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@@ -139,28 +139,28 @@ function chado_analysis_insert($node) {
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// If the analysis doesn't exist then let's create it in chado.
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if (!$analysis) {
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- // insert and then get the newly inserted analysis record
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- $values = array(
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- 'name' => $node->analysisname,
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- 'description' => $node->description,
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- 'program' => $node->program,
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- 'programversion' => $node->programversion,
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- 'algorithm' => $node->algorithm,
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- 'sourcename' => $node->sourcename,
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- 'sourceversion' => $node->sourceversion,
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- 'sourceuri' => $node->sourceuri,
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- 'timeexecuted' => $timestamp
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- );
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- if (tripal_core_chado_insert('analysis', $values)) {
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- $analysis = tripal_core_chado_select('analysis', array('*'), $values);
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- $analysis_id = $analysis[0]->analysis_id;
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- }
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+ // insert and then get the newly inserted analysis record
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+ $values = array(
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+ 'name' => $node->analysisname,
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+ 'description' => $node->description,
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+ 'program' => $node->program,
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+ 'programversion' => $node->programversion,
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+ 'algorithm' => $node->algorithm,
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+ 'sourcename' => $node->sourcename,
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+ 'sourceversion' => $node->sourceversion,
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+ 'sourceuri' => $node->sourceuri,
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+ 'timeexecuted' => $timestamp
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+ );
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+ if (tripal_core_chado_insert('analysis', $values)) {
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+ $analysis = tripal_core_chado_select('analysis', array('*'), $values);
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+ $analysis_id = $analysis[0]->analysis_id;
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+ }
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}
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// Make sure the entry for this analysis doesn't already exist in the
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// chado_analysis table if it doesn't exist then we want to add it.
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$node_check_sql = "SELECT * FROM {chado_analysis} ".
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- "WHERE analysis_id = %d";
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+ "WHERE analysis_id = %d";
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$node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
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if (!$node_check) {
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// next add the item to the drupal table
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@@ -184,16 +184,16 @@ function chado_analysis_insert($node) {
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drupal_write_record('node_revisions', $record, 'nid');
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}
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- // add the analysis to the node object for
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- // use by other analysis modules that may be using this function
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- $node->analysis = $analysis;
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- $node->analysis_id = $analysis_id; // we need to set this for children
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+ // add the analysis to the node object for
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+ // use by other analysis modules that may be using this function
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+ $node->analysis = $analysis;
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+ $node->analysis_id = $analysis_id; // we need to set this for children
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- // now add the properties
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- $properties = array(); // stores all of the properties we need to add
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- // get the list of properties for easy lookup (without doing lots of database queries
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- $properties_list = array();
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- $sql = "
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+ // now add the properties
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+ $properties = array(); // stores all of the properties we need to add
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+ // get the list of properties for easy lookup (without doing lots of database queries
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+ $properties_list = array();
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+ $sql = "
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SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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FROM {cvterm} CVT
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INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
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@@ -201,40 +201,40 @@ function chado_analysis_insert($node) {
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CV.name = 'analysis_property' AND
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NOT CVT.is_obsolete = 1
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ORDER BY CVT.name ASC
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- ";
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- $prop_types = chado_query($sql);
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- while ($prop = db_fetch_object($prop_types)) {
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- $properties_list[$prop->cvterm_id] = $prop->name;
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- }
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+ ";
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+ $prop_types = chado_query($sql);
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+ while ($prop = db_fetch_object($prop_types)) {
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+ $properties_list[$prop->cvterm_id] = $prop->name;
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+ }
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- // get the properties that should be added. Properties are in one of two forms:
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- // 1) prop_value-[type id]-[index]
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- // 2) new_value-[type id]-[index]
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- // 3) new_id, new_value
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-
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- foreach ($node as $name => $value) {
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- if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
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- $type_id = $matches[1];
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- $index = $matches[2];
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- $name = $properties_list[$type_id];
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- $properties[$name][$index] = trim($value);
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- }
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- }
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+ // get the properties that should be added. Properties are in one of two forms:
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+ // 1) prop_value-[type id]-[index]
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+ // 2) new_value-[type id]-[index]
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+ // 3) new_id, new_value
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+
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+ foreach ($node as $name => $value) {
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+ if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
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+ $type_id = $matches[1];
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+ $index = $matches[2];
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+ $name = $properties_list[$type_id];
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+ $properties[$name][$index] = trim($value);
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+ }
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+ }
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if ($node->new_id and $node->new_value) {
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- $type_id = $node->new_id;
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- $name = $properties_list[$type_id];
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- $index = count($properties[$name]);
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- $properties[$name][$index] = trim($node->new_value);
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+ $type_id = $node->new_id;
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+ $name = $properties_list[$type_id];
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+ $index = count($properties[$name]);
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+ $properties[$name][$index] = trim($node->new_value);
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}
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// now add in the properties
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foreach ($properties as $property => $elements) {
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foreach ($elements as $rank => $value) {
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- $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE);
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+ $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
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if (!$status) {
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drupal_set_message("Error cannot add property: $property", "error");
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watchdog('t_analysis', "Error cannot add property: %prop",
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array('%property' => $property), WATCHDOG_ERROR);
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- }
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+ }
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}
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}
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}
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@@ -283,113 +283,113 @@ function chado_analysis_delete($node) {
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* @ingroup tripal_analysis
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*/
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function chado_analysis_update($node) {
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- global $user;
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- if ($node->revision) {
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- // TODO -- decide what to do about revisions
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- }
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- // Create a timestamp so we can insert it into the chado database
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- $time = $node->timeexecuted;
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- $month = $time['month'];
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- $day = $time['day'];
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- $year = $time['year'];
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- $timestamp = $month . '/' . $day . '/' . $year;
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-
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- // get the analysis_id for this node:
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- $sql = "SELECT analysis_id ".
