'user', the username
'token', the authentication token"
)
);
$createPathway_sig=array(
array(
$xmlrpcStruct,
$xmlrpcString, $xmlrpcBase64,
),
array(
$xmlrpcStruct,
$xmlrpcString, $xmlrpcBase64, $xmlrpcBoolean,
),
array(
$xmlrpcStruct,
$xmlrpcString, $xmlrpcBase64, $xmlrpcBoolean,
$xmlrpcStruct
),
);
$createPathway_doc= "Create a new pathway on wikipathways.";
$createPathway_docsig = array(
array(
"A struct with the key/value pairs:" .
"
'id', the pathway id
'revision', the newest revision number
" .
"'url', the url to the pathway page",
"Description of the modifications",
"The GPML data (base64 encoded)",
),
array(
"A struct with the key/value pairs:" .
"
'id', the pathway id
'revision', the newest revision number
" .
"'url', the url to the pathway page",
"Description of the modifications",
"The GPML data (base64 encoded)",
"Boolean indicated whether the pathway should be private or not",
),
array(
"A struct with the key/value pairs:" .
"
'id', the pathway id
'revision', the newest revision number
" .
"'url', the url to the pathway page",
"Description of the modifications",
"The GPML data (base64 encoded)",
"Boolean indicated whether the pathway should be private or not",
"The authentication data, a struct with the key/value pairs:" .
"
'user', the username
'token', the authentication token"
)
);
$convertPathway_sig= array(
array(
$xmlrpcBase64,
$xmlrpcBase64, $xmlrpcString
)
);
$convertPathway_doc= "Convert GPML code to the given file format";
$convertPathway_docsig = array(
array(
"The converted file data (base64 encoded)",
"The GPML code to convert (base64 encoded)",
"The file extension to convert to (e.g. svg)",
)
);
$getPathway_sig = array(
array(
$xmlrpcStruct,
$xmlrpcString),
array(
$xmlrpcStruct,
$xmlrpcString, $xmlrpcInt),
);
$getPathway_doc = "Get the GPML code for a pathway";
$getPathway_docsig = array(
array(
"A struct containing the following key/value pairs:" .
"- gpml
- The GPML code (base64 encoded)" .
"
- revision
- The revision id of the returned GPML",
"The pathway identifier"
),
array(
"A struct containing the following key/value pairs:
" .
"- gpml
- The GPML code (base64 encoded)" .
"
- revision
- The revision id of the returned GPML",
"The pathway identifier",
"The revision id (use '0' for current revision)"
)
);
$login_sig = array(
array(
$xmlrpcString,
$xmlrpcString, $xmlrpcString
)
);
$login_doc = "Start a logged in session, using an existing WikiPathways account.
This will return an authentication code
that can be used to excecute methods that need authentication (e.g.
updatePathway)";
$login_docsig = array(
array (
"The authentication code",
"The user name",
"The password"
)
);
$getPathwayList_sig = array(
array(
$xmlrpcArray
)
);
$getPathwayList_doc = "Get a list of all pathway titles (in the form of Species:PathwayName)";
$getPathwayList_docsig = array(
array(
"An array containing all pathway titles"
)
);
$getRecentChanges_sig = array (
array(
$xmlrpcArray,
$xmlrpcString
)
);
$getRecentChanges_doc = "Get a list of recently changed pathways";
$getRecentChanges_docsig = array(
array(
"a list of names of recently changed pathways",
"a SQL timestamp cutoff"
)
);
//Definition of dispatch map
$disp_map=array(
"WikiPathways.updatePathway" =>
array("function" => "updatePathway",
"signature" => $updatePathway_sig,
"docstring" => $updatePathway_doc,
"signature_docs" => $updatePathway_docsig),
"WikiPathways.createPathway" =>
array("function" => "createPathway",
"signature" => $createPathway_sig,
"docstring" => $createPathway_doc,
"signature_docs" => $createPathway_docsig),
"WikiPathways.convertPathway" =>
array("function" => "convertPathway",
"signature" => $convertPathway_sig,
"docstring" => $convertPathway_doc,
"signature_docs" => $convertPathway_docsig),
"WikiPathways.getPathway" =>
array("function" => "getPathway",
"signature" => $getPathway_sig,
"docstring" => $getPathway_doc,
"signature_docs" => $getPathway_docsig),
"WikiPathways.login" =>
array("function" => "login",
"signature" => $login_sig,
"docstring" => $login_doc,
"signature_docs" => $login_docsig),
"WikiPathways.getPathwayList" =>
array("function" => "getPathwayList",
"signature" => $getPathwayList_sig,
"docstring" => $getPathwayList_doc,
"signature_docs" => $getPathwayList_docsig),
"WikiPathways.getRecentChanges" =>
array("function" => "getRecentChanges",
"signature" => $getRecentChanges_sig,
"docstring" => $getRecentChanges_doc,
"signature_docs" => $getRecentChanges_docsig),
);
//Setup the XML-RPC server
$s=new documenting_xmlrpc_server($disp_map,0);
$s->functions_parameters_type = 'phpvals';
//$s->setDebug(3);
$s->service();
//Function implementations
function getPathwayList() {
$pathways = Pathway::getAllPathways();
$titles = array();
foreach($pathways as $p) {
$titles[] = $p->getTitleObject()->getDbKey();
}
return $titles;
}
function updatePathway($id, $description, $gpmlData, $revision, $auth = NULL) {
global $xmlrpcerruser, $wgUser;
//Authenticate first, if token is provided
if($auth) {
try {
authenticate($auth['user'], $auth['token']);
} catch(Exception $e) {
return new xmlrpcresp(0, $xmlrpcerruser, $e);
}
}
$resp = 0;
try {
$pathway = new Pathway($id);
//Only update if the given revision is the newest
//Or if this is a new pathway
if(!$pathway->exists() || $revision == $pathway->getLatestRevision()) {
$pathway->updatePathway($gpmlData, $description);
$resp = $pathway->getLatestRevision();
} else {
wfDebug("REVISION: $revision , " . $pathway->getLatestRevision());
$resp = new xmlrpcresp(0, $xmlrpcerruser,
"Revision out of date: your GPML code originates from " .
