This function will check study submission state from database find the file ids and also check the managed tables to see what is missing. This will thus detect old files.
10 $results = chado_query(
'SELECT * FROM tpps_submission WHERE accession = :accession', [
11 ':accession' => $study_accession
14 $serialized_data =
"";
15 foreach($results as $row) {
16 $serialized_data = unserialize($row->submission_state);
21 $project_id = $serialized_data[
'ids'][
'project_id'];
24 $project_file_ids = [];
26 $results = chado_query(
'SELECT * FROM tpps_project_file_managed WHERE project_id = :project_id', [
27 ':project_id' => $project_id
29 foreach ($results as $row) {
31 array_push($project_file_ids, $row->fid);
34 sort($project_file_ids);
36 $saved_values = $serialized_data[
'saved_values'];
39 $organism_count = $saved_values[
'1'][
'organism'][
'number'];
41 for($i=1; $i<=4; $i++) {
43 for($j=1; $j<=$organism_count; $j++) {
44 if(isset($saved_values[$i][
'tree-accession'][
'species-' . $j][
'file'])) {
45 array_push($file_ids, $saved_values[$i][
'tree-accession'][
'species-' . $j][
'file']);
51 for($j=1; $j<=$organism_count; $j++) {
52 if(isset($saved_values[$i][
'organism-' . $j][
'phenotype'][
'file'])) {
53 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'phenotype'][
'file']);
55 if(isset($saved_values[$i][
'organism-' . $j][
'phenotype'][
'metadata'])) {
56 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'phenotype'][
'metadata']);
59 for($j=1; $j<=$organism_count; $j++) {
60 if(isset($saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'snps-assay'])) {
61 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'snps-assay']);
63 if(isset($saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'snps-association'])) {
64 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'snps-association']);
66 if(isset($saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'vcf'])) {
67 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'vcf']);
69 if(isset($saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'ssrs'])) {
70 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'ssrs']);
72 if(isset($saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'ssrs_extra'])) {
73 array_push($file_ids, $saved_values[$i][
'organism-' . $j][
'genotype'][
'files'][
'ssrs_extra']);
81 $markup .=
'<div style="font-size: 12px;">';
82 $markup .=
'<div style="display: inline-block; width: 30%; vertical-align: top;">';
83 $markup .=
'<h4>Project ID Managed</h4>';
84 foreach ($project_file_ids as $fid) {
85 $markup .=
'<div>' . $fid .
'-';
86 $file = file_load($fid);
88 $file_url = check_plain(file_create_url($file->uri));
89 $markup .=
"<a href='$file_url' target='blank'>$file->filename</a>";
95 $markup .=
'<div style="display: inline-block; width: 30%; vertical-align: top;">';
96 $markup .=
'<h4>Submission state</h4>';
97 foreach ($file_ids as $fid) {
98 $markup .=
'<div>' . $fid .
'-';
99 $file = file_load($fid);
101 $file_url = check_plain(file_create_url($file->uri));
102 $markup .=
"<a href='$file_url' target='blank'>$file->filename</a>";
108 $markup .=
'<div style="display: inline-block; width: 30%; vertical-align: top;">';
109 $markup .=
'<h4>History/State files</h4>';
110 $overall_file_ids = $serialized_data[
'files'];
111 sort($overall_file_ids);
112 foreach ($overall_file_ids as $fid) {
113 $markup .=
'<div>' . $fid .
'-';
114 $file = file_load($fid);
116 $file_url = check_plain(file_create_url($file->uri));
117 $markup .=
"<a href='$file_url' target='blank'>$file->filename</a>";
125 $form[
'markup'] = array(