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@@ -345,13 +345,31 @@ function tripal_chado_migrate_form_validate($form, &$form_state) {
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// Check if CV exists in the tripal_cv_defaults table. If not, do not proceed to migration
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foreach ($tv3_content_types AS $type) {
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$voc = $type['vocabulary'];
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- $cv = tripal_get_cv(array('name' => $voc));
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- if (!$cv || $voc == 'local') {
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+ $acc = $type['accession'];
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+ $term_name = $type['term_name'];
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+ $match = array(
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+ 'dbxref_id' => array(
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+ 'db_id' => array(
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+ 'name' => $voc,
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+ ),
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+ 'accession' => $acc
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+ ),
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+ );
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+ $cvterm = chado_generate_var('cvterm', $match);
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+ if ($voc == 'local' || !$cvterm) {
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+ // Ignore local terms
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continue;
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}
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- $default = tripal_get_default_cv_table($cv->cv_id);
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+ $default = tripal_get_default_cv_table($cvterm->cv_id->cv_id);
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if (!$default) {
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- form_set_error('', "'$voc' is not a " . l('Default Vocabulary', 'admin/tripal/storage/chado/vocab') . ". Migration can not be proceeded.");
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+ form_set_error('',
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+ t("'@voc' is not a ". l('Default Vocabulary', 'admin/tripal/storage/chado/vocab') . ". '@cvterm' can not be migrated.",
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+ array(
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+ '@voc' => $voc,
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+ '@cvterm' => $cvterm->name
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+ )
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+ )
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+ );
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}
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}
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}
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@@ -623,8 +641,8 @@ function tripal_chado_migrate_map_types($tv2_content_types) {
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}
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else if ($table == 'organism') {
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array_push($types, array(
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- 'vocabulary' => 'OBI',
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- 'accession' => '0100026',
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+ 'vocabulary' => 'local',
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+ 'accession' => 'organism',
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'term_name' => 'organism'
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));
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}
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