ISISDirecInelasticConfig.py

import os
import platform
import shutil
import re
import copy
from datetime import date
import time

# the list of instruments this configuration is applicable to
INELASTIC_INSTRUMENTS = ['MAPS','LET','MERLIN','MARI','HET']

class UserProperties(object):
    """Helper class to define & retrieve user properties
       as retrieved from file provided by user office
    """
    def __init__(self):
        self.instrument={}
        self.rb_dir = {}
        self.cycle_IDlist={}
        self.start_dates = {}
        self._recent_dateID=None
#
    def set_user_properties(self,instrument,start_date,cycle,rb_folder):
        """Define the information, user office provides about user. The info has the form:
           instrument -- string with full instrument name
           date       -- experiment start date in the form YYYYMMDD
           cycle      -- the cycle id in the form CYCLEYYYYN where N is the cycle number within the year
           rb_folder  -- the working folder available for all users and IS participating in the experiment.
        """
        self.check_input(instrument,start_date,cycle,rb_folder)
        #when user starts
        recent_date = date(int(start_date[0:4]),int(start_date[4:6]),int(start_date[6:8]))
        recent_date_id = str(recent_date)
        self.start_dates[recent_date_id]=recent_date

        # a data which define the cycle ID e.g 2014_3 or something
        self.cycle_IDlist[recent_date_id] = (str(cycle[5:9]),str(cycle[9:10]))
        self.instrument[recent_date_id]   = str(instrument).upper()
        self.rb_dir[recent_date_id]       = rb_folder
        if self._recent_dateID:
            max_date = self.start_dates[self._recent_dateID]
            for date_key,a_date in self.start_dates.iteritems():
                if a_date>max_date:
                    self._recent_dateID = date_key
                    max_date = a_date
        else:
            self._recent_dateID = recent_date_id
#
    def get_start_date(self):
        """Last start date"""
        if self._recent_dateID:
            return  self.start_dates[self._recent_dateID]
        else:
            raise RuntimeError("User's experiment date is not defined. User undefined")
#
    def get_last_instrument(self):
        """return instrument used in last actual experiment"""
        if self._recent_dateID:
            return  self.instrument[self._recent_dateID]
        else:
            raise RuntimeError("User's experiment date is not defined. User undefined")
#
    def get_last_rbdir(self):
        """return rb folder used in last actual instrument"""
        if self._recent_dateID:
            return  self.rb_dir[self._recent_dateID]
        else:
            raise RuntimeError("User's experiment date is not defined. User undefined")
#
    def get_last_cycleID(self):
        """return last cycle the user is participating"""
        if self._recent_dateID:
            return  self.cycle_IDlist[self._recent_dateID]
        else:
            raise RuntimeError("User's experiment date is not defined. User undefined")

    def check_input(self,instrument,start_date,cycle,rb_folder):
        """Verify that input is correct"""
        if not instrument in INELASTIC_INSTRUMENTS:
            raise RuntimeError("Instrument {0} has to be one of "\
                  "ISIS inelastic instruments".format(instrument))
        if not (isinstance(start_date,str) and len(start_date) == 8):
            raise RuntimeError("Experiment start date {0} should be defined as"\
                  " a sting in the form YYYYMMDD but it is not".format(start_date))
        if not (isinstance(cycle,str) and len(cycle) == 10 and re.match('^CYCLE',cycle)) :
            raise RuntimeError("Cycle {0} should have form CYCLEYYYYN where "\
                  "N-- the cycle's number in a year but it is not".format(cycle))
        if not (os.path.exists(rb_folder) and os.path.isdir(rb_folder)):
            raise RuntimeError("Folder {0} have to exist".format(rb_folder))
#
#--------------------------------------------------------------------#
#
class MantidConfigDirectInelastic(object):
    """Class describes Mantid server specific user's configuration,
        necessary for Direct Inelastic reduction and analysis to work

        The class should not depend on Mantid itself.

