Table support

.gitignore

@@ -2,6 +2,7 @@
 .vscode
 .DS_Store
 src/python/.loglogin
+.loglogin
 
 # Compiled files 
 *.pyc

sbin/cdb_create_configuration_openssl.sh

@@ -13,26 +13,26 @@
 #
 
 MY_DIR=`dirname $0` && cd $MY_DIR && MY_DIR=`pwd`
-if [ -z "${CDB_ROOT_DIR}" ]; then
-    CDB_ROOT_DIR=$MY_DIR/..
+if [ -z "${LOGR_ROOT_DIR}" ]; then
+    LOGR_ROOT_DIR=$MY_DIR/..
 fi
-CDB_ENV_FILE=${CDB_ROOT_DIR}/setup.sh
-if [ ! -f ${CDB_ENV_FILE} ]; then
-    echo "Environment file ${CDB_ENV_FILE} does not exist."
+LOGR_ENV_FILE=${LOGR_ROOT_DIR}/setup.sh
+if [ ! -f ${LOGR_ENV_FILE} ]; then
+    echo "Environment file ${LOGR_ENV_FILE} does not exist."
     exit 2
 fi
-. ${CDB_ENV_FILE} > /dev/null
+. ${LOGR_ENV_FILE} > /dev/null
 
-CDB_ETC_DIR=$CDB_INSTALL_DIR/etc
+LOGR_ETC_DIR=$LOGR_INSTALL_DIR/etc
 
-OPENSSL_CONFIG_FILE=$CDB_ETC_DIR/cdb.openssl.cnf
+OPENSSL_CONFIG_FILE=$LOGR_ETC_DIR/cdb.openssl.cnf
 
 if [ -f $OPENSSL_CONFIG_FILE ]; then
     echo "Configuration file $OPENSSL_CONFIG_FILE has already been created"
     exit 0;
 fi
 
-OPEN_SSL_TEMPLATE_FILE=$CDB_ROOT_DIR/etc/cdb.openssl.cnf.template
+OPEN_SSL_TEMPLATE_FILE=$LOGR_ROOT_DIR/etc/cdb.openssl.cnf.template
 
 echo "Creating the cdb openSSL configuration file."
 read -p "Enter the organizational name [company]: " SSL_ORG_NAME

sbin/cdb_create_db.sh

@@ -281,7 +281,7 @@ if [ -z "$adminWithLocalPassword" ]; then
     read -sp "Enter password for local portal admin (username: logr): [leave blank for no local password] " LOGR_LOCAL_SYSTEM_ADMIN_PASSWORD
     echo ""
     if [ ! -z "$LOGR_LOCAL_SYSTEM_ADMIN_PASSWORD" ]; then
-	adminCryptPassword=`python -c "from cdb.common.utility.cryptUtility import CryptUtility; print(str(CryptUtility.cryptPasswordWithPbkdf2('$CDB_LOCAL_SYSTEM_ADMIN_PASSWORD')))"`
+	adminCryptPassword=`python -c "from cdb.common.utility.cryptUtility import CryptUtility; print(str(CryptUtility.cryptPasswordWithPbkdf2('$LOGR_LOCAL_SYSTEM_ADMIN_PASSWORD')))"`
 	echo "update user_info set password = '$adminCryptPassword' where username='logr'" > temporaryAdminCommand.sql
         execute $mysqlCmd temporaryAdminCommand.sql
     fi

sbin/cdb_deploy_mysqld.sh

@@ -24,7 +24,7 @@ fi
 . ${LOGR_ENV_FILE} > /dev/null
 
 # Use first argument as db name, if provided
-LOGR_DB_NAME=${LOGR_DB_NAME:=cdb}
+LOGR_DB_NAME=${LOGR_DB_NAME:=logr}
 if [ ! -z "$1" ]; then
     LOGR_DB_NAME=$1
 fi

