Publication Module
Integrates the Chado Publication module with Drupal Nodes & Views, as well as, provides the ability to import publication from PubMed
The Tripal Publication module allows you to search the PubMed database for academic articles, that relate to user specified topic\s. As well, it allows management of publications so that a user can enter specified details regarding a desired publication. This allows all of the important information that is unique to a Academic Publication to be stored for access.
File
- tripal_pub/
tripal_pub.module, line 20 - Basic functionality of the pub module
Functions
Name |
Location | Description |
|---|---|---|
| chado_pub_delete |
tripal_pub/ |
Implements hook_delete(). |
| chado_pub_form |
tripal_pub/ |
Implements hook_form(). |
| chado_pub_insert |
tripal_pub/ |
Implements hook_insert(). |
| chado_pub_load |
tripal_pub/ |
Implements hook_load(). |
| chado_pub_update |
tripal_pub/ |
Implements hook_update(). |
| chado_pub_validate |
tripal_pub/ |
Implements hook_validate(). |
| chado_pub_validate_check_duplicate |
tripal_pub/ |
Check for duplicate publications. To be called from hook_validate(). Sets the form error if a duplicate |
| chado_pub_validate_check_uniquename |
tripal_pub/ |
Validate the publication uniquename. To be called from hook_validate(). |
| theme_tripal_pub_importer_setup_form_elements |
tripal_pub/ |
Theme the tripal_pub_importer_setup_form form. |
| theme_tripal_pub_search_setup_form_elements |
tripal_pub/ |
Theme the tripal_pub_search_setup_form form |
| tripal_execute_active_pub_importers |
tripal_pub/ |
Imports all publications for all active import setups. |
| tripal_execute_pub_importer |
tripal_pub/ |
Imports all publications for a given publication import setup. |
| tripal_feature_add_cvs |
tripal_feature/ |
Add cvs related to publications |
| tripal_get_remote_pub |
tripal_pub/ |
This function is used to perfom a query using one of the supported databases and return the raw query results. This may be XML or some other format as provided by the database. |
| tripal_get_remote_pubs |
tripal_pub/ |
Retrieves a list of publications as an associated array where keys correspond directly with Tripal Pub CV terms. |
| tripal_import_pub_by_dbxref |
tripal_pub/ |
Imports a singe publication specified by a remote database cross reference. |
| tripal_pubs_search_form_ajax_update |
tripal_pub/ |
Ajax callback to update the form |
| tripal_pubs_setup_form_ajax_update |
tripal_pub/ |
AJAX callback for updating the form. |
| tripal_pub_add_authors |
tripal_pub/ |
Add one or more authors to a publication |
| tripal_pub_add_custom_tables |
tripal_pub/ |
Add custom table related to publications |
| tripal_pub_add_cvs |
tripal_pub/ |
Add cvs related to publications |
| tripal_pub_add_cvterms |
tripal_pub/ |
Add cvterms related to publications |
| tripal_pub_add_publication |
tripal_pub/ |
Adds a new publication to the Chado, along with all properties and database cross-references. If the publication does not already exist in Chado then it is added. If it does exist nothing is done. If the $update parameter is TRUE then the… |
| tripal_pub_add_publications |
tripal_pub/ |
Adds publications that have been retrieved from a remote database and consolidated into an array of details. |
| tripal_pub_admin |
tripal_pub/ |
Administrative settings form |
| tripal_pub_admin_pub_view |
tripal_pub/ |
Admin launchpad |
| tripal_pub_admin_validate |
tripal_pub/ |
Validate the admin settings form |
| tripal_pub_AGL_count |
tripal_pub/ |
Retreives the total number of publications that match the search string. |
| tripal_pub_AGL_parse_pubxml |
tripal_pub/ |
Parse publication XML for a single publication |
| tripal_pub_AGL_range |
tripal_pub/ |
Retreives a range of publications from AGL. |
| tripal_pub_citation_form |
tripal_pub/ |
The admin form for submitting job to create citations |
| tripal_pub_citation_form_submit |
tripal_pub/ |
Submit form. Create Tripal job for citations |
| tripal_pub_create_citation |
tripal_pub/ |