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- "FROM {chado_analysis} ".
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- "WHERE nid = %d";
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- $analysis_id = db_fetch_object(db_query($sql, $node->nid))->analysis_id;
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-
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- $sql = "UPDATE {analysis} ".
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- "SET name = '%s', ".
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- " description = '%s', ".
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- " program = '%s', ".
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- " programversion = '%s', ".
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- " algorithm = '%s', ".
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- " sourcename = '%s', ".
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- " sourceversion = '%s', ".
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- " sourceuri = '%s', ".
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- " timeexecuted = '%s' ".
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- "WHERE analysis_id = %d ";
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-
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- chado_query($sql, $node->analysisname, $node->description, $node->program,
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- $node->programversion, $node->algorithm, $node->sourcename,
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- $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
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-
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- // Create a title for the analysis node using the unique keys so when the
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- // node is saved, it will have a title
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- $record = new stdClass();
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- // If the analysis has a name, use it as the node title. If not, construct
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- // the title using program, programversion, and sourcename
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- if ($node->analysisname) {
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- $record->title = $node->analysisname;
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- }
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- else {
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- //Construct node title as "program (version)
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- $record->title = "$node->program ($node->programversion)";
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- }
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-
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- $record->nid = $node->nid;
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- drupal_write_record('node', $record, 'nid');
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- drupal_write_record('node_revisions', $record, 'nid');
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-
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- // now update the properties
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- $properties = array(); // stores all of the properties we need to add
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- // get the list of properties for easy lookup (without doing lots of database queries
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- $properties_list = array();
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- $sql = "
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- SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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- FROM {cvterm} CVT
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- INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
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- WHERE
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- CV.name = 'analysis_property' AND
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- NOT CVT.is_obsolete = 1
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- ORDER BY CVT.name ASC
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- ";
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- $prop_types = chado_query($sql);
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- while ($prop = db_fetch_object($prop_types)) {
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- $properties_list[$prop->cvterm_id] = $prop->name;
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- }
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-
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- // get the properties that should be added. Properties are in one of three forms:
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- // 1) prop_value-[type id]-[index]
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- // 2) new_value-[type id]-[index]
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- // 3) new_id, new_value
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- // dpm($node);
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- foreach ($node as $key => $value) {
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- if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
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- $type_id = $matches[1];
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- $index = $matches[2];
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- $name = $properties_list[$type_id];
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- $properties[$name][$index] = trim($value);
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- }
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- if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
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- $type_id = $matches[1];
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- $index = $matches[2];
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- $name = $properties_list[$type_id];
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- $properties[$name][$index] = trim($value);
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- }
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- }
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- if ($node->new_id and $node->new_value) {
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- $type_id = $node->new_id;
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- $name = $properties_list[$type_id];
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- $index = count($properties[$name]);
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- $properties[$name][$index] = trim($node->new_value);
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- }
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-
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- // now add in the properties by first removing any the analysis
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- // already has and adding the ones we have
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- tripal_core_chado_delete('analysisprop', array('analysis_id' => $analysis_id));
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- foreach ($properties as $property => $elements) {
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- foreach ($elements as $rank => $value) {
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- $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE);
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- if (!$status) {
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- drupal_set_message("Error cannot add property: '$property'", "error");
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- watchdog('t_analysis', "Error cannot add property: '%prop'",
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- array('%prop' => $property), WATCHDOG_ERROR);
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- }
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- }
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- }
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+ global $user;
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+ if ($node->revision) {
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+ // TODO -- decide what to do about revisions
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+ }
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+ // Create a timestamp so we can insert it into the chado database
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+ $time = $node->timeexecuted;
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+ $month = $time['month'];
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+ $day = $time['day'];
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+ $year = $time['year'];
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+ $timestamp = $month . '/' . $day . '/' . $year;
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+
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+ // get the analysis_id for this node:
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+ $sql = "SELECT analysis_id ".
