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+<?php
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+
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+/**
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+ * @file
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+ *
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+ * These api functions are deprecated, if your site is currently using them
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+ * please update your code with the newer tripal_chado functions.
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+ */
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+
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+/**
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+ * @defgroup tripal_chado_module_DEPRECATED_api
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+ * @ingroup tripal_chado_api
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+ * @{
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+ * Deprecated legacy api code.
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+ * @}
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+ */
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+
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+
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+/**tripal_analysis_api*/
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+/**
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+ * Retrieves a chado analysis variable.
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+ *
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+ * @param $itentifier
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+ * an array with the key stating what the identifier is. Supported keys
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+ * (only on of the following unique keys is required):
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+ * - analysis_id: the chado analysis.analysis_id primary key.
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+ * - nid: the drupal node.nid primary key.
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+ * There are also some specially handled keys. They are:
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+ * - property: An array/object describing the property to select records for.
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+ * It should at least have either a type_name (if unique across cvs) or
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+ * type_id. Other supported keys include: cv_id/cv_name (of the type),
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+ * value and rank.
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+ * @param $options
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+ * An array of options. Supported keys include:
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+ * - Any keys supported by chado_generate_var(). See that function
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+ * definition for additional details.
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+ *
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+ * NOTE: the $identifier parameter can really be any array similar to $values
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+ * passed into chado_select_record(). It should fully specify the stock record
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+ * to be returned.
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+ *
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+ * @return
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+ * the analysis node matching the passed in identifier
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_analysis($identifier, $options) {
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+ chado_get_analysis($identifier, $options);
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+}
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+
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+/**
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+ * Returns a list of analyses that are currently synced with Drupal to use in
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+ * select lists.
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+ *
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+ * @param $syncd_only
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+ * Whether or not to return all chado analyses or just those sync'd with
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+ * drupal. Defaults to TRUE (only sync'd analyses).
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+ * @return
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+ * An array of analyses sync'd with Drupal where each value is the analysis
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+ * scientific name and the keys are analysis_id's.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_analysis_select_options($syncd_only = true) {
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+ chado_get_analysis_select_options($syncd_only);
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+}
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+
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+/**tripal_contact_api*/
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+/**
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+ * Adds a contact to the Chado contact table.
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+ *
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+ * @param $values
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+ * An array of values to be inserted. Valid keys include:
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+ * - name: The name of the contact.
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+ * - description: Text describing the contact.
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+ * - type_name: The type of contact. Must be a term in the tripal_contact
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+ * vocabulary.
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+ * - properties: An associative array containing a list of key value pairs for
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+ * the properites. The key's must be valid terms in the tripal_contact
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+ * vocabulary (e.g. Affiliation, Address, etc).
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+ *
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+ * @return
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+ * On success, an array is returned containing the fields of the contact
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+ * record including the newly added contact_id. On failure, FALSE is
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+ * returned.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_insert_contact($values) {
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+ chado_insert_contact($values);
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+}
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+
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+/**
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+ * This function is intended to be used in autocomplete forms for contacts.
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+ *
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+ * @param $text
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+ * The string to search for.
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+ *
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+ * @return
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+ * A json array of terms that begin with the provided string.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_autocomplete_contact($text) {
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+ chado_autocomplete_contact($text);
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+}
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+
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+/**tripal_chado_cv_api*/
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+/**
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+ * Retrieves a chado controlled vocabulary variable
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+ *
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+ * @param $identifier
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+ * An array with the key stating what the identifier is. Supported keys (only
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+ * on of the following unique keys is required):
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+ * - cv_id: the chado cv.cv_id primary key.
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+ * - name: the chado cv.name field (assume unique).
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+ * @param $options
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+ * An array of options. Supported keys include:
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+ * - Any keys supported by chado_generate_var(). See that function
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+ * definition fot additional details.
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+ *
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+ * NOTE: the $identifier parameter can really be any array similar to $values
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+ * passed into chado_select_record(). It should fully specify the cv record to
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+ * be returned.
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+ *
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+ * @return
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+ * If unique values were passed in as an identifier then an object describing
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+ * the cv will be returned (will be a chado variable from
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+ * chado_generate_var()). Otherwise, FALSE will be returned.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_cv($identifiers, $options = array()) {
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+ chado_get_cv($identifiers, $options);
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+}
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+
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+/**
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+ * Create an options array to be used in a form element which provides a
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+ * list of all chado cvs.
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+ *
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+ * @return
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+ * An array(cv_id => name) for each cv in the chado cv table.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_cv_select_options() {
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+ chado_get_cv_select_options();
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+}
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+
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+/**
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+ * Retrieves a chado controlled vocabulary term variable.
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+ *
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+ * @param $identifier
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+ * An array apropriate for use with the chado_generate_var for uniquely
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+ * identifying a cvterm record. Alternativley, there are also some specially
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+ * handled keys. They are:
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+ * - id: an ID for the term of the for [dbname]:[accession], where [dbname]
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+ * is the short name of the vocabulary and accession is the unique ID.
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+ * - cv_id: an integer indicating the cv_id or an array with 'name' => the
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+ * name of the cv.
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+ * - synonym: an array with 'name' => the name of the synonym of the cvterm
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+ * you want returned; 'cv_id' => the cv_id of the synonym; 'cv_name' =>
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+ * the name of the cv of the synonym.
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+ * - property: An array/object describing the property to select records
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+ * for. It should at least have either a type_name (if unique across cvs)
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+ * or type_id. Other supported keys include: cv_id/cv_name (of the type),
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+ * value and rank.
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+ * @param $options
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+ * An array of options. Supported keys include:
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+ * - Any keys supported by chado_generate_var(). See that function
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+ * definition for additional details.
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+ *
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+ * NOTE: the $identifier parameter can really be any array similar to $values
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+ * passed into chado_select_record(). It should fully specify the cvterm
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+ * record to be returned.
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+ *
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+ * @return
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+ * If unique values were passed in as an identifier then an object describing
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+ * the cvterm will be returned (will be a chado variable from
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+ * chado_generate_var()). Otherwise, FALSE will be returned.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_cvterm($identifiers, $options = array()) {
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+ chado_get_cvterm($identifiers, $options);
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+}
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+
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+/**
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+ * Create an options array to be used in a form element
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+ * which provides a list of all chado cvterms.
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+ *
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+ * @param $cv_id
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+ * The chado cv_id; only cvterms with the supplied cv_id will be returnedl.
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+ * @param $rel_type
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+ * Set to TRUE if the terms returned should only be relationship types in
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+ * the vocabulary. This is useful for creating drop-downs of terms
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+ * used for relationship linker tables.
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+ *
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+ * @return
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+ * An associative array with the cvterm_id's as keys. The first
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+ * element in the array has a key of '0' and a value of 'Select a Type'.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_get_cvterm_select_options($cv_id, $rel_type = false) {
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+ chado_get_cvterm_select_options($cv_id, $rel_type);
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+}
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+
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+/**
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+ * Duplicate of fill_cvtermpath() stored procedure in Chado.
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+ *
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+ * Identifies all of the root terms of the controlled vocabulary. These
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+ * root terms are then processed by calling the
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+ * chado_update_cvtermpath_root_loop() function on each one.
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+ *
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+ * @param $cvid
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+ * The controlled vocabulary ID from the cv table of Chado (i.e. cv.cv_id).
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+ * @param $job_id
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_update_cvtermpath($cv_id, $job_id = null) {
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+ chado_update_cvtermpath($cv_id, $job_id);
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+}
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+
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+/**
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+ * Duplicate of _fill_cvtermpath4root() stored procedure in Chado.
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+ *
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+ * This function process a "branch" of the ontology. Initially, the
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+ * "root" starts at the top of the tree. But, as the cvtermpath is populated
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+ * the "root" becomes terms deeper in the tree.
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+ *
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+ * @param $rootid
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+ * The term ID from the cvterm table of Chado (i.e. cvterm.cvterm_id).
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+ * @param $cvid
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+ * The controlled vocabulary ID from the cv table of Chado (i.e. cv.cv_id).