This function generates citations for publications. It requires an array structure with keys being the terms in the Tripal publication ontology. This function is intended to be used for any function that needs to generate a citation. |
| tripal_pub_create_citations |
tripal_pub/ |
Launch the Tripal job to generate citations. Called by tripal jobs |
| tripal_pub_defaultview_admin_publications |
tripal_pub/ |
Default publication administration view |
| tripal_pub_disable |
tripal_pub/ |
Implements hook_disable(). Disable default views when module is disabled |
| tripal_pub_enable |
tripal_pub/ |
Implements hook_enable(). |
| tripal_pub_form_alter |
tripal_pub/ |
Implementation of hook_form_alter(). |
| tripal_pub_get_publication_array |
tripal_pub/ |
This function generates an array suitable for use with the tripal_pub_create_citation function for any publication already stored in the Chado tables. |
| tripal_pub_help |
tripal_pub/ |
Implements hook_help(). Adds a help page to the module list |
| tripal_pub_importers_list |
tripal_pub/ |
A function to generate a table containing the list of publication importers |
| tripal_pub_importer_setup_add_criteria_fields |
tripal_pub/ |
A helper function for the importer setup form that adds the criteria to the form that belong to the importer. |
| tripal_pub_importer_setup_form |
tripal_pub/ |
The form used for creating publication importers. |
| tripal_pub_importer_setup_form_submit |
tripal_pub/ |
Submit the tripal_pub_importer_setup_form form |
| tripal_pub_importer_setup_form_validate |
tripal_pub/ |
Validate the tripal_pub_importer_setup_form form |
| tripal_pub_importer_setup_page |
tripal_pub/ |
Creates the page that contains the publication importer setup form and test results. |
| tripal_pub_importer_submit_job |
tripal_pub/ |
Add a job to import publications |
| tripal_pub_install |
tripal_pub/ |
Implementation of hook_install(). |
| tripal_pub_job_describe_args |
tripal_pub/ |
Implements hook_job_describe_args(). |
| tripal_pub_mail |
tripal_pub/ |
Implements hook_mail(). |
| tripal_pub_menu |
tripal_pub/ |
Implements hook_menu(). |
| tripal_pub_node_access |
tripal_pub/ |
Implement hook_node_access(). |
| tripal_pub_node_info |
tripal_pub/ |
Implements hook_node_info(). |
| tripal_pub_node_insert |
tripal_pub/ |
Implements hook_node_insert(). Acts on all content types. |
| tripal_pub_node_load |
tripal_pub/ |
Implements hook_node_load(). Acts on all content types. |
| tripal_pub_node_presave |
tripal_pub/ |
Implements hook_node_presave(). Acts on all content types. |
| tripal_pub_node_update |
tripal_pub/ |
Implements hook_node_update(). Acts on all content types. |
| tripal_pub_node_view |
tripal_pub/ |
Implements hook_node_view(). Acts on all content types. |
| tripal_pub_permission |
tripal_pub/ |
Implement hook_permission(). |
| tripal_pub_PMID_fetch |
tripal_pub/ |
Retreives from PubMed a set of publications from the previously initiated query. |
| tripal_pub_PMID_parse_abstract |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about the abstract |
| tripal_pub_PMID_parse_article |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about an article. |
| tripal_pub_PMID_parse_authorlist |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about the author list for a publication |
| tripal_pub_PMID_parse_date |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information regarding to dates |
| tripal_pub_PMID_parse_journal |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about a journal |
| tripal_pub_PMID_parse_journal_issue |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about a journal issue |
| tripal_pub_PMID_parse_medline_journal_info |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about the Journal |
| tripal_pub_PMID_parse_pagination |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about pagination |
| tripal_pub_PMID_parse_publication_type |
tripal_pub/ |
Parses the section from the XML returned from PubMed that contains information about a publication |
