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@@ -1,7 +1,10 @@
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<?php
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-// APPLICATION PROGRAMMER INTERFACE -------------
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-// Chado API
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+//
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+// APPLICATION PROGRAMMER INTERFACE
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+//
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+
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+// Generic Chado API functions
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require_once "api/tripal_chado.api.inc";
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require_once 'api/tripal_chado.property.api.inc';
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require_once 'api/tripal_chado.query.api.inc';
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@@ -13,6 +16,7 @@ require_once 'api/tripal_chado.schema_v1.3.api.inc';
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require_once 'api/tripal_chado.schema_v1.2.api.inc';
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require_once 'api/tripal_chado.schema_v1.11.api.inc';
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+// Chado module specific API functions
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require_once 'api/modules/tripal_chado.analysis.api.inc';
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require_once 'api/modules/tripal_chado.contact.api.inc';
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require_once 'api/modules/tripal_chado.cv.api.inc';
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@@ -22,10 +26,16 @@ require_once 'api/modules/tripal_chado.organism.api.inc';
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require_once 'api/modules/tripal_chado.pub.api.inc';
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require_once 'api/modules/tripal_chado.stock.api.inc';
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+//
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+// REQUIRED INCLUDE FILES
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+//
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+// These require files implement hooks and therefore must
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+// ways be included when the module is interpreted.
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require_once "includes/tripal_chado.entity.inc";
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require_once "includes/tripal_chado.schema.inc";
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require_once "includes/tripal_chado.term_storage.inc";
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require_once "includes/tripal_chado.field_storage.inc";
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+require_once "includes/tripal_chado.fields.inc";
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tripal_chado_set_globals();
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@@ -504,643 +514,35 @@ function tripal_chado_permission() {
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);
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}
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-/**
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- * Implements hook_field_info().
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- */
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-function tripal_chado_field_info() {
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- $fields = array(
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- 'organism_id' => array(
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- 'label' => t('Organism'),
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- 'description' => t('A field for specifying an organism.'),
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- 'default_widget' => 'tripal_chado_organism_select_widget',
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- 'default_formatter' => 'tripal_chado_organism_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- 'dbxref_id' => array(
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- 'label' => t('Cross reference'),
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- 'description' => t('This record can be cross referenced with a record in
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- another online database. This field is intended for the most prominent
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- reference. At a minimum, the database and accession must be provided.'),
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- 'default_widget' => 'tripal_chado_dbxref_id_widget',
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- 'default_formatter' => 'tripal_chado_dbxref_id_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- 'residues' => array(
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- 'label' => t('Residues'),
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- 'description' => t('A field for managing nucleotide and protein residues.'),
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- 'default_widget' => 'tripal_chado_residue_textarea_widget',
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- 'default_formatter' => 'tripal_chado_residues_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- 'md5checksum' => array(
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- 'label' => t('MD5 checksum'),
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- 'description' => t('A field for generating MD5 checksum for a sequence.'),
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- 'default_widget' => 'tripal_chado_md5checksum_checkbox_widget',
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- 'default_formatter' => 'tripal_chado_md5checksum_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- 'seqlen' => array(
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- 'label' => t('Sequence length'),
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- 'description' => t('A field for calculating the length of a sequence.'),
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- 'default_widget' => 'tripal_chado_seqlen_hidden_widget',
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- 'default_formatter' => 'tripal_chado_seqlen_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- // The field provides a widget for adding new properties
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- // to an entity that is connected to a base table that has a prop table
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- // in Chado.
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- 'kvproperty_adder' => array(
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- 'label' => t('Add a Property Type'),
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- 'description' => t('This record may have any number of properties. Use
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- this field to first add the type.'),
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- 'default_widget' => 'tripal_chado_kvproperty_adder_widget',
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- //'default_formatter' => 'tripal_chado_kvproperty_adder_formatter',
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- 'default_formatter' => 'hidden',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- // The field provides form elements for adding a property to an entity
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- // that in turn gets stored in a prop table of Chado (e.g. featureprop,
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- // stockprop, etc).
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- 'kvproperty' => array(
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- 'label' => t('Add a Property'),
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- 'description' => t('Add details about this property.'),
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- 'default_widget' => 'tripal_chado_kvproperty_widget',
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- 'default_formatter' => 'tripal_chado_kvproperty_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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-
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- // The field provides form elements for adding multiple dbxrefs to an
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- // entity that in turn get stored in a [base]_dbxref table of Chado
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- // (e.g. organism_dbxref, feature_dbxref). This is different
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- // from the dbxref_id field as that is specific to a dbxref_id in
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- // a base table.
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- 'dbxref' => array(
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- 'label' => t('Cross references'),
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- 'description' => t('This record can be cross referenced with a record in
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- another online database. This field is intended for one or more
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- references. At a minimum, the database and accession must be provided.'),
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- 'default_widget' => 'tripal_chado_dbxref_widget',
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- 'default_formatter' => 'tripal_chado_dbxref_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- // The field provides a widget for adding new vocabularies for cvterm
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- // linker tables. This will allow cvterms to be grouped by vocabulary
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- // ('category').
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- 'cvterm_class_adder' => array(
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- 'label' => t('Add an Annotation Type'),
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- 'description' => t('This record may have any number of types of
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- annotations. Use this field to first add the type.'),
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- 'default_widget' => 'tripal_chado_cvterm_class_adder_widget',
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- //'default_formatter' => 'tripal_chado_cvterm_class_adder_formatter',
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- 'default_formatter' => 'hidden',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- // The field provides form elements for adding multiple cvterms to an
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- // entity that in turn get stored in a [base]_cvterm table of Chado
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- // (e.g. feature_cvterm).
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- 'cvterm' => array(
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- 'label' => t('Annotations'),
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- 'description' => t('This record can be annotated with terms
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- from other vocabularies.'),
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- 'default_widget' => 'tripal_chado_cvterm_widget',
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- 'default_formatter' => 'tripal_chado_cvterm_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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-
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- 'synonym' => array(
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- 'label' => t('Synonyms'),
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- 'description' => t('Adds an alternative name (synonym or alias) to this record.'),
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- 'default_widget' => 'tripal_chado_synonym_widget',
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- 'default_formatter' => 'tripal_chado_synonym_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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-
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- 'pub' => array(
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- 'label' => t('Publications'),
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- 'description' => t('Associates a publication (e.g. journal article, conference proceedings, book chapter, etc.) with this record.'),
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- 'default_widget' => 'tripal_chado_pub_widget',
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- 'default_formatter' => 'tripal_chado_pub_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- ),
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- );
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- return $fields;
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-}
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-
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-/**
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- * Implements hook_field_widget_info().
