source: trunk/CifFile/CifFile.py @ 4082

# To maximize python3/python2 compatibility
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import

try:
    from cStringIO import StringIO
except ImportError:
    from io import StringIO

# Python 2,3 compatibility
try:
    from urllib import urlopen         # for arbitrary opening
    from urlparse import urlparse, urlunparse,urljoin
except:
    from urllib.request import urlopen
    from urllib.parse import urlparse,urlunparse,urljoin

# The unicode type does not exist in Python3 as the str type
# encompasses unicode.  PyCIFRW tests for 'unicode' would fail
# Suggestions for a better approach welcome.

if isinstance(u"abc",str):   #Python3
    unicode = str
    
__copyright = """
PYCIFRW License Agreement (Python License, Version 2)
-----------------------------------------------------

1. This LICENSE AGREEMENT is between the Australian Nuclear Science
and Technology Organisation ("ANSTO"), and the Individual or
Organization ("Licensee") accessing and otherwise using this software
("PyCIFRW") in source or binary form and its associated documentation.

2. Subject to the terms and conditions of this License Agreement,
ANSTO hereby grants Licensee a nonexclusive, royalty-free, world-wide
license to reproduce, analyze, test, perform and/or display publicly,
prepare derivative works, distribute, and otherwise use PyCIFRW alone
or in any derivative version, provided, however, that this License
Agreement and ANSTO's notice of copyright, i.e., "Copyright (c)
2001-2014 ANSTO; All Rights Reserved" are retained in PyCIFRW alone or
in any derivative version prepared by Licensee.

3. In the event Licensee prepares a derivative work that is based on
or incorporates PyCIFRW or any part thereof, and wants to make the
derivative work available to others as provided herein, then Licensee
hereby agrees to include in any such work a brief summary of the
changes made to PyCIFRW.

4. ANSTO is making PyCIFRW available to Licensee on an "AS IS"
basis. ANSTO MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, ANSTO MAKES NO AND
DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYCIFRW WILL NOT
INFRINGE ANY THIRD PARTY RIGHTS.

5. ANSTO SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYCIFRW
FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A
RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYCIFRW, OR ANY
DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.

6. This License Agreement will automatically terminate upon a material
breach of its terms and conditions.

7. Nothing in this License Agreement shall be deemed to create any
relationship of agency, partnership, or joint venture between ANSTO
and Licensee. This License Agreement does not grant permission to use
ANSTO trademarks or trade name in a trademark sense to endorse or
promote products or services of Licensee, or any third party.

8. By copying, installing or otherwise using PyCIFRW, Licensee agrees
to be bound by the terms and conditions of this License Agreement.

"""


import re,sys
from . import StarFile
from .StarFile import StarList  #put in global scope for exec statement
try:
    import numpy                   #put in global scope for exec statement
    from .drel import drel_runtime  #put in global scope for exec statement
except ImportError:
    pass                       #will fail when using dictionaries for calcs
from copy import copy          #must be in global scope for exec statement

def track_recursion(in_this_func):
    """Keep an eye on a function call to make sure that the key argument hasn't been
    seen before"""
    def wrapper(*args,**kwargs):
        key_arg = args[1]
        if key_arg in wrapper.called_list:
            print('Recursion watch: %s already called %d times' % (key_arg,wrapper.called_list.count(key_arg)))
            raise CifRecursionError( key_arg,wrapper.called_list[:])    #failure
        if len(wrapper.called_list) == 0:   #first time
            wrapper.stored_use_defaults = kwargs.get("allow_defaults",False)
            print('All recursive calls will set allow_defaults to ' + repr(wrapper.stored_use_defaults))
        else:
            kwargs["allow_defaults"] = wrapper.stored_use_defaults
        wrapper.called_list.append(key_arg)
        print('Recursion watch: call stack: ' + repr(wrapper.called_list))
        try:
            result = in_this_func(*args,**kwargs)
        except StarFile.StarDerivationError as s:
            if len(wrapper.called_list) == 1: #no more
                raise StarFile.StarDerivationFailure(wrapper.called_list[0])
            else:
                raise
        finally:
            wrapper.called_list.pop()
            if len(wrapper.called_list) == 0:
                wrapper.stored_used_defaults = 'error'
        return result
    wrapper.called_list = []
    return wrapper