src/java/LogrPortal/nbproject/project.properties

@@ -48,6 +48,7 @@ file.reference.dm-api-3.3.1.jar=lib/dm-api-3.3.1.jar
 file.reference.dm-base-3.3.1.jar=lib/dm-base-3.3.1.jar
 file.reference.ejb-api-3.0.jar=lib/ejb-api-3.0.jar
 file.reference.flexmark-0.64.8.jar=lib/flexmark-0.64.8.jar
+file.reference.flexmark-ext-tables-0.64.8.jar=lib/flexmark-ext-tables-0.64.8.jar
 file.reference.flexmark-util-ast-0.64.8.jar=lib/flexmark-util-ast-0.64.8.jar
 file.reference.flexmark-util-builder-0.64.8.jar=lib/flexmark-util-builder-0.64.8.jar
 file.reference.flexmark-util-collection-0.64.8.jar=lib/flexmark-util-collection-0.64.8.jar
@@ -169,7 +170,8 @@ javac.classpath=\
     ${file.reference.flexmark-util-collection-0.64.8.jar}:\
     ${file.reference.flexmark-util-format-0.64.8.jar}:\
     ${file.reference.flexmark-util-visitor-0.64.8.jar}:\
-    ${file.reference.flexmark-util-html-0.64.8.jar}
+    ${file.reference.flexmark-util-html-0.64.8.jar}:\
+    ${file.reference.flexmark-ext-tables-0.64.8.jar}
 # Space-separated list of extra javac options
 javac.compilerargs=
 javac.debug=true

src/java/LogrPortal/nbproject/project.xml

@@ -243,6 +243,10 @@
                     <file>${file.reference.flexmark-util-html-0.64.8.jar}</file>
                     <path-in-war>WEB-INF/lib</path-in-war>
                 </library>
+                <library dirs="200">
+                    <file>${file.reference.flexmark-ext-tables-0.64.8.jar}</file>
+                    <path-in-war>WEB-INF/lib</path-in-war>
+                </library>
             </web-module-libraries>
             <web-module-additional-libraries/>
             <source-roots>

src/java/LogrPortal/src/java/gov/anl/aps/logr/portal/utilities/MarkdownParser.java

@@ -21,6 +21,7 @@
 import com.vladsch.flexmark.util.misc.Extension;
 import com.vladsch.flexmark.util.sequence.BasedSequence;
 import com.vladsch.flexmark.util.sequence.Escaping;
+import com.vladsch.flexmark.ext.tables.TablesExtension;
 import gov.anl.aps.logr.common.constants.CdbPropertyValue;
 
 import java.util.HashSet;
@@ -60,13 +61,15 @@ public class MarkdownParser {
             + "monospaced code content goes here\n"
             + "```\n"
             + "\n\n"
-            + "# Heading Levels:\n"
+            + "### Table\n\n"
+            + "| Column1 | Column2 | Column3 |\n"
+            + "| --- | --- | --- |\n"
+            + "| Cell 1 | Cell 2 | Cell 3 |\n"
+            + "\n\n"
+            + "### Heading Levels\n"
             + "# Level 1 Heading\n"
             + "## Level 2 Heading\n"
-            + "### Level 3 Heading\n"
-            + "#### Level 4 Heading\n"
-            + "##### Level 5 Heading\n"
-            + "###### Level 6 Heading\n";
+            + "### Level 3 Heading\n";
 
 
     private static String contextRoot = null;
@@ -79,7 +82,8 @@ public class MarkdownParser {
     private static MutableDataHolder options = new MutableDataSet()
             .set(Parser.EXTENSIONS, Arrays.asList(
                     new Extension[]{
-                        LogrFlexmarkExtension.create()
+                        LogrFlexmarkExtension.create(),
+                        TablesExtension.create()
                     }
             ));
 

src/java/LogrPortal/web/resources/css/logbook.css

@@ -133,7 +133,28 @@ pre:has([class^="language-"]) {
 }
 
 .logEntry img {
-    max-width: 450px; 
+    max-width: 450px;
+}
+
+/* Markdown table styles */
+.logEntry table {
+    border-collapse: collapse;
+    width: 100%;
+    margin: 1em 0;
+    font-size: 14px;
+    line-height: 1.5;
+}
+
+.logEntry th,
+.logEntry td {
+    border: 1px solid #ddd;
+    padding: 10px 12px;
+}
+
+.logEntry th {
+    background-color: #f5f5f5;
+    font-weight: 600;
+    color: #333;
 }
 
