Merge branch 'devel' for releasing '3.3.0'

.gitignore

@@ -1,9 +1,15 @@
 # Configuration files
+config.local/
 config/*_config.inc
 config/hrm.conf
 resources/hrmd.plist
 user/login_user.inc
 
+# Customization files
+images/hrm_custom.ico
+images/logo_custom.png
+css/custom.css
+
 # IDE project settings
 /nbproject/
 /.idea/

.htaccess

@@ -1 +1,5 @@
+# if nothing is requested explicitly, go to the login page:
 DirectoryIndex login.php
+
+# prevent serving git stuff:
+RedirectMatch 404 /\.git

aberration_correction.php

@@ -63,6 +63,8 @@
 
 if ( $_SESSION['setting']->isSted() || $_SESSION['setting']->isSted3D()) {
     $back = "sted_parameters.php";
+} else if ( $_SESSION['setting']->isSpim()) {
+    $back = "spim_parameters.php";
 } else {
     $back = "capturing_parameter.php";
 }

bin/hrm_config.py

@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+"""Helper module to parse the HRM (shell style) config file.
+
+Usually, the config is located at /etc/hrm.conf and written in shell syntax as
+this file simply gets sourced by the bash init script and other shell based
+tools.
+
+This module is not meant to be executed directly and doesn't do anything in
+this case.
+"""
+
+# NOTE:
+# It might be worth checking out the solution described on stackoverflow [1]
+# using an approach based on a real shell subprocess like this:
+"""
+>>> command = ['bash', '-c', 'source init_env && env']
+>>> proc = subprocess.Popen(command, stdout = subprocess.PIPE)
+>>> for line in proc.stdout:
+...    (key, _, value) = line.partition("=")
+...    os.environ[key] = value
+>>> proc.communicate()
+"""
+# [1]: http://stackoverflow.com/questions/3503719/
+
+
+import shlex
+import sys
+
+
+def parse_hrm_conf(filename):
+    """Assemble a dict from the HRM config file (shell syntax).
+
+    Parameters
+    ==========
+    filename: str  - the filename to parse
+
+    Returns
+    =======
+    config: dict
+
+    Example
+    =======
+    {
+        'HRM_DATA': '/export/hrm_data',
+        'HRM_DEST': 'dst',
+        'HRM_HOME': '/var/www/hrm',
+        'HRM_LOG': '/var/log/hrm',
+        'HRM_SOURCE': 'src',
+        'OMERO_HOSTNAME': 'omero.mynetwork.xy',
+        'OMERO_PKG': '/opt/OMERO/OMERO.server',
+        'OMERO_PORT': '4064',
+        'PHP_CLI': '/usr/local/php/bin/php',
+        'SUSER': 'hrm'
+    }
+    """
+    config = dict()
+    body = file(filename, 'r').read()
+    lexer = shlex.shlex(body)
+    lexer.wordchars += '-./'
+    while True:
+        token = lexer.get_token()
+        if token is None or token == '':
+            break
+        # it's valid sh syntax to use a semicolon to join lines, so accept it:
+        if token == ';':
+            continue
+        # we assume entries of the following form:
+        # KEY="some-value"
+        key = token
+        try:
+            equals = lexer.get_token()
+            assert equals == '='
+        except AssertionError:
+            raise SyntaxError(
+                "Can't parse %s, invalid syntax in line %s "
+                "(expected '=', found '%s')." %
+                (filename, lexer.lineno, equals))
+        value = lexer.get_token()
+        value = value.replace('"', '')  # remove double quotes
+        value = value.replace("'", '')  # remove single quotes
+        config[key] = value
+    return config
+
+
+def check_hrm_conf(config):
+    """Check the config dict for required entries."""
+    required = ['OMERO_PKG', 'OMERO_HOSTNAME']
+    for entry in required:
+        if entry not in config:
+            raise SyntaxError('Missing "%s" in the HRM config file.' % entry)
+
+
+if __name__ == "__main__":
+    print __doc__
+    sys.exit(1)
+
+CONFIG = parse_hrm_conf('/etc/hrm.conf')
+check_hrm_conf(CONFIG)