Author: pwang
Date: 2010-09-14 16:34:55 -0700 (Tue, 14 Sep 2010)
New Revision: 21856
Modified:
new_cytoscape_website/plugin_website/plugins/pluginPropsUtil.inc
Log:
Check class version with "get_class_major" program
Modified: new_cytoscape_website/plugin_website/plugins/pluginPropsUtil.inc
===================================================================
--- new_cytoscape_website/plugin_website/plugins/pluginPropsUtil.inc
2010-09-14 22:35:39 UTC (rev 21855)
+++ new_cytoscape_website/plugin_website/plugins/pluginPropsUtil.inc
2010-09-14 23:34:55 UTC (rev 21856)
@@ -1,430 +1,458 @@
-<?php
-
-function isPluginVersionExists($connection, $pluginProps) {
-
- $query = 'SELECT version_auto_id FROM categories, plugin_list,
plugin_version' .
- ' WHERE categories.category_id = plugin_list.category_id ' .
- ' and plugin_list.plugin_auto_id = plugin_version.plugin_id ' .
- ' and categories.name ="' . $pluginProps['pluginCategory'] . "\"
" .
- ' and plugin_list.name = "' . $pluginProps['pluginName']
. "\" " .
- ' and plugin_version.version = "' .
$pluginProps['pluginVersion'] . "\"";
-
- // Run the query
- if (!($result = @ mysql_query($query, $connection)))
- showerror();
-
- if (@ mysql_num_rows($result) != 0) {
- $retValue = true;
-?>
- <strong>Error:</strong> <span class="style4">This
version of this plugin already exists.</span><br>
- <?php
- }
- else {
- $retValue = false;
- }
-
- return $retValue;
-}
-
-
-function validatePluginProps($pluginProps) {
- $retVal = true;
- if ($pluginProps == NULL || count($pluginProps) == 0) {
-?>
- <strong>Error: plugin.props in the jar/zip file is missing or
empty.</strong><br>
- <?php
- return false;
- }
-
- if (!array_key_exists('pluginName', $pluginProps)) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: pluginName is
required.</strong><br>
- <?php
-
-
- }
- else if (strpos($pluginProps['pluginName'],' ')>0) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: white space is not allowed in the
plugin name.</strong><br>
- <?php
-
- }
- if (!array_key_exists('pluginVersion', $pluginProps)) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: PluginVersion is
required.</strong><br>
- <?php
- }
- else {
- if (!preg_match('/^[0-9]+\.[0-9]+$/',
$pluginProps['pluginVersion'])) {
- $retVal = false;
-
-?>
- <strong>Error in plugin.prop: plugin version must be double
type, two numbers seperated by a dot (.).</strong><br>
- <?php
-
- }
- }
-
-
- if (!array_key_exists('pluginDescription', $pluginProps)) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: pluginDescription is
required.</strong><br>
- <?php
-
-
- }
- if (!array_key_exists('pluginCategory', $pluginProps)) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: pluginCategory is
required.</strong><br>
- <?php
-
-
- }
- else {
- if (!((strnatcasecmp($pluginProps['pluginCategory'], 'Core') ==
0) ||
- (strnatcasecmp($pluginProps['pluginCategory'], 'Analysis')
== 0) ||
- (strnatcasecmp($pluginProps['pluginCategory'], 'Network and
Attribute I/O') == 0) ||
- (strnatcasecmp($pluginProps['pluginCategory'], 'Network
Inference') == 0) ||
- (strnatcasecmp($pluginProps['pluginCategory'], 'Functional
Enrichment') == 0) ||
- (strnatcasecmp($pluginProps['pluginCategory'],
'Communication/Scripting') == 0) ||
- (strnatcasecmp($pluginProps['pluginCategory'], 'Other') ==
0)))
- {
- $retVal = false;
- ?>
- <strong>Error in plugin.prop: pluginCategory must be one of the
categories listed at <a href =
"http://cytoscape.org/plugins25/index.php";>Cytoscape plugin web
site</a>.</strong><br>
- <?php
-
- }
-
- }
-
- if (!array_key_exists('cytoscapeVersion', $pluginProps)) {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: cytoscapeVersion is
required.</strong><br>
- <?php
-
-
- }
- else {
- if ($pluginProps['cytoscapeVersion'] == null ||
$pluginProps['cytoscapeVersion'] == "") {
- $retVal = false;
-?>
- <strong>Error in plugin.prop: cytoscapeVersion is
required.</strong><br>
- <?php
- }
- }
-
- //If release Date is not provided, set it to today (system date).
