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@@ -135,11 +135,6 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => $column_name,
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- 'base_table' => $table_name,
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- ),
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);
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// Alter the field info array depending on the column details.
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@@ -235,11 +230,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => 'organism_id',
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -255,12 +245,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => 'dbxref_id',
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- 'base_table' => $table_name,
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- 'semantic_web' => tripal_get_chado_semweb_term($table_name, 'dbxref_id'),
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- ),
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);
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}
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@@ -276,12 +260,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => 'md5checksum',
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- 'base_table' => $table_name,
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- 'semantic_web' => tripal_get_chado_semweb_term($table_name, 'md5checksum'),
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- ),
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);
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}
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@@ -297,11 +275,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => 'residues',
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -317,11 +290,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $table_name,
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- 'chado_column' => 'seqlen',
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -338,11 +306,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $rel_table,
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- 'chado_column' => '',
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -359,8 +322,6 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
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// 'type' => 'field_chado_storage',
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// ),
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// 'settings' => array(
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-// 'chado_table' => 'organism',
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-// 'chado_column' => 'type_id',
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// ),
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// );
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// }
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@@ -393,20 +354,12 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $contact_table,
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- 'base_table' => $table_name,
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- 'chado_column' => 'contact_id',
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- ),
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);
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}
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// DBXREF
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$dbxref_table = $table_name . '_dbxref';
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if (chado_table_exists($dbxref_table)) {
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- $dbxref_table = $table_name . '_dbxref';
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- $schema = chado_get_schema($dbxref_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'sbo__database_cross_reference';
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$field_type = 'sbo__database_cross_reference';
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$info[$field_name] = array(
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@@ -417,19 +370,12 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $dbxref_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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// EXPRESSION
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$expression_table = $table_name . '_expression';
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if (chado_table_exists($expression_table)) {
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- $schema = chado_get_schema($expression_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'go__gene_expression';
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$field_type = 'go__gene_expression';
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$info[$field_name] = array(
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@@ -440,18 +386,11 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $expression_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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// FEATURELOC
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if ($table_name == 'feature') {
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- $schema = chado_get_schema('featureloc');
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- $pkey = $schema['primary key'][0];
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$field_name = 'data__sequence_coordinates';
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$field_type = 'data__sequence_coordinates';
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$info[$field_name] = array(
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@@ -462,18 +401,11 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => 'featureloc',
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- 'chado_column' => $pkey,
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- 'base_table' => 'feature',
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- ),
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);
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}
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// FEATUREPOS
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if ($table_name == 'feature') {
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- $schema = chado_get_schema('featurepos');
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- $pkey = $schema['primary key'][0];
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$field_name = 'ogi__location_on_map';
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$field_type = 'ogi__location_on_map';
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$info[$field_name] = array(
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@@ -484,19 +416,12 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => 'featurepos',
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- 'chado_column' => $pkey,
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- 'base_table' => 'feature',
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- ),
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);
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}
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// GENOTYPE
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$genotype_table = $table_name . '_genotype';
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if (chado_table_exists($genotype_table)) {
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- $schema = chado_get_schema($genotype_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'so__genotype';
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$field_type = 'so__genotype';
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$info[$field_name] = array(
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@@ -507,19 +432,12 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $genotype_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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// PHENOTYPE
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$phenotype_table = $table_name . '_phenotype';
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if (chado_table_exists($phenotype_table)) {
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- $schema = chado_get_schema($phenotype_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'sbo__phenotype';
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$field_type = 'sbo__phenotype';
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$info[$field_name] = array(
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@@ -530,11 +448,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $phenotype_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -544,11 +457,9 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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// Get the list of existing property types for this table.