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_update_cvtermpath_root_loop($rootid, $cvid, &$roots) {
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+ chado_update_cvtermpath_root_loop($rootid, $cvid, $roots);
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+}
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+
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+/**
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+ *
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+ * @param $origin
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+ * The root terms cvterm_id.
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+ * @param $child_id
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+ * The cvterm_id of the current child term. The child term is a descendent
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+ * of the origin.
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+ * @param $cv_id
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+ * The controlled vocabulary ID from the cv table of Chado (i.e. cv.cv_id).
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+ * @param $type_id
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+ * The relationship type between the origin term and the child.
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+ * @param $depth
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+ * The depth of the recursion.
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+ * @param $increment_of_depth.
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+ * An integer tailing the number of children that have been walked down.
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+ * @param $tree_path.
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+ * The array of every term between the current child and the origin. Each
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+ * element in the array is an associative array with the keys:
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+ * -build_id: an string identifier for the child that combines the origin,
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+ * child cvterm_id,cv_id, and the type_id.
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+ * -depth: the depth that a child was inserted into the cvtermpath table.
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+ * @param $possible_loop
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+ * A boolean flag.
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+ * @param $matched_row
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+ * An array of rows that are currently in the cvtermpath table that match the
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+ * build_id of the current term trying to be written to the table
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+ * @param $possible_start_of_ loop
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+ * The array of the possible loop item between the current child and the
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+ * origin. Each element in the array is an associative array with the keys:
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+ * - cvid : $cv_id
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+ * - subject_id:
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+ * - child_id : $child_id,
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+ * - type_id : $type_id,
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+ * - depth : $depth,
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+ * @param $no_loop_skip_test
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+ * A boolean used when the possible loop has been ruled out as a loop.
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+ *
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_update_cvtermpath_loop(
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+ $origin,
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+ $child_id,
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+ $cv_id,
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+ $type_id,
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+ $depth,
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+ $increment_of_depth,
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+ $tree_path,
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+ $possible_loop,
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+ $matched_rows,
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+ $possible_start_of_loop,
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+ $no_loop_skip_test
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+) {
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+ chado_update_cvtermpath_loop($origin, $child_id, $cv_id, $type_id, $depth,
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+ $increment_of_depth, $tree_path, $possible_loop, $matched_rows,
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+ $possible_start_of_loop, $no_loop_skip_test);
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+}
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+
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+/**
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+ *
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+ * @param $origin
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+ * The root terms cvterm_id.
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+ * @param $child_id
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+ * The cvterm_id of the current child term. The child term is a descendent
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+ * of the origin.
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+ * @param $cv_id
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+ * The controlled vocabulary ID from the cv table of Chado (i.e. cv.cv_id).
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+ * @param $type_id
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+ * The relationship type between the origin term and the child.
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+ * @param $depth
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+ * The depth of the recursion.
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+ * @param $increment_of_depth.
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+ * An integer.
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+ * @param $tree_path.
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+ * The array of every term between the current child and the origin. Each
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+ * element in the array is an associative array with the keys:
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+ * -build_id: an string identifier for the child that combines the origin,
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+ * child cvterm_id,cv_id, and the type_id.
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+ * -depth: the depth that a child was inserted into the cvtermpath table.
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+ * @param $possible_loop
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+ * A boolean flag.
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+ * @param $matched_row
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+ * An array of rows that are currently in the cvtermpath table that match the
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+ * build_id of the current term trying to be written to the table
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+ * @param $possible_start_of_ loop
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+ * The array of the possible loop item between the current child and the origin.
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+ * Each element in the array is an associative array with the keys:
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+ * - cvid : $cv_id
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+ * - subject_id:
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+ * - child_id : $child_id,
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+ * - type_id : $type_id,
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+ * - depth : $depth,
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+ * @param $no_loop_skip_test
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+ * A boolean used when the possible loop has been ruled out as a loop.
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+ * @return multitype: Either a number that represents the row count of existing
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+ * rows that already match these specification or a Boolean false.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_update_cvtermpath_loop_increment(
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+ $origin,
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+ $child_id,
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+ $cv_id,
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+ $type_id,
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+ $depth,
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+ $increment_of_depth,
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+ $tree_path,
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+ $possible_loop,
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+ $matched_rows,
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+ &$possible_start_of_loop,
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+ $no_loop_skip_test
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+) {
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+ chado_update_cvtermpath_loop_increment($origin, $child_id, $cv_id, $type_id,
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+ $depth, $increment_of_depth, $tree_path, $possible_loop, $matched_rows,
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+ $possible_start_of_loop, $no_loop_skip_test);
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+}
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+
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+/**
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+ * Adds a controlled vocabulary to the CV table of Chado.
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+ *
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+ * @param $name
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+ * The name of the controlled vocabulary. These are typically all lower case
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+ * with no special characters other than an undrescore (for spaces).
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+ * @param $comment
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+ * A description or definition of the vocabulary.
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+ *
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+ * @return
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+ * An object populated with fields from the newly added database.
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+ *
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+ * @ingroup tripal_chado_module_DEPRECATED_api
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+ */
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+function tripal_insert_cv($name, $definition) {
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+ chado_insert_cv($name, $definition);
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+}
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+
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+/**
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+ * Add's a controlled vocabulary term to Chado.
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+ *
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+ * This function will add a cvterm record (and a dbxref record if appropriate
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+ * values are provided). If the parent vocabulary does not exist then
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+ * that also is added to the cv table. If the cvterm is a relationship term
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+ * then the 'is_relationship' value should be set. All
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+ * terms must also have a corresponding database. This is specified in the
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+ * term's ID just before the colon (e.g. GO:003824). If the database does not
|
|
|
+ * exist in the DB table then it will be added automatically. The accession
|
|
|
+ * (the value just after the colon in the term's ID) will be added to the
|
|
|
+ * dbxref table. If the CVterm already exists and $update is set (default)
|
|
|
+ * then the cvterm is updated. If the CVTerm already exists and $update is
|
|
|
+ * not set, then no changes are made and the CVTerm object is returned.
|
|
|
+ *
|
|
|
+ * @param $term
|
|
|
+ * An associative array with the following keys:
|
|
|
+ * - id: the term accession. must be of the form <DB>:<ACCESSION>, where
|
|
|
+ * <DB> is the name of the database to which the cvterm belongs and the
|
|
|
+ * <ACCESSION> is the term's accession number in the database.
|
|
|
+ * - name: the name of the term. usually meant to be human-readable.
|
|
|
+ * - is_obsolete: is present and set to 1 if the term is defunct.
|
|
|
+ * - definition: the definition of the term.
|
|
|
+ * - cv_name: The CV name to which the term belongs. If this arugment is
|
|
|
+ * null or not provided then the function tries to find a record in the
|
|
|
+ * CV table with the same name provided in the $term[namespace]. If
|
|
|
+ * this field is provided then it overrides what the value in
|
|
|
+ * $term[namespace].
|
|
|
+ * - is_relationship: If this term is a relationship term then this value
|
|
|
+ * should be 1.
|
|
|
+ * - db_name: In some cases the database name will not be part of the
|
|
|
+ * $term['id'] and it needs to be explicitly set. Use this argument
|
|
|
+ * only if the database name cannot be specififed in the term ID
|
|
|
+ * (e.g. <DB>:<ACCESSION>).
|
|
|
+ * @param $options
|
|
|
+ * An associative array with the following keys:
|
|
|
+ * - update_existing: By default this is TRUE. If the term exists it is
|
|
|
+ * automatically updated.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A cvterm object
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_insert_cvterm($term, $options = array()) {
|
|
|
+ chado_insert_cvterm($term, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * TODO: deprecate this function
|
|
|
+ *
|
|
|
+ * Avoid using this function as it will be deprecated in future releases.
|
|
|
+ *
|
|
|
+ * This function allows other modules to programatically
|
|
|
+ * submit an ontology for loading into Chado.
|
|
|
+ *
|
|
|
+ * This function will add a job to the Jobs subsystem for parsing the ontology.