- if (!array_key_exists('releaseDate', $pluginProps)) {
- $pluginProps['releaseDate'] =
date('Y').'-'.date('m').'-'.date('d');
- } elseif ($pluginProps['releaseDate']=='invalidDate') {
- $retVal = false;
- ?>
- <strong>Error in plugin.prop: Invalid release date.</strong><br>
- <?php
- }
-
- if ($retVal == false) {
- ?>
- <br>Please check the definition of Cytoscape plugin
propertiies at <a
href="http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_Plugin_Tutorial";>Cytoscape
wiki</a> for detail. </p>
- <br><br>
-
- <?php
- }
-
- return $retVal;
-}
-
-function getReleaseDateFromStr($releaseDateStr) {
- // The releaseDateStr will have the format like "May 1, 2007"
- // The return value will be have the format like "2007-5-1"
- // If the input string is invlalid date Str, return null
-
- $elements = sscanf($releaseDateStr, "%s%d,%d");
-
- if (count($elements) == 3) {
- $month = trim($elements[0]);
- $day = $elements[1];
- $year = $elements[2];
- } else {
- return null;
- }
-
- if (strnatcasecmp($month, "January") == 0) {
- $month = '1';
- }
- elseif (strnatcasecmp($month, "February") == 0) {
- $month = '2';
- }
- elseif (strnatcasecmp($month, "March") == 0) {
- $month = '3';
- }
- elseif (strnatcasecmp($month, "April") == 0) {
- $month = '4';
- }
- elseif (strnatcasecmp($month, "May") == 0) {
- $month = '5';
- }
- elseif (strnatcasecmp($month, "June") == 0) {
- $month = '6';
- }
- elseif (strnatcasecmp($month, "July") == 0) {
- $month = '7';
- }
- elseif (strnatcasecmp($month, "August") == 0) {
- $month = '8';
- }
- elseif (strnatcasecmp($month, "September") == 0) {
- $month = '9';
- }
- elseif (strnatcasecmp($month, "October") == 0) {
- $month = '10';
- }
- elseif (strnatcasecmp($month, "November") == 0) {
- $month = '11';
- }
- elseif (strnatcasecmp($month, "December") == 0) {
- $month = '12';
- }
- else {
- return 'invalidDate';
- }
-
- return $year . '-' . $month . '-' . $day;
-} // End of function getReleaseDateFromStr()
-
-//Parse the authInstStr and save the data into an Array of Array
-function getAuthorInstArray($authorInstStr) {
-
- if (empty($authorInstStr)) {
- return null;
- }
-
- $tmpArray = preg_split("{;}", $authorInstStr); // Split into an array
-
- foreach ($tmpArray as $record) {
- $tmpArray2 = preg_split("{:}", $record);
- $names[] =$tmpArray2[0];
- $insts[] =$tmpArray2[1];
- }
-
- $retValue['names'] = $names;
- $retValue['insts'] = $insts;
-
- return $retValue;
-}
-
-
-//Get the plugin properties from a Jar/Zip file
-function getPluginProps($zipFileName) {
-
- $pluginProps = NULL;
-
- $zip = zip_open($zipFileName);
- if ($zip) {
- while ($zip_entry = zip_read($zip)) {
- $cur_file_name = zip_entry_name($zip_entry);
-
- if (substr_count($cur_file_name, "plugin.props") > 0) {
-
- $position = strpos($cur_file_name,"plugin.props");
//find position of plugin.props
- if ($position != (strlen($cur_file_name) - 12)) {
- continue;
- }
- // This is the plugin.prop file
- if (zip_entry_open($zip, $zip_entry, "r")) {
- $buf = zip_entry_read($zip_entry,
zip_entry_filesize($zip_entry));
-
- $all_lines = explode("\n", $buf);
- $lineCount = count($all_lines);
-
- // Remove blank and comment lines
- for ($i = 0; $i < $lineCount; $i++) {
- $cur_line =
trim($all_lines[$i]);
- if (($cur_line == "") ||
(strstr($cur_line, '#') == $cur_line)) {
- continue;
- }
- $lines[] = trim($all_lines[$i]);
- }
-
- for ($i = 0; $i < count($lines); $i++) {
- $cur_line = $lines[$i];
- if (stristr($cur_line,
'pluginName') == $lines[$i]) { // the line starts with pluginName
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['pluginName'] = trim(substr($cur_line, $pos +1));
- }
- if (stristr($cur_line,
'pluginDescription') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
- $desText =
trim(substr($cur_line, $pos +1));
-
- $supportMultilineDes =
true;
- // Begin of
multiple-line description
- if
