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Convert README.md to README.json

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intendo
2020-11-01 21:55:32 -08:00
parent be2c12a563
commit 0221f9d4aa
3 changed files with 246 additions and 8 deletions
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10
examples/bem-pKa/README.md
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@@ -17,8 +17,8 @@ This directory contains five example .in files:
These files can be used to demonstrate TABI-PB pKa calculations, documented at:
http://www.poissonboltzmann.org/examples/Lysozyme_pKa_example/
File Input| APBS Version| Result (kJ/mol)| Expected (kJ/mol)
---|---|---|---
[ASH66.in](ASH66.in)| **3.0**| **-4.026**| **-4.026**
[2LTZ-ASH66.in](2LTZ-ASH66.in)| **3.0**| **-369.020**| **-369.020**
[2LTZ-noASH66.in](2LTZ-noASH66.in)| **3.0**| **-367.795**| **-367.795**
Input File | Description | APBS Version| Result (kJ/mol)| Expected (kJ/mol)
---|---|---|---|---
[ASH66.in](ASH66.in)|| **3.0**| **-4.026**| **-4.026**
[2LTZ-ASH66.in](2LTZ-ASH66.in)|| **3.0**| **-369.020**| **-369.020**
[2LTZ-noASH66.in](2LTZ-noASH66.in)|| **3.0**| **-367.795**| **-367.795**

6
examples/geoflow/README.md
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@@ -14,8 +14,8 @@ al](http://www.ncbi.nlm.nih.gov/pubmed/23212974).
The parameters used in the input files (imidazol and glycerol) came from Thomas et al.
| Input File | Description | APBS Version | Global Net ELEC Energy | Global Net APOL Energy |
|-------------|-----------------------------|------------------|------------------------|------------------------|
| imidazol.in | Serial, mdh boundary condts.| **3.0** | **-10.3022** | **0.541742** |
Input File | Description | APBS Version | Global Net ELEC Energy | Global Net APOL Energy
---|---|---|---|---
imidazol.in | Serial, mdh boundary condts.| **3.0** | **-10.3022** | **0.541742**
|||1.5|-10.3022|0.541742
|||1.4.2|-10.3022|0.541742

238
tools/create_example_readme_json.pl Executable file
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@@ -0,0 +1,238 @@
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long; Getopt::Long::Configure('bundling');
my @COPY_ARGV = @ARGV;
my $HELP = 0;
my $INPUT_FILE = '';
my $PROG = $0;
$PROG =~ s#.*/##;
GetOptions(
'h+' => \$HELP,
'i=s' => \$INPUT_FILE,
);
sub usage($)
{
my($help) = @_;
print("\n$PROG " . join(' ', @COPY_ARGV) . "\n") if (! $help);
print("\n");
print(" Usage: $0 [-h] | [-i input_file]\n\n");
print(" -h = Help\n");
print(" -i = Input file to process ($INPUT_FILE)\n");
print("\n");
exit(0) if ($help);
return;
}
sub get_title() {
my $title = '';
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
chomp();
last if m/^={20,}/;
$title .= $_;
}
close(FD);
return $title;
}
sub get_description() {
my @descriptions;
my $description;
my $skip;
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
last until m/^={20,}/;
}
$skip = <FD>;
$skip = <FD>;
while(<FD>) {
last if m/^Input File/;
chomp();
push(@descriptions, ' "' . $_ . '"');
}
close(FD);
$description = '[ ' . "\n" . join(",\n", @descriptions) . "\n" . ' ]';
return $description;
}
sub get_table_header() {
my $header;
my @fields;
my @header;
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
chomp();
if (m/^Input File\|/) {
@fields = split(/\s*\|\s*/, $_);
last;
}
}
foreach (@fields) {
push(@header, ' "' . $_ . '"');
}
close(FD);
$header = '[ ' . "\n" . join(",\n", @header) . "\n" . ' ]';
return $header;
}
sub get_table_rows() {
my @rows;
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
last if m/^Input File\|/;
}
my $skip = <FD>;
while(<FD>) {
last if m/^\s*$/;
if (m/.*?\|/) {
chomp();
push @rows, $_;
}
}
close(FD);
return @rows;
}
sub get_notes() {
my $note;
my @notes;
my $skip;
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
last if m/^Input File\|/;
}
$skip = <FD>;
while(<FD>) {
last if m/^\s*$/;
}
$skip = <FD>;
$skip = <FD>;
while(<FD>) {
chomp();
push(@notes, ' "' . $_ . '"');
}
close(FD);
$note = '[ ' . "\n" . join(",\n", @notes) . "\n" . ' ]';
return $note;
}
sub get_output() {
my $output;
my $title = get_title();
my $description = get_description();
my $table_header = get_table_header();
my @row_data = get_table_rows();
my $notes = get_notes();
$output = "{\n";
$output .= ' "title": "' . $title . '",' . "\n";
$output .= ' "introduction": ' . $description . ',' . "\n";
$output .= ' "tableheader": ' . $table_header . ',' . "\n";
$output .= ' "data": [' . "\n";
my @rows;
foreach (@row_data) {
my($blank, $file, $desc, $version, $result, $aresult) = 0;
if (/^\|/) {
($blank, $file, $desc, $version, $result, $aresult) = split('\|', $_);
$aresult = "";
}
else {
($file, $desc, $version, $result, $aresult) = split('\|', $_);
}
my $row;
$row = ' {' . "\n";
$row .= ' "filename": "' . $file . '",' . "\n";
$row .= ' "description": "' . $desc . '",' . "\n";
$row .= ' "version": "' . $version . '",' . "\n";
$row .= ' "results": ';
if ($result =~ m/[+\-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)?/ &&
$result !~ m/[<>]/ &&
$result !~ m/^[*]/) {
$row .= $result . ",\n";
}
else {
$row .= '"' . $result . '",' . "\n";
}
$row .= ' "analytical": ';
if ($aresult =~ m/[+\-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)?/ &&
$aresult !~ m/[<>]/ &&
$aresult !~ m/^[*]/) {
$row .= $aresult . "\n";
}
else {
$row .= '"' . $aresult . '"' . "\n";
}
$row .= ' }';
push(@rows, $row);
}
$output .= join(",\n", @rows);
$output .= "\n" . ' ],' . "\n";
$output .= ' "notes": ' . $notes . "\n}\n";
return $output;
}
sub write_output($) {
my($output) = @_;
my $output_file = $INPUT_FILE;
$output_file =~ s/\.md$/.json/;
open(FD, ">$output_file") || die("Can't create $output_file\n");
print(FD $output);
close(FD);
}
sub is_data_file() {
open(FD, $INPUT_FILE) || die("Can't open $INPUT_FILE\n");
while(<FD>) {
if (/^Input File\s*\|/) {
return 1;
}
}
close(FD);
return 0;
}
sub main()
{
usage(1) if (1 == $HELP);
if (! -f "$INPUT_FILE")
{
usage(0);
croak("ERROR: Can't find input file, $INPUT_FILE: $!\n");
}
if (is_data_file()) {
print("PROCESSING File: $INPUT_FILE\n");
my $output = get_output();
write_output($output);
}
else {
print("SKIPPING File: $INPUT_FILE\n");
}
}
main();
exit(0);