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update_module_details.php
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update_module_details.php
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<?php
echo "\n\nUpdating module details - " . date("Y-m-d h:i:s") . "\n";
// Allow PHP fopen to work with remote links
ini_set("allow_url_fopen", 1);
// Load yaml parser
require "vendor/autoload.php";
use Symfony\Component\Yaml\Yaml;
// Get auth secrets
$config = parse_ini_file("config.ini");
$gh_auth = base64_encode($config['github_username'] . ':' . $config['github_access_token']);
$conn = mysqli_connect($config['host'], $config['username'], $config['password'], $config['dbname'], $config['port']);
if ($conn === false) {
die("ERROR: Could not connect. " . mysqli_connect_error());
}
//
//
// GitHub API calls
//
//
function github_query($gh_query_url)
{
global $config;
$gh_auth = base64_encode($config['github_username'] . ':' . $config['github_access_token']);
// HTTP header to use on GitHub API GET requests
$gh_api_opts = stream_context_create([
'http' => [
'method' => 'GET',
'header' => [
'User-Agent: PHP',
"Authorization: Basic $gh_auth"
]
]
]);
$first_page = true;
$next_page = false;
$res = [];
while ($first_page || $next_page) {
// reset loop vars
$first_page = false;
// Get GitHub API results
if ($next_page) {
$gh_query_url = $next_page;
}
$tmp_results = json_decode(file_get_contents($gh_query_url, false, $gh_api_opts), true);
if (strpos($http_response_header[0], "HTTP/1.1 200") === false) {
var_dump($http_response_header);
echo ("\nCould not fetch $gh_query_url");
continue;
}
if(substr($gh_query_url,0,29) == "https://api.github.com/repos/" ){
$res = $tmp_results;
} else{
array_push($res, ...$tmp_results);
}
// Look for URL to next page of API results
$next_page = false;
$m_array = preg_grep('/rel="next"/', $http_response_header);
if (count($m_array) > 0) {
preg_match('/<([^>]+)>; rel="next"/', array_values($m_array)[0], $matches);
if (isset($matches[1])) {
$next_page = $matches[1];
}
}
}
return $res;
}
//
// nf-core modules table
//
$gh_modules = github_query('https://api.github.com/repos/nf-core/modules/git/trees/master?recursive=1');
$modules = [];
foreach($gh_modules['tree'] as $f){
if(substr($f['path'],-8)=='meta.yml' && substr($f['path'],0,8)=='modules/'){
$meta = github_query($f['url']);
$meta_content = base64_decode($meta['content']);
$meta_content = Yaml::parse($meta_content);
$meta_content['keywords'] = is_array($meta_content['keywords']) ? implode(';', $meta_content['keywords']) : $meta_content['keywords'];
$meta_content['authors'] = is_array($meta_content['authors']) ? implode(';', $meta_content['authors']) : $meta_content['authors'];
$meta_content['sha'] = $meta['sha'];
$meta_content['api_url'] = $meta['url'];
$meta_content['github_path'] = $f['path'];
$modules[] = $meta_content;
}
}
// Drop existing table if query was successful
if (count($modules)>1){
$sql = "DROP TABLE IF EXISTS nfcore_modules";
if (!mysqli_query($conn, $sql)) {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
$sql = "CREATE TABLE nfcore_modules (
id INT AUTO_INCREMENT PRIMARY KEY,
github_sha VARCHAR (400) NOT NULL,
github_path VARCHAR (400) NOT NULL,
api_url VARCHAR (400) NOT NULL,
name VARCHAR (400) NOT NULL,
description VARCHAR (4000) DEFAULT NULL,
keywords VARCHAR (2000) DEFAULT NULL,
tools JSON NOT NULL,