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$sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
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$props = chado_query($sql);
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- $schema = chado_get_schema($prop_table);
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- $pkey = $schema['primary key'][0];
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while ($prop = $props->fetchObject()) {
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$term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));
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- $field_name = strtolower($term->dbxref_id->db_id->name . '__' . $term->name);
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+ $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
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$field_type = 'chado_linker__prop';
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$info[$field_name] = array(
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'field_name' => $field_name,
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@@ -558,11 +469,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'base_table' => $table_name,
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- 'chado_table' => $prop_table,
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- 'chado_column' => $pkey,
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- ),
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);
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}
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}
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@@ -570,8 +476,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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// PUBLICATIONS
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$pub_table = $table_name . '_pub';
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if (chado_table_exists($pub_table)) {
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- $schema = chado_get_schema($pub_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'schema__publication';
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$field_type = 'schema__publication';
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$info[$field_name] = array(
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@@ -582,11 +486,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $pub_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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@@ -594,8 +493,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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// If the linker table does not exists then we don't want to add attach.
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$rel_table = $table_name . '_relationship';
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if (chado_table_exists($rel_table)) {
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- $schema = chado_get_schema($rel_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'sbo__relationship';
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$field_type = 'sbo__relationship';
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$info[$field_name] = array(
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@@ -606,19 +503,12 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'storage' => array(
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'type' => 'field_chado_storage',
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),
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- 'settings' => array(
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- 'chado_table' => $rel_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- ),
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);
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}
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// SYNONYMS
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$syn_table = $table_name . '_synonym';
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if (chado_table_exists($syn_table)) {
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- $schema = chado_get_schema($syn_table);
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- $pkey = $schema['primary key'][0];
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$field_name = 'schema__alternate_name';
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$field_type = 'schema__alternate_name';
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$info[$field_name] = array(
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@@ -630,9 +520,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
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'type' => 'field_chado_storage',
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),
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'settings' => array(
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- 'chado_table' => $syn_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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),
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);
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}
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@@ -745,6 +632,9 @@ function tripal_chado_bundle_create_instances_base(&$info, $entity_type, $bundle
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'term_vocabulary' => $cvterm->dbxref_id->db_id->name,
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'term_name' => $cvterm->name,
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'term_accession' => $cvterm->dbxref_id->accession,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => $column_name,
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'settings' => array(
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@@ -906,6 +796,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => $is_required,
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'settings' => array(
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'auto_attach' => TRUE,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => 'organism_id',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'type' => 'obi__organism_widget',
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@@ -936,6 +829,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => FALSE,
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'settings' => array(
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'auto_attach' => TRUE,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => 'dbxref_id',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'type' => 'data__accession_widget',