($supportMultilineDes) {
- $i=$i+1;
- while ($i <
count($lines)) {
-
-
$cur_line = $lines[$i];
-
- if
(!(stristr($cur_line, 'pluginVersion') == $lines[$i])) {
-
$desText = $desText.$cur_line;
-
$i=$i+1;
- }
- else {
-
// reach the end of description text
-
$i=$i-1;
-
break;
- }
- }
- }
- // End of multiple-line
description
-
-
$pluginProps['pluginDescription'] = $desText;
-
- }
- if (stristr($cur_line,
'pluginVersion') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['pluginVersion'] = trim(substr($cur_line, $pos +1));
- }
- if (stristr($cur_line,
'cytoscapeVersion') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['cytoscapeVersion'] = trim(substr($cur_line, $pos +1));
- //remove any white space
-
$pluginProps['cytoscapeVersion'] = ereg_replace('
','',$pluginProps['cytoscapeVersion']);
-
$pluginProps['cytoscapeVersion'] =
ereg_replace('\t','',$pluginProps['cytoscapeVersion']);
-
- }
- if (stristr($cur_line,
'pluginCategory') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['pluginCategory'] = trim(substr($cur_line, $pos +1));
- }
- if (stristr($cur_line,
'projectURL') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['projectURL'] = trim(substr($cur_line, $pos +1));
- }
- if ((stristr($cur_line,
'pluginAuthorsInstitutions') == $lines[$i]) || (stristr($cur_line,
'pluginAuthorsIntsitutions') == $lines[$i])) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['pluginAuthorsInstitutions'] =
getAuthorInstArray(trim(substr($cur_line, $pos +1)));
- }
- if (stristr($cur_line,
'releaseDate') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['releaseDate'] = getReleaseDateFromStr(trim(substr($cur_line, $pos
+1)));
- }
- if (stristr($cur_line,
'themeOnly') == $lines[$i]) {
- $pos =
strpos($cur_line, "="); // find first "="
-
$pluginProps['themeOnly'] = trim(substr($cur_line, $pos +1));
- }
- }
-
- //If themeOnly is not provided, set it
to "no".
- if (!array_key_exists('themeOnly',
$pluginProps)) {
- $pluginProps['themeOnly'] =
'no';
- }
-
- //If release Date is not provided, set
it to today (system date).
- if (!array_key_exists('releaseDate',
$pluginProps)) {
- $pluginProps['releaseDate'] =
date('Y').'-'.date('m').'-'.date('d');
- }
-
- //Not defined yet, may need it, in the
future
- $pluginProps['minimumJavaVersion'] =
'0.0';
- zip_entry_close($zip_entry);
- }
- break;
- }
- } // end while loop
- zip_close($zip);
- }
- else {
- //failed to open the zip file
- }
-
- return $pluginProps;
-
-}// end of getPluginProps()
-
-//Get the contents of MANIFEST file from a Jar/Zip file
-// Then check if any line start with "Cytoscape-Plugin"
-function validateManifestFile($zipFileName) {
- $retValue = false;
- $javaVersion_tooHigh = false;
- $zip = zip_open($zipFileName);
- if ($zip) {
- while ($zip_entry = zip_read($zip)) {
- $cur_file_name = zip_entry_name($zip_entry);
-
- if (substr_count($cur_file_name, "MANIFEST.MF") > 0) {
- // This is the MANIFEST.MF file
- if (zip_entry_open($zip, $zip_entry, "r")) {
- $buf = zip_entry_read($zip_entry,
zip_entry_filesize($zip_entry));
-
- $all_Lines = explode("\n", $buf);
-
- for ($i = 0; $i < count($all_Lines);
$i++) {
- $cur_line = $all_Lines[$i];
- if ((!empty($cur_line))&&
stristr($cur_line,'Cytoscape-Plugin') == $cur_line) {
- //echo "MANIFEST.MF:
Found attribute Cytoscape-Plugin<br>";
-
- $pluginClassName =
substr($cur_line, 16);
-
- $version =
getJavaVersion($zipFileName, $javaClassName);
-
- if ($version > 49){ //
49 is the jdk version (java platform version 1.5)
-
$javaVersion_tooHigh = true;
- }
- // debug only
- $javaVersion_tooHigh =
true;
-
- $retValue = true;
- }
- }
- }
- break;
- }
- } //while loop
- zip_close($zip);
- }
- else {
- //failed to open the zip file
- }
-
- if ($retValue == false && $javaVersion_tooHigh == false) {
- ?>
- <br><b>Error</b>: MANIFEST.MF is either missing or the attribute
Cytoscape-Plugin is not defined.
