Public Member Functions | |
| formSubmit (array $form, \Drupal\Core\Form\FormStateInterface &$form_state) | |
| form_submit (array $form, \Drupal\Core\Form\FormStateInterface $form_state, array &$criteria) | |
| form (array $form, \Drupal\Core\Form\FormStateInterface &$form_state) | |
| formValidate (array $form, \Drupal\Core\Form\FormStateInterface &$form_state) | |
| run (array $query) | |
| retrieve (array $query, int $limit=10, int $page=0) | |
| remoteSearchPMID ($search_array, $num_to_retrieve, $page, $row_mode=1) | |
| parse_xml (string $pub_xml) | |
 Public Member Functions inherited from Drupal\tripal\TripalPubLibrary\TripalPubLibraryBase | |
| __construct (array $configuration, $plugin_id, $plugin_definition, Connection $public, \Drupal\tripal\Services\TripalLogger $logger, \Drupal\tripal\Services\TripalCitationManager $citation_manager, TripalFileRetriever $fileretriever) | |
Protected Attributes | |
| array | $webquery = [] |
| array | $retrieval_options |
| Protected Attributes inherited from Drupal\tripal\TripalPubLibrary\TripalPubLibraryBase | |
| $public | |
| $logger | |
| $fileretriever = NULL | |
| $citation_manager = NULL | |
| $plugin_id | |
| $plugin_definition | |
Additional Inherited Members | |
| Static Public Member Functions inherited from Drupal\tripal\TripalPubLibrary\TripalPubLibraryBase | |
| static | create (ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition) |
| Protected Member Functions inherited from Drupal\tripal\TripalPubLibrary\TripalPubLibraryBase | |
| xmlIsValid (string $xml) | |
Member Function Documentation
◆ form()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::form | ( | array | $form, |
| \Drupal\Core\Form\FormStateInterface & | $form_state | ||
| ) |
Adds plugin specific form items and returns the $form array
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
◆ form_submit()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::form_submit | ( | array | $form, |
| \Drupal\Core\Form\FormStateInterface | $form_state, | ||
| array & | $criteria | ||
| ) |
Plugin specific form submit to add form values to the criteria array. The criteria array eventually gets serialized and stored in the tripal_pub_import database table. (This code gets called from ChadoNewPublicationForm)
◆ formSubmit()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::formSubmit | ( | array | $form, |
| \Drupal\Core\Form\FormStateInterface & | $form_state | ||
| ) |
Handles submission of the form elements.
The form elements provided in the implementation of the form() function can be used for special submit if needed.
- Parameters
-
array $form The form array definition. \Drupal\Core\Form\FormStateInterface $form_state The form state object.
- Returns
- void
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
◆ formValidate()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::formValidate | ( | array | $form, |
| \Drupal\Core\Form\FormStateInterface & | $form_state | ||
| ) |
- See also
- TripalImporter::formValidate()
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
◆ parse_xml()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::parse_xml | ( | string | $pub_xml | ) |
This function parses the XML containing details of a publication and converts it into an associative array of where keys are Tripal Pub ontology terms and the values are extracted from the XML. The XML should contain only a single publication record.
Information about the valid elements in the PubMed XML can be found here: https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html
Information about PubMed's citation format can be found here https://www.nlm.nih.gov/bsd/policy/cit_format.html
- Parameters
-
string $pub_xml An XML string describing a single publication
- Returns
- array An array describing the publication
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
◆ remoteSearchPMID()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::remoteSearchPMID | ( | $search_array, | |
| $num_to_retrieve, | |||
| $page, | |||
$row_mode = 1 |
|||
| ) |
A function for performing the search on the PubMed database.
- Parameters
-
$search_array An array containing the search criteria for the search $num_to_retrieve Indicates the maximum number of publications to retrieve from the remote database $page Indicates the page to retrieve. This corresponds to a paged table, where each page has $num_to_retrieve publications.
- Returns
- array|NULL
- 'total_records' = The number of records available for retrieval
- 'skipped_records' = The number of records where download failed
- 'search_str' = The query string used for the search
- 'pubs' = The uniform publication information array. or NULL if query failed and an exception was caught
◆ retrieve()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::retrieve | ( | array | $query, |
| int | $limit = 10, |
||
| int | $page = 0 |
||
| ) |
More documentation can be found in TripalPubLibraryInterface
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
◆ run()
| Drupal\tripal\Plugin\TripalPubLibrary\TripalPubLibraryPubMed::run | ( | array | $query | ) |
Retrieves one or more publications from PubMed based on a search query specification
- Parameters
-
array $query An associative array defining a publication query, specifying the database and query parameters for a particular publication repository.
- Returns
- array|NULL
- 'total_records' = The number of records available for retrieval
- 'skipped_records' = The number of records where download failed
- 'search_str' = The query string used for the search
- 'pubs' = The uniform publication information array. or NULL if query failed and an exception was caught
Implements Drupal\tripal\TripalPubLibrary\Interfaces\TripalPubLibraryInterface.
Member Data Documentation
◆ $retrieval_options
|
protected |
◆ $webquery
|
protected |
Stores information of an initialized search. Array keys are 'Count', 'WebEnv', and 'QueryKey' with values as returned by PubMed's esearch utility
The documentation for this class was generated from the following file:
- tripal/src/Plugin/TripalPubLibrary/TripalPubLibraryPubMed.php