class CifBlock(StarFile.StarBlock):
    """
    A class to hold a single block of a CIF file.  A `CifBlock` object can be treated as
    a Python dictionary, in particular, individual items can be accessed using square
    brackets e.g. `b['_a_dataname']`.  All other Python dictionary methods are also
    available (e.g. `keys()`, `values()`).  Looped datanames will return a list of values.

    ## Initialisation

    When provided, `data` should be another `CifBlock` whose contents will be copied to
    this block.

    * if `strict` is set, maximum name lengths will be enforced

    * `maxoutlength` is the maximum length for output lines

    * `wraplength` is the ideal length to make output lines

    * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
    is raised).

    * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
    the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
    after setting the dataitem value.
    """
    def __init__(self,data = (), strict = 1, compat_mode=False, **kwargs):
        """When provided, `data` should be another CifBlock whose contents will be copied to
        this block.

        * if `strict` is set, maximum name lengths will be enforced

        * `maxoutlength` is the maximum length for output lines

        * `wraplength` is the ideal length to make output lines

        * When set, `overwrite` allows the values of datanames to be changed (otherwise an error
        is raised).

        * `compat_mode` will allow deprecated behaviour of creating single-dataname loops using
        the syntax `a[_dataname] = [1,2,3,4]`.  This should now be done by calling `CreateLoop`
        after setting the dataitem value.
        """
        if strict: maxnamelength=75
        else:
           maxnamelength=-1
        super(CifBlock,self).__init__(data=data,maxnamelength=maxnamelength,**kwargs)
        self.dictionary = None   #DDL dictionary referring to this block
        self.compat_mode = compat_mode   #old-style behaviour of setitem

    def RemoveCifItem(self,itemname):
        """Remove `itemname` from the CifBlock"""
        self.RemoveItem(itemname)

    def __setitem__(self,key,value):
        self.AddItem(key,value)
        # for backwards compatibility make a single-element loop
        if self.compat_mode:
            if isinstance(value,(tuple,list)) and not isinstance(value,StarFile.StarList):
                 # single element loop
                 self.CreateLoop([key])

    def copy(self):
        newblock = super(CifBlock,self).copy()
        return self.copy.im_class(newblock)   #catch inheritance

    def AddCifItem(self,data):
        """ *DEPRECATED*. Use `AddItem` instead."""
        # we accept only tuples, strings and lists!!
        if not (isinstance(data[0],(unicode,tuple,list,str))):
                  raise TypeError('Cif datanames are either a string, tuple or list')
        # we catch single item loops as well...
        if isinstance(data[0],(unicode,str)):
            self.AddSingleCifItem(data[0],list(data[1]))
            if isinstance(data[1],(tuple,list)) and not isinstance(data[1],StarFile.StarList):  # a single element loop
                self.CreateLoop([data[0]])
            return
        # otherwise, we loop over the datanames
        keyvals = zip(data[0][0],[list(a) for a in data[1][0]])
        [self.AddSingleCifItem(a,b) for a,b in keyvals]
        # and create the loop
        self.CreateLoop(data[0][0])

    def AddSingleCifItem(self,key,value):
        """*Deprecated*. Use `AddItem` instead"""
        """Add a single data item. If it is part of a loop, a separate call should be made"""
        self.AddItem(key,value)

    def loopnames(self):
        return [self.loops[a] for a in self.loops]