input JSON NOT NULL,
output JSON NOT NULL,
authors VARCHAR (2000) NOT NULL,
date_added datetime DEFAULT current_timestamp
)";
if (mysqli_query($conn, $sql)) {
echo "`nfcore_modules` table created successfully.\n";
} else {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
}
// Prepare an insert statement
$sql = "INSERT INTO nfcore_modules (github_sha,github_path,api_url,name,description,keywords,tools,input,output,authors) VALUES (?,?,?,?,?,?,?,?,?,?)";
if ($stmt = mysqli_prepare($conn, $sql)) {
// Bind variables to the prepared statement as parameters
mysqli_stmt_bind_param($stmt, "ssssssssss", $github_sha, $github_path, $api_url, $name, $description, $keywords, $tools, $input, $output, $authors);
foreach ($modules as $idx => $module) {
// check if module already exists
$check = "SELECT * FROM nfcore_modules WHERE name = '$module[name]'";
$res = mysqli_query($conn, $check);
if ($res->num_rows) {
continue;
}else{
$github_sha = $module['sha'];
$github_path = $module['github_path'];
$api_url = $module['api_url'];
$name = $module['name'];
$description = $module['description'];
$keywords = $module['keywords'];
$tools = json_encode($module['tools']);
$input = json_encode($module['input']);
$output = json_encode($module['output']);
$authors = $module['authors'];
mysqli_stmt_execute($stmt);
}
}
} else {
echo "ERROR: Could not prepare query: $sql. " . mysqli_error($conn);
}
//
// nf-core pipelines table
//
$gh_pipelines = github_query('https://api.github.com/orgs/nf-core/repos?per_page=100');
$ignored_repos = parse_ini_file("ignored_repos.ini")['repos'];
// Drop existing table if query was successful
if (count($gh_pipelines) > 1) {
$sql = "DROP TABLE IF EXISTS nfcore_pipelines";
if (!mysqli_query($conn, $sql)) {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
$sql = "CREATE TABLE nfcore_pipelines (
id INT AUTO_INCREMENT PRIMARY KEY,
github_id VARCHAR (400) NOT NULL,
html_url VARCHAR (400) NOT NULL,
name VARCHAR (400) NOT NULL,
description VARCHAR (4000) DEFAULT NULL,
gh_created_at datetime NOT NULL,
gh_updated_at datetime NOT NULL,
gh_pushed_at datetime NOT NULL,
stargazers_count INT NOT NULL,
watchers_count INT NOT NULL,
forks_count INT NOT NULL,
open_issues_count INT NOT NULL,
topics VARCHAR (4000) DEFAULT NULL,
watchers INT NOT NULL,
default_branch VARCHAR (400) NOT NULL,
pipeline_type VARCHAR (400) NOT NULL,
date_added datetime DEFAULT current_timestamp
)";
if (mysqli_query($conn, $sql)) {
echo "`nfcore_pipelines` table created successfully.\n";
} else {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
}
// Prepare an insert statement
$sql = "INSERT INTO nfcore_pipelines (github_id,html_url,name,description,gh_created_at,gh_updated_at,gh_pushed_at,stargazers_count,watchers_count,forks_count,open_issues_count,topics,watchers,default_branch,pipeline_type) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)";
if ($stmt = mysqli_prepare($conn, $sql)) {
// Bind variables to the prepared statement as parameters
mysqli_stmt_bind_param($stmt, "sssssssiiiisiss",$github_id,$html_url,$name,$description,$gh_created_at,$gh_updated_at,$gh_pushed_at,$stargazers_count,$watchers_count,$forks_count,$open_issues_count,$topics,$watchers,$default_branch,$pipeline_type);
foreach ($gh_pipelines as $pipeline) {
// check if module already exists
$check = "SELECT * FROM nfcore_pipelines WHERE name = '$pipeline[name]'";
$res = mysqli_query($conn, $check);