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- */
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-function tripal_chado_field_widget_info() {
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- return array(
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- 'tripal_chado_organism_select_widget' => array(
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- 'label' => t('Organism Select'),
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- 'field types' => array('organism_id')
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- ),
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- 'tripal_chado_dbxref_id_widget' => array(
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- 'label' => t('Cross reference'),
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- 'field types' => array('dbxref_id'),
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- 'description' => t('This record can be cross referenced with a record in
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- another online database. This field is intended for the most
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- prominent reference. At a minimum, the database and accession
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- must be provided.'),
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- ),
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- 'tripal_chado_dbxref_widget' => array(
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- 'label' => t('Cross references'),
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- 'field types' => array('dbxref'),
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- 'description' => t('This record can be cross referenced with a record
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- in another online database. This field is intended for the most
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- prominent reference. At a minimum, the database and accession
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- must be provided.'),
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- ),
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- 'tripal_chado_cvterm_class_adder_widget' => array(
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- 'label' => t('Add an Annotation'),
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- 'field types' => array('cvterm_class_adder'),
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- ),
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- 'tripal_chado_cvterm_widget' => array(
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- 'label' => t('Annotations'),
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- 'field types' => array('cvterm'),
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- 'description' => t('This record can be annotated with terms
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- from other vocabularies.'),
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- ),
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- 'tripal_chado_md5checksum_checkbox_widget' => array(
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- 'label' => t('MD5 Checksum Checkbox'),
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- 'field types' => array('md5checksum'),
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- ),
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- 'tripal_chado_residues_textarea_widget' => array(
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- 'label' => t('Residues'),
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- 'field types' => array('residues'),
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- ),
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- 'tripal_chado_seqlen_hidden_widget' => array(
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- 'label' => t('Sequence Length'),
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- 'field types' => array('seqlen'),
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- ),
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- 'tripal_chado_kvproperty_adder_widget' => array(
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- 'label' => t('Add a Property'),
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- 'field types' => array('kvproperty_adder'),
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- ),
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- 'tripal_chado_kvproperty_widget' => array(
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- 'label' => t('Property'),
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- 'field types' => array('kvproperty'),
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- ),
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- 'tripal_chado_synonym_widget' => array(
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- 'label' => t('Synonyms'),
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- 'field types' => array('synonym'),
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- ),
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- 'tripal_chado_pub_widget' => array(
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- 'label' => t('Publications'),
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- 'field types' => array('pub'),
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- ),
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- );
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-}
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-/**
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- * Implements hook_field_formatter_info().
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- */
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-function tripal_chado_field_formatter_info() {
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- return array(
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- 'tripal_chado_organism_formatter' => array(
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- 'label' => t('Organism'),
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- 'field types' => array('organism_id')
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- ),
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- 'tripal_chado_dbxref_id_formatter' => array(
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- 'label' => t('Cross reference'),
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- 'field types' => array('dbxref_id')
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- ),
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- 'tripal_chado_dbxref_formatter' => array(
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- 'label' => t('Cross references'),
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- 'field types' => array('dbxref')
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- ),
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- 'tripal_chado_cvterm_class_adder_formatter' => array(
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- 'label' => t('Add an Annotation'),
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- 'field types' => array('cvterm_class_adder')
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- ),
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- 'tripal_chado_cvterm_formatter' => array(
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- 'label' => t('Annotations'),
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- 'field types' => array('cvterm')
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- ),
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- 'tripal_chado_md5checksum_formatter' => array(
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- 'label' => t('MD5 checksum'),
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- 'field types' => array('md5checksum')
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- ),
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- 'tripal_chado_residues_formatter' => array(
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- 'label' => t('Residues'),
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- 'field types' => array('residues')
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- ),
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- 'tripal_chado_seqlen_formatter' => array(
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- 'label' => t('Sequence length'),
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- 'field types' => array('seqlen')
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- ),
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- 'tripal_chado_kvproperty_adder_formatter' => array(
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- 'label' => t('Add a Property'),
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- 'field types' => array('kvproperty_adder')
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- ),
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- 'tripal_chado_kvproperty_formatter' => array(
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- 'label' => t('Property'),
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- 'field types' => array('kvproperty')
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- ),
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- 'tripal_chado_synonym_formatter' => array(
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- 'label' => t('Synonyms'),
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- 'field types' => array('synonym')
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- ),
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- 'tripal_chado_pub_formatter' => array(
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- 'label' => t('Publications'),
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- 'field types' => array('pub')
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- ),
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- );
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-}
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-
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-/**
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- * Implements hook_field_widget_form_alter().
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- */
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-function tripal_chado_field_widget_form_alter(&$element, &$form_state, $context) {
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-
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- if (array_key_exists('#field_name', $element)) {
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- $field_name = $element['#field_name'];
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- $matches = array();
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-
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- if (preg_match('/(.+?)__(.+?)$/', $field_name, $matches)) {
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- $tablename = $matches[1];
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- $colname = $matches[2];
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- $schema = chado_get_schema($tablename);
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-
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- // The timelastmodified field exists in many Chado tables. We want
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- // the form element to update to the most recent time rather than the time
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- // in the database.
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- if ($colname == 'timelastmodified' and $schema['fields'][$colname]['type'] == 'datetime') {
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- // We want the default value for the field to be the current time.
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- $element['#default_value']['value'] = format_date(time(), 'custom', "Y-m-d H:i:s", 'UTC');
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- $element['#date_items']['value'] = $element['#default_value']['value'];
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- }
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- // We want the date combo fieldset to be collaspible so we will
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- // add our own theme_wrapper to replace the one added by the date
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- // module.