 .activeLogEntry {
@@ -160,7 +181,7 @@ div.logbookSection {
 .markdown-example-field {
     background: white;
     width: 400px;
-    height: 700px;    
+    height: 750px;
 }
 
 .markdown-example-field > pre {

support/bin/install_netbeans.sh

@@ -8,7 +8,7 @@ CDB_HOSTNAME=`hostname -f`
 
 NETBEANS_VERSION=16
 NETBEANS_ZIP_FILE=netbeans-$NETBEANS_VERSION-bin.zip
-DOWNLOAD_URL=https://dlcdn.apache.org/netbeans/netbeans/$NETBEANS_VERSION/$NETBEANS_ZIP_FILE
+DOWNLOAD_URL=https://archive.apache.org/dist/netbeans/netbeans/$NETBEANS_VERSION/$NETBEANS_ZIP_FILE
 
 currentDir=`pwd`
 cd `dirname $0`/.. && topDir=`pwd`

tools/developer_tools/logr_plugins/utilities/plugin_configuration.py

@@ -28,23 +28,23 @@ def update_plugin_configuration(self, plugin_name, destination_path, configurati
             ext = ext_split[-1]
             # Verify that file is not simply called the same as extension adn
             if ext_split.__len__() > 1 and ext.upper() == configuration_extension.upper():
-                print '\n\nUpdating configuration for plugin: %s (%s)' % (plugin_name, listing)
+                print('\n\nUpdating configuration for plugin: %s (%s)' % (plugin_name, listing))
                 plugin_listing_path = '%s/%s' % (destination_path, listing)
                 default_configuration = open(plugin_listing_path).read()
                 plugin_configuration_directory = "%s/%s" % (self.cdb_plugin_configuration_storage, plugin_name)
                 plugin_stored_configuration_file = "%s/%s" % (plugin_configuration_directory, listing)
 
                 if os.path.exists(plugin_stored_configuration_file):
-                    print "Using stored configuration file: %s" % plugin_stored_configuration_file
+                    print("Using stored configuration file: %s" % plugin_stored_configuration_file)
                 else:
-                    print "\n\nNo configuration exists, follow prompts\n"
+                    print("\n\nNo configuration exists, follow prompts\n")
                     resulting_configuration = ''
                     for configuration_line in default_configuration.split('\n'):
                         if configuration_line.startswith('#'):
-                            print 'Configuration Comment: %s' % configuration_line[1:]
+                            print('Configuration Comment: %s' % configuration_line[1:])
                             resulting_configuration += configuration_line
                         elif configuration_line.startswith('['):
-                            print "Section: %s" % configuration_line
+                            print("Section: %s" % configuration_line)
                             resulting_configuration += configuration_line
                         else:
                             configuration_split = configuration_line.split('=')
@@ -56,7 +56,7 @@ def update_plugin_configuration(self, plugin_name, destination_path, configurati
                             if configuration_split.__len__() == 2:
                                 config_default_value = configuration_split[1]
 
-                            config_value = raw_input("%s [%s]: " % (config_key, config_default_value))
+                            config_value = input("%s [%s]: " % (config_key, config_default_value))
                             if config_value is None or config_value == '':
                                 config_value = config_default_value
                             new_config_line = "%s=%s" % (config_key, config_value)
@@ -76,7 +76,7 @@ def update_plugin_configuration(self, plugin_name, destination_path, configurati
 
                 # Update the configuration stored.
                 shutil.copyfile(plugin_stored_configuration_file, plugin_listing_path)
-                print 'New configuration stored in deployment: %s' % plugin_listing_path
+                print('New configuration stored in deployment: %s' % plugin_listing_path)
 
