Formatters¶
Formatters take the output from an XML parser and return a Drupal-form friendly array. Typically a formatter will return a table each for:
The base Chado record
Properties
DBXrefs
New Chado records created and linked, including organisms, contacts, projects, analyses, etc
EUtilsFormatter¶
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class EUtilsFormatter¶
Subclassed by EUtilsAssemblyFormatter, EUtilsBioProjectFormatter, EUtilsBioSampleFormatter
Public Functions
- format (array $data)
Format a parser’s output.
- Parameters
$data – The data array returned by a parser.
- Returns
array This function does not return anything. It directly manipulates the elements array.
- getDbLink (string $accession, string $db)
Generates a URL link given a db string and accession.
- Parameters
$accession – Accession string.
$db – Database lookup string.
- Returns
mixed returns either the accession string, or the accession with a link to the xref.
- getNCBIDB (string $db_name)
Fetch the DB object for an NCBI DB.
- Parameters
$db_name – The DB name as passed by the parser.
- Returns
bool Returns a database object or FALSE.
EUtilsFormatterFactory¶
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class EUtilsFormatterFactory : public EUtilsFactoryInterface¶
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Creates a formatter given the db.
Public Functions
- get (string $db)
- Parameters
$db – The database name.
- Throws
- Returns
The formatter for the given DB.
EUtilsAssemblyFormatter¶
-
class EUtilsAssemblyFormatter : public EUtilsFormatter¶
Parse EUtilsAssemblyParser output for display on a form.
Public Functions
- format (array $data)
Add the formatted data into a table.
- Parameters
$data – The parsed XML data.
- Returns
array Drupal form elements array of each section in a fieldset.
EUtilsBioProjectFormatter¶
-
class EUtilsBioProjectFormatter : public EUtilsFormatter¶
Class EutilsBioProject Formatter.
Public Functions
- format (array $data)
Add the formatted data into a table.
- Parameters
$data – The parsed XML data.
- Returns
array Drupal form elements array of each section in a fieldset.
EUtilsBioSampleFormatter¶
-
class EUtilsBioSampleFormatter : public EUtilsFormatter¶
Class EUtilsBioSampleFormatter.
Public Functions
- format (array $data)
Add the formatted data into a table.
- Parameters
$data – The parsed XML data.
- Returns
array Drupal form elements array of each section in a fieldset.
EUtilsPubmedFormatter¶
Pubmed records are not directly imported via this module, as this functionality is already provided via Tripal core.