|
|
|
+ * You can either pass a known OBO ID to the function or the URL
|
|
|
+ * or full path the the ontology file. If a URL or file name is
|
|
|
+ * passed then the $obo_name argument must also be provided. If
|
|
|
+ * this is the first time the ontology has been provided to Tripal
|
|
|
+ * then it will be added to the database and will be assigned a
|
|
|
+ * unique OBO ID.
|
|
|
+ *
|
|
|
+ * @param $obo_id
|
|
|
+ * If the ontology is already loaded into the Tripal tables then
|
|
|
+ * use this argument to specify the unique ID for the ontology
|
|
|
+ * that will be loaded.
|
|
|
+ * @param $obo_name
|
|
|
+ * If the OBO has not been added before then use this argument
|
|
|
+ * to specify the human readable name of the ontology.
|
|
|
+ * @param $obo_url
|
|
|
+ * If the OBO to be loaded is located on a remote server then
|
|
|
+ * use this argument to provide the URL.
|
|
|
+ * @param $obo_file
|
|
|
+ * If the OBO is housed on the local file system of the server then
|
|
|
+ * use this argument to specify the full path.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * returns the job_id of the submitted job or FALSE if the job was not added
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_submit_obo_job($obo) {
|
|
|
+ chado_submit_obo_job($obo);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add the OBO to the tripal_cv_obo table in the Drupal database.
|
|
|
+ *
|
|
|
+ * If the OBO name already exists in the table then the path is updated.
|
|
|
+ *
|
|
|
+ * @param $name
|
|
|
+ * The human readable name of this ontology.
|
|
|
+ * @param $path
|
|
|
+ * The file path or URL of the ontology.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * Returns the ontology ID.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_insert_obo($name, $path) {
|
|
|
+ chado_insert_obo($name, $path);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves an OBO record.
|
|
|
+ *
|
|
|
+ * @param $values
|
|
|
+ * An associate array with the following allowed keys: obo_id, name.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An instance of an OBO record object.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_obo($values) {
|
|
|
+ chado_get_obo($values);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is intended to be used in autocomplete forms.
|
|
|
+ *
|
|
|
+ * This function searches for a matching controlled vobulary name.
|
|
|
+ *
|
|
|
+ * @param $string
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_cv($string = '') {
|
|
|
+ chado_autocomplete_cv($string);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is intended to be used in autocomplete forms
|
|
|
+ * for searching for CV terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @param $cv_id
|
|
|
+ * The CV ID in which to search for the term.
|
|
|
+ * @param $string
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_cvterm($cv_id, $string = '') {
|
|
|
+ chado_autocomplete_cvterm($cv_id, $string);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add a record to a cvterm linking table (ie: feature_cvterm).
|
|
|
+ *
|
|
|
+ * @param $basetable
|
|
|
+ * The base table to which the cvterm should be linked/associated. Thus to
|
|
|
+ * associate a cvterm to a feature the basetable=feature and cvterm_id is
|
|
|
+ * added to the feature_cvterm table.
|
|
|
+ * @param $record_id
|
|
|
+ * The primary key of the basetable to associate the cvterm with. This should
|
|
|
+ * be in integer.
|
|
|
+ * @param $cvterm
|
|
|
+ * An associative array describing the cvterm. Valid keys include:
|
|
|
+ * - name: the name for the cvterm,
|
|
|
+ * - cv_name: the name of the cv the cvterm belongs to.
|
|
|
+ * - cv_id: the primary key of the cv the cvterm belongs to.
|
|
|
+ * @param $options
|
|
|
+ * An associative array of options. Valid keys include:
|
|
|
+ * - insert_cvterm: Insert the cvterm if it doesn't already exist. FALSE is
|
|
|
+ * the default.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_associate_cvterm($basetable, $record_id, $cvterm, $options = array()) {
|
|
|
+ chado_associate_cvterm($basetable, $record_id, $cvterm, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**tripal_chado_database_api*/
|
|
|
+/**
|
|
|
+ * Retrieves a chado db variable.
|
|
|
+ *
|
|
|
+ * Example Usage:
|
|
|
+ * @code
|
|
|
+ * $select_values = array(
|
|
|
+ * 'name' => 'SOFP'
|
|
|
+ * );
|
|
|
+ * $db_object = tripal_get_db($select_values);
|
|
|
+ * @endcode
|
|
|
+ * The above code selects the SOFP db and returns the following object:
|
|
|
+ * @code
|
|
|
+ * $db_object = stdClass Object (
|
|
|
+ * [db_id] => 49
|
|
|
+ * [name] => SOFP
|
|
|
+ * [description] =>
|
|
|
+ * [urlprefix] =>
|
|
|
+ * [url] =>
|
|
|
+ * );
|
|
|
+ * @endcode
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array with the key stating what the identifier is. Supported keys (only
|
|
|
+ * on of the following unique keys is required):
|
|
|
+ * - db_id: the chado db.db_id primary key.
|
|
|
+ * - name: the chado db.name field (assume unique).
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * NOTE: the $identifier parameter can really be any array similar to $values
|
|
|
+ * passed into chado_select_record(). It should fully specify the db record to
|
|
|
+ * be returned.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If unique values were passed in as an identifier then an object describing
|
|
|
+ * the cv will be returned (will be a chado variable from
|
|
|
+ * chado_generate_var()). Otherwise, an array of objects will be returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_db($identifiers, $options = array()) {
|
|
|
+ chado_get_db($identifiers, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Create an options array to be used in a form element
|
|
|
+ * which provides a list of all chado dbs.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array(db_id => name) for each db in the chado db table.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_db_select_options() {
|
|
|
+ chado_get_db_select_options();
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves a chado database reference variable.
|
|
|
+ *
|
|
|
+ * Example Usage:
|
|
|
+ * @code
|
|
|
+ * $identifiers = array(
|
|
|
+ * 'accession' => 'synonym',
|
|
|
+ * 'db_id' => array(
|
|
|
+ * 'name' => 'SOFP'
|
|
|
+ * )
|
|
|
+ * );
|
|
|
+ * $dbxref_object = tripal_get_dbxref($identifiers);
|
|
|
+ * @endcode
|
|
|
+ * The above code selects the synonym database reference and returns the
|
|
|
+ * following object:
|
|
|
+ * @code
|
|
|
+ * $dbxref_object = stdClass Object (
|
|
|
+ * [dbxref_id] => 2581
|
|
|
+ * [accession] => synonym
|
|
|
+ * [description] =>
|
|
|
+ * [version] =>
|
|
|
+ * [db_db_id] => 49
|
|
|
+ * [db_name] => SOFP
|
|
|
+ * [db_description] =>
|
|
|
+ * [db_urlprefix] =>
|
|
|
+ * [db_url] =>
|
|
|
+ * );
|
|
|
+ * @endcode
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array apropriate for use with the chado_generate_var for uniquely
|
|
|
+ * identifying a dbxref record. Alternatively, there are also some specially
|
|
|
+ * handled keys. They are:
|
|
|
+ * - property: An array/object describing the property to select records for.
|
|
|
+ * It should at least have either a type_name (if unique across cvs) or
|
|
|
+ * type_id. Other supported keys include: cv_id/cv_name (of the type),
|
|
|
+ * value and rank.
