XML Parsers¶
XML parsers take the response from the EUtils resources and extract information from the returned XML.
EUtilsXMLParserFactory¶
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class EUtilsXMLParserFactory : public EUtilsFactoryInterface¶
Class EUtilsXMLParserFactory.
This is the base EUTILS XML parser class. The plan is to extend this base class to be specific for each DB type.
Public Functions
- get (string $db)
Get the appropriate XML parser.
- Parameters
$db – The name of the DB.
- Throws
- Returns
EUtilsAssemblyParser¶
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class EUtilsAssemblyParser : public EUtilsParserInterface¶
Parser for NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/ XML.
Public Functions
- getFTPData ($url)
Get the fields the assembly object will need from the FTP.
- Parameters
$url –
the ftp site url extracted form the metadata
- Returns
array
- parse (SimpleXMLElement $xml)
- Parameters
$xml –
- Returns
array
- parseMeta ($x)
Parse the <Meta> tag, which containts CDATA but all of the Assembly props.
- Parameters
$x –
- Returns
array
EUtilsBioProjectParser¶
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class EUtilsBioProjectParser : public EUtilsParserInterface¶
Class EUtilsBioProjectParser.
Note that projects don’t have reliable attribute listings.
Public Functions
- bioProjectSubmission (SimpleXMLElement $xml)
- Parameters
$xml –
- Returns
array
- parse (SimpleXMLElement $xml)
Parse an NCBI BioProject XML.
- Parameters
$xml – Simple XML Element.
- Throws
- Returns
array|mixed Array.
EUtilsBioSampleParser¶
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class EUtilsBioSampleParser : public EUtilsParserInterface¶
Parses BioSample XML.
Public Functions
- parse (SimpleXMLElement $xml)
Parse the XML into an array.
- Parameters
$xml –
- Throws
- Returns
array An array of parsed data
EUtilsPubmedParser¶
Pubmed records are parsed via the Tripal Core API.
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class EUtilsPubmedParser : public EUtilsParserInterface¶
Class EUtilsPubmedParser.
Public Functions
- parse (SimpleXMLElement $xml)
Parse an NCBI Pubmed XML. Uses the core parser code.
- Parameters
$xml – Simple XML Element.
- Throws
- Returns
array|mixed Array.