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Publications.md

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Tripal v4 - Publications Design Document

This design documents includes multiple classes that are needed for querying, retrieving and importing publications into Tripal using a database-backend agnostic approach.

Search Query Form Classes

ManagePubSearchQueriesForm

Provides the form interface for managing a publication query.

AddPubSearchQueryForm

Provides the form interface for adding a single query for a given publication library.

DeletePubSearchQueryForm

Deletes a single search query.

TripalPubLibrary Plugin

TripalPubLibrary (Annotation Class)

This is the annotation class for the plugin

Member Variables

  • id: the plugin id
  • label: the label for the plugin
  • description: the description for the plugin

TripalPubLibraryInterface

Interface class for the TripalPubLibrary class. This interface provides the functions that all TripalPubLibrary classes must implement.

Member Variables

Functions

  • form(): provides the form elements for library that is used by AddPubSearchQueryForm
  • formSubmit():
  • formValidate():
  • parse():
  • retrieve(): runs a query and retrieves results. This function is used by the AddPubSearchQueryForm to retrieve results using a query definition array.
  • run(): runs the retrieve() and parse() functions for a given query. Requires that the query is already saved and pulls the query definition from the database.

TripalPubLibraryBase

The base class for all TripalPubLibrary implementation. It provides common functionality that all TripalPubLibrary implementations will need.

TripalPubLibraryPubmed

An instance of a TripalPubLibrary plugin that talks directly to PubMed. It should retrieve and parse the results of a query into a common publication object.

TripalPubLibraryAgricola

An instance of a TripalPubLibrary plugin that talks directly to the USDA Agricola database. It should retrieve and parse the results of a query into a common publication object.

TripalPubLibraryBibTex

An instance of a TripalPubLibrary plugin that can import from a file.

PubBuddyService

A base class that manages a ChadoBuddyRecord instance to store the publication. It is used in place of the old associative array for storing publications.

Member Variables

  • record: an instance of ChadoBuddyRecord

Functions

  • setAttribute($attribute, $value)
  • checkAuthors()
  • getAttribute($attribute)
  • getCitation(): retrieves the citation for a publication.

ChadoPubBuddyService

Implements a PubBuddyService and is responsible for saving the publication to Chado

Neo4jPubBuddyService

Theoretical example for storing in another database.

TripalImporter Plugins

PubFileImporter

Implementation of the TripalImporter plugin for loading publication data into Chado using a file.

Functions:

  • form(): Lets the user upload a file. Lets the user select the file TripalPubLibrary plugin that can upload files
  • run(): Instantiate the proper instance of the TripalPubLibrary plugin (e.g. TripalPubLibraryBibTex) call the library->run() and pass the query id iterate through the array returned by the call above and store the records in Chado.

PubSearchQueryImporter

Implementation of the TripalImporter plugin for loading publication data into Chado using a search query. It will allow the user to select from a set of already created search queries.

Form Elements

  • Select list for the database (eg. PubMed)
  • Autocomplete text field (the name of the search query name)

Functions:

  • form(): Let's the user select a search query – no file upload needed.
  • run(): Query the tripal_pub_library_query table, for the query information to get the TripalPubLibrary plugin id. Instantiate the proper instance of the TripalPubLibrary plugin (e.g. TripalPubLibraryPubmed). call the library->run() and pass the query id iterate through the array returned by the call above and store the records in Chado.
    • Tables (pub, pub_dbxref, dbxref, pubauthor, pubprop) - Look at GFF importer which does procedural functions to check for publications first and then insert publications not found in the CHADO schema.