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * NOTE: the $identifier parameter can really be any array similar to $values
|
|
|
+ * passed into chado_select_record(). It should fully specify the dbxref record
|
|
|
+ * to be returned.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If unique values were passed in as an identifier then an object describing
|
|
|
+ * the dbxref will be returned (will be a chado variable from
|
|
|
+ * chado_generate_var()). Otherwise, FALSE will be returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_dbxref($identifiers, $options = array()) {
|
|
|
+ chado_get_dbxref($identifiers, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Generates a URL for the controlled vocabulary term.
|
|
|
+ *
|
|
|
+ * If the URL and URL prefix are provided for the database record of a cvterm
|
|
|
+ * then a URL can be created for the term. By default, the db.name and
|
|
|
+ * dbxref.accession are concatenated and appended to the end of the db.urlprefix.
|
|
|
+ * But Tripal supports the use of {db} and {accession} tokens when if present
|
|
|
+ * in the db.urlprefix string will be replaced with the db.name and
|
|
|
+ * dbxref.accession respectively.
|
|
|
+ *
|
|
|
+ * @param $dbxref
|
|
|
+ * A dbxref object as created by the chado_generate_var() function.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A string containing the URL.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_dbxref_url($dbxref) {
|
|
|
+ chado_get_dbxref_url($dbxref);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Adds a new database to the Chado DB table and returns the DB object.
|
|
|
+ *
|
|
|
+ * @param $values
|
|
|
+ * An associative array of the values of the db (those to be inserted):
|
|
|
+ * - name: The name of the database. This name is usually used as the prefix
|
|
|
+ * for CV term accessions.
|
|
|
+ * - description: (Optional) A description of the database. By default no
|
|
|
+ * description is required.
|
|
|
+ * - url: (Optional) The URL for the database.
|
|
|
+ * - urlprefix: (Optional) The URL that is to be used as a prefix when
|
|
|
+ * constructing a link to a database term.
|
|
|
+ * @param $options
|
|
|
+ * Optional. An associative array of options that can include:
|
|
|
+ * - update_existing: Set this to '1' to force an update of the database if it
|
|
|
+ * already exists. The default is to not update. If the database exists
|
|
|
+ * then nothing is added.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An object populated with fields from the newly added database. If the
|
|
|
+ * database already exists it returns the values in the current entry.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_insert_db($values, $options = array()) {
|
|
|
+ chado_insert_db($values, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add a database reference.
|
|
|
+ *
|
|
|
+ * @param $values
|
|
|
+ * An associative array of the values to be inserted including:
|
|
|
+ * - db_id: the database_id of the database the reference is from.
|
|
|
+ * - accession: the accession.
|
|
|
+ * - version: (Optional) The version of the database reference.
|
|
|
+ * - description: (Optional) A description of the database reference.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * The newly inserted dbxref as an object, similar to that returned by
|
|
|
+ * the chado_select_record() function.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_insert_dbxref($values) {
|
|
|
+ chado_insert_dbxref($values);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add a record to a database reference linking table (ie: feature_dbxref).
|
|
|
+ *
|
|
|
+ * @param $basetable
|
|
|
+ * The base table for which the dbxref should be associated. Thus to associate
|
|
|
+ * a dbxref with a feature the basetable=feature and dbxref_id is added to the
|
|
|
+ * feature_dbxref table.
|
|
|
+ * @param $record_id
|
|
|
+ * The primary key of the basetable to associate the dbxref with. This should
|
|
|
+ * be in integer.
|
|
|
+ * @param $dbxref
|
|
|
+ * An associative array describing the dbxref. Valid keys include:
|
|
|
+ * 'accession' => the accession for the dbxref, 'db_name' => the name of the
|
|
|
+ * database the dbxref belongs to.
|
|
|
+ * 'db_id' => the primary key of the database the dbxref belongs to.
|
|
|
+ * @param $options
|
|
|
+ * An associative array of options. Valid keys include:
|
|
|
+ * - insert_dbxref: Insert the dbxref if it doesn't already exist. TRUE is
|
|
|
+ * the default.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_associate_dbxref($basetable, $record_id, $dbxref, $options = array()) {
|
|
|
+ chado_associate_dbxref($basetable, $record_id, $dbxref, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is intended to be used in autocomplete forms
|
|
|
+ * for searching for accession that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @param $db_id
|
|
|
+ * The DB ID in which to search for the term.
|
|
|
+ * @param $string
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_dbxref($db_id, $string = '') {
|
|
|
+ chado_autocomplete_dbxref($db_id, $string);
|
|
|
+}
|
|
|
+
|
|
|
+/**tripal_feature_api*/
|
|
|
+/**
|
|
|
+ * Used for autocomplete in forms for identifying for publications.
|
|
|
+ *
|
|
|
+ * @param $field
|
|
|
+ * The field in the publication to search on.
|
|
|
+ * @param $string
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_feature($string = '') {
|
|
|
+ chado_autocomplete_feature($string);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Performs a reverse compliment of a nucleotide sequence.
|
|
|
+ *
|
|
|
+ * @param $sequence
|
|
|
+ * The nucelotide sequence.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * an upper-case reverse complemented sequence.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_reverse_compliment_sequence($sequence) {
|
|
|
+ chado_reverse_compliment_sequence($sequence);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves the sequences for a given feature.
|
|
|
+ *
|
|
|
+ * If a feature has multiple alignments or multiple relationships then
|
|
|
+ * multiple sequences will be returned.
|
|
|
+ *
|
|
|
+ * @param $feature
|
|
|
+ * An associative array describing the feature. Valid keys include:
|
|
|
+ * - feature_id: The feature_id of the feature for which the sequence will
|
|
|
+ * be retrieved.
|
|
|
+ * - name: The feature name. This will appear on the FASTA definition line.
|
|
|
+ * - parent_id: (optional) only retrieve a sequence if 'derive_from_parent'
|
|
|
+ * is true and the parent matches this ID.
|
|
|
+ * - featureloc_id: (optional) only retrieve a sequence if
|
|
|
+ * 'derive_from_parent' is true and the alignment is defined with this
|
|
|
+ * featureloc_id.
|
|
|
+ * @param $options
|
|
|
+ * An associative array of options. Valid keys include:
|
|
|
+ * - width: Indicate the number of bases to use per line. A new line will
|
|
|
+ * be added after the specified number of bases on each line.
|
|
|
+ * - is_html: Set to '1' if the sequence is meant to be displayed on a web
|
|
|
+ * page. This will cause a <br> tag to separate lines of the FASTA sequence.
|
|
|
+ * - derive_from_parent: Set to '1' if the sequence should be obtained from
|
|
|
+ * the parent to which this feature is aligned.
|
|
|
+ * - aggregate: Set to '1' if the sequence should only contain sub features,
|
|
|
+ * excluding intro sub feature sequence. For example, set this option to
|
|
|
+ * obtain just the coding sequence of an mRNA.
|
|
|
+ * - upstream: An integer specifing the number of upstream bases to include
|
|
|
+ * in the output.
|
|
|
+ * - downstream: An integer specifying the number of downstream bases to
|
|
|
+ * include in the output.
|
|
|
+ * - sub_feature_types: Only include sub features (or child features) of
|
|
|
+ * the types provided in the array.
|
|
|
+ * - relationship_type: If a relationship name is provided (e.g. sequence_of)
|
|
|
+ * then any sequences that are in relationships of this type with matched
|
|
|
+ * sequences are also included.
|
|
|
+ * - relationship_part: If a relationship is provided in the preceeding
|
|
|
+ * argument then the rel_part must be either 'object' or 'subject' to
|
|
|
+ * indicate which side of the relationship the matched features belong.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * an array of matching sequence in the following keys for each sequence:
|
|
|
+ * - types: an array of feature types that were used to derive
|
|
|
+ * the sequence (e.g. from an aggregated sequence)
|
|
|
+ * - upstream: the number of upstream bases included in the sequence
|
|
|
+ * - downstream: the number of downstream bases included in the
|
|
|
+ * sequence
|
|
|
+ * - defline: the definintion line used to create a FASTA sequence
|
|
|
+ * - residues: the residues
|
|
|
+ * - featureloc_id: the featureloc_id if the sequences is from an
|
|
|
+ * alignment
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_feature_sequences($feature, $options) {
|
|
|
+ chado_get_feature_sequences($feature, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves the bulk sequences for a given feature.
|
|
|
+ *
|
|
|
+ * @param $options
|
|
|
+ * An associative array of options for selecting a feature. Valid keys include:
|
|
|
+ * - org_commonname: The common name of the organism for which sequences
|
|
|
+ * should be retrieved
|
|
|
+ * - genus: The genus of the organism for which sequences should be retrieved
|
|
|
+ * - species: The species of the organism for which sequences should be
|
|
|
+ * retrieved
|
|
|
+ * - analysis_name: The name of an analysis to which sequences belong. Only
|
|
|
+ * those that are associated with the analysis will be retrieved.