- <br>Please check the definition of Cytoscape plugin
MANIFEST.MF at <a
href="http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_Plugin_Tutorial";>Cytoscape
wiki</a> for detail. </p>
- <br><br>
- <?php
- }
-
- if ($javaVersion_tooHigh == true) {
-
- ?>
- <br><b>Error</b>: Plugin should be compiled with Java 1.5 or less.
- <br><br>
- <?php
- $retValue = false;
-
- }
-
-
-
- return $retValue;
-} // end of validateManifestFile()
-
-
-function getJavaVersion($javaFileName, $javaClassName) {
-
- $cmd = 'javap -v -classpath '.$jarFile.' '.$pluginClassName.'|grep
"major version"';
- $results = shell_exec($cmd);
- $version = substr($results,16);
-
- echo "version = ".$version."<br><br>";
- return $version;
-}
-
-?>
+<?php
+
+function isPluginVersionExists($connection, $pluginProps) {
+
+ $query = 'SELECT version_auto_id FROM categories, plugin_list,
plugin_version' .
+ ' WHERE categories.category_id = plugin_list.category_id ' .
+ ' and plugin_list.plugin_auto_id = plugin_version.plugin_id ' .
+ ' and categories.name ="' . $pluginProps['pluginCategory'] . "\"
" .
+ ' and plugin_list.name = "' . $pluginProps['pluginName']
. "\" " .
+ ' and plugin_version.version = "' .
$pluginProps['pluginVersion'] . "\"";
+
+ // Run the query
+ if (!($result = @ mysql_query($query, $connection)))
+ showerror();
+
+ if (@ mysql_num_rows($result) != 0) {
+ $retValue = true;
+?>
+ <strong>Error:</strong> <span class="style4">This
version of this plugin already exists.</span><br>
+ <?php
+ }
+ else {
+ $retValue = false;
+ }
+
+ return $retValue;
+}
+
+
+function validatePluginProps($pluginProps) {
+ $retVal = true;
+ if ($pluginProps == NULL || count($pluginProps) == 0) {
+?>
+ <strong>Error: plugin.props in the jar/zip file is missing or
empty.</strong><br>
+ <?php
+ return false;
+ }
+
+ if (!array_key_exists('pluginName', $pluginProps)) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: pluginName is
required.</strong><br>
+ <?php
+
+
+ }
+ else if (strpos($pluginProps['pluginName'],' ')>0) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: white space is not allowed in the
plugin name.</strong><br>
+ <?php
+
+ }
+ if (!array_key_exists('pluginVersion', $pluginProps)) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: PluginVersion is
required.</strong><br>
+ <?php
+ }
+ else {
+ if (!preg_match('/^[0-9]+\.[0-9]+$/',
$pluginProps['pluginVersion'])) {
+ $retVal = false;
+
+?>
+ <strong>Error in plugin.prop: plugin version must be double
type, two numbers seperated by a dot (.).</strong><br>
+ <?php
+
+ }
+ }
+
+
+ if (!array_key_exists('pluginDescription', $pluginProps)) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: pluginDescription is
required.</strong><br>
+ <?php
+
+
+ }
+ if (!array_key_exists('pluginCategory', $pluginProps)) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: pluginCategory is
required.</strong><br>
+ <?php
+
+
+ }
+ else {
+ if (!((strnatcasecmp($pluginProps['pluginCategory'], 'Core') ==
0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'], 'Analysis')
== 0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'], 'Network and
Attribute I/O') == 0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'], 'Network
Inference') == 0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'], 'Functional