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- if (array_key_exists($colname, $schema['fields']) and $schema['fields'][$colname]['type'] == 'datetime') {
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- $element['#theme_wrappers'] = array('tripal_chado_date_combo');
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- }
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- }
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- }
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-}
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-
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-
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-/**
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- * Implements hook_field_formatter_view().
|
|
|
- */
|
|
|
-function tripal_chado_field_formatter_view($entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display) {
|
|
|
-
|
|
|
- $element = array();
|
|
|
- switch ($display['type']) {
|
|
|
- case 'tripal_chado_organism_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
|
|
|
- tripal_chado_organism_select_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_dbxref_id_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
|
|
|
- tripal_chado_dbxref_id_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_dbxref_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref');
|
|
|
- tripal_chado_dbxref_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_cvterm_class_adder_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
|
|
|
- tripal_chado_cvterm_class_adder_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_cvterm_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm');
|
|
|
- tripal_chado_cvterm_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_md5checksum_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
|
|
|
- tripal_chado_md5checksum_checkbox_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_residues_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
|
|
|
- tripal_chado_residues_textarea_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_seqlen_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
|
|
|
- tripal_chado_seqlen_hidden_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_kvproperty_adder_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
|
|
|
- tripal_chado_kvproperty_adder_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_kvproperty_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
|
|
|
- tripal_chado_kvproperty_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_synonym_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
|
|
|
- tripal_chado_synonym_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- case 'tripal_chado_pub_formatter':
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/pub');
|
|
|
- tripal_chado_pub_formatter($element, $entity_type, $entity, $field,
|
|
|
- $instance, $langcode, $items, $display);
|
|
|
- break;
|
|
|
- }
|
|
|
- return $element;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_widget_form().
|
|
|
- */
|
|
|
-function tripal_chado_field_widget_form(&$form, &$form_state, $field,
|
|
|
- $instance, $langcode, $items, $delta, $element) {
|
|
|
-
|
|
|
- $widget = $element;
|
|
|
- switch ($instance['widget']['type']) {
|
|
|
- case 'tripal_chado_organism_select_widget':
|
|
|
- // Make sure the include files get parsed now and for the form submits.
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/organism_id');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
|
|
|
- // Update the widget with the new field.
|
|
|
- tripal_chado_organism_select_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_dbxref_id_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/dbxref_id');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
|
|
|
- tripal_chado_dbxref_id_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_dbxref_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/dbxref');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref');
|
|
|
- tripal_chado_dbxref_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_cvterm_class_adder_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
|
|
|
- tripal_chado_cvterm_class_adder_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_cvterm_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/cvterm');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm');
|
|
|
- tripal_chado_cvterm_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_md5checksum_checkbox_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/md5checksum');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
|
|
|
- tripal_chado_md5checksum_checkbox_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_residues_textarea_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/residues');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
|
|
|
- tripal_chado_residues_textarea_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_seqlen_hidden_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/seqlen');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
|
|
|
- tripal_chado_seqlen_hidden_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_kvproperty_adder_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
|
|
|
- tripal_chado_kvproperty_adder_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_kvproperty_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
|
|
|
- tripal_chado_kvproperty_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_synonym_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/synonym');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
|
|
|
- tripal_chado_synonym_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- case 'tripal_chado_pub_widget':
|
|
|
- form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/pub');
|
|
|
- module_load_include('inc', 'tripal_chado', 'includes/fields/pub');
|
|
|
- tripal_chado_pub_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
|
|
|
- break;
|
|
|
- }
|
|
|
- return $widget;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_form_FORM_ID_alter().
|
|
|
- *
|
|
|
- * The field_ui_display_overview_form is used for formatting the display
|
|
|
- * or layout of fields attached to an entity and shown on the entity view page.
|
|
|
- *
|
|
|
- * This function removes the cvterm class and property adder field as those are
|
|
|
- * really not meant for users to show or manage.
|
|
|
- */
|
|
|
-function tripal_chado_form_field_ui_display_overview_form_alter(&$form, &$form_state, $form_id) {
|
|
|
- // Remove the kvproperty_addr field as it isn't ever displayed. It's just used
|
|
|
- // on the add/edit form of an entity for adding new property fields.
|
|
|
- $fields_names = element_children($form['fields']);
|
|
|
- foreach ($fields_names as $field_name) {
|
|
|
- $field_info = field_info_field($field_name);
|
|
|
- if ($field_info['type'] == 'kvproperty_adder') {
|
|
|
- unset($form['fields'][$field_name]);
|
|
|
- }
|
|
|
- if ($field_info['type'] == 'cvterm_class_adder') {
|
|
|
- unset($form['fields'][$field_name]);
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_form_FORM_ID_alter().
|
|
|
- *
|
|
|
- * The field_ui_field_overview_form is used for ordering and configuring the
|
|
|
- * fields attached to an entity.
|
|
|
- *
|
|
|
- * This function removes the property adder field as that is really not meant
|
|
|
- * for users to show or manage.
|
|
|
- */
|
|
|
-function tripal_chado_form_field_ui_field_overview_form_alter(&$form, &$form_state, $form_id) {
|
|
|
- // Remove the kvproperty_addr field as it isn't ever displayed. It's just used
|
|
|
- // on the add/edit form of an entity for adding new property fields.
|
|
|
- $fields_names = element_children($form['fields']);
|
|
|
- foreach ($fields_names as $field_name) {
|
|
|
- $field_info = field_info_field($field_name);
|
|
|
- if ($field_info['type'] == 'kvproperty_adder') {
|
|
|
- unset($form['fields'][$field_name]);
|
|
|
- }
|
|
|
- if ($field_info['type'] == 'cvterm_class_adder') {
|
|
|
- unset($form['fields'][$field_name]);
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_field_is_empty().
|
|
|
- */
|
|
|
-function tripal_chado_field_is_empty($item, $field) {
|
|
|
-
|
|
|
- // If there is no value field then the field is empty.
|
|
|
- if (!array_key_exists('value', $item)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
-
|
|
|
- // Iterate through all of the fields and if at least one has a value
|
|
|
- // the field is not empty.
|
|
|
- foreach ($item as $form_field_name => $value) {
|
|
|
- if (isset($value) and $value != NULL and $value != '') {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Otherwise, the field is empty.
|
|
|
- return TRUE;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Returns the values of the field from the $form_state.
|
|
|
- */
|
|
|
-function tripal_chado_get_field_form_values($field_name, $form_state, $delta = 0, $child = NULL) {
|
|
|
- $value = NULL;
|
|
|
- // The form_state must have the 'values' key. If not then just return.
|
|
|
- if (!array_key_exists('values', $form_state)) {
|
|
|
- return $value;
|
|
|
- }
|
|
|
-
|
|
|
- // If the field name is not in the form_state['values'] then return.