|
|
|
+ * - type: The type of feature (a sequence ontology term).
|
|
|
+ * - feature_name: the name of the feature. Can be an array of feature names.
|
|
|
+ * - feature_uname: the uniquename of the feature. Can be an array of
|
|
|
+ * feature unique names.
|
|
|
+ * - upstream: An integer specifing the number of upstream bases to include
|
|
|
+ * in the output
|
|
|
+ * - downstream: An integer specifying the number of downstream bases to
|
|
|
+ * include in the output.
|
|
|
+ * - derive_from_parent: Set to '1' if the sequence should be obtained from
|
|
|
+ * the parent to which this feature is aligned.
|
|
|
+ * - aggregate: Set to '1' if the sequence should only contain sub features,
|
|
|
+ * excluding intro sub feature sequence. For example, set this option to
|
|
|
+ * obtain just the coding sequence of an mRNA.
|
|
|
+ * - sub_feature_types: Only include sub features (or child features) of
|
|
|
+ * the types provided in the array
|
|
|
+ * - relationship_type: If a relationship name is provided (e.g. sequence_of)
|
|
|
+ * then any sequences that are in relationships of this type with matched
|
|
|
+ * sequences are also included
|
|
|
+ * - relationship_part: If a relationship is provided in the preceeding
|
|
|
+ * argument then the rel_part must be either 'object' or 'subject' to
|
|
|
+ * indicate which side of the relationship the matched features belong
|
|
|
+ * - width: Indicate the number of bases to use per line. A new line will
|
|
|
+ * be added after the specified number of bases on each line.
|
|
|
+ * - is_html: Set to '1' if the sequence is meant to be displayed on a
|
|
|
+ * web page. This will cause a <br> tag to separate lines of the FASTA
|
|
|
+ * sequence.
|
|
|
+ * @return
|
|
|
+ * Returns an array of sequences. The sequences will be in an array with the
|
|
|
+ * following keys for each sequence:
|
|
|
+ * 'types' => an array of feature types that were used to derive
|
|
|
+ * the sequence (e.g. from an aggregated sequence)
|
|
|
+ * 'upstream' => the number of upstream bases in the sequence
|
|
|
+ * 'downstream' => the number of downstream bases in the sequence
|
|
|
+ * 'defline' => the definintion line used to create a FASTA sequence
|
|
|
+ * 'residues' => the residues
|
|
|
+ * 'featureloc_id' => the featureloc_id if from an alignment
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_bulk_feature_sequences($options) {
|
|
|
+ chado_get_bulk_feature_sequences($options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Returns a definition line that can be used in a FASTA file.
|
|
|
+ *
|
|
|
+ * @param $feature
|
|
|
+ * A single feature object containing all the fields from the chado.feature
|
|
|
+ * table. Best case is to provide an object generated by the
|
|
|
+ * chado_generate_var() function.
|
|
|
+ * @param $notes
|
|
|
+ * Optional: additional notes to be added to the definition line.
|
|
|
+ * @param $featureloc
|
|
|
+ * Optional: a single featureloc object generated using chado_generate_var
|
|
|
+ * that contains a record from the chado.featureloc table. Provide this if the
|
|
|
+ * sequence was obtained by using the alignment rather than from the
|
|
|
+ * feature.residues column.
|
|
|
+ * @param $type
|
|
|
+ * Optional: the type of sequence. By default the feature type is used.
|
|
|
+ * @param $length
|
|
|
+ * Optional: the length of the sequence.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A string of the format: uniquename|name|type|feature_id
|
|
|
+ * or if an alignment: srcfeature_name:fmin..fmax[+-]; alignment of
|
|
|
+ * uniquename|name|type|feature_id.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_fasta_defline($feature, $notes = '', $featureloc = null, $type = '', $length = 0) {
|
|
|
+ chado_get_fasta_defline($feature, $notes, $featureloc, $type, $length);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Returns a string representing a feature location in an alignment.
|
|
|
+ *
|
|
|
+ * @param $featureloc
|
|
|
+ * A single featureloc object generated using chado_generate_var that
|
|
|
+ * contains a record from the chado.featureloc table.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A string of the format: uniquename:featurelocmin..featurelocmax.strand
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_location_string($featureloc) {
|
|
|
+ chado_get_location_string($featureloc);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Quickly retrieves relationships for a feature.
|
|
|
+ *
|
|
|
+ * Using the chado_expand_var function to retrieve a set
|
|
|
+ * of relationships can be very slow, especialy if there are many relationships.
|
|
|
+ * This function is intended to help speed up the retrieval of relationships
|
|
|
+ * by only retrieving the base information for the relationship and returning
|
|
|
+ * an array.
|
|
|
+ *
|
|
|
+ * @param $feature
|
|
|
+ * The feature object
|
|
|
+
|
|
|
+ * @return
|
|
|
+ * An array with two objects
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_feature_relationships($feature) {
|
|
|
+ chado_get_feature_relationships($feature);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves a chado organism variable.
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array with the key stating what the identifier is. Supported keys (only
|
|
|
+ * on of the following unique keys is required):
|
|
|
+ * - organism_id: the chado organism.organism_id primary key.
|
|
|
+ * - genus & species: the chado organism.genus field & organism.species field.
|
|
|
+ * There are also some specially handled keys. They are:
|
|
|
+ * - property: An array/object describing the property to select records for.
|
|
|
+ * It should at least have either a type_name (if unique across cvs) or
|
|
|
+ * type_id. Other supported keys include: cv_id/cv_name (of the type),
|
|
|
+ * value and rank.
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * NOTE: the $identifier parameter can really be any array similar to $values
|
|
|
+ * passed into chado_select_record(). It should fully specify the organism
|
|
|
+ * record to be returned.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If unique values were passed in as an identifier then an object describing
|
|
|
+ * the organism will be returned (will be a chado variable from
|
|
|
+ * chado_generate_var()). Otherwise, FALSE will be returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_organism($identifiers, $options = array()) {
|
|
|
+ chado_get_organism($identifiers, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Returns the full scientific name of an organism.
|
|
|
+ *
|
|
|
+ * @param $organism
|
|
|
+ * An organism object.
|
|
|
+ * @return
|
|
|
+ * The full scientific name of the organism.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_organism_scientific_name($organism) {
|
|
|
+ chado_get_organism_scientific_name($organism);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Returns a list of organisms that are currently synced with Drupal to use in
|
|
|
+ * select lists.
|
|
|
+ *
|
|
|
+ * @param $syncd_only
|
|
|
+ * Whether or not to return all chado organisms or just those sync'd with
|
|
|
+ * drupal. Defaults to TRUE (only sync'd organisms).
|
|
|
+ * @return
|
|
|
+ * An array of organisms sync'd with Drupal where each value is the organism
|
|
|
+ * scientific name and the keys are organism_id's.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_organism_select_options($syncd_only = true) {
|
|
|
+ chado_get_organism_select_options($syncd_only);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Return the path for the organism image.
|
|
|
+ *
|
|
|
+ * @param $organism
|
|
|
+ * An organism table record.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If the type parameter is 'url' (the default) then the fully qualified
|
|
|
+ * url to the image is returend. If no image is present then NULL is returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_organism_image_url($organism) {
|
|
|
+ chado_get_organism_image_url($organism);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is intended to be used in autocomplete forms
|
|
|
+ * for searching for organisms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @param $text
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_organism($text) {
|
|
|
+ chado_autocomplete_organism($text);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * A handy function to abbreviate the infraspecific rank.
|
|
|
+ *
|
|
|
+ * @param $rank
|
|
|
+ * The rank below species.
|
|
|
+ * @return
|
|
|
+ * The proper abbreviation for the rank.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_abbreviate_infraspecific_rank($rank) {
|
|
|
+ chado_abbreviate_infraspecific_rank($rank);
|
|
|
+}
|
|
|
+
|
|
|
+/** tripal_phylotree_api */
|
|
|
+/**
|
|
|
+ * Validates an $options array for insert or update of a phylotree record.