Enrichment') == 0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'],
'Communication/Scripting') == 0) ||
+ (strnatcasecmp($pluginProps['pluginCategory'], 'Other') ==
0)))
+ {
+ $retVal = false;
+ ?>
+ <strong>Error in plugin.prop: pluginCategory must be one of the
categories listed at <a href =
"http://cytoscape.org/plugins25/index.php";>Cytoscape plugin web
site</a>.</strong><br>
+ <?php
+
+ }
+
+ }
+
+ if (!array_key_exists('cytoscapeVersion', $pluginProps)) {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: cytoscapeVersion is
required.</strong><br>
+ <?php
+
+
+ }
+ else {
+ if ($pluginProps['cytoscapeVersion'] == null ||
$pluginProps['cytoscapeVersion'] == "") {
+ $retVal = false;
+?>
+ <strong>Error in plugin.prop: cytoscapeVersion is
required.</strong><br>
+ <?php
+ }
+ }
+
+ //If release Date is not provided, set it to today (system date).
+ if (!array_key_exists('releaseDate', $pluginProps)) {
+ $pluginProps['releaseDate'] =
date('Y').'-'.date('m').'-'.date('d');
+ } elseif ($pluginProps['releaseDate']=='invalidDate') {
+ $retVal = false;
+ ?>
+ <strong>Error in plugin.prop: Invalid release date.</strong><br>
+ <?php
+ }
+
+ if ($retVal == false) {
+ ?>
+ <br>Please check the definition of Cytoscape plugin
propertiies at <a
href="http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_Plugin_Tutorial";>Cytoscape
wiki</a> for detail. </p>
+ <br><br>
+
+ <?php
+ }
+
+ return $retVal;
+}
+
+function getReleaseDateFromStr($releaseDateStr) {
+ // The releaseDateStr will have the format like "May 1, 2007"
+ // The return value will be have the format like "2007-5-1"
+ // If the input string is invlalid date Str, return null
+
+ $elements = sscanf($releaseDateStr, "%s%d,%d");
+
+ if (count($elements) == 3) {
+ $month = trim($elements[0]);
+ $day = $elements[1];
+ $year = $elements[2];
+ } else {
+ return null;
+ }
+
+ if (strnatcasecmp($month, "January") == 0) {
+ $month = '1';
+ }
+ elseif (strnatcasecmp($month, "February") == 0) {
+ $month = '2';
+ }
+ elseif (strnatcasecmp($month, "March") == 0) {
+ $month = '3';
+ }
+ elseif (strnatcasecmp($month, "April") == 0) {
+ $month = '4';
+ }
+ elseif (strnatcasecmp($month, "May") == 0) {
+ $month = '5';
+ }
+ elseif (strnatcasecmp($month, "June") == 0) {
+ $month = '6';
+ }
+ elseif (strnatcasecmp($month, "July") == 0) {
+ $month = '7';
+ }
+ elseif (strnatcasecmp($month, "August") == 0) {
+ $month = '8';
+ }
+ elseif (strnatcasecmp($month, "September") == 0) {
+ $month = '9';
+ }
+ elseif (strnatcasecmp($month, "October") == 0) {
+ $month = '10';
+ }
+ elseif (strnatcasecmp($month, "November") == 0) {
+ $month = '11';
+ }
+ elseif (strnatcasecmp($month, "December") == 0) {
+ $month = '12';
+ }
+ else {
+ return 'invalidDate';
+ }
+
+ return $year . '-' . $month . '-' . $day;
+} // End of function getReleaseDateFromStr()
+
+//Parse the authInstStr and save the data into an Array of Array
+function getAuthorInstArray($authorInstStr) {
+
+ if (empty($authorInstStr)) {
+ return null;
+ }
+
+ $tmpArray = preg_split("{;}", $authorInstStr); // Split into an array
+
+ foreach ($tmpArray as $record) {
+ $tmpArray2 = preg_split("{:}", $record);
+ $names[] =$tmpArray2[0];
+ $insts[] =$tmpArray2[1];
+ }
+
+ $retValue['names'] = $names;
+ $retValue['insts'] = $insts;
+
+ return $retValue;
+}
+
+
