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+<?php
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+namespace Tests\tripal_chado\api;
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+
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+use StatonLab\TripalTestSuite\DBTransaction;
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+use StatonLab\TripalTestSuite\TripalTestCase;
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+
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+class TripalChadoMViewsAPITest extends TripalTestCase {
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+
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+ // Use a transaction to roll back changes after every test.
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+ use DBTransaction;
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+
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+ // This variable holds example materialized views that can be used
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+ // by the unit tests below.
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+ private $example_mviews = [
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+ 'analysis_organism_test' => [
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+ 'schema' => [
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+ 'table' => 'analysis_organism_test',
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+ 'description' => 'This view is for associating an organism (via it\'s associated features) to an analysis.',
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+ 'fields' => [
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+ 'analysis_id' => [
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => true,
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+ ],
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+ 'organism_id' => [
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => true,
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+ ],
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+ ],
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+ 'indexes' => [
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+ 'networkmod_qtl_indx0' => [
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+ 0 => 'analysis_id',
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+ ],
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+ 'networkmod_qtl_indx1' => [
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+ 0 => 'organism_id',
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+ ],
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+ ],
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+ 'foreign keys' => [
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+ 'analysis' => [
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+ 'table' => 'analysis',
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+ 'columns' => [
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+ 'analysis_id' => 'analysis_id',
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+ ],
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+ ],
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+ 'organism' => [
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+ 'table' => 'organism',
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+ 'columns' => [
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+ 'organism_id' => 'organism_id',
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+ ],
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+ ],
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+ ],
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+ ],
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+ 'sql' => "
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+ SELECT DISTINCT A.analysis_id, O.organism_id
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+ FROM analysis A
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+ INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id
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+ INNER JOIN feature F ON AF.feature_id = F.feature_id
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+ INNER JOIN organism O ON O.organism_id = F.organism_id
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+ ",
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+ 'comment' => 'This view is for associating an organism (via it\'s associated features) to an analysis.',
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+ 'module' => 'tripal_chado',
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+ ],
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+ ];
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+
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+ /**
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+ * Test creation of a new materialized view.
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+ *
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+ * @group api
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+ */
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+ public function test_chado_add_mview() {
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+
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+ // Add the analysis_organism mview.
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+ $mview_name = 'analysis_organism_test';
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+ $mview_module = $this->example_mviews[$mview_name]['module'];
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+ $mview_sql = $this->example_mviews[$mview_name]['sql'];
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+ $mview_schema = $this->example_mviews[$mview_name]['schema'];
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+ $mview_comment = $this->example_mviews[$mview_name]['comment'];
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+ $success = chado_add_mview($mview_name, $mview_module, $mview_schema, $mview_sql, $mview_comment, FALSE);
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+ $this->assertTrue($success, "Failed to create materialized view: $mview_name");
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+
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+ // Make sure that the entry is now there.
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+ $mview = db_select('tripal_mviews', 'tm')
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+ ->fields('tm')
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+ ->condition('name', $mview_name)
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+ ->execute()
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+ ->fetchObject();
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+ $this->assertTrue(is_object($mview),
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+ "Failed to find the materialized view, $mview_name, in the tripal_mviews table");
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+
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+ // Make sure that all of the fields exist and were properly added.
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+ $this->assertTrue($mview->modulename == $mview_module,
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+ "Failed to create a proper materialized the modulename field is incorrect: '$mview_module' != '$mview->modulename'");
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+ $this->assertTrue($mview->mv_table == $mview_name,
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+ "Failed to create a proper materialized the mv_table field does not match input.");
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+ $this->assertTrue($mview->query == $mview_sql,
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+ "Failed to create a proper materialized the query field does not match input.");
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+ $this->assertTrue($mview->comment == $mview_comment,
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+ "Failed to create a proper materialized the comment field does not match input.");
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+ $this->assertNULL($mview->status,
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+ "Failed to create a proper materialized the status field should be NULL.");
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+ $this->assertNULL($mview->last_update,
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+ "Failed to create a proper materialized the last_update field should be NULL.");
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+
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+ // Make sure the table exists.
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+ $this->assertTrue(chado_table_exists($mview_name),
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+ "Materialized view, $mview_name, was added to the tripal_mviews table but the table was not created.");
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+
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+ $this->reset_tables();
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+ }
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+ /**
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+ * Test deletion of a materialized view.
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+ *
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+ * @group api
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+ */
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+ public function test_chado_delete_mview() {
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+
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+ // Make sure the mview is present.
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+ $mview_name = 'analysis_organism_test';
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+ $mview_module = $this->example_mviews[$mview_name]['module'];
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+ $mview_sql = $this->example_mviews[$mview_name]['sql'];
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+ $mview_schema = $this->example_mviews[$mview_name]['schema'];
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+ $mview_comment = $this->example_mviews[$mview_name]['comment'];
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+ $success = chado_add_mview($mview_name, $mview_module, $mview_schema, $mview_sql, $mview_comment, FALSE);
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+ $this->assertTrue($success, "Failed to create materialized view: $mview_name");
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+
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+ // Get the mview_id.
