# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details. """ dna_updater_globals.py -- global variables or mutables for dna_updater, and their lowest-level accessors. @author: Bruce @version: $Id$ @copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details. """ from utilities import debug_flags from foundation.changedicts import refreshing_changedict_subscription from foundation.changedicts import _cdproc_for_dictid # but it's private! from model.global_model_changedicts import _changed_structure_Atoms # todo: rename to be non-private from model.global_model_changedicts import _changed_parent_Atoms from utilities.debug import print_compact_stack _DEBUG_ATOM_KEY = None # None, or a value of atom.key for which all ignored changes should be printed # == # _rcdp1 and _rcdp2 will be replaced in initialize_globals() # with refreshing_changedict_subscription instances: _rcdp1 = None _rcdp2 = None # REVIEW: when we reload this module during development, # do we need to preserve those global objects? # I would guess so, but I didn't yet see a bug from not doing so. # [bruce 071119] def initialize_globals(): """ Meant to be called only from master_model_updater.py (perhaps indirectly). Do whatever one-time initialization is needed before our other public functions should be called. [Also should be called if this module is reloaded.] """ # set up this module's private global changedict subscription handlers global _rcdp1, _rcdp2 _rcdp = _refreshing_changedict_subscription_for_dict _rcdp1 = _rcdp(_changed_structure_Atoms) _rcdp2 = _rcdp(_changed_parent_Atoms) return def _refreshing_changedict_subscription_for_dict(dict1): cdp = _cdproc_for_dictid[ id(dict1)] # error if not found; depends on import/initialize order rcdp = refreshing_changedict_subscription( cdp) return rcdp def get_changes_and_clear(): """ Grab copies of the global atom changedicts we care about, returning them in a single changed atom dict, and resubscribe so we don't grab the same changes next time. """ dict1 = _rcdp1.get_changes_and_clear() dict2 = _rcdp2.get_changes_and_clear() # combine them into one dict to return (which caller will own) # optim: use the likely-bigger one, dict2 (from _changed_parent_Atoms), # to hold them all dict2.update(dict1) return dict2 def ignore_new_changes( from_what, changes_ok = True, debug_print_even_if_none = False): """ Discard whatever changes occurred since the last time we called get_changes_and_clear, of the changes we normally monitor and respond to. @param from_what: a string for debug prints, saying what the changes are from, e.g. "from fixing classes". @type from_what: string @param changes_ok: whether it's ok (not an error) if we see changes. @type changes_ok: boolean @param debug_print_even_if_none: do our debug prints even if there were no changes @type debug_print_even_if_none: boolean """ ignore_these = get_changes_and_clear() if ignore_these or debug_print_even_if_none: if (not ignore_these) or changes_ok: if debug_flags.DEBUG_DNA_UPDATER: print "dna updater: ignoring %d new changes %s" % (len(ignore_these), from_what) else: msg = "\nBUG: dna updater: ignoring %d new changes %s -- any such changes are a bug: " % \ (len(ignore_these), from_what) print_compact_stack(msg) print if ignore_these.has_key(_DEBUG_ATOM_KEY): msg = "*** _DEBUG_ATOM_KEY %r: %r seen in those changes" % (_DEBUG_ATOM_KEY, ignore_these[_DEBUG_ATOM_KEY]) if changes_ok: print_compact_stack(msg + ": ") # since we didn't print stack just above else: print msg del ignore_these return # == # globals and accessors # (some can be set outside of dna updater runs, noticed during them) # (not yet here: _f_are_there_any_homeless_dna_markers, etc) _f_invalid_dna_ladders = {} # moved here from DnaLadder.py, bruce 080413 [rename with _f_?] def _f_get_invalid_dna_ladders(): # moved here from DnaLadder.py, bruce 080413 """ Return the invalid dna ladders, and clear the list so they won't be returned again (unless they are newly made invalid). Friend function for dna updater. Other calls would cause it to miss newly invalid ladders, causing serious bugs. """ res = _f_invalid_dna_ladders.values() _f_invalid_dna_ladders.clear() res = filter( lambda ladder: not ladder.valid, res ) # probably not needed return res def _f_clear_invalid_dna_ladders(): #bruce 080413; see comment in caller about need for review/testing if _f_invalid_dna_ladders: print "fyi: dna updater: ignoring %d newly invalid dnaladders" % \ len( _f_invalid_dna_ladders) _f_invalid_dna_ladders.clear() return _f_baseatom_wants_pam = {} # maps baseatom.key to a PAM_MODEL it wants updater to convert it to #bruce 080411, for use instead of chunk attrs like .display_as_pam # by commands for manual conversion of PAM model # note: Pl atoms are not baseatoms! To use _f_baseatom_wants_pam on them, # you need this function: def _f_anyatom_wants_pam(atom): #bruce 080411 # not counting its chunk attrs, just looking at _f_baseatom_wants_pam properly if atom.element.symbol == 'Pl5': atom = atom.Pl_preferred_Ss_neighbor() if atom is None: # that method printed a bug note already return None return _f_baseatom_wants_pam.get(atom.key) # == # These should be cleared at the start and end of any dna updater run. _f_DnaGroup_for_homeless_objects_in_Part = {} _f_ladders_with_up_to_date_baseframes_at_ends = {} #bruce 080409, replacing ladders_dict params (whose passing into enough # methods/functions was unfinished) _f_atom_to_ladder_location_dict = {} #bruce 080411, to permit finding ladder/rail/index of atoms in freshly # made ladders which didn't yet remake their chunks # (needn't store all end atoms, since those can be found using # rail_end_atom_to_ladder -- important for bridging Pls # between fresh and old-untouched ladders) DNALADDER_INVAL_IS_OK = 0 DNALADDER_INVAL_IS_ERROR = 1 DNALADDER_INVAL_IS_NOOP_BUT_OK = 2 dnaladder_inval_policy = DNALADDER_INVAL_IS_OK ### todo: make private; only used directly in this file # and this rule should be maintained # [bruce 080413] def get_dnaladder_inval_policy(): # (use this to prevent bugs from importing a mutable value # and having only the initial value defined globally in a # client module) return dnaladder_inval_policy def clear_updater_run_globals(): #bruce 080218 """ Clear globals which are only used during individual runs of the dna updater. """ # Note: perhaps not all such globals are here yet, which should be. # And there are some in fix_bond_directions (IIRC) which can't be here. _f_DnaGroup_for_homeless_objects_in_Part.clear() _f_ladders_with_up_to_date_baseframes_at_ends.clear() _f_atom_to_ladder_location_dict.clear() global dnaladder_inval_policy dnaladder_inval_policy = DNALADDER_INVAL_IS_OK # important in case of exceptions during updater return def temporarily_set_dnaladder_inval_policy(new): # bruce 080413 """ Must be used in matching pairs with restore_dnaladder_inval_policy, and only within the dna updater. """ global dnaladder_inval_policy old = dnaladder_inval_policy dnaladder_inval_policy = new return old def restore_dnaladder_inval_policy(old): # bruce 080413 global dnaladder_inval_policy dnaladder_inval_policy = old return # == def rail_end_atom_to_ladder(atom): """ Atom is believed to be the end-atom of a rail in a valid DnaLadder. Return that ladder. If anything looks wrong, either console print an error message and return None (which is likely to cause exceptions in the caller), or raise some kind of exception (which is what we do now, since easiest). """ #bruce 080510 moved this from DnaLadder.py to avoid import cycles # various exceptions are possible from the following; all are errors try: ladder = atom._DnaLadder__ladder # note: this attribute name is hardcoded in several files ## assert isinstance(ladder, DnaLadder) # (not worth the trouble, since we don't want the DnaLadder import) assert ladder is not None assert ladder.valid, "%r not valid" % ladder # note: changes in _ladder_set_valid mean this will become common for bugs, attrerror will be rare [080413] # or: if not, print "likely bug: invalid ladder %r found on %r during merging" % (ladder, atom) #k # REVIEW: it might be better to return an invalid ladder than no ladder or raise an exception, # so we might change this to return one, provided the atom is in the end_baseatoms. #### assert atom in ladder.rail_end_baseatoms() return ladder except: error = atom._dna_updater__error and ("[%s]" % atom._dna_updater__error) or "" print "\nfollowing exception is an error in rail_end_atom_to_ladder(%r%s): " % \ (atom, error) raise pass # end