resource	id ID or uniquename of subject resource
	$relationship_name	Optionally delimit by relationship type by providing the type name
	$name_as_key	A boolean, if TRUE then the return array has uniquename as key
	$limit	A string. Optionally pass a string to add as LIMIT to the query.

Returns:

A 2D associative array with primary key the object_id and secondary the column names object_type,object_name for each object resource

Definition at line 1028 of file icbasic.module.

References icbasic_get_add_cv_withnames().

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

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icbasic_get_resource_cvterm_and_prop

(

$

resource

)

Get cvterms and properties for a resource

Parameters:

$resource

ID or name of resource to get cvterms and properties for.

Returns:

An associative array where the primary key is 'cvterm' and 'prop' for cvterms and properties respectively. 'cvterm' is has cvterm.names in a list array foreach cv_name. 'prop' does likewise for values of each cvterm.name

Definition at line 872 of file icbasic.module.

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

icbasic_get_resource_name_id	(	$	resource,
		$	name_as_key = FALSE
	)

Get 1+ resource names/IDs by providing 1+ resource IDs/names

Parameters:

	$resource	A string or list array of IDs or uniquename of resources to fetch
	$name_as_key	A boolean, if true then the key of the returned array is the uniquename.

Returns:

An associative array with the ID and uniquename of each resource The key is the ID unless $name_as_key is set.

Definition at line 736 of file icbasic.module.

icbasic_init

(

)

Implements of hook_init

Definition at line 27 of file icbasic.module.

icbasic_link_unlink_resources	(	$	subject,
		$	rel,
		$	object = NULL,
		$	replace = FALSE
	)

Link two resources with a relationship

Parameters:

	$subject	The resource_ID or uniquename of the subject of the relationship
	$rel	The name of a relationship such as 'part_of' or 'uses'
	$object	The resource_ID or uniquename object of the relationship
	$replace	Whether to fail if an existing relationship exists (FALSE), replace it (TRUE) or simply delete it ('DELETE'). If $object is NULL and $replace is DELETE then all relationships $rel for $subject are removed.

Returns:

TRUE on success.

Definition at line 923 of file icbasic.module.

References icbasic_get_add_cv_withnames().

Referenced by dbsf_admin_newdataset_form_submit().

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icbasic_populate_cvterms	(	$	table_type,
		$	object_name,
		$	cvname,
		$	cvterm_array
	)

Populate a _cvterm Chado table

Parameters:

	$table_type	Type of table linked to teh _cvterm table Currently, only feature and resource table sets are supported
	$object_name	Name of reference feature/resourc
	$cvname	Name of CV to which the cvterms belong to

See also:

icbasic_add_cv()

Parameters:

$cvterm_array

A list array of cvterms to add to the _cvterm table

See also:

icbasic_add_cv()

Returns:

FALSE on failure, TRUE on success

Definition at line 474 of file icbasic.module.

References icbasic_add_cv().

Referenced by dbsf_add_software_blast(), dbsf_add_software_ssaha2(), and dbsf_admin_newdataset_form_submit().

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icbasic_populate_prop	(	$	table_type,
		$	object_name,
		$	cvterm_id,
		$	property_array
	)

Populate a IC Chado property table

Parameters:

	$table_type	Type of table linked to the -prop table. Currently only feature and resource are allowed
	$object_name	Name of reference feature/resource
	$cvterm_id	CV term ID used to link the property
	$property_array	An array of property values to insert with the above cvterm and reference

Returns:

FALSE on failure, TRUE on success

Definition at line 404 of file icbasic.module.

Referenced by dbsf_add_software_blast(), and dbsf_add_software_ssaha2().

icbasic_validate_ic_id

(

$

accession = NULL

)

Validate and InsectaCentral accession ID.

Parameters:

$accession

ID to validate

Returns:

Returns correct/cleaned part of accession or FALSE on failure

Definition at line 184 of file icbasic.module.

icbasic_validate_seq_dna

(

$

seq = NULL

)

Validate that a sequence is with IUPAC DNA alphabet only

Xs are allowed

See also:

icbasic_validate_seq_protein()

Parameters:

$seq

string of sequence to validate

Returns:

Cleaned sequence or (int) number of errors detected (or FLASE on failure)

Definition at line 209 of file icbasic.module.

Referenced by dbsf_blast_form_validate(), and dbsf_ssaha2_form_validate().

icbasic_validate_seq_protein

(

$

seq = NULL

)

Validate a protein sequence using IUPAC amino acids

Xs are allowed

See also:

icbasic_validate_seq_dna()

Parameters:

$seq

Sequence string to validate

Returns:

Returns cleaned string or number of errors found (or FALSE on failure)

Definition at line 266 of file icbasic.module.

Referenced by dbsf_blast_form_validate().

icbasic_write_fastafile	(	$	infile = NULL,
		$	outfile = NULL,
		$	delete = NULL
	)

Write a FASTA file to a destination

Used when uploading from a form

Parameters:

	$infile	Full path to input file, e.g. one uploaded into temp dir /tmp/temp.txt
	$outfile	Desired destination (including filename) for FASTA file.
	$delete	A boolean of whether to delete the input file after transfer.

Returns:

TRUE on success

Definition at line 1089 of file icbasic.module.

Referenced by dbsf_batch_upload_fasta().