from __future__ import absolute_import, division, print_function import os from iotbx.phil import parse from libtbx.utils import Sorry master_phil_str = """ dispatcher = cctbx.xfel.process .type = str .help = Which program to run. cctbx.xfel.process should be used in most cases. dry_run = False .type = bool .help = If True, the program will create the trial directory but not submit the job, \ and will show the command that would have been executed. monitoring_mode = False .type = bool .help = If True, will hide the submit jobs buttons and remove tabs for configuring \ Trials and Datasets. facility { name = lcls *standalone .type = choice .help = Facility for the XFEL gui. LCLS configures the GUI to use LCLS services \ for data monitoring, job submission, and so forth. Standlone runs the \ GUI for all other data sources. lcls { experiment = "" .type = str .help = Experiment name, eg cxid9114 web { location = "SLAC" .type = str .help = Where to look for XTC streams. Can be SLAC, SLACFFB (active experiment \ only, retired), SRCF_FFB (active experiment only), SDF or NERSC \ (contact LCLS staff to arrange file mover for SDF or NERSC). user = "" .type = str .help = Username for LCLS run database web service password = "" .type = str .help = Web password. Will be cached in plain text! enforce80 = False .type = bool .help = report only on stream 81, FEE spectrometer enforce81 = False .type = bool .help = report only on stream 81, FEE spectrometer } use_ffb = False .type = bool .help = Run on the ffb if possible. Only for active users! dump_shots = False .type = bool .help = Write images to disk whether they index or not. \ Helpful for tuning spotfinding and indexing parameters, and necessary \ for the "Should have indexed" feature of the Run Stats tab. } standalone { data_dir = None .type = path .help = Folder to monitor for new data monitor_for = *files folders .type = choice .help = Whether to monitor for new files or new folders with files in them folders { method = *status_file n_files .type = choice .help = How to determine if a run is complete. status_file: look for a \ status.txt file. n_files: run is complete when at least \ n_files_needed files are found n_files_needed = 0 .type = int .help = If criteria is n_files, this is how many files are needed \ before a run is complete } files { last_modified = 0 .type = float .help = This is the miniumum number of seconds since a file was last \ modified before the run is complete minimum_file_size = 0 .type = int .help = Minimum file size (in bytes) before the run is complete } template = None .type = str .help = File matching pattern for new data. Example: *.h5 composite_files = True .type = bool .help = If True, files are submitted as individual runs. Otherwise, groups \ of files are submitted as single runs } } output_folder = "" .type = path .help = Processing results will go in this folder include scope xfel.command_line.cxi_mpi_submit.mp_phil_scope """ db_phil_str = """ experiment_tag = None .type = str .help = User defined tag to describe the set of trials being performed. All database tables will \ be pre-pended with this string db { host = psdb-user.slac.stanford.edu .type = str .help = Host name for mysql databse server name = "" .type = str .help = Database name user = "" .type=str .help = Database user name password = "" .type = str .help = Database password. Will be cached as plain text! verbose = False .type = bool .expert_level = 2 .help = Print to the terminal all database queries port = 3306 .type = int .help = Port number to be used for connection logging_batch_size = 3 .type = int .help = Number of images to log at once. Increase if using many (thousands) of processors. server { basedir = None .type = path .help = Root folder for mysql database prompt_for_root_password = False .type = bool .help = Whether to always ask for the root password. Note, root password is always \ needed when the database is initialized. root_user = 'root' .type = str .help = username for root .expert_level = 2 root_password = None .type = str .help = Password for root user .expert_level = 2 } } """ master_phil_scope = parse(master_phil_str + db_phil_str, process_includes=True) settings_dir = os.path.join(os.path.expanduser('~'), '.cctbx.xfel') settings_file = os.path.join(settings_dir, 'settings.phil') known_dials_dispatchers = { 'cctbx.xfel.xtc_process': 'xfel.command_line.xtc_process', 'cctbx.xfel.process': 'xfel.command_line.xfel_process', 'dials.stills_process': 'dials.command_line.stills_process', 'cctbx.xfel.small_cell_process': 'xfel.small_cell.command_line.xfel_small_cell_process', 'cctbx.xfel.stripe_experiment': 'xfel.command_line.striping', 'cctbx.xfel.merge': 'xfel.merging.application.phil.phil' } def load_phil_scope_from_dispatcher(dispatcher): import importlib try: phil_scope = importlib.import_module(known_dials_dispatchers[dispatcher]).phil_scope except KeyError: import imp mod = imp.load_source('module', dispatcher) phil_scope = mod.phil_scope return phil_scope def load_cached_settings(): if os.path.exists(settings_file): user_phil = parse(file_name = settings_file) params, unused = master_phil_scope.fetch(source = user_phil, track_unused_definitions=True) params = params.extract() if len(unused) > 0: from .phil_patch import sync_phil sync_phil(params, unused) return params else: return master_phil_scope.extract() def save_cached_settings(params): if not os.path.exists(settings_dir): os.makedirs(settings_dir) working_phil = master_phil_scope.format(python_object = params) diff_phil = master_phil_scope.fetch_diff(source = working_phil) try: f = open(settings_file.encode('utf8'), 'wb') f.write(diff_phil.as_str().encode('utf8')) f.close() except IOError: raise Sorry('Unable to write %s.' % settings_file)