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+ $mview = db_select('tripal_mviews', 'tm')
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+ ->fields('tm')
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+ ->condition('name', $mview_name)
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+ ->execute()
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+ ->fetchObject();
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+ $this->assertTrue(is_object($mview),
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+ "Failed to find the materialized view, $mview_name, in the tripal_mviews table");
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+ $mview_id = $mview->mview_id;
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+
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+ // Now run the API function to delete it.
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+ $success = chado_delete_mview($mview_id);
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+ $this->assertTrue($success,
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+ "Materialized view, $mview_name, could not be deleted.");
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+
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+ $this->reset_tables();
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+
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+ // Make sure the table is gone.
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+ $this->assertFalse(chado_table_exists($mview_name),
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+ "Materialized view, $mview_name, table failed to be removed after deletion.");
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+
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+ }
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+
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+ /**
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+ * Test modifications to a materialized view
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+ *
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+ * @group api
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+ */
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+ public function test_chado_edit_mview() {
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+
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+ $this->reset_tables();
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+ }
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+ /**
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+ * Test adding a Tripal Job to re-populate a materialized view
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+ *
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+ * @group api
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+ */
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+ public function test_chado_refresh_mview() {
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+
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+ $this->reset_tables();
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+ }
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+ /**
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+ * Test re-populating a materialized view.
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+ *
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+ * @group api
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+ */
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+ public function test_chado_populate_mview() {
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+
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+ $this->reset_tables();
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+ }
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+ /**
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+ * Test modifications to a materialized view
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+ *
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+ * @group api
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+ */
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+ public function test_chado_get_mview_id() {
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+
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+ $this->reset_tables();
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+ }
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+ /**
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+ * Test retrieving names of the materialized views.
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+ *
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+ * @group api
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+ */
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+ public function test_chado_get_mview_table_names() {
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+ $this->reset_tables();
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+ }
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+ /**
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+ * Test retrieving all materialized view objects.
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+ *
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+ * @group api
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+ */
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+ public function test_chado_get_mviews() {
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+
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+ // TODO: this is currently a stub for a test function that neds
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+ // implementation. For now it returns true to get past unit testing.
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+ $this->assertTrue(true);
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+
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+ $this->reset_tables();
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+ }
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+
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+ /**
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+ * Issue 322 reported the problem of re-adding a materialized view after
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+ * the actual table had been manually removed outside of Tripal. The
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+ * function reported errors.
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+ *
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+ * @ticket 322
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+ */
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+ public function test_re_adding_deleted_mview_issue_322() {
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+
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+ // Add the analysis_organism mview.
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+ $mview_name = 'analysis_organism_test';
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+ $mview_module = $this->example_mviews[$mview_name]['module'];
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+ $mview_sql = $this->example_mviews[$mview_name]['sql'];
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+ $mview_schema = $this->example_mviews[$mview_name]['schema'];
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+ $mview_comment = $this->example_mviews[$mview_name]['comment'];
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+ $success = chado_add_mview($mview_name, $mview_module, $mview_schema, $mview_sql, $mview_comment, FALSE);
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+ $this->assertTrue($success, "Failed to create materialized view: $mview_name");
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+
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+ // Now simulate manual deletion of the table outside of the API.
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+ chado_query('DROP TABLE {' . $mview_name . '}');
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+
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+ // Make sure the table no longer exists.
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+ $this->assertFalse(chado_table_exists($mview_name),
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+ "Failed to manually remove the materialized view, cannot complete the test.");
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+
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+ // Now try to read the mview. Previously, the behavior was the the mview
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+ // table would not be created because Tripal thinks it's already there.
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+ $success = chado_add_mview($mview_name, $mview_module, $mview_schema, $mview_sql, $mview_comment, FALSE);
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+ $this->assertTrue($success, "Failed to re-create materialized view: $mview_name");
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+
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+ // Now make sure the mview table exists.
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+ $this->reset_tables();
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+ $this->assertTrue(chado_table_exists($mview_name),
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+ "Manually removing a materialized views throws off the chado_add_mview function when the mview is re-added. See Issue #322");
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+
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+ $this->reset_tables();
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+ }
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+
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+ /**
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+ * The chado_table_exists() function mantains a global variable to keep track
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+ * of which tables exist. If the table exists then it stores that info in
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+ * the global variable. This is because lots of queries perform a check to
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+ * see if the tables exist and that can have a major performance hit.
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+ *
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+ * Because we are creating and dropping Chado tables in our tests it throws
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+ * off the array and we need to reset it. Normally this isn't a problem
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+ * because this would get reset on every page load anyone. For testing it
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+ * doesn't.
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+ */
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+ public function reset_tables() {
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+ $GLOBALS["chado_tables"] = [];
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+ }
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+}
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Lacey-Anne Sanderson