class CifFile(StarFile.StarFile):
    def __init__(self,datasource=None,strict=1,standard='CIF',**kwargs):
        super(CifFile,self).__init__(datasource=datasource,standard=standard, **kwargs)
        self.strict = strict
        self.header_comment = \
"""
##########################################################################
#               Crystallographic Information Format file
#               Produced by PyCifRW module
#
#  This is a CIF file.  CIF has been adopted by the International
#  Union of Crystallography as the standard for data archiving and
#  transmission.
#
#  For information on this file format, follow the CIF links at
#  http://www.iucr.org
##########################################################################
"""


class CifError(Exception):
    def __init__(self,value):
        self.value = value
    def __str__(self):
        return '\nCif Format error: '+ self.value

class ValidCifError(Exception):
    def __init__(self,value):
        self.value = value
    def __str__(self):
        return '\nCif Validity error: ' + self.value

class CifRecursionError(Exception):
    def __init__(self,key_value,call_stack):
        self.key_value = key_value
        self.call_stack = call_stack
    def __str__(self):
        return "Derivation has recursed, %s seen twice (call stack %s)" % (self.key_value,repr(self.call_stack))


class CifDic(StarFile.StarFile):
    """Create a Cif Dictionary object from the provided source, which can
    be a filename/URL or a CifFile.  Optional arguments (relevant to DDLm
    only):

    * do_minimum (Boolean):
         Do not set up the dREL system for auto-calculation or perform
         imports.  This implies do_imports=False and do_dREL=False

    * do_imports = No/Full/Contents/All:
         If not 'No', replace _import.get statements with the imported contents for
         Full mode/Contents mode/Both respectively.

    * do_dREL = True/False:
         Parse and convert all dREL methods to Python. Implies do_imports=All

    """
    def __init__(self,dic,do_minimum=False,do_imports='All', do_dREL=True,
                                                             grammar='auto',**kwargs):
        self.do_minimum = do_minimum
        if do_minimum:
            do_imports = 'No'
            do_dREL = False
        if do_dREL: do_imports = 'All'
        self.template_cache = {}    #for DDLm imports
        self.ddlm_functions = {}    #for DDLm functions
        self.switch_numpy(False)    #no Numpy arrays returned
        super(CifDic,self).__init__(datasource=dic,grammar=grammar,**kwargs)
        self.standard = 'Dic'    #for correct output order
        self.scoping = 'dictionary'
        (self.dicname,self.diclang) = self.dic_determine()
        print('%s is a %s dictionary' % (self.dicname,self.diclang))
        self.scopes_mandatory = {}
        self.scopes_naughty = {}
        # rename and expand out definitions using "_name" in DDL dictionaries
        if self.diclang == "DDL1":
            self.DDL1_normalise()   #this removes any non-definition entries
        self.create_def_block_table() #From now on, [] uses definition_id
        if self.diclang == "DDL1":
            self.ddl1_cat_load()
        elif self.diclang == "DDL2":
            self.DDL2_normalise()   #iron out some DDL2 tricky bits
        elif self.diclang == "DDLm":
            self.scoping = 'dictionary'   #expose all save frames
            if do_imports is not 'No':
               self.ddlm_import(import_mode=do_imports)#recursively calls this routine
            self.create_alias_table()
            self.create_cat_obj_table()
            self.create_cat_key_table()
            if do_dREL:
                print('Doing full dictionary initialisation')
                self.initialise_drel()
        self.add_category_info(full=do_dREL)
        # initialise type information
        self.typedic={}
        self.primdic = {}   #typecode<->primitive type translation
        self.add_type_info()
        self.install_validation_functions()