        1) Valid for Mantid 3.4 available on 18/05/2015 and expects server
        to have:
        Map/masks folder with layout defined on (e.g. svn checkout)
        https://svn.isis.rl.ac.uk/InstrumentFiles/trunk
        2) User scripts folder with layout defined on 
        (e.g. git checkout or Mantid script repository set-up):
        git@github.com:mantidproject/scriptrepository.git
        see https://github.com/mantidproject/scriptrepository for details
        3) The data can be found in archive, mounted at /archive/NDXxxxxx/Instrument/data/cycle_XX_Y

        4)There are number of other assumptions about script path, used scripts, Mantid confg,
          and other folders
          All these assumptions are summarized within __init__

       The class have to change/to be amended if the configuration 
       changes or has additional features.
    """
    def __init__(self,mantid='/opt/Mantid/',home='/home/',\
                 script_repo='/opt/UserScripts/',\
                 map_mask_folder='/usr/local/mprogs/InstrumentFiles/'):
        """Initialize generic config variables and variables specific to a server"""

        self._mantid_path = str(mantid)
        self._home_path  = str(home)
        self._script_repo = str(script_repo)
        self._map_mask_folder = str(map_mask_folder)
        # check if all necessary server folders specified as class parameters are present
        self._check_server_folders_present()
        #
        # Static Parts of dynamic contents of Mantid configuration file
        self._root_data_folder='/archive' # root folder for all experimental results -- particular one will depend on
                                          # instrument and cycle number.
        # the common part of all strings, generated dynamically as function of input class parameters.
        self._dynamic_options_base = ['default.facility=ISIS']
        # Path to python scripts, defined and used by mantid wrt to Mantid Root (this path may be version specific)
        self._python_mantid_path = ['scripts/Calibration/','scripts/Examples/','scripts/Interface/','scripts/Vates/']
        # Static paths to user scripts, defined wrt script repository root
        self._python_user_scripts = set(['direct_inelastic/ISIS/qtiGenie/'])
        # File name, used as source of reduction scripts for particular instrument
        self._sample_reduction_file = lambda InstrName : '{0}Reduction_Sample.py'.format(InstrName)
        # File name, used as target for copying to user folder for user to deploy as the base for his reduction script
        self._target_reduction_file = lambda InstrName,cycleID : '{0}Reduction_{1}_{2}.py'.format(InstrName,cycleID[0],cycleID[1])

        # Static contents of the Mantid Config file
        self._header = ("# This file can be used to override any properties for this installation.\n"
                        "# Any properties found in this file will override any that are found in the Mantid.Properties file\n"
                        "# As this file will not be replaced with further installations of Mantid it is a safe place to put\n"
                        "# properties that suit your particular installation.\n"
                        "#\n"
                        "# See here for a list of possible options:''# http://www.mantidproject.org/Properties_File#Mantid.User.Properties''\n"
                        "#\n"
                        "#uncomment to enable archive search - ICat and Orbiter\n"
                        "datasearch.searcharchive = On #  may be important for autoreduction to work,\n")
        #
        self._footer = ("##\n"
                        "## LOGGING\n"
                        "##\n"
                        "\n"
                        "## Uncomment to change logging level\n"
                        "## Default is information\n"
                        "## Valid values are: error, warning, notice, information, debug\n"
                        "#logging.loggers.root.level=information\n"
                        "\n"
                        "## Sets the lowest level messages to be logged to file\n"
                        "## Default is warning\n"
                        "## Valid values are: error, warning, notice, information, debug\n"
                        "#logging.channels.fileFilterChannel.level=debug\n"
                        "## Sets the file to write logs to\n"
                        "#logging.channels.fileChannel.path=../mantid.log\n"
                        "##\n"
                        "## MantidPlot\n"
                        "##\n"
                        "## Show invisible workspaces\n"
                        "#MantidOptions.InvisibleWorkspaces=0\n"
                        "## Re-use plot instances for different plot types\n"
                        "#MantidOptions.ReusePlotInstances=Off\n\n"
                        "## Uncomment to disable use of OpenGL to render unwrapped instrument views\n"
                        "#MantidOptions.InstrumentView.UseOpenGL=Off\n")