"an old revision. This means somebody else modified the pathway " .
"since you downloaded it. Please apply your changes on the newest version"
);
}
} catch(Exception $e) {
wfDebug("XML-RPC ERROR: $e");
$resp = new xmlrpcresp(0, $xmlrpcerruser, $e);
}
ob_clean(); //Clean the output buffer, so nothing is printed before the xml response
return $resp;
}
function createPathway($description, $gpmlData, $private = false, $auth = NULL) {
global $xmlrpcerruser, $wgUser;
//Authenticate first, if token is provided
if($auth) {
try {
authenticate($auth['user'], $auth['token']);
} catch(Exception $e) {
return new xmlrpcresp(0, $xmlrpcerruser, $e);
}
}
$resp = 0;
try {
$pathway = Pathway::createNewPathway($gpmlData, $description);
$title = $pathway->getTitleObject();
$resp = array(
"id" => $pathway->getIdentifier(),
"url" => $title->getFullUrl(),
"revision" => $pathway->getLatestRevision()
);
if($private) {
$pathway->makePrivate($wgUser);
}
} catch(Exception $e) {
wfDebug("XML-RPC ERROR: $e");
$resp = new xmlrpcresp(0, $xmlrpcerruser, $e);
}
ob_clean(); //Clean the output buffer, so nothing is printed before the xml response
return $resp;
}
function convertPathway($gpmlData64, $fileType) {
global $xmlrpcerruser;
$gpmlData = base64_decode($gpmlData64);
$gpmlFile = tempnam(WPI_TMP_PATH, "gpml");
writeFile($gpmlFile, $gpmlData);
$imgFile = tempnam(WPI_TMP_PATH, $fileType) . ".$fileType";
$cmd = "cd " . WPI_SCRIPT_PATH . "; java -jar bin/pathvisio_core.jar $gpmlFile $imgFile 2>&1";
wfDebug($cmd);
exec($cmd, $output, $status);
foreach ($output as $line) {
$msg .= $line . "\n";
}
wfDebug("Converting to $fileType:\nStatus:$status\nMessage:$msg");
if($status != 0 ) {
return new xmlrpcresp(0, $xmlrpcerruser, "Unable to convert:\nStatus:$status\nMessage:$msg");
}
$imgData = file_get_contents($imgFile);
$imgData64 = base64_encode($imgData);
unlink($gpmlFile);
unlink($imgFile);
ob_clean(); //Clean the output buffer, so nothing is printed before the xml response
return $imgData64;
}
function getPathway($id, $revision = 0) {
global $xmlrpcerruser;
try {
$pathway = new Pathway($id);
$revision = $pathway->getLatestRevision();
$gpmlData64 = base64_encode($pathway->getGPML());
ob_clean();
return array(
"gpml" => $gpmlData64,
"revision" => $revision
);
} catch(Exception $e) {
wfDebug("XML-RPC ERROR: $e");
$resp = new xmlrpcresp(0, $xmlrpcerruser, $e);
}
}
function login($name, $pass) {
global $wgUser, $wgAuth, $xmlrpcerruser;
$user = User::newFromName( $name );
if( is_null($user) || $user->getID() == 0) {
return new xmlrpcresp(0, $xmlrpcerruser, "Invalid user name");
}
$user->load();
if ($user->checkPassword( $pass )) {
$wgAuth->updateUser($user);
$wgUser = $user;
return $user->mToken;
} else {
return new xmlrpcresp(0, $xmlrpcerruser, "Wrong password");
}
}
function getRecentChanges($timestamp)
{
global $xmlrpcerruser;
//check safety of $timestamp, must be exactly 14 digits and nothing else.
if (!preg_match ("/^\d{14}$/", $timestamp))
{
return new xmlrpcresp(0, $xmlrpcerruser, "Invalid timestamp " . htmlentities ($timestamp));
}
$dbr =& wfGetDB( DB_SLAVE );
$forceclause = $dbr->useIndexClause("rc_timestamp");
$recentchanges = $dbr->tableName( 'recentchanges');
$sql = "SELECT
rc_namespace,
rc_title,
MAX(rc_timestamp)
FROM $recentchanges $forceclause
WHERE
rc_namespace = " . NS_PATHWAY . "
AND
rc_timestamp > '$timestamp'
GROUP BY rc_title
ORDER BY rc_timestamp DESC
";
//~ wfDebug ("SQL: $sql");
$res = $dbr->query( $sql, "getRecentChanges" );
$titles = array();
while ($row = $dbr->fetchRow ($res))
{
$titles[] = $row['rc_title'];
}
return $titles;
}
//Non-rpc functions
function authenticate($username, $token) {
global $wgUser, $wgAuth;
$user = User::newFromName( $username );
if( is_null($user) || $user->getID() == 0) {
throw new Exception("Invalid user name");
}
$user->load();
if ($user->mToken == $token) {
$wgAuth->updateUser($user);
$wgUser = $user;
} else {
throw new Exception("Wrong authentication token");
}
}
?>