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Fix front-end skipping "Incertae sedis" leaf nodes #11

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Fix front-end skipping "Incertae sedis" leaf nodes #11

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8188769
Fix front-end skipping "Incertae sedis" leaf nodes
maxpatiiuk May 2, 2023
32bad0d
Filter out out of order ranks
maxpatiiuk May 2, 2023
736cb10
Fix column's being off by one
maxpatiiuk May 2, 2023
aca81a8
Merge pull request #12 from specify/catalogue_of_life_3
grantfitzsimmons May 2, 2023
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7 changes: 7 additions & 0 deletions back_end/refresh_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -244,6 +244,7 @@ def list_flip(original_list):
orders_fixed = 0

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

Expand All @@ -257,6 +258,12 @@ def list_flip(original_list):
if parent_tsn not in rows:
continue

if row[1] <= rows[parent_tsn][1]:
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]
rows[parent_tsn][2].append(tsn)
modified = True
Expand Down
62 changes: 28 additions & 34 deletions front_end/generate_tree/index.php
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Original file line number Diff line number Diff line change
Expand Up @@ -147,31 +147,28 @@ 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';

//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 @@ -230,7 +227,7 @@ function show_node(
$node,
$parent_choice_tree = [],
$parent_rank = FALSE,
$line = ''
$line = []
){

global $column_separator;
Expand Down Expand Up @@ -272,38 +269,35 @@ 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 $parent_rank
//var_dump('<br><br>',$node);
$line .= handle_missing_ranks($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 . $node[0][2];
$line []= $node[0][2];

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

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++;

}

if($line_limit !== FALSE){
if($line_limit !== FALSE && $lines_count >= $line_limit){
$result .= $local_result;
if($lines_count >= $line_limit)
save_result();
save_result();
}


Expand Down Expand Up @@ -332,7 +326,6 @@ function handle_missing_ranks(
global $kingdom;
global $ranks;
global $selected_ranks;
global $column_separator;
global $include_authors;
global $include_common_names;
global $required_ranks;
Expand All @@ -341,31 +334,32 @@ function handle_missing_ranks(
if($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[] = '';

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

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

if($include_common_names)
$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
4 changes: 2 additions & 2 deletions front_end/index.php
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@

//Show the tree and other options

$display_down_to = 'Order'; ?>
$display_down_to = 'Family'; ?>

<h3>Step 2: Choose export data type</h3>
<label>
Expand All @@ -95,7 +95,7 @@

foreach($ranks[$kingdom] as $rank_id => &$rank_data){

if($rank_data[0]==$display_down_to)
if(ucfirst($rank_data[0])==ucfirst($display_down_to))
$stop_rank = $rank_id;

if($parent_rank_id!=0)
Expand Down
2 changes: 1 addition & 1 deletion front_end/static/js/main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ $( function () {
const ul = child.find('> ul');
//if(child_name.substr(0,4)==='(no ')
if(child_name==='incertae sedis')
tree = get_children(ul);
tree = {...tree, ...get_children(ul)};

else if(child.hasClass('mixed')){
if(ul.length===1)
Expand Down