    def dic_determine(self):
        if "on_this_dictionary" in self: 
            self.master_block = super(CifDic,self).__getitem__("on_this_dictionary")
            self.def_id_spec = "_name"
            self.cat_id_spec = "_category.id"   #we add this ourselves 
            self.type_spec = "_type"
            self.enum_spec = "_enumeration"
            self.cat_spec = "_category"
            self.esd_spec = "_type_conditions"
            self.must_loop_spec = "_list"
            self.must_exist_spec = "_list_mandatory"
            self.list_ref_spec = "_list_reference"
            self.key_spec = "_list_mandatory"
            self.unique_spec = "_list_uniqueness"
            self.child_spec = "_list_link_child"
            self.parent_spec = "_list_link_parent"
            self.related_func = "_related_function"
            self.related_item = "_related_item"
            self.primitive_type = "_type"
            self.dep_spec = "xxx"
            self.cat_list = []   #to save searching all the time
            name = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_name"]
            version = super(CifDic,self).__getitem__("on_this_dictionary")["_dictionary_version"]
            return (name+version,"DDL1")
        elif len(self.get_roots()) == 1:              # DDL2/DDLm
            self.master_block = super(CifDic,self).__getitem__(self.get_roots()[0][0])      
            # now change to dictionary scoping
            self.scoping = 'dictionary'
            name = self.master_block["_dictionary.title"]
            version = self.master_block["_dictionary.version"]
            if self.master_block.has_key("_dictionary.class"):   #DDLm
                self.enum_spec = '_enumeration_set.state'
                self.key_spec = '_category.key_id'
                self.must_exist_spec = None
                self.cat_spec = '_name.category_id'
                self.primitive_type = '_type.contents'
                self.cat_id_spec = "_definition.id"
                self.def_id_spec = "_definition.id"
                return(name+version,"DDLm") 
            else:   #DDL2
                self.cat_id_spec = "_category.id"
                self.def_id_spec = "_item.name"
                self.key_spec = "_category_mandatory.name"
                self.type_spec = "_item_type.code"
                self.enum_spec = "_item_enumeration.value"
                self.esd_spec = "_item_type_conditions.code"
                self.cat_spec = "_item.category_id"
                self.loop_spec = "there_is_no_loop_spec!"
                self.must_loop_spec = "xxx"
                self.must_exist_spec = "_item.mandatory_code"
                self.child_spec = "_item_linked.child_name"
                self.parent_spec = "_item_linked.parent_name"
                self.related_func = "_item_related.function_code"
                self.related_item = "_item_related.related_name"
                self.unique_spec = "_category_key.name"
                self.list_ref_spec = "xxx"
                self.primitive_type = "_type"
                self.dep_spec = "_item_dependent.dependent_name"
                return (name+version,"DDL2")
        else:
            raise CifError("Unable to determine dictionary DDL version")

    def DDL1_normalise(self):
        # switch off block name collision checks
        self.standard = None
        # add default type information in DDL2 style
        # initial types and constructs
        base_types = ["char","numb","null"]
        prim_types = base_types[:]
        base_constructs = [".*",
            '(-?(([0-9]*[.][0-9]+)|([0-9]+)[.]?)([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|\?|\.',
            "\"\" "]
        for key,value in self.items():
           newnames = [key]  #keep by default
           if "_name" in value:
               real_name = value["_name"]
               if isinstance(real_name,list):        #looped values
                   for looped_name in real_name:
                      new_value = value.copy()
                      new_value["_name"] = looped_name  #only looped name
                      self[looped_name] = new_value
                   newnames = real_name
               else:
                      self[real_name] = value
                      newnames = [real_name]
           # delete the old one
           if key not in newnames:
              del self[key]
        # loop again to normalise the contents of each definition
        for key,value in self.items():
           #unlock the block
           save_overwrite = value.overwrite
           value.overwrite = True
           # deal with a missing _list, _type_conditions
           if "_list" not in value: value["_list"] = 'no'
           if "_type_conditions" not in value: value["_type_conditions"] = 'none'
           # deal with enumeration ranges
           if "_enumeration_range" in value:
               max,min = self.getmaxmin(value["_enumeration_range"])
               if min == ".":
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max),(max,min))))
               elif max == ".":
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,min),(min,min))))
               else:
                   self[key].AddLoopItem((("_item_range.maximum","_item_range.minimum"),((max,max,min),(max,min,min))))
           #add any type construct information
           if "_type_construct" in value:
               base_types.append(value["_name"]+"_type")   #ie dataname_type
               base_constructs.append(value["_type_construct"]+"$")
               prim_types.append(value["_type"])     #keep a record
               value["_type"] = base_types[-1]   #the new type name