| tripal_pub_PMID_parse_pubxml |
tripal_pub/ |
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. |
| tripal_pub_PMID_search_init |
tripal_pub/ |
Initailizes a PubMed Search using a given search string |
| tripal_pub_preprocess_tripal_pub_relationships |
tripal_pub/ |
|
| tripal_pub_remote_alter_form_AGL |
tripal_pub/ |
A hook for altering the publication importer form. |
| tripal_pub_remote_alter_form_PMID |
tripal_pub/ |
A hook for altering the publication importer form. It Changes the 'Abstract' filter to be 'Abstract/Title'. |
| tripal_pub_remote_search_AGL |
tripal_pub/ |
A hook for performing the search on the AGL database. |
| tripal_pub_remote_search_AGL_get_author |
tripal_pub/ |
Used for parsing of the XML results to get details about an author |
| tripal_pub_remote_search_AGL_get_subfield |
tripal_pub/ |
Used for parsing of the XML results to get a set of subfields |
| tripal_pub_remote_search_get_language |
tripal_pub/ |
Get the name of the language based on an abbreviation |
| tripal_pub_remote_search_PMID |
tripal_pub/ |
A hook for performing the search on the PubMed database. |
| tripal_pub_remote_validate_form_AGL |
tripal_pub/ |
A hook for providing additional validation of importer setup form. |
| tripal_pub_remote_validate_form_PMID |
tripal_pub/ |
A hook for providing additional validation of importer setup form. |
| tripal_pub_requirements |
tripal_pub/ |
Implementation of hook_requirements(). |
| tripal_pub_schema |
tripal_pub/ |
Implementation of hook_schema(). |
| tripal_pub_search_form |
tripal_pub/ |
Provides the form to search pubmed |
| tripal_pub_search_form_ajax_button_submit |
tripal_pub/ |
This function is used to rebuild the form if an ajax call is made vai a button. The button causes the form to be submitted. We don't want this so we override the validate and submit routines on the form button. Therefore, this function only needs… |
| tripal_pub_search_form_ajax_button_validate |
tripal_pub/ |
This function is just a dummy to override the default form submit on ajax calls for buttons |
| tripal_pub_search_form_submit |
tripal_pub/ |
Submit the tripal_pub_search_form form |
| tripal_pub_search_form_validate |
tripal_pub/ |
Validate the tripal_pub_search_form form |
| tripal_pub_search_page |
tripal_pub/ |
The page that contains the publication search form and the results for the search |
| tripal_pub_setup_form_ajax_button_submit |
tripal_pub/ |
This function is just a dummy to override the default form submit on ajax calls for buttons |
| tripal_pub_setup_form_ajax_button_validate |
tripal_pub/ |
This function is used to rebuild the form if an ajax call is made vai a button. The button causes the form to be submitted. We don't want this so we override the validate and submit routines on the form button. Therefore, this function only needs… |
| tripal_pub_set_pub_url |
tripal_pub/ |
Set the URL for a publication |
| tripal_pub_theme |
tripal_pub/ |
Implements hook_theme(). Register themeing functions for this module |
| tripal_pub_uninstall |
tripal_pub/ |
Implementation of hook_uninstall(). |
| tripal_pub_views_api |
tripal_pub/ |
Implements hook_views_api(). |
| tripal_pub_views_default_views |
tripal_pub/ |
Implements hook_views_default_views(). |
| tripal_reimport_publications |
tripal_pub/ |
Updates publication records that currently exist in the Chado pub table with the most recent data in the remote database. |
| tripal_search_publications |
tripal_pub/ |
Builds the SQL statement need to search Chado for the publications that match the user supplied criteria. Tpyically, this function is called by the search form generated by the tripal_pub_search_form() function but this function is included in the… |
| tripal_stock_add_cvs |
tripal_stock/ |
Add cvs related to publications |
| tripal_stock_add_cvterms |
tripal_stock/ |
Add cvterms related to publications |
Files
|
Name |
Location | Description |
|---|---|---|
| tripal_pub.chado_node.inc |
tripal_pub/ |
Implements Drupal Node hooks to create the chado_analysis node content type. |