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@@ -969,6 +865,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => FALSE,
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'settings' => array(
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'auto_attach' => TRUE,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => 'md5checksum',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'type' => 'data__sequence_checksum_widget',
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@@ -999,6 +898,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => FALSE,
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'settings' => array(
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'auto_attach' => FALSE,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => 'residues',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'type' => 'data__sequence_widget',
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@@ -1031,6 +933,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => FALSE,
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'settings' => array(
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'auto_attach' => TRUE,
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+ 'chado_table' => $table_name,
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+ 'chado_column' => 'seqlen',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
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'type' => 'data__sequence_length_widget',
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@@ -1061,6 +966,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
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'required' => FALSE,
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'settings' => array(
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'auto_attach' => FALSE,
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+ 'chado_table' => $rel_table,
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+ 'chado_column' => '',
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+ 'base_table' => $table_name,
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),
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'widget' => array(
|
|
|
'type' => 'so__transcript_widget',
|
|
|
@@ -1090,6 +998,9 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
|
|
|
// 'required' => FALSE,
|
|
|
// 'settings' => array(
|
|
|
// 'auto_attach' => TRUE,
|
|
|
+// 'chado_table' => 'organism',
|
|
|
+// 'chado_column' => 'type_id',
|
|
|
+// 'base_table' => 'organism',
|
|
|
// ),
|
|
|
// 'widget' => array(
|
|
|
// 'type' => 'taxarank__infraspecific_taxon_widget',
|
|
|
@@ -1135,6 +1046,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $contact_table,
|
|
|
+ 'base_table' => $table_name,
|
|
|
+ 'chado_column' => 'contact_id',
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'local__contact_widget',
|
|
|
@@ -1144,7 +1058,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
),
|
|
|
'display' => array(
|
|
|
'default' => array(
|
|
|
- 'label' => 'inline',
|
|
|
+ 'label' => 'above',
|
|
|
'type' => 'local__contact_formatter',
|
|
|
'settings' => array(),
|
|
|
),
|
|
|
@@ -1156,6 +1070,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$dbxref_table = $table_name . '_dbxref';
|
|
|
if (chado_table_exists($dbxref_table)) {
|
|
|
$field_name = 'sbo__database_cross_reference';
|
|
|
+ $schema = chado_get_schema($dbxref_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1165,6 +1081,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $dbxref_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'sbo__database_cross_reference_widget',
|
|
|
@@ -1186,6 +1105,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$expression_table = $table_name . '_expression';
|
|
|
if (chado_table_exists($expression_table)) {
|
|
|
$field_name = 'go__gene_expression';
|
|
|
+ $schema = chado_get_schema($expression_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1195,6 +1116,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $expression_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'go__gene_expression_widget',
|
|
|
@@ -1215,6 +1139,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
// FEATURELOC
|
|
|
if ($table_name == 'feature') {
|
|
|
$field_name = 'data__sequence_coordinates';
|
|
|
+ $schema = chado_get_schema('featureloc');
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1225,6 +1151,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => 'featureloc',
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => 'feature',
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'data__sequence_coordinates_widget',
|
|
|
@@ -1245,6 +1174,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
// FEATUREPOS
|
|
|
if ($table_name == 'feature') {
|
|
|
$field_name = 'ogi__location_on_map';
|
|
|
+ $schema = chado_get_schema('featurepos');
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1254,6 +1185,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => 'featurepos',
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => 'feature',
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'ogi__location_on_map_widget',
|
|
|
@@ -1275,6 +1209,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$genotype_table = $table_name . '_genotype';
|
|
|
if (chado_table_exists($genotype_table)) {
|
|
|
$field_name = 'so__genotype';
|
|
|
+ $schema = chado_get_schema($genotype_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1284,6 +1220,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $genotype_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'so__genotype_widget',
|
|
|
@@ -1305,6 +1244,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$phenotype_table = $table_name . '_phenotype';
|
|
|
if (chado_table_exists($phenotype_table)) {
|
|
|
$field_name = 'sbo__phenotype';
|
|
|
+ $schema = chado_get_schema($phenotype_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1314,6 +1255,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $phenotype_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'sbo__phenotype_widget',
|
|
|
@@ -1331,17 +1275,17 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
);
|
|
|
}
|
|
|
|
|
|
- // TODO: we need to add a property for each type that already exists
|
|
|
- // in the prop table.
|
|
|
- // PROPERTIES
|
|
|
- $prop_table = $table_name . 'prop';
|
|
|
- if (chado_table_exists($prop_table)) {
|
|
|
+ // PROPERTIES
|
|
|
+ $prop_table = $table_name . 'prop';
|
|
|
+ if (chado_table_exists($prop_table)) {
|
|
|
// Get the list of existing property types for this table.