        #make categories conform with ddl2
        #note that we must remove everything from the last underscore
           if value.get("_category",None) == "category_overview":
                last_under = value["_name"].rindex("_")
                catid = value["_name"][1:last_under]
                value["_category.id"] = catid  #remove square bracks
                if catid not in self.cat_list: self.cat_list.append(catid)
           value.overwrite = save_overwrite
        # we now add any missing categories before filling in the rest of the
        # information
        for key,value in self.items():
            #print('processing ddl1 definition %s' % key)
            if "_category" in self[key]:
                if self[key]["_category"] not in self.cat_list:
                    # rogue category, add it in
                    newcat = self[key]["_category"]
                    fake_name = "_" + newcat + "_[]"
                    newcatdata = CifBlock()
                    newcatdata["_category"] = "category_overview"
                    newcatdata["_category.id"] = newcat
                    newcatdata["_type"] = "null"
                    self[fake_name] = newcatdata
                    self.cat_list.append(newcat)
        # write out the type information in DDL2 style
        self.master_block.AddLoopItem((
            ("_item_type_list.code","_item_type_list.construct",
              "_item_type_list.primitive_code"),
            (base_types,base_constructs,prim_types)
            ))

    def ddl1_cat_load(self):
        deflist = self.keys()       #slight optimization
        cat_mand_dic = {}
        cat_unique_dic = {}
        # a function to extract any necessary information from each definition
        def get_cat_info(single_def):
            if self[single_def].get(self.must_exist_spec)=='yes':
                thiscat = self[single_def]["_category"]
                curval = cat_mand_dic.get(thiscat,[])
                curval.append(single_def)
                cat_mand_dic[thiscat] = curval
            # now the unique items...
            # cif_core.dic throws us a curly one: the value of list_uniqueness is
            # not the same as the defined item for publ_body_label, so we have
            # to collect both together.  We assume a non-listed entry, which
            # is true for all current (May 2005) ddl1 dictionaries.
            if self[single_def].get(self.unique_spec,None)!=None:
                thiscat = self[single_def]["_category"]
                new_unique = self[single_def][self.unique_spec]
                uis = cat_unique_dic.get(thiscat,[])
                if single_def not in uis: uis.append(single_def)
                if new_unique not in uis: uis.append(new_unique)
                cat_unique_dic[thiscat] = uis

        [get_cat_info(a) for a in deflist] # apply the above function
        for cat in cat_mand_dic.keys():
            self[cat]["_category_mandatory.name"] = cat_mand_dic[cat]
        for cat in cat_unique_dic.keys():
            self[cat]["_category_key.name"] = cat_unique_dic[cat]

    def create_pcloop(self,definition):
        old_children = self[definition].get('_item_linked.child_name',[])
        old_parents = self[definition].get('_item_linked.parent_name',[])
        if isinstance(old_children,unicode):
             old_children = [old_children]
        if isinstance(old_parents,unicode):
             old_parents = [old_parents]
        if (len(old_children)==0 and len(old_parents)==0) or \
           (len(old_children) > 1 and len(old_parents)>1):
             return
        if len(old_children)==0:
             old_children = [definition]*len(old_parents)
        if len(old_parents)==0:
             old_parents = [definition]*len(old_children)
        newloop = CifLoopBlock(dimension=1)
        newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
        newloop.AddLoopItem(('_item_linked.child_name',old_children))
        try:
            del self[definition]['_item_linked.parent_name']
            del self[definition]['_item_linked.child_name']
        except KeyError:
            pass
        self[definition].insert_loop(newloop)



