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@@ -1,4 +1,5 @@
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<?php
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+
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/**
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* @file
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* The functions for the Tripal bulk loader.
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@@ -218,11 +219,11 @@ function tripal_bulk_loader_theme() {
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* @return
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* If the permission for the specified operation is not set then return FALSE. If the
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* permission is set then return NULL as this allows other modules to disable
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- * access. The only exception is when the $op == 'create'. We will always
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+ * access. The only exception is when the $op == 'create'. We will always
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* return TRUE if the permission is set.
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* @ingroup tripal_bulk_loader
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*/
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-function tripal_bulk_loader_access($op, $node, $account) {
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+function tripal_bulk_loader_node_access($node, $op, $account) {
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if ($op == 'create') {
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if (!user_access('create tripal_bulk_loader', $account)) {
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return FALSE;
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@@ -252,7 +253,7 @@ function tripal_bulk_loader_access($op, $node, $account) {
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*
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* @ingroup tripal_bulk_loader
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*/
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-function tripal_bulk_loader_perm() {
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+function tripal_bulk_loader_permission() {
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return array(
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'access tripal_bulk_loader',
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'create tripal_bulk_loader',
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@@ -275,7 +276,7 @@ function tripal_bulk_loader_node_info() {
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$nodes = array();
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$nodes['tripal_bulk_loader'] = array(
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'name' => t('Bulk Loading Job'),
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- 'module' => 'tripal_bulk_loader',
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+ 'base' => 'tripal_bulk_loader',
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'description' => t('A bulk loader for inserting tab-delimited data into chado database'),
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'has_title' => TRUE,
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'has_body' => FALSE,
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@@ -299,9 +300,9 @@ function tripal_bulk_loader_form($node, $form_state) {
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}
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$sql = "SELECT * FROM {tripal_bulk_loader_template}";
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- $results = db_query($sql);
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+ $results = db_query($sql)->execute();
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$templates = array();
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- while ($template = db_fetch_object ($results)) {
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+ foreach ($results as $template) {
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$templates [$template->template_id] = $template->name;
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}
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@@ -376,27 +377,27 @@ function tripal_bulk_loader_form($node, $form_state) {
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* @ingroup tripal_bulk_loader
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*/
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function tripal_bulk_loader_load($node) {
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- $sql = "SELECT * FROM {tripal_bulk_loader} WHERE nid = %d";
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- $node = db_fetch_object(db_query($sql, $node->nid));
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+ $sql = "SELECT * FROM {tripal_bulk_loader} WHERE nid = :nid";
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+ $node = db_query($sql, array(':nid' => $node->nid))->fetchObject();
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$node->title = 'Bulk Loading Job: ' . $node->loader_name;
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// Add job details
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$progress = tripal_bulk_loader_progess_file_get_progress($node->job_id);
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- $sql = "SELECT * FROM {tripal_jobs} WHERE job_id=%d";
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- $node->job = db_fetch_object(db_query($sql, $node->job_id));
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+ $sql = "SELECT * FROM {tripal_jobs} WHERE job_id=:job_id";
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+ $node->job = db_query($sql, array(':job_id' => $node->job_id))->fetchObject();
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// Add the loader template
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- $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
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- $results = db_fetch_object(db_query($sql, $node->template_id));
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+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=:template";
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+ $results = db_query($sql, array(':template' => $node->template_id))->fetchObject();
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$template = unserialize($results->template_array);
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$node->template = $results;
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$node->template->template_array = $template;
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// Add inserted records
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- $sql = 'SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d';
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- $resource = db_query($sql, $node->nid);
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- while ($r = db_fetch_object($resource)) {
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+ $sql = 'SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=:nid';
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+ $resource = db_query($sql, array(':nid' => $node->nid))->execute();
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+ foreach ($resource as $r) {
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$r->num_inserted = sizeof(preg_split('/,/', $r->ids_inserted));
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$node->inserted_records->{$r->table_inserted_into} = $r;
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}
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@@ -423,9 +424,9 @@ function tripal_bulk_loader_load($node) {
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// Add constants
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- $sql = 'SELECT * FROM {tripal_bulk_loader_constants} WHERE nid=%d ORDER BY group_id, record_id, field_id';