        # Methods, which build & verify various parts of Mantid configuration
        self._dynamic_options = [self._set_default_inst,
                        self._set_script_repo, # this would be necessary to have on an Instrument scientist account, disabled on generic setup
                        self._def_python_search_path,
                        self._set_datasearch_directory,self._set_rb_directory]
        self._user = None
        self._cycle_data_folder=set()
        # this is the list, containing configuration strings
        # generated by the class. No configuration is present initially.
        # Its contents is generated by _init_config method from server and user specific
        # input parameters together.
        self._dynamic_configuration = None
        # Unconditionally rewrite Mantid Configuration
        self._force_change_config = False
        # Unconditionally rewrite copy of sample reduction script
        self._force_change_script = False
#
    def config_need_replacing(self,config_file_name):
        """Method specifies conditions when existing configuration file should be replaced"""
        if self._force_change_config:
            return True
        # missing file should always be replaced
        if not os.path.isfile(config_file_name):
           return True
        modification_date = date.fromtimestamp(os.path.getmtime(config_file_name))
        start_date = self._user.get_start_date()
        if modification_date<start_date:
            return True
        else:
            return False
#
    def script_need_replacing(self,source_script_name,target_script_name):
        """Method specifies conditions when existing reduction file should be replaced
           by a sample file.
        """
        if self._force_change_script:
            return True
        # non-existing file should always be replaced
        if not os.path.isfile(target_script_name):
           return True
        #Always replace sample file if it has not been touched
        start_date = self._user.get_start_date()
        # this time is set up to the file, copied from the repository
        sample_file_time = time.mktime(start_date.timetuple())
        targ_file_time  = os.path.getmtime(target_script_name)
        if sample_file_time  ==  targ_file_time:
            return True
        else: # somebody have modified the target file. Leave it alone
            return False
#
    def copy_reduction_sample(self,InstrName,CycleID,rb_folder):
        """Method copies sample reduction script from user script repository
           to user folder.
        """

        source_file = self._sample_reduction_file(InstrName)

        source_path = os.path.join(self._script_repo,'direct_inelastic',InstrName.upper())
        full_source = os.path.join(source_path,source_file)

        if not os.path.isfile(full_source):
            return

        target_file = self._target_reduction_file(InstrName,CycleID)
        full_target = os.path.join(rb_folder,target_file)
        # already have target file or modified by user
        if not self.script_need_replacing(full_source,full_target):
            return
        if os.path.isfile(full_target):
            os.remove(full_target)
        shutil.copyfile(full_source,full_target)
        os.chmod(full_target,0777)

        if platform.system() != 'Windows':
            os.system('chown '+self._fedid+':'+self._fedid+' '+full_target)
        # Set up the file  creation and modification dates to the users start date
        start_date = self._user.get_start_date()
        file_time = time.mktime(start_date.timetuple())
        os.utime(full_target,(file_time,file_time))


    def get_data_folder_name(self,instr,cycle_ID):
        """Method to generate a data folder from instrument name and the cycle start date
           (cycle ID)
           The agreement on the naming as currently in ISIS:
           e.g: /archive/NDXMERLIN/Instrument/data/cycle_08_1
        """
        folder = os.path.join(self._root_data_folder,'NDX'+instr.upper(),\
                              'Instrument/data/cycle_'+str(cycle_ID[0])+'_'+str(cycle_ID[1]))
        return folder

    def is_inelastic(self,instr_name):
        """Check if the instrument is inelastic"""
        if instr_name in INELASTIC_INSTRUMENTS:
            return True
        else:
            return False
    #
    def init_user(self,fedid,theUser):
        """Define settings, specific to a user"""
        #
        for instr in theUser.instrument.values():
            if not self.is_inelastic(instr):
                raise RuntimeError('Instrument {0} is not among acceptable instruments'.format(instrument))
        self._user=theUser

        self._fedid = str(fedid)
        user_folder = os.path.join(self._home_path,self._fedid)
        if not os.path.exists(user_folder):
            raise RuntimeError("User with fedID {0} does not exist. Create such user folder first".format(fedid))
        for rb_folder in theUser.rb_dir.values():
            if not os.path.exists(str(rb_folder)):
                raise RuntimeError("Experiment folder with {0} does not exist. Create such folder first".format(rb_folder))
        #
        # how to check cycle folders, they may not be available
        self._cycle_data_folder=set()
        for date_key,folder_id in theUser.cycle_IDlist.items():
            self._cycle_data_folder.add(self.get_data_folder_name(theUser.instrument[date_key],folder_id))
        # Initialize configuration settings 
        self._dynamic_configuration = copy.deepcopy(self._dynamic_options_base)
        self._init_config()
    #

    def  _check_server_folders_present(self):
        """Routine checks all necessary server folder are present"""
        if not os.path.exists(self._mantid_path):
            raise RuntimeError("SERVER ERROR: no correct mantid path defined at {0}".format(self._mantid_path))
        if not os.path.exists(self._home_path):
            raise RuntimeError("SERVER ERROR: no correct home path defined at {0}".format(self._home_path))
        if not os.path.exists(self._script_repo):
            raise RuntimeError(("SERVER ERROR: no correct user script repository defined at {0}\n"
                                "Check out Mantid script repository from account, which have admin rights").format(self._script_repo))
        if not os.path.exists(self._map_mask_folder):
            raise RuntimeError(("SERVER ERROR: no correct map/mask folder defined at {0}\n"
                                "Check out Mantid map/mask files from svn at https://svn.isis.rl.ac.uk/InstrumentFiles/trunk")\
                                .format(self._map_mask_folder))