|
|
|
- if (!array_key_exists($field_name, $form_state['values'])) {
|
|
|
- return $value;
|
|
|
- }
|
|
|
-
|
|
|
- // Iterate through the values looking for the field_name provided.
|
|
|
- foreach ($form_state['values'][$field_name] as $langcode => $items) {
|
|
|
- if (!array_key_exists($delta, $items)) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- $item = $items[$delta];
|
|
|
- if ($child){
|
|
|
- if(array_key_exists($child, $item) and $item[$child] != '') {
|
|
|
- $value = $item[$child];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $value = $item['value'];
|
|
|
- }
|
|
|
- }
|
|
|
- return $value;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Sets the values of the field from the $form_state.
|
|
|
- */
|
|
|
-function tripal_chado_set_field_form_values($field_name, &$form_state, $newvalue, $delta = 0, $child = NULL) {
|
|
|
- // The form_state must have the 'values' key. If not then just return.
|
|
|
- if (!array_key_exists('values', $form_state)) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // If the field name is not in the form_state['values'] then reutrn.
|
|
|
- if (!array_key_exists($field_name, $form_state['values'])) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- foreach ($form_state['values'][$field_name] as $langcode => $items) {
|
|
|
- if ($child) {
|
|
|
- $form_state['values'][$field_name][$langcode][$delta][$child] = $newvalue;
|
|
|
- }
|
|
|
- else {
|
|
|
- $form_state['values'][$field_name][$langcode][$delta]['value'] = $newvalue;
|
|
|
- }
|
|
|
- }
|
|
|
- return TRUE;
|
|
|
-}
|
|
|
-
|
|
|
/**
|
|
|
* Implements hook_theme().
|
|
|
*/
|
|
|
function tripal_chado_theme($existing, $type, $theme, $path) {
|
|
|
return array(
|
|
|
// Theme fields.
|
|
|
- 'tripal_chado_dbxref_id_widget' => array(
|
|
|
+ 'chado_base__dbxref_id_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/dbxref_id.inc',
|
|
|
+ 'file' => 'includes/fields/chado_base__dbxref_id.inc',
|
|
|
),
|
|
|
- 'tripal_chado_dbxref_widget' => array(
|
|
|
+ 'chado_linker__dbxref_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/dbxref.inc',
|
|
|
+ 'file' => 'includes/fields/chado_linker__dbxref.inc',
|
|
|
),
|
|
|
- 'tripal_chado_cvterm_widget' => array(
|
|
|
+ 'chado_linker__cvterm_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/cvterm.inc',
|
|
|
+ 'file' => 'includes/fields/chado_linker__cvterm.inc',
|
|
|
),
|
|
|
- 'tripal_chado_synonym_widget' => array(
|
|
|
+ 'chado_linker__synonym_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/synonym.inc',
|
|
|
+ 'file' => 'includes/fields/chado_linker__synonym.inc',
|
|
|
),
|
|
|
- 'tripal_chado_pub_widget' => array(
|
|
|
+ 'chado_linker__pub_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/pub.inc',
|
|
|
+ 'file' => 'includes/fields/chado_linker__pub.inc',
|
|
|
),
|
|
|
- 'tripal_chado_kvproperty_addr_widget' => array(
|
|
|
+ 'chado_linker__prop_adder_widget' => array(
|
|
|
'render element' => 'element',
|
|
|
- 'file' => 'includes/fields/dbxref_id.inc',
|
|
|
+ 'file' => 'includes/fields/chado_linker__prop_adder.inc',
|
|
|
),
|
|
|
'tripal_chado_date_combo' => array(
|
|
|
'render element' => 'element',
|
|
|
@@ -1159,622 +561,8 @@ function tripal_chado_theme($existing, $type, $theme, $path) {
|
|
|
);
|
|
|
}
|
|
|
|
|
|
-/**
|
|
|
- * Implements hook_add_bundle_fields().
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
|
|
|
-
|
|
|
- $bundle_name = $bundle->name;
|
|
|
-
|
|
|
- // This array will hold details that map the bundle to tables in Chado.
|
|
|
- $bundle_data = array();
|
|
|
-
|
|
|
- // Get the cvterm that corresponds to this TripalTerm object.
|
|
|
- $vocab = entity_load('TripalVocab', array($term->vocab_id));
|
|
|
- $vocab = reset($vocab);
|
|
|
- $match = array(
|
|
|
- 'dbxref_id' => array(
|
|
|
- 'db_id' => array(
|
|
|
- 'name' => $vocab->namespace,
|
|
|
- ),
|
|
|
- 'accession' => $term->accession
|
|
|
- ),
|
|
|
- );
|
|
|
- $cvterm = chado_generate_var('cvterm', $match);
|
|
|
-
|
|
|
- // The organism table does not have a type_id so we won't ever find
|
|
|
- // a record for it in the tripal_cv_defaults table.
|
|
|
- if ($cvterm->name == 'organism') {
|
|
|
- $bundle_data = array(
|
|
|
- 'cv_id' => $cvterm->cv_id->cv_id,
|
|
|
- 'cvterm_id' => $cvterm->cvterm_id,
|
|
|
- 'data_table' => 'organism',
|
|
|
- 'type_table' => 'organism',
|
|
|
- 'field' => '',
|
|
|
- );
|
|
|
- }
|
|
|
- // The analysis table does not have a type_id so we won't ever find
|
|
|
- // a record for it in the tripalcv_defaults table.
|
|
|
- else if ($cvterm->name == 'analysis') {
|
|
|
- $bundle_data = array(
|
|
|
- 'cv_id' => $cvterm->cv_id->cv_id,
|
|
|
- 'cvterm_id' => $cvterm->cvterm_id,
|
|
|
- 'data_table' => 'analysis',
|
|
|
- 'type_table' => 'analysis',
|
|
|
- 'field' => '',
|
|
|
- );
|
|
|
- }
|
|
|
- else if ($cvterm->name == 'project') {
|
|
|
- $bundle_data = array(
|
|
|
- 'cv_id' => $cvterm->cv_id->cv_id,
|
|
|
- 'cvterm_id' => $cvterm->cvterm_id,
|
|
|
- 'data_table' => 'project',
|
|
|
- 'type_table' => 'project',
|
|
|
- 'field' => '',
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- // TODO: WHAT TO DO IF A VOCABULARY IS USED AS A DEFAULT FOR MULTIPLE
|
|
|
- // TABLES.