|
|
|
+ *
|
|
|
+ * If validation passes then any values that needed validation lookups
|
|
|
+ * (such as the dbxref, analysis, leaf_type, etc) will have their approriate
|
|
|
+ * primary_keys added to the $options array, and missing default values
|
|
|
+ * will also be added.
|
|
|
+ *
|
|
|
+ * @param $val_type
|
|
|
+ * The type of validation. Can be either 'insert' or 'update'.
|
|
|
+ * @param $options
|
|
|
+ * An array of key/value pairs containing any of the valid keys for
|
|
|
+ * either the tripal_insert_phylotree() or tripal_update_phylotree()
|
|
|
+ * functions.
|
|
|
+ * @param $errors
|
|
|
+ * An empty array where validation error messages will be set. The keys
|
|
|
+ * of the array will be name of the field from the options array and the
|
|
|
+ * value is the error message.
|
|
|
+ * @param $warnings
|
|
|
+ * An empty array where validation warning messagges will be set. The
|
|
|
+ * warnings should not stop an insert or an update but should be provided
|
|
|
+ * to the user as information by a drupal_set_message() if appropriate. The
|
|
|
+ * keys of the array will be name of the field from the options array and the
|
|
|
+ * value is the error message.
|
|
|
+ * @return
|
|
|
+ * If validation failes then FALSE is returned. Any options that do not pass
|
|
|
+ * validation checks will be added in the $errors array with the key being
|
|
|
+ * the option and the value being the error message. If validation
|
|
|
+ * is successful then TRUE is returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_validate_phylotree($val_type, &$options, &$errors, &$warnings) {
|
|
|
+ chado_validate_phylotree($val_type, $options, $errors, $warnings);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Inserts a phylotree record into Chado.
|
|
|
+ *
|
|
|
+ * This function validates the options passed prior to insertion of the record,
|
|
|
+ * and if validation passes then any values in the options array that needed
|
|
|
+ * validation lookups (such as the dbxref, analysis, leaf_type, etc) will have
|
|
|
+ * their approriate primary key values added to the options array.
|
|
|
+ *
|
|
|
+ * @param $options
|
|
|
+ * An array of key value pairs with the following keys required:
|
|
|
+ * 'name': The name of the tree. This will be displayed to users.
|
|
|
+ * 'description: A description about the tree
|
|
|
+ * 'anlaysis_id: The ID of the analysis to which this phylotree should be
|
|
|
+ * associated.
|
|
|
+ * 'analysis': If the analysis_id key is not used then the analysis name
|
|
|
+ * may be provided to identify the analysis to which the tree
|
|
|
+ * should be associated.
|
|
|
+ * 'leaf_type': A sequence ontology term or the word 'organism'. If the
|
|
|
+ * type is 'organism' then this tree represents a
|
|
|
+ * taxonomic tree. The default, if not specified, is the
|
|
|
+ * term 'polypeptide'.
|
|
|
+ * 'tree_file': The path of the file containing the phylogenetic tree to
|
|
|
+ * import or a Drupal managed_file numeric ID.
|
|
|
+ * 'format': The file format. Currently only 'newick is supported'.
|
|
|
+ *
|
|
|
+ * Optional keys:
|
|
|
+ * 'dbxref': A database cross-reference of the form DB:ACCESSION.
|
|
|
+ * Where DB is the database name, which is already present
|
|
|
+ * in Chado, and ACCESSION is the unique identifier for
|
|
|
+ * this tree in the remote database.
|
|
|
+ * 'name_re': If the leaf type is NOT 'taxonomy', then the value of
|
|
|
+ * this field can be a regular expression to pull out
|
|
|
+ * the name of the feature from the node label in the
|
|
|
+ * intput tree. If no value is provided the entire label is
|
|
|
+ * used.
|
|
|
+ * 'match': Set to 'uniquename' if the leaf nodes should be matched
|
|
|
+ * with the feature uniquename.
|
|
|
+ * 'load_now': If set, the tree will be loaded immediately if a tree_file
|
|
|
+ * is provided. Otherwise, the tree will be loaded via
|
|
|
+ * a Tripal jobs call.
|
|
|
+ * 'no_load': If set the tree file will not be loaded.
|
|
|
+ * @param $errors
|
|
|
+ * An empty array where validation error messages will be set. The keys
|
|
|
+ * of the array will be name of the field from the options array and the
|
|
|
+ * value is the error message.
|
|
|
+ * @param $warnings
|
|
|
+ * An empty array where validation warning messagges will be set. The
|
|
|
+ * warnings should not stop an insert or an update but should be provided
|
|
|
+ * to the user as information by a drupal_set_message() if appropriate. The
|
|
|
+ * keys of the array will be name of the field from the options array and the
|
|
|
+ * value is the error message.
|
|
|
+ * @return
|
|
|
+ * TRUE for success and FALSE for failure.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_insert_phylotree(&$options, &$errors, &$warnings) {
|
|
|
+ chado_insert_phylotree($options, $errors, $warnings);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Updates a phylotree record into Chado.
|
|
|
+ *
|
|
|
+ * This function validates the options passed prior to update of the record
|
|
|
+ * and if validation passes then any values in the options array that needed
|
|
|
+ * validation lookups (such as the dbxref, analysis, leaf_type, etc) will have
|
|
|
+ * their approriate primary key values added to the options array. A Drupal
|
|
|
+ * File object will be added to the options array for the tree file if one
|
|
|
+ * is provided.
|
|
|
+ *
|
|
|
+ *
|
|
|
+ * @param $phylotree_id
|
|
|
+ * The ID of the phylotree to update.
|
|
|
+ * @param $options
|
|
|
+ * An array of key value pairs with the following optional keys:
|
|
|
+ * 'name': The name of the tree. This will be displayed to users.
|
|
|
+ * 'description: A description about the tree
|
|
|
+ * 'anlaysis_id: The ID of the analysis to which this phylotree should be
|
|
|
+ * associated.
|
|
|
+ * 'analysis': If the analysis_id key is not used then the analysis name
|
|
|
+ * may be provided to identify the analysis to which the tree
|
|
|
+ * should be associated.
|
|
|
+ * 'leaf_type': A sequence ontology term or the word 'organism'. If the
|
|
|
+ * type is 'organism' then this tree represents a
|
|
|
+ * taxonomic tree. The default, if not specified, is the
|
|
|
+ * term 'polypeptide'.
|
|
|
+ * 'tree_file': The path of the file containing the phylogenetic tree to
|
|
|
+ * import or a Drupal managed_file numeric ID.
|
|
|
+ * 'format': The file format. Currently only 'newick is supported'
|
|
|
+ * 'dbxref': A database cross-reference of the form DB:ACCESSION.
|
|
|
+ * Where DB is the database name, which is already present
|
|
|
+ * in Chado, and ACCESSION is the unique identifier for
|
|
|
+ * this tree in the remote database.
|
|
|
+ * 'name_re': If the leaf type is NOT 'taxonomy', then the value of
|
|
|
+ * this field can be a regular expression to pull out
|
|
|
+ * the name of the feature from the node label in the
|
|
|
+ * intput tree. If no value is provided the entire label is
|
|
|
+ * used.
|
|
|
+ * 'match': Set to 'uniquename' if the leaf nodes should be matched
|
|
|
+ * with the feature uniquename.
|
|
|
+ * 'load_now': If set, the tree will be loaded immediately if a tree_file
|
|
|
+ * is provided. Otherwise, the tree will be loaded via
|
|
|
+ * a Tripal jobs call.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_update_phylotree($phylotree_id, &$options) {
|
|
|
+ chado_update_phylotree($phylotree_id, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Deletes a phylotree record from Chado.
|
|
|
+ *
|
|
|
+ * @param $phylotree_id
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * TRUE on success, FALSE on failure.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_delete_phylotree($phylotree_id) {
|
|
|
+ chado_delete_phylotree($phylotree_id);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Iterates through the tree and sets the left and right indicies.
