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46 tv3 php8 warnings #47

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46 tv3 php8 warnings #47

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1f65b8d
Issue 46 fix for undefined variable $db
dsenalik Dec 15, 2022
a85e48e
Issue 46 fix read property "value" on null
dsenalik Dec 15, 2022
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24 changes: 14 additions & 10 deletions api/tripal_analysis_blast.api.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ function tripal_get_feature_blast_results($feature_id, $db_id = NULL) {

$analysis = chado_generate_var('analysis', array('analysis_id' => $analysisfeature[0]->analysis_id));
$analysis_id = $analysis->analysis_id;
$adb_id = NULL;

// Get the blast_hit_data record for this analysis feature. For Tripal v3
// all blast files imported will use this table. Previously it was optional.
Expand Down Expand Up @@ -80,7 +81,9 @@ function tripal_get_feature_blast_results($feature_id, $db_id = NULL) {
// database id
else {
$blastdb = chado_get_property(array('table'=> 'analysis', 'id' => $analysis_id), array('type_name' => 'analysis_blast_blastdb', 'cv_name' => 'tripal'));
$adb_id = $blastdb->value;
if ($blastdb) {
$adb_id = $blastdb->value;
}
}
}

Expand All @@ -93,19 +96,20 @@ function tripal_get_feature_blast_results($feature_id, $db_id = NULL) {
continue;
}

// get the database
// analysis db will be null if no blast hits for this feature
if ($adb_id) {
// get the database
$db_arr = chado_select_record('db', array('*'), array('db_id' => $adb_id));
$db = $db_arr[0];
}

// parse the XML and add it to the array of blast results to be returned
module_load_include('inc', 'tripal_analysis_blast', 'includes/TripalImporter/BlastImporter');
$importer = new BlastImporter();
$blast_obj =$importer->getResultObject($blast_xml, $db, $feature_id, $analysis);
$blast_obj->analysis = $analysis;
$blast_obj_array [$blast_obj_counter] = $blast_obj;
$blast_obj_counter ++;
// parse the XML and add it to the array of blast results to be returned
module_load_include('inc', 'tripal_analysis_blast', 'includes/TripalImporter/BlastImporter');
$importer = new BlastImporter();
$blast_obj =$importer->getResultObject($blast_xml, $db, $feature_id, $analysis);
$blast_obj->analysis = $analysis;
$blast_obj_array [$blast_obj_counter] = $blast_obj;
$blast_obj_counter ++;
}
}

return $blast_obj_array;
Expand Down