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+ "FROM {chado_analysis} ".
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+ "WHERE nid = %d";
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+ $analysis_id = db_fetch_object(db_query($sql, $node->nid))->analysis_id;
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+
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+ $sql = "UPDATE {analysis} ".
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+ "SET name = '%s', ".
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+ " description = '%s', ".
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+ " program = '%s', ".
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+ " programversion = '%s', ".
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+ " algorithm = '%s', ".
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+ " sourcename = '%s', ".
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+ " sourceversion = '%s', ".
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+ " sourceuri = '%s', ".
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+ " timeexecuted = '%s' ".
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+ "WHERE analysis_id = %d ";
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+
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+ chado_query($sql, $node->analysisname, $node->description, $node->program,
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+ $node->programversion, $node->algorithm, $node->sourcename,
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+ $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
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+
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+ // Create a title for the analysis node using the unique keys so when the
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+ // node is saved, it will have a title
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+ $record = new stdClass();
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+ // If the analysis has a name, use it as the node title. If not, construct
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+ // the title using program, programversion, and sourcename
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+ if ($node->analysisname) {
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+ $record->title = $node->analysisname;
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+ }
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+ else {
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+ //Construct node title as "program (version)
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+ $record->title = "$node->program ($node->programversion)";
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+ }
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+
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+ $record->nid = $node->nid;
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+ drupal_write_record('node', $record, 'nid');
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+ drupal_write_record('node_revisions', $record, 'nid');
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+
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+ // now update the properties
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+ $properties = array(); // stores all of the properties we need to add
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+ // get the list of properties for easy lookup (without doing lots of database queries
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+ $properties_list = array();
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+ $sql = "
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+ SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ CV.name = 'analysis_property' AND
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+ NOT CVT.is_obsolete = 1
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+ ORDER BY CVT.name ASC
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+ ";
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+ $prop_types = chado_query($sql);
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+ while ($prop = db_fetch_object($prop_types)) {
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+ $properties_list[$prop->cvterm_id] = $prop->name;
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+ }
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+
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+ // get the properties that should be added. Properties are in one of three forms:
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+ // 1) prop_value-[type id]-[index]
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+ // 2) new_value-[type id]-[index]
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+ // 3) new_id, new_value
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+ // dpm($node);
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+ foreach ($node as $key => $value) {
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+ if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
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+ $type_id = $matches[1];
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+ $index = $matches[2];
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+ $name = $properties_list[$type_id];
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+ $properties[$name][$index] = trim($value);
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+ }
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+ if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
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+ $type_id = $matches[1];
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+ $index = $matches[2];
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+ $name = $properties_list[$type_id];
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+ $properties[$name][$index] = trim($value);
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+ }
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+ }
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+ if ($node->new_id and $node->new_value) {
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+ $type_id = $node->new_id;
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+ $name = $properties_list[$type_id];
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+ $index = count($properties[$name]);
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+ $properties[$name][$index] = trim($node->new_value);
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+ }
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+
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+ // now add in the properties by first removing any the analysis
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+ // already has and adding the ones we have
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+ tripal_core_chado_delete('analysisprop', array('analysis_id' => $analysis_id));
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+ foreach ($properties as $property => $elements) {
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+ foreach ($elements as $rank => $value) {
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+ $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
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+ if (!$status) {
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+ drupal_set_message("Error cannot add property: '$property'", "error");
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+ watchdog('t_analysis', "Error cannot add property: '%prop'",
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+ array('%prop' => $property), WATCHDOG_ERROR);
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+ }
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+ }
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+ }
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}
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/**
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@@ -516,7 +516,7 @@ function tripal_analysis_perm() {
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* @ingroup tripal_analysis
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*/
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function tripal_analysis_theme() {
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- return array(
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+ $items = array(
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'tripal_analysis_base' => array(
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'arguments' => array('node' => NULL),
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'template' => 'tripal_analysis_base',
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@@ -530,14 +530,16 @@ function tripal_analysis_theme() {
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'arguments' => array(NULL),
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'path' => drupal_get_path('module', 'tripal_analysis') . '/theme',
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),
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- 'tripal_analysis_properties' => array(
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- 'arguments' => array('node' => NULL)
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- ),
|
|
|
+ 'tripal_analysis_properties' => array(
|
|
|
+ 'arguments' => array('node' => NULL)
|
|
|
+ ),
|
|
|
// Themed Forms
|
|
|
'chado_analysis_node_form' => array(
|
|
|
'arguments' => array('form'),
|
|
|
),
|
|
|
);
|
|
|
+
|
|
|
+ return $items;
|
|
|
}
|
|
|
/**
|
|
|
*
|
spficklin