|
|
|
- // Look to see if this vocabulary is used as a default for any table.
|
|
|
- $default = db_select('tripal_cv_defaults', 't')
|
|
|
- ->fields('t')
|
|
|
- ->condition('cv_id', $cvterm->cv_id->cv_id)
|
|
|
- ->execute()
|
|
|
- ->fetchObject();
|
|
|
- if ($default) {
|
|
|
- $bundle_data = array(
|
|
|
- 'cv_id' => $cvterm->cv_id->cv_id,
|
|
|
- 'cvterm_id' => $cvterm->cvterm_id,
|
|
|
- 'data_table' => $default->table_name,
|
|
|
- 'type_table' => $default->table_name,
|
|
|
- 'field' => $default->field_name,
|
|
|
- );
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Save the mapping information so that we can reuse it when we need to
|
|
|
- // look things up for later for an entity
|
|
|
- tripal_set_bundle_variable('chado_cvterm_id', $bundle->id, $bundle_data['cvterm_id']);
|
|
|
- tripal_set_bundle_variable('chado_table', $bundle->id, $bundle_data['data_table']);
|
|
|
- tripal_set_bundle_variable('chado_column', $bundle->id, $bundle_data['field']);
|
|
|
-
|
|
|
- //////////////////////////////////////////////////////////////////////////////
|
|
|
- // ADD FIELDS TO BUNDLE
|
|
|
- ////////////////////////////////////////////////////////////////////////////
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Base table fields.
|
|
|
- //
|
|
|
- // Adds the fields for the base table to the entity. Adds fields
|
|
|
- // for all columns including FK fields. Excludes primary key and the
|
|
|
- // type_id field (that's inherent in the bundle).
|
|
|
- tripal_chado_add_bundle_base_fields($entity_type, $bundle_name, $bundle_data);
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Property table fields.
|
|
|
- //
|
|
|
- // Check to see if there are any property tables with FKs to this
|
|
|
- // base table. If so, add the fields for that type of table.
|
|
|
- $prop_table = $bundle_data['data_table'] . 'prop';
|
|
|
- if (chado_table_exists($prop_table)) {
|
|
|
- tripal_chado_add_bundle_kvproperty_adder_field($entity_type, $bundle_name, $prop_table, $bundle_data['data_table']);
|
|
|
- }
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Dbxref table fields.
|
|
|
- //
|
|
|
- // Check to see if there are any dbxref tables with FKs to this
|
|
|
- // base table. If so, add the fields for that type of table.
|
|
|
- $dbxref_table = $bundle_data['data_table'] . '_dbxref';
|
|
|
- if (chado_table_exists($dbxref_table)) {
|
|
|
- tripal_chado_add_bundle_dbxref_field($entity_type, $bundle_name, $dbxref_table, $bundle_data['data_table']);
|
|
|
- }
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Cvterm table fields.
|
|
|
- //
|
|
|
- // Check to see if there are any cvterm tables with FKs to this
|
|
|
- // base table. If so, add the fields for that type of table.
|
|
|
- $cvterm_table = $bundle_data['data_table'] . '_cvterm';
|
|
|
- if (chado_table_exists($cvterm_table)) {
|
|
|
- tripal_chado_add_bundle_cvterm_class_adder_field($entity_type, $bundle_name, $cvterm_table, $bundle_data['data_table']);
|
|
|
- }
|
|
|
-
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Synonym table fields.
|
|
|
- //
|
|
|
- // Check to see if there are any synonym tables with FKs to this
|
|
|
- // base table. If so, add the fields for that type of table.
|
|
|
- $syn_table = $bundle_data['data_table'] . '_synonym';
|
|
|
- if (chado_table_exists($syn_table)) {
|
|
|
- tripal_chado_add_bundle_synonym_field($entity_type, $bundle_name, $syn_table, $bundle_data['data_table']);
|
|
|
- }
|
|
|
-
|
|
|
- ////
|
|
|
- //
|
|
|
- // Pub table fields.
|
|
|
- //
|
|
|
- // Check to see if there are any pub tables with FKs to this
|
|
|
- // base table. If so, add the fields for that type of table.
|
|
|
- $pub_table = $bundle_data['data_table'] . '_pub';
|
|
|
- if (chado_table_exists($pub_table)) {
|
|
|
- tripal_chado_add_bundle_pub_field($entity_type, $bundle_name, $pub_table, $bundle_data['data_table']);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Adds the fields for managing xrefs that are stored in a [base]_dbxref table.
|
|
|
- *
|
|
|
- * @param $entity_type
|
|
|
- * @param $bundle_name
|
|
|
- * @param $base_table
|
|
|
- * @param $dbxref_table
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_dbxref_field($entity_type_name, $bundle_name, $dbxref_table, $base_table) {
|
|
|
- // We already have a dbxref_id field.
|
|
|
- $field_name = $dbxref_table;
|
|
|
- $schema = chado_get_schema($dbxref_table);
|
|
|
- $pkey = $schema['primary key'][0];
|
|
|
-
|
|
|
- // Initialize the field array.
|
|
|
- $field_info = array(
|
|
|
- 'field_type' => 'dbxref',
|
|
|
- 'widget_type' => 'tripal_fields_dbxfref_widget',
|
|
|
- 'widget_settings' => array('display_label' => 1),
|
|
|
- 'description' => '',
|
|
|
- 'label' => 'Cross References',
|
|
|
- 'is_required' => 0,
|
|
|
- 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'field_settings' => array(
|
|
|
- // The Chado table that this field maps to.
|
|
|
- 'chado_table' => $dbxref_table,
|
|
|
- // The column in the chado table that this field maps to.
|
|
|
- 'chado_column' => $pkey,
|
|
|
- // The base table that this field is connected to.
|
|
|
- 'base_table' => $base_table,
|
|
|
- 'semantic_web' => array(
|
|
|
- // The type is the term from a vocabulary that desribes this field..
|
|
|
- 'type' => '',
|
|
|
- // The namepsace for the vocabulary (e.g. 'foaf').
|
|
|
- 'ns' => '',
|
|
|
- // The URL for the namespace. It must be that the type can be
|
|
|
- // appended to the URL.
|
|
|
- 'nsurl' => '',
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- // If the base table has a 'dbxref_id' then change the label to
|
|
|
- // indicate these are secondary cross references.