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- $resource = db_query($sql, $node->nid);
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- while ($r = db_fetch_object($resource)) {
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+ $sql = 'SELECT * FROM {tripal_bulk_loader_constants} WHERE nid=:nid ORDER BY group_id, record_id, field_id';
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+ $resource = db_query($sql, array(':nid' => $node->nid))->execute();
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+ foreach ($resource as $r) {
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$node->constants[$r->group_id][$r->record_id][$r->field_id] = array(
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'constant_id' => $r->constant_id,
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'group_id' => $r->group_id,
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@@ -452,8 +453,17 @@ function tripal_bulk_loader_load($node) {
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function tripal_bulk_loader_insert($node) {
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// Insert into tripal_bulk_loader
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- $sql = "INSERT INTO {tripal_bulk_loader} (nid, loader_name, template_id, file, file_has_header, job_status, keep_track_inserted) VALUES (%d, '%s', %d, '%s', %d, '%s', %d)";
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- db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, 'Initialized', $node->keep_track_inserted);
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+ $sql = "INSERT INTO {tripal_bulk_loader} (nid, loader_name, template_id, file, file_has_header, job_status, keep_track_inserted) VALUES (:nid, :loader, :template, :file, :header, :status, :ids)";
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+ db_query($sql,
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+ array(':nid' => $node->nid,
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+ ':loader' => $node->loader_name,
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+ ':template' => $node->template_id,
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+ ':file' => $node->file,
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+ ':header' => $node->has_header,
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+ ':status' => 'Initialized',
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+ ':ids' => $node->keep_track_inserted
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+ )
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+ )->execute();
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// Update title
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$node->title =$node->loader_name;
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@@ -471,8 +481,8 @@ function tripal_bulk_loader_insert($node) {
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* @ingroup tripal_bulk_loader
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*/
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function tripal_bulk_loader_delete($node) {
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- $sql = "DELETE FROM {tripal_bulk_loader} WHERE nid = %d";
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- db_query($sql, $node->nid);
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+ $sql = "DELETE FROM {tripal_bulk_loader} WHERE nid = :nid";
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+ db_query($sql, array(':nid' => $node->nid))->execute();
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}
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/**
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@@ -484,8 +494,17 @@ function tripal_bulk_loader_delete($node) {
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function tripal_bulk_loader_update($node) {
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// Update tripal_bulk_loader
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- $sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s', keep_track_inserted = %d WHERE nid = %d";
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- db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, $node->keep_track_inserted, $node->nid);
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+ $sql = "UPDATE {tripal_bulk_loader} SET nid = :nid, loader_name = :loader, template_id = :template, file = :file, file_has_header = :header, keep_track_inserted = :ids WHERE nid = :wherenid";
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+ db_query($sql,
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+ array(':nid' => $node->nid,
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+ ':loader' => $node->loader_name,
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+ ':template' => $node->template_id,
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+ ':file' => $node->file,
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+ ':header' => $node->has_header,
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+ ':ids' => $node->keep_track_inserted,
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+ ':wherenid' => $node->nid
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+ )
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+ )->execute();
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// Add a job if the user want to load the data
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global $user;
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@@ -514,7 +533,7 @@ function tripal_bulk_loader_update($node) {
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function tripal_bulk_loader_preprocess_tripal_bulk_loader_template(&$variables) {
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$sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
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- $template = db_fetch_object(db_query($sql, $variables['template_id']));
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+ $template = db_query($sql, array(':template' => $variables['template_id']))->fetchObject();
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$template->template_array = unserialize($template->template_array);
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$variables['template'] = $template;
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@@ -550,7 +569,7 @@ function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress
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$num_lines = trim(`wc --lines < $filename`);
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$num_records = trim(`grep -o "." $filename | wc --lines`);
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- $job = db_fetch_object(db_query("SELECT j.*, b.file, b.file_has_header, c.num as num_constant_sets
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+ $job = db_query("SELECT j.*, b.file, b.file_has_header, c.num as num_constant_sets
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FROM {tripal_jobs} j
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LEFT JOIN {tripal_bulk_loader} b ON b.job_id=j.job_id
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LEFT JOIN (
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@@ -558,7 +577,7 @@ function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress
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FROM {tripal_bulk_loader_constants}
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GROUP BY nid
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) c ON c.nid=b.nid
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- WHERE j.job_id=%d", $job_id));
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+ WHERE j.job_id=:job", array(':job' =>$job_id))->execute();
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if ($job->num_constant_sets) {
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$num_constant_sets_loaded = round($job->progress / (100 / $job->num_constant_sets), 4);
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Lacey Sanderson