|
|
|
+ *
|
|
|
+ * @param $tree
|
|
|
+ * The tree array.
|
|
|
+ * @param $index
|
|
|
+ * This parameters is not used when the function is first called. It
|
|
|
+ * is used for recursive calls.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_assign_phylogeny_tree_indices(&$tree, &$index = 1) {
|
|
|
+ chado_assign_phylogeny_tree_indices($tree, $index);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Iterates through the tree array and creates phylonodes in Chado.
|
|
|
+ *
|
|
|
+ * The function iterates through the tree in a top-down approach adding
|
|
|
+ * parent internal nodes prior to leaf nodes. Each node of the tree should have
|
|
|
+ * the following fields:
|
|
|
+ *
|
|
|
+ * -name: The name (or label) for this node.
|
|
|
+ * -depth: The depth of the node in the tree.
|
|
|
+ * -is_root: Set to 1 if this node is a root node.
|
|
|
+ * -is_leaf: Set to 1 if this node is a leaf node.
|
|
|
+ * -is_internal: Set to 1 if this node is an internal node.
|
|
|
+ * -left_index: The index of the node to the left in the tree.
|
|
|
+ * -right_index: The index of the node to the right in the tree.
|
|
|
+ * -branch_set: An array containing a list of nodes of that are children
|
|
|
+ * of the node.
|
|
|
+ * -parent: The name of the parent node.
|
|
|
+ * -organism_id: The organism_id for associtating the node with an organism.
|
|
|
+ * -properties: An array of key/value pairs where the key is the cvterm_id
|
|
|
+ * and the value is the property value. These properties
|
|
|
+ * will be assocaited with the phylonode.
|
|
|
+ *
|
|
|
+ * Prior to importing the tree the indicies can be set by using the
|
|
|
+ * chado_assign_phylogeny_tree_indices() function.
|
|
|
+ *
|
|
|
+ * @param $tree
|
|
|
+ * The tree array.
|
|
|
+ * @param $phylotree.
|
|
|
+ * The phylotree object (from Chado).
|
|
|
+ * @param $options
|
|
|
+ * The options provide some direction for how the tree is imported. The
|
|
|
+ * following keys can be used:
|
|
|
+ * -taxonomy: Set to 1 if this tree is a taxonomic tree. Set to 0
|
|
|
+ * otherwise.
|
|
|
+ * -leaf_type: Set to the leaf type name. If this is a non-taxonomic tree
|
|
|
+ * that is associated with features, then this should be the
|
|
|
+ * Sequence Ontology term for the feature (e.g. polypeptide).
|
|
|
+ * If this is a taxonomic tree then this option is not needed.
|
|
|
+ * -match: Set to either 'name' or 'uniquename'. This is used for
|
|
|
+ * matching the feature name or uniquename with the node name.
|
|
|
+ * This is not needed for taxonomic trees.
|
|
|
+ * -match_re: Set to a regular that can be used for matching the node
|
|
|
+ * name with the feature name if the node name is not
|
|
|
+ * identical to the feature name.
|
|
|
+ * @param $vocab
|
|
|
+ * Optional. An array containing a set of key/value pairs that maps node
|
|
|
+ * types to CV terms. The keys must be 'root', 'internal' or 'leaf'. If
|
|
|
+ * no vocab is provded then the terms provided by the tripal_phylogeny
|
|
|
+ * CV will be used.
|
|
|
+ * @param $parent
|
|
|
+ * This argument is not needed when the funtion is first called. This
|
|
|
+ * function is recursive and this argument is used on recursive calls.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_phylogeny_import_tree(&$tree, $phylotree, $options, $vocab = array(), $parent = null) {
|
|
|
+ chado_phylogeny_import_tree($tree, $phylotree, $options, $vocab, $parent);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Get the vocabulary terms used to describe nodes in the tree.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * Array of vocab info or FALSE on failure.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_phylogeny_get_node_types_vocab() {
|
|
|
+ chado_phylogeny_get_node_types_vocab();
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Imports a tree file.
|
|
|
+ *
|
|
|
+ * This function is used as a wrapper for loading a phylogenetic tree using
|
|
|
+ * any number of file loaders.
|
|
|
+ *
|
|
|
+ * @param $file_name
|
|
|
+ * The name of the file containing the phylogenetic tree to import.
|
|
|
+ * @param $format
|
|
|
+ * The format of the file. Currently only the 'newick' file format is
|
|
|
+ * supported.
|
|
|
+ * @param $options
|
|
|
+ * Options if the phylotree record already exists:
|
|
|
+ * 'phylotree_id': The imported nodes will be associated with this tree.
|
|
|
+ * 'leaf_type': A sequence ontology term or the word 'organism'. If the
|
|
|
+ * type is 'organism' then this tree represents a
|
|
|
+ * taxonomic tree. The default, if not specified, is the
|
|
|
+ * term 'polypeptide'.
|
|
|
+ * 'name_re': If the leaf type is NOT 'taxonomy', then the value of
|
|
|
+ * this field can be a regular expression to pull out
|
|
|
+ * the name of the feature from the node label in the
|
|
|
+ * intput tree. If no value is provided the entire label is
|
|
|
+ * used.
|
|
|
+ * 'match': Set to 'uniquename' if the leaf nodes should be matched
|
|
|
+ * with the feature uniquename.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_phylogeny_import_tree_file($file_name, $format, $options = array(), $job_id = null) {
|
|
|
+ chado_phylogeny_import_tree_file($file_name, $format, $options, $job_id);
|
|
|
+}
|
|
|
+
|
|
|
+/** tripal_pub_api */
|
|
|
+/**
|
|
|
+ * Retrieves a chado publication array.
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array used to uniquely identify a publication. This array has the same
|
|
|
+ * format as that used by the chado_generate_var(). The following keys can be
|
|
|
+ * useful for uniquely identifying a publication as they should be unique:
|
|
|
+ * - pub_id: the chado pub.pub_id primary key.
|
|
|
+ * - nid: the drupal nid of the publication.
|
|
|
+ * - uniquename: A value to matach with the pub.uniquename field.
|
|
|
+ * There are also some specially handled keys. They are:
|
|
|
+ * - property: An array describing the property to select records for. It
|
|
|
+ * should at least have either a 'type_name' key (if unique across cvs) or
|
|
|
+ * 'type_id' key. Other supported keys include: 'cv_id', 'cv_name'
|
|
|
+ * (of the type), 'value' and 'rank'
|
|
|
+ * - dbxref: The database cross reference accession. It should be in the
|
|
|
+ * form DB:ACCESSION, where DB is the database name and ACCESSION is the
|
|
|
+ * unique publication identifier (e.g. PMID:4382934)
|
|
|
+ * - dbxref_id: The dbxref.dbxref_id of the publication.
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * NOTE: the $identifier parameter can really be any array similar to $values
|
|
|
+ * passed into chado_select_record(). It should fully specify the pub record to
|
|
|
+ * be returned.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If a singe publication is retreived using the identifiers, then a
|
|
|
+ * publication array will be returned. The array is of the same format
|
|
|
+ * returned by the chado_generate_var() function. Otherwise, FALSE will be
|
|
|
+ * returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_publication($identifiers, $options = array()) {
|
|
|
+ chado_get_publication($identifiers, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * The publication table of Chado only has a unique constraint for the
|
|
|
+ * uniquename of the publiation, but in reality a publication can be considered
|
|
|
+ * unique by a combination of the title, publication type, published year and
|
|
|
+ * series name (e.g. journal name or conference name). The site administrator
|
|
|
+ * can configure how publications are determined to be unique. This function
|
|
|
+ * uses the configuration specified by the administrator to look for publications
|
|
|
+ * that match the details specified by the $pub_details argument
|
|
|
+ * and indicates if one ore more publications match the criteria.
|
|
|
+ *
|
|
|
+ * @param $pub_details
|
|
|
+ * An associative array with details about the publications. The expected keys
|
|
|
+ * are:
|
|
|
+ * 'Title': The title of the publication.
|
|
|
+ * 'Year': The published year of the publication.
|
|
|
+ * 'Publication Type': An array of publication types. A publication can
|
|
|
+ * have more than one type.
|
|
|
+ * 'Series Name': The series name of the publication.
|
|
|
+ * 'Journal Name': An alternative to 'Series Name'.
|
|
|
+ * 'Conference Name': An alternative to 'Series Name'.
|
|
|
+ * 'Citation': The publication citation (this is the value saved
|
|
|
+ * in the pub.uniquename field and must be unique).
|
|
|
+ *
|
|
|
+ * If this key is present it will also be checked
|
|
|
+ * 'Publication Dbxref': A database cross reference of the form DB:ACCESSION
|
|
|
+ * where DB is the name of the database and ACCESSION
|
|
|
+ * is the unique identifier (e.g PMID:3483139).