+//Get the plugin properties from a Jar/Zip file
+function getPluginProps($zipFileName) {
+
+ $pluginProps = NULL;
+
+ $zip = zip_open($zipFileName);
+ if ($zip) {
+ while ($zip_entry = zip_read($zip)) {
+ $cur_file_name = zip_entry_name($zip_entry);
+
+ if (substr_count($cur_file_name, "plugin.props") > 0) {
+
+ $position = strpos($cur_file_name,"plugin.props");
//find position of plugin.props
+ if ($position != (strlen($cur_file_name) - 12)) {
+ continue;
+ }
+ // This is the plugin.prop file
+ if (zip_entry_open($zip, $zip_entry, "r")) {
+ $buf = zip_entry_read($zip_entry,
zip_entry_filesize($zip_entry));
+
+ $all_lines = explode("\n", $buf);
+ $lineCount = count($all_lines);
+
+ // Remove blank and comment lines
+ for ($i = 0; $i < $lineCount; $i++) {
+ $cur_line =
trim($all_lines[$i]);
+ if (($cur_line == "") ||
(strstr($cur_line, '#') == $cur_line)) {
+ continue;
+ }
+ $lines[] = trim($all_lines[$i]);
+ }
+
+ for ($i = 0; $i < count($lines); $i++) {
+ $cur_line = $lines[$i];
+ if (stristr($cur_line,
'pluginName') == $lines[$i]) { // the line starts with pluginName
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['pluginName'] = trim(substr($cur_line, $pos +1));
+ }
+ if (stristr($cur_line,
'pluginDescription') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+ $desText =
trim(substr($cur_line, $pos +1));
+
+ $supportMultilineDes =
true;
+ // Begin of
multiple-line description
+ if
($supportMultilineDes) {
+ $i=$i+1;
+ while ($i <
count($lines)) {
+
+
$cur_line = $lines[$i];
+
+ if
(!(stristr($cur_line, 'pluginVersion') == $lines[$i])) {
+
$desText = $desText.$cur_line;
+
$i=$i+1;
+ }
+ else {
+
// reach the end of description text
+
$i=$i-1;
+
break;
+ }
+ }
+ }
+ // End of multiple-line
description
+
+
$pluginProps['pluginDescription'] = $desText;
+
+ }
+ if (stristr($cur_line,
'pluginVersion') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['pluginVersion'] = trim(substr($cur_line, $pos +1));
+ }
+ if (stristr($cur_line,
'cytoscapeVersion') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['cytoscapeVersion'] = trim(substr($cur_line, $pos +1));
+ //remove any white space
+
$pluginProps['cytoscapeVersion'] = ereg_replace('
','',$pluginProps['cytoscapeVersion']);
+
$pluginProps['cytoscapeVersion'] =
ereg_replace('\t','',$pluginProps['cytoscapeVersion']);
+
+ }
+ if (stristr($cur_line,
'pluginCategory') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['pluginCategory'] = trim(substr($cur_line, $pos +1));
+ }
+ if (stristr($cur_line,
'projectURL') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['projectURL'] = trim(substr($cur_line, $pos +1));
+ }
+ if ((stristr($cur_line,
'pluginAuthorsInstitutions') == $lines[$i]) || (stristr($cur_line,
'pluginAuthorsIntsitutions') == $lines[$i])) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['pluginAuthorsInstitutions'] =
getAuthorInstArray(trim(substr($cur_line, $pos +1)));
+ }
+ if (stristr($cur_line,
'releaseDate') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['releaseDate'] = getReleaseDateFromStr(trim(substr($cur_line, $pos
+1)));
+ }
+ if (stristr($cur_line,
'themeOnly') == $lines[$i]) {
+ $pos =
strpos($cur_line, "="); // find first "="
+
$pluginProps['themeOnly'] = trim(substr($cur_line, $pos +1));
+ }
+ }
+
+ //If themeOnly is not provided, set it
to "no".