     @classmethod
     def backup_original_plugin_configurations(cls, plugin_storage_path, configuration_extension):
@@ -98,7 +98,7 @@ def backup_original_plugin_configurations(cls, plugin_storage_path, configuratio
                     if not os.path.exists(configuration_backup_dir):
                         os.makedirs(configuration_backup_dir)
                     configuration_backup_path = "%s/%s" % (configuration_backup_dir, listing)
-                    print "Storing a default plugin configuration file %s to %s: " % (listing, configuration_backup_path)
+                    print("Storing a default plugin configuration file %s to %s: " % (listing, configuration_backup_path))
                     shutil.copyfile(configuration_storage_path, configuration_backup_path)
 
         return configuration_backup_dir
@@ -119,6 +119,6 @@ def restore_configuration(cls, configuration_backup_dir, plugin_storage_path):
                 for listing in directory_listings:
                     configuration_storage_path = "%s/%s" % (plugin_storage_path, listing)
                     configuration_backup_storage_path = "%s/%s" % (configuration_backup_dir, listing)
-                    print "Reverting backup file %s to %s" % (listing, configuration_storage_path)
+                    print("Reverting backup file %s to %s" % (listing, configuration_storage_path))
                     shutil.move(configuration_backup_storage_path, configuration_storage_path)
 

tools/developer_tools/logr_plugins/utilities/plugin_java_parser.py

@@ -5,7 +5,7 @@
 """
 
 import os
-from plugin_configuration import PluginConfiguration
+from .plugin_configuration import PluginConfiguration
 
 JAVA_PLUGIN_PACKAGE="gov.anl.aps.logr.portal.plugins.support"
 

tools/developer_tools/logr_plugins/utilities/plugin_manager.py

@@ -3,7 +3,7 @@
 Copyright (c) UChicago Argonne, LLC. All rights reserved.
 See LICENSE file.
 """
-from utilities.plugin_python_parser import PluginPythonParser
+from .plugin_python_parser import PluginPythonParser
 
 try:
     # attempt to import unique package of cdb python web service to ensure loaded environment
@@ -12,17 +12,16 @@
     import os, sys
     directory = os.path.dirname(__file__)
     fullPath = os.path.abspath(directory + "/../../../..")
-    print >> sys.stderr, "Environment not loaded. Please run `source %s/setup.sh` before running this script." % (
-    fullPath)
+    print("Environment not loaded. Please run `source %s/setup.sh` before running this script." % fullPath, file=sys.stderr)
     exit(1)
 
 import os
 import sys
 
-from plugin_java_parser import PluginJavaParser
-from plugin_xhtml_parser import PluginXhtmlParser
+from .plugin_java_parser import PluginJavaParser
+from .plugin_xhtml_parser import PluginXhtmlParser
 
-from objects.cdb_plugin import CdbPlugin
+from .objects.cdb_plugin import CdbPlugin
 
 LOGR_INSTALL_DIRECTORY = os.environ['LOGR_INSTALL_DIR']
 LOGR_DIST_DIRECTORY = os.environ['LOGR_ROOT_DIR']
@@ -62,11 +61,11 @@ def __select_stored_plugin_directory(self):
         options.append(LOGR_INSTALL_PLUGIN_DIRECTORY)
         options.append('Specify different directory.')
 
-        print 'Select directory for storage of cdb plugins: '
+        print('Select directory for storage of cdb plugins: ')
         for i in range(0, options.__len__()):
-            print '%i - %s' % (i, options[i])
+            print('%i - %s' % (i, options[i]))
 
-        selection = raw_input("%i %s [%i]: " % (i, options[i], default_option))
+        selection = input("%i %s [%i]: " % (i, options[i], default_option))
         if selection is None or selection == '':
             selection = default_option
 
@@ -76,7 +75,7 @@ def __select_stored_plugin_directory(self):
             exit(1)
 
         if selection == 2:
-            result = raw_input("Please enter the path to directory with all plug-ins: ")
+            result = input("Please enter the path to directory with all plug-ins: ")
         else:
             result = options[selection]
 