|
|
|
$sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
|
|
|
$props = chado_query($sql);
|
|
|
+ $schema = chado_get_schema($prop_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
while ($prop = $props->fetchObject()) {
|
|
|
$term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));
|
|
|
- $field_name = strtolower($term->dbxref_id->db_id->name . '__' . $term->name);
|
|
|
+ $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1354,6 +1298,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'term_vocabulary' => $term->dbxref_id->db_id->name,
|
|
|
'term_accession' => $term->dbxref_id->accession,
|
|
|
'term_name' => $term->name,
|
|
|
+ 'base_table' => $table_name,
|
|
|
+ 'chado_table' => $prop_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'chado_linker__prop_widget',
|
|
|
@@ -1377,16 +1324,20 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$pub_table = $table_name . '_pub';
|
|
|
if (chado_table_exists($pub_table)) {
|
|
|
$field_name = 'schema__publication';
|
|
|
+ $schema = chado_get_schema($pub_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
'bundle' => $bundle->name,
|
|
|
'label' => 'Publication',
|
|
|
- 'description' => 'This record has been referenced or is sourced from
|
|
|
- these publications.',
|
|
|
+ 'description' => 'This record has been referenced or is sourced from these publications.',
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $pub_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'schema__publication_widget',
|
|
|
@@ -1409,6 +1360,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$rel_table = $table_name . '_relationship';
|
|
|
if (chado_table_exists($rel_table)) {
|
|
|
$field_name = 'sbo__relationship';
|
|
|
+ $schema = chado_get_schema($rel_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1418,6 +1371,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $rel_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'sbo__relationship_widget',
|
|
|
@@ -1439,6 +1395,8 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
$syn_table = $table_name . '_synonym';
|
|
|
if (chado_table_exists($syn_table)) {
|
|
|
$field_name = 'schema__alternate_name';
|
|
|
+ $schema = chado_get_schema($syn_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
$info[$field_name] = array(
|
|
|
'field_name' => $field_name,
|
|
|
'entity_type' => $entity_type,
|
|
|
@@ -1448,6 +1406,9 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
|
|
|
'required' => FALSE,
|
|
|
'settings' => array(
|
|
|
'auto_attach' => FALSE,
|
|
|
+ 'chado_table' => $syn_table,
|
|
|
+ 'chado_column' => $pkey,
|
|
|
+ 'base_table' => $table_name,
|
|
|
),
|
|
|
'widget' => array(
|
|
|
'type' => 'schema__alternate_name_widget',
|
|
|
@@ -1628,3 +1589,76 @@ function tripal_chado_form_field_ui_field_overview_add_new($new_field, $bundle)
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Allows for altering of a field's instance setting form.
|
|
|
+ *
|
|
|
+ * This appears to be a Drupal hook but is actually a custom function created
|
|
|
+ * by this module. It is called by the tripal_form_alter() function of this
|
|
|
+ * module.
|
|
|
+ *
|
|
|
+ * Here we put additional form elements for any field, regardless if it is
|
|
|
+ * a tripalField or not.
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form array. Alterations to the form can be made within this array.
|
|
|
+ * @param $form_state
|
|
|
+ * The form state array.
|
|
|
+ */
|
|
|
+function tripal_chado_field_instance_settings_form_alter(&$form, $form_state) {
|
|
|
+ global $language;
|
|
|
+ $field = $form['#field'];
|
|
|
+ $instance = $form['#instance'];
|
|
|
+
|
|
|
+ // Construct a table for the vocabulary information.
|
|
|
+ $headers = array();
|
|
|
+ $rows = array();
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Base Table',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ $instance['settings']['base_table']
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'Record Table',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ $instance['settings']['chado_table']
|
|
|
+ );
|
|
|
+ $rows[] = array(
|
|
|
+ array(
|
|
|
+ 'data' => 'ID Column',
|
|
|
+ 'header' => TRUE,
|
|
|
+ 'width' => '20%',
|
|
|
+ ),
|
|
|
+ $instance['settings']['chado_column']
|
|
|
+ );
|
|
|
+ $table = array(
|
|
|
+ 'header' => $headers,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => array(
|
|
|
+ ),
|
|
|
+ 'sticky' => FALSE,
|
|
|
+ 'caption' => '',
|
|
|
+ 'colgroups' => array(),
|
|
|
+ 'empty' => '',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['chado_mapping'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Chado Mapping',
|
|
|
+ '#description' => t('This field maps to data in Chado to the following table:'),
|
|
|
+ '#prefix' => '<div id = "tripal-field-term-fieldset">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+ $form['chado_mapping']['details'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#markup' => theme_table($table),
|
|
|
+ );
|
|
|
+
|
|
|
+}
|
Stephen Ficklin