if ($res->num_rows) {
continue;
} else {
$github_id = $pipeline['id'];
$html_url = $pipeline['html_url'];
$name = $pipeline['name'];
$description = $pipeline['description'];
$gh_created_at = date('Y-m-d H:i:s',$pipeline['created_at']);
$gh_updated_at = date('Y-m-d H:i:s',$pipeline['updated_at']);
$gh_pushed_at = date('Y-m-d H:i:s',$pipeline['pushed_at']);
$stargazers_count = $pipeline['stargazers_count'];
$watchers_count = $pipeline['watchers_count'];
$forks_count = $pipeline['forks_count'];
$open_issues_count = $pipeline['open_issues_count'];
$topics = is_array($pipeline['topics']) ? implode(';', $pipeline['topics']) : $pipeline['topics'];
$watchers = $pipeline['watchers'];
$default_branch = $pipeline['default_branch'];
if (in_array($pipeline['name'], $ignored_repos)) {
$pipeline_type = 'core_repos';
} else {
$pipeline_type = 'pipelines';
}
mysqli_stmt_execute($stmt);
}
}
} else {
echo "ERROR: Could not prepare query: $sql. " . mysqli_error($conn);
}
//
// pipelines modules link table
//
$sql = "SELECT * FROM nfcore_pipelines WHERE pipeline_type = 'pipelines' ORDER BY LOWER(name) ";
$pipelines = [];
if ($result = mysqli_query($conn, $sql)) {
if (mysqli_num_rows($result) > 0) {
$pipelines = mysqli_fetch_all($result, MYSQLI_ASSOC);
// Free result set
mysqli_free_result($result);
} else {
echo "Oops! Something went wrong. Please try again later.";
}
}
// Drop existing table if query was successful
if (count($pipelines) > 1) {
$sql = "DROP TABLE IF EXISTS pipelines_modules";
if (!mysqli_query($conn, $sql)) {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
// create pipelines_modules table with foreign keys to pipelines and modules
$sql = "CREATE TABLE pipelines_modules (
id INT AUTO_INCREMENT PRIMARY KEY,
pipeline_id INT NOT NULL,
module_id INT NOT NULL,
FOREIGN KEY (pipeline_id) REFERENCES nfcore_pipelines(id),
FOREIGN KEY (module_id) REFERENCES nfcore_modules(id)
)";
if (mysqli_query($conn, $sql)) {
echo "`pipelines_modules` table created successfully.\n";
} else {
echo "ERROR: Could not execute $sql. " . mysqli_error($conn);
}
}
// Prepare an insert statement
$sql = "INSERT INTO pipelines_modules (pipeline_id,module_id) VALUES (?,?)";
foreach ($pipelines as $pipeline) {
$modules_json = github_query('https://api.github.com/repos/nf-core/'.$pipeline["name"].'/contents/modules.json');
$modules_json = json_decode(base64_decode($modules_json['content']),true);
$modules = $modules_json['repos']['nf-core/modules'];
// catch repos with no modules.json
if($modules == null){
continue;
}
foreach ($modules as $name=>$content) {
$stmt = mysqli_prepare($conn, $sql);
// Bind variables to the prepared statement as parameters
mysqli_stmt_bind_param($stmt, "ii", $pipeline_id, $module_id);
$name = str_replace('/','_',$name);
// pepare a select statment for nfcore_modules based on name
$get_module = "SELECT * FROM nfcore_modules WHERE name = '$name'";
if ($result = mysqli_query($conn, $get_module)) {
if (mysqli_num_rows($result) > 0) {
$repo_module = mysqli_fetch_all($result, MYSQLI_ASSOC);
$pipeline_id = $pipeline['id'];
$module_id = $repo_module[0]['id'];
mysqli_stmt_execute($stmt);
print_r($stmt->error);
// Free result set
mysqli_free_result($result);
} else {
echo "Oops! Something went wrong. Please try again later.";
}
}
}
}
mysqli_close($conn);
echo ("\nupdate_module_details done " . date("Y-m-d h:i:s") . "\n\n");