Connecting to NCBI: Eutils

The Eutils resource classes (located in includes/resources) are for connecting to the NCBI repository. Not all databses are supported by the ESearch API: we therefore use the Eutils class to provide the correct service.

group resources

Some explanation.

Functions

__construct ($create_linked_records=TRUE, $job=NULL)

EUtils constructor.

Parameters

  • $create_linked_records – Records referenced in the XML will spawn new EUtils to import if true.

  • $job – Tripal Job object.

checkResponseSuccess ($response, string $db, string $accession)

Checks that the resource was found.

Parameters

  • $response – Response object.

  • $db – NCBI db string.

  • $accession – Accession.

Throws

convertAccessionsToUID (string $db, string $accession)

Checks the accession and converts to uid accession if neccesary.

Parameters

  • $db –

  • $accession – The accession for the NCBI record.

Throws

Returns

bool|string

get ($db, $accession)

Queries and parses an NCBI record.

Parameters

  • $db – NCBI database.

  • $accession – Numeric only accession.

Throws

Returns

mixed Chado object record.

getAccessionField ($db)
getResourceProvider ($db)

Returns the appropriate NCBI query method given the database.

Parameters

$db – NCBI database.

Throws

Returns

|| NCBI DB query object.

setPreview ($preview=TRUE)

Sets the object to not insert, but only preview the XML.

Parameters

$preview – TRUE will set to preview mode, FALSE unsets.

Variables

$create_linked_records
$job
$preview   = FALSE
static static $visited   = []
class BiosamplePropertyLookup

Fetch the published biosample attributes to feed our property list.

Public Functions

lookupAll (string $url=NULL)

Looks up all attributes.

Parameters

$url – Optional URL string to lookup.

Returns

array Array of terms keyed by harmonized (machine name) with human readable label and definition.

class EFetch : public EUtilsRequest

Https://www.ncbi.nlm.nih.gov/books/NBK25499/ NCBI Efetch docs.

Public Functions

__construct (string $db)

EFetch constructor.

Parameters

$db – NCBI database string.

Throws

class EFTP

Right now responsible for getting a single value from the Assembly.

Public Functions

getField (string $field)

Find all records of line starting with a specific item.

Parameters

$field – The field is the substring to look for at the start of a line.

Returns

array

setURL ($url)

Get the contents of a file at a given URL.

Parameters

$url – The FTP URL.

Throws

class ESearch : public EUtilsRequest

Queries the EUtils esearch API.

Public Functions

__construct (string $db)

ESearch constructor.

Parameters

$db –

Throws

class ESummary : public EUtilsRequest

Queries the NCBI ESummary API.

Public Functions

__construct ($db)

ESummary constructor.

Parameters

$db –

Throws

class EUtils

Factory class which returns the appropriate NCBI resource provider.

Public Functions

__construct ($create_linked_records=TRUE, $job=NULL)

EUtils constructor.

Parameters

  • $create_linked_records – Records referenced in the XML will spawn new EUtils to import if true.

  • $job – Tripal Job object.

convertAccessionsToUID (string $db, string $accession)

Checks the accession and converts to uid accession if neccesary.

Parameters

  • $db –

  • $accession – The accession for the NCBI record.

Throws

Returns

bool|string

get ($db, $accession)

Queries and parses an NCBI record.

Parameters

  • $db – NCBI database.

  • $accession – Numeric only accession.

Throws

Returns

mixed Chado object record.

setPreview ($preview=TRUE)

Sets the object to not insert, but only preview the XML.

Parameters

$preview – TRUE will set to preview mode, FALSE unsets.

class EUtilsRequest

Builds and executes the API request to NCBI.

Subclassed by EFetch, ESearch, ESummary

Public Functions

addHeader ($key, $value)
Parameters

  • $key –

  • $value –

Returns

$this

addHeaders ($headers)
Parameters

$headers –

Returns

$this

addParam ($key, $value)

Add a single parameter.

Parameters

  • $key –

  • $value –

Returns

$this

addParams ($params)

Add an array of parameters.

Parameters

$params –

Returns

$this

get ($url='')

Send a GET request.

Parameters

$url –

Returns

post ($url='')

Send a POST request.

Parameters

$url –

Returns

setBaseURL ($url)
Parameters

$url –

Returns

$this

class EUtilsResource

Interacts with a response from the EUtils API.

Public Functions

__construct ($response)

EUtilsResource constructor.

See also

drupal_http_request()

Parameters

$response – The object returned by drupal_http_request()

dom()

Parse response into DOMDocument.

Returns

The response as DOMDocument.

errorMessage()

Get the error message.

Returns

string|null The message or null if none exist.

hasError()

Find and set errors.

Returns

bool Whether the response has an error element.

headers()

Get an array of response headers.

Returns

array

isSuccessful()

Check if the request is successful.

Returns

bool TRUE for success.

originalBody()

Get raw body response.

Returns

string The raw body response string.

originalResponseObject()

Get the response object.

Returns

object The original response object.

status()

Get the response status code.

Returns

int Status code.

xml()

Parse response into XML.

Returns

The response in XML.