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Fix missing column separator in the file #5

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Fix missing column separator in the file #5

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1b1bcfa
Fix missing column separator in the file
maxpatiiuk Mar 23, 2023
e805ecf
Fix column's being off by one
maxpatiiuk Mar 25, 2023
ea4df04
Improve wrong order node detection
maxpatiiuk Mar 25, 2023
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5 changes: 4 additions & 1 deletion back_end/refresh_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -235,6 +235,7 @@ def list_flip(original_list):
print('Finding parent nodes')

modified = True
wrong_order_nodes = []
while modified:
modified = False

Expand All @@ -249,7 +250,9 @@ def list_flip(original_list):
continue

if row[1] < rows[parent_tsn][1]:
print("Skipping node with wrong rank order: " + row[0][3])
if row not in wrong_order_nodes:
print("Skipping node with wrong rank order. Child:", row, "Parent: ", rows[parent_tsn])
wrong_order_nodes.append(row)
continue

del row[3]
Expand Down
65 changes: 30 additions & 35 deletions front_end/generate_tree/index.php
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Original file line number Diff line number Diff line change
Expand Up @@ -146,33 +146,30 @@ function truthy($val){


//Output the header row
$line = '';
$line = [];
foreach($ranks[$kingdom] as $rank_id => $rank_data){

if(!in_array($rank_id, $selected_ranks))
continue;

if($line != '')
$line .= $column_separator;

$rank_name = $rank_data[0];
$line .= $rank_name;
$line .= $column_separator.$rank_name.' GUID';
$line[] = $rank_name;
$line[] = $rank_name.' GUID';

if($include_authors)
$line .= $column_separator . $rank_name . ' Author';
$line[] = $rank_name . ' Author';

if($include_common_names)
$line .= $column_separator . $rank_name . ' Common Name';
$line[] = $rank_name . ' Common Name';

$line .= $column_separator . $rank_name . ' Remarks';
$line[] = $rank_name . ' Remarks';

//if($fill_in_links)
$line .= $column_separator . $rank_name . ' Source';
$line[] = $rank_name . ' Source';

}

$header_line = $line . $line_separator;
$header_line = implode($column_separator, $line) . $line_separator;

//send stats data
if(STATS_URL!=''){
Expand Down Expand Up @@ -231,7 +228,7 @@ function show_node(
$node,
$parent_choice_tree = [],
$parent_rank = FALSE,
$line = ''
$line = []
){

global $column_separator;
Expand Down Expand Up @@ -273,35 +270,33 @@ function show_node(
$local_result = '';
if(in_array($rank, $selected_ranks)){ // The rank of this element is selected

if($line != '')
$line .= $column_separator;

if($parent_rank !== FALSE && $ranks[$kingdom][$rank][1] != $parent_rank) // If current $rank is not a direct parent of $parent_rank
$line .= handle_missing_ranks($rank, $parent_rank);
$line = array_merge($line, handle_missing_ranks($rank, $parent_rank));

$line .= $node_name.$column_separator.$taxon_number;
$line[] = $node_name;
$line[] = $taxon_number;

if($include_authors)
$line .= $column_separator . substr($node[0][2], 0, 128);
$line[] = substr($node[0][2], 0, 128);

if($include_common_names)
$line .= $column_separator . substr($node[0][1], 0, 128);
$line[] = substr($node[0][1], 0, 128);

$line .= $column_separator . 'WoRMS Editorial Board (2021). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. Accessed 10-22-2021. http://doi.org/10.14284/170';
$line[] = 'WoRMS Editorial Board (2021). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. Accessed 10-22-2021. http://doi.org/10.14284/170';

if($fill_in_links)
$line .= $column_separator . 'https://www.catalogueoflife.org/data/taxon/'. $taxon_number;
$line[] = 'https://www.catalogueoflife.org/data/taxon/'. $taxon_number;
else
$line .= $column_separator . $node[0][3];
$line[] = $node[0][3];

$local_result .= $line . $line_separator;
$local_result .= implode($column_separator, $line) . $line_separator;

$lines_count++;

}
else
// Handle cases when one of the required ranks is not selected/missing in the data
$line .= handle_missing_ranks($rank, $parent_rank);
$line = array_merge($line, handle_missing_ranks($rank, $parent_rank));

if($line_limit !== FALSE){
$result .= $local_result;
Expand Down Expand Up @@ -344,35 +339,35 @@ function handle_missing_ranks(
if($rank == 0)
return '';

$line = '';
$line = [];
if(!$direct_call && in_array($rank, $selected_ranks)){

if(in_array($rank, $required_ranks))//show required && missing ranks
$line .= 'incertae sedis';
$line[] = 'incertae sedis';
else
$line[] = '';

// Name and GUID
$count = 2;
// For Guid
$line[] = '';

if($include_authors)
$count++;
$line[] = '';

if($include_common_names)
$count++;
$line[] = '';

// Remarks
$count++;
$line[] = '';

//if($fill_in_links)
$count++;

$line .= str_repeat($column_separator, $count);
$line[] = '';

}

$parent_rank = $ranks[$kingdom][$rank][1];

if($parent_rank != $target_rank)
$line = handle_missing_ranks($parent_rank, $target_rank, FALSE) . $line;
$line = array_merge(handle_missing_ranks($parent_rank, $target_rank, FALSE), $line);

return $line;

Expand Down