|
|
|
- $schema = chado_get_schema($base_table);
|
|
|
- if (array_key_exists('dbxref_id', $schema['fields'])) {
|
|
|
- $field_info['label'] = 'Secondary Cross References';
|
|
|
- }
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Adds the fields for managing xrefs that are stored in a [base]_dbxref table.
|
|
|
- *
|
|
|
- * @param $entity_type
|
|
|
- * @param $bundle_name
|
|
|
- * @param $base_table
|
|
|
- * @param $dbxref_table
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_synonym_field($entity_type_name, $bundle_name, $syn_table, $base_table) {
|
|
|
- // We already have a dbxref_id field.
|
|
|
- $field_name = $syn_table;
|
|
|
- $schema = chado_get_schema($syn_table);
|
|
|
- $pkey = $schema['primary key'][0];
|
|
|
-
|
|
|
- // Initialize the field array.
|
|
|
- $field_info = array(
|
|
|
- 'field_type' => 'synonym',
|
|
|
- 'widget_type' => 'tripal_fields_synonym_widget',
|
|
|
- 'widget_settings' => array('display_label' => 1),
|
|
|
- 'description' => '',
|
|
|
- 'label' => 'Synonyms',
|
|
|
- 'is_required' => 0,
|
|
|
- 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'field_settings' => array(
|
|
|
- // The Chado table that this field maps to.
|
|
|
- 'chado_table' => $syn_table,
|
|
|
- // The column in the chado table that this field maps to.
|
|
|
- 'chado_column' => $pkey,
|
|
|
- // The base table that this field is connected to.
|
|
|
- 'base_table' => $base_table,
|
|
|
- 'semantic_web' => array(
|
|
|
- // The type is the term from a vocabulary that desribes this field..
|
|
|
- 'type' => '',
|
|
|
- // The namepsace for the vocabulary (e.g. 'foaf').
|
|
|
- 'ns' => '',
|
|
|
- // The URL for the namespace. It must be that the type can be
|
|
|
- // appended to the URL.
|
|
|
- 'nsurl' => '',
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Adds the fields for managing xrefs that are stored in a [base]_dbxref table.
|
|
|
- *
|
|
|
- * @param $entity_type
|
|
|
- * @param $bundle_name
|
|
|
- * @param $base_table
|
|
|
- * @param $dbxref_table
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_pub_field($entity_type_name, $bundle_name, $pub_table, $base_table) {
|
|
|
- // We already have a dbxref_id field.
|
|
|
- $field_name = $pub_table;
|
|
|
- $schema = chado_get_schema($pub_table);
|
|
|
- $pkey = $schema['primary key'][0];
|
|
|
-
|
|
|
- // Initialize the field array.
|
|
|
- $field_info = array(
|
|
|
- 'field_type' => 'pub',
|
|
|
- 'widget_type' => 'tripal_fields_pub_widget',
|
|
|
- 'widget_settings' => array('display_label' => 1),
|
|
|
- 'description' => '',
|
|
|
- 'label' => 'Publications',
|
|
|
- 'is_required' => 0,
|
|
|
- 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'field_settings' => array(
|
|
|
- // The Chado table that this field maps to.
|
|
|
- 'chado_table' => $pub_table,
|
|
|
- // The column in the chado table that this field maps to.
|
|
|
- 'chado_column' => $pkey,
|
|
|
- // The base table that this field is connected to.
|
|
|
- 'base_table' => $base_table,
|
|
|
- 'semantic_web' => array(
|
|
|
- // The type is the term from a vocabulary that desribes this field..
|
|
|
- 'type' => '',
|
|
|
- // The namepsace for the vocabulary (e.g. 'foaf').
|
|
|
- 'ns' => '',
|
|
|
- // The URL for the namespace. It must be that the type can be
|
|
|
- // appended to the URL.
|
|
|
- 'nsurl' => '',
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Adds the fields for managing properties that are stored in a prop table.
|
|
|
- *
|
|
|
- * @param $entity_type_name
|
|
|
- * @param $bundle_name
|
|
|
- * @param $kv_table
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, $kv_table, $base_table) {
|
|
|
- $field_name = $kv_table;
|
|
|
-
|
|
|
- // Initialize the field array.
|
|
|
- $field_info = array(
|
|
|
- 'field_type' => 'kvproperty_adder',
|
|
|
- 'widget_type' => 'tripal_fields_kvproperty_adder_widget',
|
|
|
- 'field_settings' => array(
|
|
|
- 'base_table' => $base_table,
|
|
|
- ),
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'widget_settings' => array('display_label' => 1),
|
|
|
- 'description' => '',
|
|
|
- 'label' => 'Additional Properties',
|
|
|
- 'is_required' => 0,
|
|
|
- );
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Adds the fields for managing properties that are stored in a prop table.
|
|
|
- *
|
|
|
- * @param $entity_type_name
|
|
|
- * @param $bundle_name
|
|
|
- * @param $kv_table
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_cvterm_class_adder_field($entity_type_name, $bundle_name, $cvterm_table, $base_table) {
|
|
|
- // First add a generic property field so that users can add new property types.
|
|
|
- $field_name = $cvterm_table;
|
|
|
-
|
|
|
- // Initialize the field array.
|
|
|
- $field_info = array(
|
|
|
- 'field_type' => 'cvterm_class_adder',
|
|
|
- 'widget_type' => 'tripal_fields_cvterm_class_adder_widget',
|
|
|
- 'field_settings' => array(
|
|
|
- 'base_table' => $base_table,
|
|
|
- ),
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'widget_settings' => array('display_label' => 1),
|
|
|
- 'description' => '',
|
|
|
- 'label' => 'Additional Annotation Types',
|
|
|
- 'is_required' => 0,
|
|
|
- );
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Adds the fields for the base table to the entity.
|
|
|
- */
|
|
|
-function tripal_chado_add_bundle_base_fields($entity_type_name, $bundle_name, $bundle_data) {
|
|
|
-
|
|
|
- $table_name = $bundle_data['data_table'];
|
|
|
- $type_table = $bundle_data['type_table'];
|
|
|
- $type_field = $bundle_data['field'];
|
|
|
-
|
|
|
- // Iterate through the columns of the table and see if fields have been
|
|
|
- // created for each one. If not, then create them.