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array containing the pub_id's of matching publications. Returns an
|
|
|
+ * empty array if no pubs match.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_publication_exists($pub_details) {
|
|
|
+ chado_publication_exists($pub_details);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Used for autocomplete in forms for identifying for publications.
|
|
|
+ *
|
|
|
+ * @param $field
|
|
|
+ * The field in the publication to search on.
|
|
|
+ * @param $string
|
|
|
+ * The string to search for.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A json array of terms that begin with the provided string.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_autocomplete_pub($string = '') {
|
|
|
+ chado_autocomplete_pub($string);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Imports a singe publication specified by a remote database cross reference.
|
|
|
+ *
|
|
|
+ * @param $pub_dbxref
|
|
|
+ * The unique database ID for the record to update. This value must
|
|
|
+ * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
|
|
|
+ * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
|
|
|
+ * for the record in the database.
|
|
|
+ * @param $do_contact
|
|
|
+ * Set to TRUE if authors should automatically have a contact record added
|
|
|
+ * to Chado.
|
|
|
+ * @param $do_update
|
|
|
+ * If set to TRUE then the publication will be updated if it already exists
|
|
|
+ * in the database.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = false, $do_update = true) {
|
|
|
+ chado_import_pub_by_dbxref($pub_dbxref, $do_contact, $do_update);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Imports all publications for all active import setups.
|
|
|
+ *
|
|
|
+ * @param $report_email
|
|
|
+ * A list of email address, separated by commas, that should be notified
|
|
|
+ * once importing has completed.
|
|
|
+ * @param $do_update
|
|
|
+ * If set to TRUE then publications that already exist in the Chado database
|
|
|
+ * will be updated, whereas if FALSE only new publications will be added.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_execute_active_pub_importers($report_email = false, $do_update = false) {
|
|
|
+ chado_execute_active_pub_importers($report_email, $do_update);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Updates publication records.
|
|
|
+ *
|
|
|
+ * Updates publication records that currently exist in the Chado pub table
|
|
|
+ * with the most recent data in the remote database.
|
|
|
+ *
|
|
|
+ * @param $do_contact
|
|
|
+ * Set to TRUE if authors should automatically have a contact record added
|
|
|
+ * to Chado. Contacts are added using the name provided by the remote
|
|
|
+ * database.
|
|
|
+ * @param $dbxref
|
|
|
+ * The unique database ID for the record to update. This value must
|
|
|
+ * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
|
|
|
+ * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
|
|
|
+ * for the record in the database.
|
|
|
+ * @param $db
|
|
|
+ * The name of the remote database to update. If this value is provided and
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|
|
+ * no dbxref then all of the publications currently in the Chado database
|
|
|
+ * for this remote database will be updated.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_reimport_publications($do_contact = false, $dbxref = null, $db = null) {
|
|
|
+ chado_reimport_publications($do_contact, $dbxref, $db);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Launch the Tripal job to generate citations.
|
|
|
+ *
|
|
|
+ * This function will recreate citations for all publications currently
|
|
|
+ * loaded into Tripal. This is useful to create a consistent format for
|
|
|
+ * all citations.
|
|
|
+ *
|
|
|
+ * @param $options
|
|
|
+ * Options pertaining to what publications to generate citations for.
|
|
|
+ * One of the following must be present:
|
|
|
+ * - all: Create and replace citation for all pubs.
|
|
|
+ * - new: Create citation for pubs that don't already have one.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_pub_create_citations($options) {
|
|
|
+ chado_pub_create_citations($options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * 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.
|
|
|
+ *
|
|
|
+ * @param $pub
|
|
|
+ * An array structure containing publication details where the keys
|
|
|
+ * are the publication ontology term names and values are the
|
|
|
+ * corresponding details. The pub array can contain the following
|
|
|
+ * keys with corresponding values:
|
|
|
+ * - Publication Type: an array of publication types. a publication can
|
|
|
+ * have more than one type.
|
|
|
+ * - Authors: a string containing all of the authors of a publication.
|
|
|
+ * - Journal Name: a string containing the journal name.
|
|
|
+ * - Journal Abbreviation: a string containing the journal name abbreviation.
|
|
|
+ * - Series Name: a string containing the series (e.g. conference
|
|
|
+ * proceedings) name.
|
|
|
+ * - Series Abbreviation: a string containing the series name abbreviation
|
|
|
+ * - Volume: the serives volume number.
|
|
|
+ * - Issue: the series issue number.
|
|
|
+ * - Pages: the page numbers for the publication.
|
|
|
+ * - Publication Date: A date in the format "Year Month Day".
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A text string containing the citation.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_pub_create_citation($pub) {
|
|
|
+ chado_pub_create_citation($pub);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves the minimal information to uniquely describe any publication.
|
|
|
+ *
|
|
|
+ * The returned array is an associative array where the keys are
|
|
|
+ * the controlled vocabulary terms in the form [vocab]:[accession].
|
|
|
+ *
|
|
|
+ * @param $pub
|
|
|
+ * A publication object as created by chado_generate_var().
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array with the following keys: 'Citation', 'Abstract', 'Authors',
|
|
|
+ * 'URL'. All keys are term names in the Tripal Publication Ontology :TPUB.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_minimal_pub_info($pub) {
|
|
|
+ chado_get_minimal_pub_info($pub);
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/** tripal_stock_api */
|
|
|
+/**
|
|
|
+ * Retrieves a chado stock variable
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array with the key stating what the identifier is. Supported keys (only
|
|
|
+ * one of the following unique keys is required):
|
|
|
+ * - stock_id: the chado stock.stock_id primary key
|
|
|
+ * - nid: the drupal nid of the stock
|
|
|
+ * There are also some specially handled keys. They are:
|
|
|
+ * - property: An array/object describing the property to select records for.
|
|
|
+ * It should at least have either a type_name (if unique across cvs) or
|
|
|
+ * type_id. Other supported keys include: cv_id/cv_name (of the type),
|
|
|
+ * value and rank
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * NOTE: the $identifier parameter can really be any array similar to $values
|
|
|
+ * passed into chado_select_record(). It should fully specify the stock record
|
|
|
+ * to be returned.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If unique values were passed in as an identifier then an object describing
|
|
|
+ * the stock will be returned (will be a chado variable from
|
|
|
+ * chado_generate_var()). Otherwise, FALSE will be returned.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_stock($identifiers, $options = array()) {
|
|
|
+ chado_get_stock($identifiers, $options);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Retrieves a chado stock variable.
|
|
|
+ *
|
|
|
+ * @param $identifier
|
|
|
+ * An array with the key stating what the identifier is. Supported keys
|
|
|
+ * include any field in the stock table. See the chado_select_record() $values
|
|
|
+ * parameter for additional details including an example.
|
|
|
+ * @param $options
|
|
|
+ * An array of options. Supported keys include:
|
|
|
+ * - Any keys supported by chado_generate_var(). See that function
|
|
|
+ * definition for additional details.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array of stock objects matching the criteria.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_module_DEPRECATED_api
|
|
|
+ */
|
|
|
+function tripal_get_multiple_stocks($identifiers, $options = array()) {
|
|
|
+ chado_get_multiple_stocks($identifiers, $options);
|
|
|
+}
|
Shawna Spoor