    def DDL2_normalise(self):
       listed_defs = filter(lambda a:isinstance(self[a].get('_item.name'),list),self.keys())
       # now filter out all the single element lists!
       dodgy_defs = filter(lambda a:len(self[a]['_item.name']) > 1, listed_defs)
       for item_def in dodgy_defs:
                # print("DDL2 norm: processing %s" % item_def)
                thisdef = self[item_def]
                packet_no = thisdef['_item.name'].index(item_def)
                realcat = thisdef['_item.category_id'][packet_no]
                realmand = thisdef['_item.mandatory_code'][packet_no]
                # first add in all the missing categories
                # we don't replace the entry in the list corresponding to the
                # current item, as that would wipe out the information we want
                for child_no in range(len(thisdef['_item.name'])):
                    if child_no == packet_no: continue
                    child_name = thisdef['_item.name'][child_no]
                    child_cat = thisdef['_item.category_id'][child_no]
                    child_mand = thisdef['_item.mandatory_code'][child_no]
                    if child_name not in self:
                        self[child_name] = CifBlock()
                        self[child_name]['_item.name'] = child_name
                    self[child_name]['_item.category_id'] = child_cat
                    self[child_name]['_item.mandatory_code'] = child_mand
                self[item_def]['_item.name'] = item_def
                self[item_def]['_item.category_id'] = realcat
                self[item_def]['_item.mandatory_code'] = realmand

       target_defs = [a for a in self.keys() if '_item_linked.child_name' in self[a] or \
                                     '_item_linked.parent_name' in self[a]]
       # now dodgy_defs contains all definition blocks with more than one child/parent link
       for item_def in dodgy_defs: self.create_pcloop(item_def)           #regularise appearance
       for item_def in dodgy_defs:
             print('Processing %s' % item_def)
             thisdef = self[item_def]
             child_list = thisdef['_item_linked.child_name']
             parents = thisdef['_item_linked.parent_name']
             # for each parent, find the list of children.
             family = list(zip(parents,child_list))
             notmychildren = family         #We aim to remove non-children
             # Loop over the parents, relocating as necessary
             while len(notmychildren):
                # get all children of first entry
                mychildren = [a for a in family if a[0]==notmychildren[0][0]]
                print("Parent %s: %d children" % (notmychildren[0][0],len(mychildren)))
                for parent,child in mychildren:   #parent is the same for all
                         # Make sure that we simply add in the new entry for the child, not replace it,
                         # otherwise we might spoil the child entry loop structure
                         try:
                             childloop = self[child].GetLoop('_item_linked.parent_name')
                         except KeyError:
                             print('Creating new parent entry %s for definition %s' % (parent,child))
                             self[child]['_item_linked.parent_name'] = [parent]
                             childloop = self[child].GetLoop('_item_linked.parent_name')
                             childloop.AddLoopItem(('_item_linked.child_name',[child]))
                             continue
                         else:
                             # A parent loop already exists and so will a child loop due to the
                             # call to create_pcloop above
                             pars = [a for a in childloop if getattr(a,'_item_linked.child_name','')==child]
                             goodpars = [a for a in pars if getattr(a,'_item_linked.parent_name','')==parent]
                             if len(goodpars)>0:   #no need to add it
                                 print('Skipping duplicated parent - child entry in %s: %s - %s' % (child,parent,child))
                                 continue
                             print('Adding %s to %s entry' % (parent,child))
                             newpacket = childloop.GetPacket(0)   #essentially a copy, I hope
                             setattr(newpacket,'_item_linked.child_name',child)
                             setattr(newpacket,'_item_linked.parent_name',parent)
                             childloop.AddPacket(newpacket)
                #
                # Make sure the parent also points to the children.  We get
                # the current entry, then add our
                # new values if they are not there already
                #
                parent_name = mychildren[0][0]
                old_children = self[parent_name].get('_item_linked.child_name',[])
                old_parents = self[parent_name].get('_item_linked.parent_name',[])
                oldfamily = zip(old_parents,old_children)
                newfamily = []
                print('Old parents -> %s' % repr(old_parents))
                for jj, childname in mychildren:
                    alreadythere = [a for a in oldfamily if a[0]==parent_name and a[1] ==childname]
                    if len(alreadythere)>0: continue
                    'Adding new child %s to parent definition at %s' % (childname,parent_name)
                    old_children.append(childname)
                    old_parents.append(parent_name)
                # Now output the loop, blowing away previous definitions.  If there is something
                # else in this category, we are destroying it.
                newloop = CifLoopBlock(dimension=1)
                newloop.AddLoopItem(('_item_linked.parent_name',old_parents))
                newloop.AddLoopItem(('_item_linked.child_name',old_children))
                del self[parent_name]['_item_linked.parent_name']
                del self[parent_name]['_item_linked.child_name']
                self[parent_name].insert_loop(newloop)
                print('New parents -> %s' % repr(self[parent_name]['_item_linked.parent_name']))
                # now make a new,smaller list
                notmychildren = [a for a in notmychildren if a[0]!=mychildren[0][0]]