|
|
|
- $schema = chado_get_schema($table_name);
|
|
|
- $columns = $schema['fields'];
|
|
|
- foreach ($columns as $column_name => $details) {
|
|
|
- $field_name = $table_name . '__' . $column_name;
|
|
|
-
|
|
|
- // Skip the primary key field.
|
|
|
- if ($column_name == $schema['primary key'][0]) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Skip the type field.
|
|
|
- if ($table_name == $type_table and $column_name == $type_field) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // Get the field defaults for this column.
|
|
|
- $field_info = tripal_chado_get_table_column_field_default($table_name, $schema, $column_name);
|
|
|
-
|
|
|
-
|
|
|
- // TODO: add in a call to drupal_alter to allow other modules to change
|
|
|
- // the field settings.
|
|
|
-
|
|
|
- // Determine if the field is required.
|
|
|
- if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
|
|
|
- $field_info['is_required'] = array_key_exists('default', $details) ? 0 : 1;
|
|
|
- }
|
|
|
-
|
|
|
- // If we don't have a field type then we don't need to create a field.
|
|
|
- if (!$field_info['field_type']) {
|
|
|
- // If we don't have a field type but it is required and doesn't have
|
|
|
- // a default value then we are in trouble.
|
|
|
- if ($field_info['is_required'] and !array_key_exists('default', $details)) {
|
|
|
- throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
|
|
|
- array('%table' => $table_name, '%field' => $column_name, '%type' => $details['type'])));
|
|
|
- }
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // If this field is a foreign key field then we will have a custom field.
|
|
|
- $is_fk = FALSE;
|
|
|
- if (array_key_exists('foreign keys', $schema)) {
|
|
|
- foreach ($schema['foreign keys'] as $remote_table => $fk_details) {
|
|
|
- if (array_key_exists($column_name, $fk_details['columns'])) {
|
|
|
- $is_fk = TRUE;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Add the field to the bundle.
|
|
|
- tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Returns a $field_info array for a field based on a database column.
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_get_table_column_field_default($table_name, $schema, $column_name) {
|
|
|
- $details = $schema['fields'][$column_name];
|
|
|
-
|
|
|
- // Create an array with information about this field.
|
|
|
- $field = array(
|
|
|
- 'field_type' => '',
|
|
|
- 'widget_type' => '',
|
|
|
- 'description' => '',
|
|
|
- 'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
|
|
|
- 'is_required' => 0,
|
|
|
- 'storage' => 'field_chado_storage',
|
|
|
- 'widget_settings' => array(
|
|
|
- 'display_label' => 1
|
|
|
- ),
|
|
|
- 'field_settings' => array(
|
|
|
- // The table in Chado where this field maps to.
|
|
|
- 'chado_table' => $table_name,
|
|
|
- // The column in the Chado table that this field maps to.
|
|
|
- 'chado_column' => $column_name,
|
|
|
- 'semantic_web' => array(
|
|
|
- // The type is the term from a vocabulary that desribes this field..
|
|
|
- 'type' => '',
|
|
|
- // The namepsace for the vocabulary (e.g. 'foaf').
|
|
|
- 'ns' => '',
|
|
|
- // The URL for the namespace. It must be that the type can be
|
|
|
- // appended to the URL.
|
|
|
- 'nsurl' => '',
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- // Alter the field info array depending on the column details.
|
|
|
- switch($details['type']) {
|
|
|
- case 'char':
|
|
|
- $field['field_type'] = 'text';
|
|
|
- $field['widget_type'] = 'text_textfield';
|
|
|
- $field['field_settings']['max_length'] = $details['length'];
|
|
|
- break;
|
|
|
- case 'varchar':
|
|
|
- $field['field_type'] = 'text';
|
|
|
- $field['widget_type'] = 'text_textfield';
|
|
|
- $field['field_settings']['max_length'] = $details['length'];
|
|
|
- break;
|
|
|
- case 'text':
|
|
|
- $field['field_type'] = 'text';
|
|
|
- $field['widget_type'] = 'text_textarea';
|
|
|
- $field['field_settings']['max_length'] = 17179869184;
|
|
|
- $field['field_settings']['text_processing'] = 1;
|
|
|
- $field['format'] = filter_default_format();
|
|
|
- break;
|
|
|
- case 'blob':
|
|
|
- // not sure how to support a blob field.
|
|
|
- continue;
|
|
|
- break;
|
|
|
- case 'int':
|
|
|
- $field['field_type'] = 'number_integer';
|
|
|
- $field['widget_type'] = 'number';
|
|
|
- break;
|
|
|
- case 'float':
|
|
|
- $field['field_type'] = 'number_float';
|
|
|
- $field['widget_type'] = 'number';
|
|
|
- $field['field_settings']['precision'] = 10;
|
|
|
- $field['field_settings']['scale'] = 2;
|
|
|
- $field['field_settings']['decimal_separator'] = '.';
|
|
|
- break;
|
|
|
- case 'numeric':
|
|
|
- $field['field_type'] = 'number_decimal';
|
|
|
- $field['widget_type'] = 'number';
|
|
|
- break;
|
|
|
- case 'serial':
|
|
|
- // Serial fields are most likely not needed as a field.
|
|
|
- break;
|
|
|
- case 'boolean':
|
|
|
- $field['field_type'] = 'list_boolean';
|
|
|
- $field['widget_type'] = 'options_onoff';
|
|
|
- $field['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
|
|
|
- break;
|
|
|
- case 'datetime':
|
|
|
- // Use the Drupal Date and Date API to create the field/widget
|
|
|
- $field['field_type'] = 'datetime';
|
|
|
- $field['widget_type'] = 'date_select';
|
|
|
- $field['widget_settings']['increment'] = 1;
|
|
|
- $field['widget_settings']['tz_handling'] = 'none';
|
|
|
- $field['widget_settings']['collapsible'] = TRUE;
|
|
|
-
|
|
|
- // TODO: Add settings so that the minutes increment by 1.
|
|
|
- // And turn off the timezone, as the Chado field doesn't support it.