+ if (!array_key_exists('themeOnly',
$pluginProps)) {
+ $pluginProps['themeOnly'] =
'no';
+ }
+
+ //If release Date is not provided, set
it to today (system date).
+ if (!array_key_exists('releaseDate',
$pluginProps)) {
+ $pluginProps['releaseDate'] =
date('Y').'-'.date('m').'-'.date('d');
+ }
+
+ //Not defined yet, may need it, in the
future
+ $pluginProps['minimumJavaVersion'] =
'0.0';
+ zip_entry_close($zip_entry);
+ }
+ break;
+ }
+ } // end while loop
+ zip_close($zip);
+ }
+ else {
+ //failed to open the zip file
+ }
+
+ return $pluginProps;
+
+}// end of getPluginProps()
+
+//Get the contents of MANIFEST file from a Jar/Zip file
+// Then check if any line start with "Cytoscape-Plugin"
+function validateManifestFile($zipFileName) {
+ $retValue = false;
+ $javaVersion_tooHigh = false;
+ $pluginClassName ="";
+
+ $zip = zip_open($zipFileName);
+ if ($zip) {
+ while ($zip_entry = zip_read($zip)) {
+ $cur_file_name = zip_entry_name($zip_entry);
+
+ if (substr_count($cur_file_name, "MANIFEST.MF") > 0) {
+ // This is the MANIFEST.MF file
+ if (zip_entry_open($zip, $zip_entry, "r")) {
+ $buf = zip_entry_read($zip_entry,
zip_entry_filesize($zip_entry));
+
+ $all_Lines = explode("\n", $buf);
+
+ for ($i = 0; $i < count($all_Lines);
$i++) {
+ $cur_line = $all_Lines[$i];
+ if ((!empty($cur_line))&&
stristr($cur_line,'Cytoscape-Plugin') == $cur_line) {
+ //echo "MANIFEST.MF:
Found attribute Cytoscape-Plugin<br>";
+
+ $pluginClassName =
substr($cur_line, 17);
+
+ $retValue = true;
+ }
+ }
+ }
+ break;
+ }
+ } //while loop
+ zip_close($zip);
+ }
+ else {
+ //failed to open the zip file
+ }
+
+ $version = getJavaVersion($zipFileName, $pluginClassName);
+
+ if ($version > 49){ // 49 is the jdk version (java platform version 1.5)
+ $javaVersion_tooHigh = true;
+ }
+
+ if ($retValue == false && $javaVersion_tooHigh == false) {
+ ?>
+ <br><b>Error</b>: MANIFEST.MF is either missing or the attribute
Cytoscape-Plugin is not defined.
+ <br>Please check the definition of Cytoscape plugin
MANIFEST.MF at <a
href="http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_Plugin_Tutorial";>Cytoscape
wiki</a> for detail. </p>
+ <br><br>
+ <?php
+ }
+
+ if ($javaVersion_tooHigh == true) {
+
+ ?>
+ <br><b>Error</b>: Plugin should be compiled with Java 1.5 or less.
+ <br><br>
+ <?php
+ $retValue = false;
+
+ }
+
+ return $retValue;
+} // end of validateManifestFile()
+
+
+// Get the version of java class
+function getJavaVersion($jarFileName, $javaClassName) {
+
+ $tokens = explode('.', trim($javaClassName));
+ $baseClassName = $tokens[count($tokens)-1];
+
+ $zip = zip_open($jarFileName);
+
+ if ($zip) {
+ while ($zipcontent = zip_read($zip)) {
+ $zip_entry_name = zip_entry_name($zipcontent);
+
+ if (strstr($zip_entry_name,
'/'.$baseClassName.'.class')){
+
+ if (zip_entry_open($zip, $zipcontent)){
+ $content =
zip_entry_read($zipcontent,1024);
+ // save the content in file
+ // Open the file and erase the contents
if any
+ $fp = fopen("./_tmp/tmp.class", "w");
+ fwrite($fp, $content);
+ fclose($fp);
+
+ zip_entry_close($zipcontent);
+ }
+ break;
+ }
+ }
+ zip_close($zip);
+ }
+ else {
+ //failed to open the zip file
+ return -1;
+ }
+
+ $cmd = "./get_class_major ./_tmp/tmp.class";
+ $result =shell_exec($cmd);
+
+ return $result;
+}
+
+?>
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