    def _init_config(self):
        """Execute Mantid properties setup methods"""
        for fun in self._dynamic_options:
            fun()
    #
    def _set_default_inst(self):
        """Set up last instrument, deployed by user"""
        if self._user:
            InstrName = self._user.get_last_instrument()
            self._dynamic_configuration.append('default.instrument={0}'.format(InstrName))
        else:
            self._dynamic_configuration.append('default.instrument={0}'.format('MARI'))
    #
    def _set_script_repo(self):
        self._dynamic_configuration.append('#ScriptLocalRepository={0}'.format(self._script_repo))
    #
    def _def_python_search_path(self):
        """Define path for Mantid Inelastic python scripts"""
        # Note, instrument name script folder is currently upper case on GIT
        if not self._user:
            raise RuntimeError("Can not define python search path without defined user")

        # define main Mantid scripts search path
        path = os.path.join(self._mantid_path,'scripts/')
        for part in self._python_mantid_path:
            path +=';'+os.path.join(self._mantid_path,part)

        # define and append user scrips search path
        user_path_part = copy.deepcopy(self._python_user_scripts)
        for instr in self._user.instrument.values():
            user_path_part.add(os.path.join('direct_inelastic',instr.upper()))
        for part in user_path_part:
            path +=';'+os.path.join(self._script_repo,part)+'/'

        self._dynamic_configuration.append('pythonscripts.directories=' + path)
    #
    def _set_rb_directory(self):
        """Set up default save directory, the one where data are saved by default"""
        if self._user:
            rb_folder = self._user.get_last_rbdir()
            self._dynamic_configuration.append('defaultsave.directory={0}'.format(rb_folder))
        else:
            raise RuntimeError("Can not define RB folder without user being defined")
    #
    def _set_datasearch_directory(self):
        """Note, map/mask instrument folder is lower case as if loaded from SVN. 
           Autoreduction may have it upper case"""
        if not self._user:
            raise RuntimeError("Can not define Data search path without user being defined")

        instr_name = self._user.get_last_instrument()
        map_mask_dir  = os.path.abspath(os.path.join('{0}'.format(self._map_mask_folder),\
                                                     '{0}'.format(str.lower(instr_name))))
        # set up all data folders
        all_data_folders=list(self._cycle_data_folder)
        data_dir = os.path.abspath('{0}'.format(all_data_folders[0]))
        for folder in all_data_folders[1:]:
             data_dir +=';'+os.path.abspath('{0}'.format(folder))

        all_rb_folders = self._user.rb_dir
        for folder in all_rb_folders.values():
            data_dir+=';'+os.path.abspath('{0}'.format(folder))

        self._dynamic_configuration.append('datasearch.directories='+map_mask_dir+';'+data_dir)
    #
    def generate_config(self):
        """Save generated Mantid configuration file into user's home folder
           and copy other files, necessary for Mantid to work properly
        """

        config_path = os.path.join(self._home_path,self._fedid,'.mantid')
        if not os.path.exists(config_path):
            err = os.makedirs(config_path)
            if err: 
                raise RuntimeError('can not find or create Mantid configuration path {0}'.format(config_path))

        config_file = os.path.join(config_path,'Mantid.user.properties')
        if self.config_need_replacing(config_file):
            self._write_user_config_file(config_file)
        else:
            pass
        if platform.system() != 'Windows':
            os.system('chown -R {0}:{0} {1}'.format(self._fedid,config_path))

        InstrName = self._user.get_last_instrument()
        cycleID   = self._user.get_last_cycleID()
        rb_folder = self._user.get_last_rbdir()
        self.copy_reduction_sample(InstrName,cycleID,rb_folder)

    def _write_user_config_file(self,config_file_name):
        """Write existing dynamic configuration from memory to
           user defined configuration file
        """
        fp = open(config_file_name,'w')
        fp.write(self._header)
        fp.write('## -----   Generated user properties ------------ \n')
        fp.write('##\n')
        for opt in self._dynamic_configuration:
            fp.write(opt)
            fp.write('\n##\n')
        fp.write(self._footer)
        fp.close()
        if platform.system() != 'Windows':
            os.system('chown -R {0}:{0} {1}'.format(self._fedid,config_file_name))