@@ -139,19 +138,19 @@ def __deploy_portal_plugin(self, selection):
 
     def __prompt_plugin_action(self, actionPrompt, actionMethod):
         self.list_plugins()
-        selection = raw_input("%s [All]: " % actionPrompt)
+        selection = input("%s [All]: " % actionPrompt)
         if selection == "" or selection == "All":
             selection = None
         else:
             selection = int(selection)
 
         actionMethod(selection)
 
-        print "\n\nCompleted: result plugin list."
+        print("\n\nCompleted: result plugin list.")
         self.list_plugins()
 
     def update_auto_generated_files(self, update_configuration=True):
-        print 'Updating auto-generated CDB plugin files'
+        print('Updating auto-generated CDB plugin files')
         self.__update_autogenerated_files(update_configuration)
 
     def __update_autogenerated_files(self, update_configuration=True):
@@ -194,11 +193,11 @@ def __update_autogenerated_files(self, update_configuration=True):
             # Create a __init__.py file for all python plugins.
             init_file_path = "%s/%s" % (LOGR_PYTHON_PLUGIN_PATH, '__init__.py')
             init_file = os.open(init_file_path, os.O_CREAT|os.O_WRONLY)
-            os.write(init_file, "#!/usr/bin/env python\n")
-            os.write(init_file, "\"\"\"\n")
-            os.write(init_file, "Copyright (c) UChicago Argonne, LLC. All rights reserved.\n")
-            os.write(init_file, "See LICENSE file.\n")
-            os.write(init_file, "\"\"\"")
+            os.write(init_file, b"#!/usr/bin/env python\n")
+            os.write(init_file, b"\"\"\"\n")
+            os.write(init_file, b"Copyright (c) UChicago Argonne, LLC. All rights reserved.\n")
+            os.write(init_file, b"See LICENSE file.\n")
+            os.write(init_file, b"\"\"\"")
             os.close(init_file)
 
     @staticmethod
@@ -254,13 +253,13 @@ def __print_selection_list(self, selection_list, title):
 
         listItemFormat = '*%4s - %-' + str(width - 36) + 's %-6s %-6s %-12s*'
 
-        print '\nSaved plugins are located in plug-in directory: %s' % self.plugin_storage_directory
-        print 'for xhtml, java, python (s = stored d=deployed)'
+        print('\nSaved plugins are located in plug-in directory: %s' % self.plugin_storage_directory)
+        print('for xhtml, java, python (s = stored d=deployed)')
 
-        print "\n%s %s %s" % (header_before, title, header_after)
-        print listItemFormat % ('#', 'Plugin Name', 'Xhtml', 'Java', 'Python')
+        print("\n%s %s %s" % (header_before, title, header_after))
+        print(listItemFormat % ('#', 'Plugin Name', 'Xhtml', 'Java', 'Python'))
         column_header_seperator = '-' * (width-2)
-        print '*%s*' % (column_header_seperator)
+        print('*%s*' % (column_header_seperator))
         for i in range(0, selection_list.__len__()):
             plugin = selection_list[i]
             xhtml = ''
@@ -281,8 +280,8 @@ def __print_selection_list(self, selection_list, title):
                 xhtml += 'd'
 
 
-            print listItemFormat % (str(i), plugin.plugin_name, xhtml, java, python)
-        print '*' * width
+            print(listItemFormat % (str(i), plugin.plugin_name, xhtml, java, python))
+        print('*' * width)
 
 if __name__ == '__main__':
     plugin_manager = PluginManager()

tools/developer_tools/logr_plugins/utilities/plugin_python_parser.py

@@ -4,7 +4,7 @@
 See LICENSE file.
 """
 
-from plugin_configuration import PluginConfiguration
+from .plugin_configuration import PluginConfiguration
 
 CONFIGURATION_FILE_EXTENSION = "cfg"