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@@ -0,0 +1,112 @@
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+<?php
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+
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+/**
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+ * This function populates the Tripal entity tables using existing
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+ * data in the database.
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+ */
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+function tripal_entities_populate_entity_tables() {
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+ // Get the cvterm table and look for all of the tables that link to it.
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+ $schema = chado_get_schema('cvterm');
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+ $referring = $schema['referring_tables'];
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+
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+ // Perform this action in a transaction
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+ $transaction = db_transaction();
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+ print "\nNOTE: Populating of tripal entity tables is performed using a database transaction. \n" .
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+ "If the load fails or is terminated prematurely then the entire set of \n" .
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+ "insertions/updates is rolled back and will not be found in the database\n\n";
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+ try {
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+
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+ // Iterate through the referring tables to see what records are there.
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+ foreach ($referring as $tablename) {
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+
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+ // We only want to look at base tables.
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+ if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
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+ $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
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+ $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
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+ preg_match('/_cvterm$/', $tablename)) {
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+ continue;
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+ }
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+
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+ print "Examining $tablename...\n";
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+ $ref_schema = chado_get_schema($tablename);
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+ $fkeys = $ref_schema['foreign keys'];
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+ foreach ($fkeys['cvterm']['columns'] as $local_id => $remote_id) {
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+
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+ // Get the list of cvterm_ids from existing records in the table.
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+ $sql = "
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+ SELECT $local_id
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+ FROM { " . $tablename . "}
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+ GROUP BY $local_id
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+ ";
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+ $results = chado_query($sql);
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+ while ($cvterm_id = $results->fetchField()) {
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+
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+ // Get the CV term details and add it to the tripal_entity_type table if
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+ // it doesn't already exist.
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+ $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
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+
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+ // First add a record to the tripal_entity_type table.
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+ $values = array(
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+ 'cv_id' => $cvterm->cv_id->cv_id,
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+ 'db_id' => $cvterm->dbxref_id->db_id->db_id,
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+ 'publish' => 0,
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+ );
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+ $entity_type_id = 0;
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+ $entity_type = chado_select_record('tripal_entity_type', array('entity_type_id'), $values);
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+ if (count($entity_type) == 0) {
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+ $entity_type = chado_insert_record('tripal_entity_type', $values);
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+ $entity_type_id = $entity_type['entity_type_id'];
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+ }
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+ else {
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+ $entity_type_id = $entity_type[0]->entity_type_id;
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+ }
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+
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+ // Next add a record to the tripal_entity_bundle table.
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+ $values = array(
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+ 'entity_type_id' => $entity_type_id,
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+ 'cvterm_id' => $cvterm_id,
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+ 'publish' => 0
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+ );
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+ $bundle_id = 0;
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+ $bundle = chado_select_record('tripal_entity_bundle', array('bundle_id'), $values);
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+ if (count($bundle) == 0) {
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+ $bundle = chado_insert_record('tripal_entity_bundle', $values);
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+ $bundle_id = $bundle['bundle_id'];
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+ }
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+ else {
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+ $bundle_id = $bundle[0]->bundle_id;
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+ }
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+
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+ // Add the table where the records are found.
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+ $values = array(
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+ 'bundle_id' => $bundle_id,
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+ 'data_table' => $tablename,
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+ 'type_table' => $tablename,
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+ 'field' => $local_id
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+ );
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+ if (!chado_select_record('tripal_entity_bundle_source', array('bundle_source_id'), $values, array('has_record' => TRUE))) {
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+ chado_insert_record('tripal_entity_bundle_source', $values);
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+ }
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+
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+ // Add the table where the records are found.
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+ $values = array(
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+ 'entity_type_id' => $entity_type_id,
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+ 'data_table' => $tablename,
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+ 'type_table' => $tablename,
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+ 'field' => $local_id
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+ );
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+ if (!chado_select_record('tripal_entity_type_source', array('entity_type_id'), $values, array('has_record' => TRUE))) {
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+ chado_insert_record('tripal_entity_type_source', $values);
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+ }
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+ }
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+ }
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+ }
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+ }
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+ catch (Exception $e) {
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+ print "\n"; // make sure we start errors on new line
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+ $transaction->rollback();
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+ watchdog_exception('tripal_ws', $e);
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+ print "FAILED: Rolling back database changes...\n";
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+ }
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+ print "\nDone.\n";
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+}
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Stephen Ficklin