|
|
|
- break;
|
|
|
- }
|
|
|
|
|
|
- // Set some default semantic web information
|
|
|
- if ($column_name == 'name') {
|
|
|
- $field['field_settings']['semantic_web']['type'] = 'name';
|
|
|
- $field['field_settings']['semantic_web']['ns'] = 'foaf';
|
|
|
- $field['field_settings']['semantic_web']['nsurl'] = 'http://xmlns.com/foaf/0.1/';
|
|
|
- }
|
|
|
- if ($column_name == 'description' or $column_name == 'definition' or
|
|
|
- $column_name == 'comment') {
|
|
|
- $field['field_settings']['semantic_web']['type'] = 'description';
|
|
|
- $field['field_settings']['semantic_web']['ns'] = 'hydra';
|
|
|
- $field['field_settings']['semantic_web']['nsurl'] = 'http://www.w3.org/ns/hydra/core#';
|
|
|
- }
|
|
|
|
|
|
- //
|
|
|
- // GENERIC COLUMNS
|
|
|
- //
|
|
|
- if ($field['field_settings']['chado_column'] =='organism_id') {
|
|
|
- $field['field_type'] = 'organism_id';
|
|
|
- $field['widget_type'] = 'tripal_chado_organism_select_widget';
|
|
|
- $field['label'] = 'Organism';
|
|
|
- $field['description'] = 'Select an organism.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_column'] =='dbxref_id') {
|
|
|
- $field['field_type'] = 'dbxref_id';
|
|
|
- $field['widget_type'] = 'tripal_chado_primary_dbxref_widget';
|
|
|
- $field['label'] = 'Cross Reference';
|
|
|
- $field['description'] = 'This record can be cross referenced with a ' .
|
|
|
- 'record in another online database. The primary reference is for the ' .
|
|
|
- 'most prominent reference. At a minimum, the database and accession ' .
|
|
|
- 'must be provided. To remove a set reference, change the database ' .
|
|
|
- 'field to "Select a Database".';
|
|
|
- }
|
|
|
- elseif ($field['label'] == 'Timeaccessioned') {
|
|
|
- $field['label'] = 'Time Accessioned';
|
|
|
- $field['description'] = 'Please enter the time that this record was first added to the database.';
|
|
|
- }
|
|
|
- elseif ($field['label'] == 'Timelastmodified') {
|
|
|
- $field['label'] = 'Time Last Modified';
|
|
|
- $field['description'] = 'Please enter the time that this record was last modified. The default is the current time.';
|
|
|
- }
|
|
|
- //
|
|
|
- // ORGANISM TABLE
|
|
|
- //
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'organism' and $field['field_settings']['chado_column'] == 'comment') {
|
|
|
- $field['label'] = 'Description';
|
|
|
- }
|
|
|
- //
|
|
|
- // FEATURE TABLE
|
|
|
- //
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'uniquename') {
|
|
|
- $field['field_type'] = 'text';
|
|
|
- $field['widget_type'] = 'text_textfield';
|
|
|
- $field['field_settings']['text_processing'] = 0;
|
|
|
- $field['field_settings']['semantic_web']['type'] = 'name';
|
|
|
- $field['field_settings']['semantic_web']['ns'] = 'foaf';
|
|
|
- $field['field_settings']['semantic_web']['nsurl'] = 'http://xmlns.com/foaf/0.1/';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'md5checksum') {
|
|
|
- $field['field_type'] = 'md5checksum';
|
|
|
- $field['widget_type'] = 'tripal_chado_md5checksum_checkbox_widget';
|
|
|
- $field['label'] = 'MD5 Checksum';
|
|
|
- $field['description'] = 'Generate an MD5 checksum for the sequence.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'seqlen') {
|
|
|
- $field['field_type'] = 'seqlen';
|
|
|
- $field['widget_type'] = 'tripal_chado_seqlen_hidden_widget';
|
|
|
- $field['label'] = 'Seqlen';
|
|
|
- $field['description'] = 'The length of the residues.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'residues') {
|
|
|
- $field['field_type'] = 'residues';
|
|
|
- $field['widget_type'] = 'tripal_chado_residues_textarea_widget';
|
|
|
- $field['label'] = 'Residues';
|
|
|
- $field['description'] = 'Please provide an IUPAC compatible residues for this feature. Spaces and new lines are allowed.';
|
|
|
- }
|
|
|
- //
|
|
|
- // ANALYSIS TABLE
|
|
|
- //
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'program') {
|
|
|
- $field['field_settings']['semantic_web']['type'] = 'SoftwareApplication';
|
|
|
- $field['field_settings']['semantic_web']['ns'] = 'schema';
|
|
|
- $field['field_settings']['semantic_web']['nsurl'] = 'https://schema.org/';
|
|
|
- $field['description'] = 'The program name (e.g. blastx, blastp, sim4, genscan. If the analysis was not derived from a software package then provide a very brief description of the pipeline, workflow or method.';
|
|
|
- $field['label'] = 'Program, Pipeline, Workflow or Method Name.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'sourceuri') {
|
|
|
- $field['field_type'] = 'text';
|
|
|
- $field['widget_type'] = 'text_textfield';
|
|
|
- $field['field_settings']['text_processing'] = 0;
|
|
|
- $field['label'] = 'Source URL';
|
|
|
- $field['description'] = 'The URL where the original source data was derived. Ideally, this should link to the page where more information about the source data can be found.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'sourcename') {
|
|
|
- $field['label'] = 'Source Name';
|
|
|
- $field['description'] = 'The name of the source data. This could be a file name, data set or a small description for how the data was collected. For long descriptions use the larger description field.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'sourceversion') {
|
|
|
- $field['label'] = 'Source Version';
|
|
|
- $field['description'] = 'If hte source data set has a version include it here.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'algorithm') {
|
|
|
- $field['label'] = 'Source Version';
|
|
|
- $field['description'] = 'The name of the algorithm used to produce the dataset if different from the program.';
|
|
|
- }
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'analysis' and $field['field_settings']['chado_column'] == 'programversion') {
|
|
|
- $field['label'] = 'Program Version';
|
|
|
- $field['description'] = 'The version of the program used to perform this analysis. (e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. Enter "n/a" if no version is available or applicable.';
|
|
|
- }
|
|
|
- //
|
|
|
- // PROJECT TABLE
|
|
|
- //
|
|
|
- elseif ($field['field_settings']['chado_table'] == 'project' and $field['field_settings']['chado_column'] == 'description') {
|
|
|
- $field['label'] = 'Short Description';
|
|
|
- }
|
|
|
- return $field;
|
|
|
-}
|
|
|
|
|
|
/**
|
|
|
* Implements hook_exclude_type_by_default()
|
Stephen Ficklin