       # now flatten any single element lists
       single_defs = filter(lambda a:len(self[a]['_item.name'])==1,listed_defs)
       for flat_def in single_defs:
           flat_keys = self[flat_def].GetLoop('_item.name').keys()
           for flat_key in flat_keys: self[flat_def][flat_key] = self[flat_def][flat_key][0]
       # now deal with the multiple lists
       # next we do aliases
       all_aliases = [a for a in self.keys() if self[a].has_key('_item_aliases.alias_name')]
       for aliased in all_aliases:
          my_aliases = listify(self[aliased]['_item_aliases.alias_name'])
          for alias in my_aliases:
              self[alias] = self[aliased].copy()   #we are going to delete stuff...
              del self[alias]["_item_aliases.alias_name"]
 
    def ddlm_parse_valid(self):
        if "_dictionary_valid.application" not in self.master_block:
            return
        for scope_pack in self.master_block.GetLoop("_dictionary_valid.application"):
            scope = getattr(scope_pack,"_dictionary_valid.application")
            valid_info = getattr(scope_pack,"_dictionary_valid.attributes")
            if scope[1] == "Mandatory":
                self.scopes_mandatory[scope[0]] = self.expand_category_opt(valid_info)
            elif scope[1] == "Prohibited":
                self.scopes_naughty[scope[0]] = self.expand_category_opt(valid_info)
                
    def ddlm_import(self,import_mode='All'):
        import_frames = list([(a,self[a]['_import.get']) for a in self.keys() if '_import.get' in self[a]])
        print ('Import mode %s applied to following frames' % import_mode)
        print (str([a[0] for a in import_frames]))
        if import_mode != 'All':
           for i in range(len(import_frames)):
                import_frames[i] = (import_frames[i][0],[a for a in import_frames[i][1] if a.get('mode','Contents') == import_mode])
           print('Importing following frames in mode %s' % import_mode)
           print(str(import_frames))
        #resolve all references
        for parent_block,import_list in import_frames:
          for import_ref in import_list:
            file_loc = import_ref["file"]
            full_uri = self.resolve_path(file_loc)
            if full_uri not in self.template_cache:
                dic_as_cif = CifFile(urlopen(full_uri),grammar=self.grammar)
                self.template_cache[full_uri] = CifDic(dic_as_cif,do_imports=import_mode,do_dREL=False)  #this will recurse internal imports
                print('Added %s to cached dictionaries' % full_uri)
            import_from = self.template_cache[full_uri]
            dupl = import_ref.get('dupl','Exit')
            miss = import_ref.get('miss','Exit')
            target_key = import_ref["save"]
            try:
                import_target = import_from[target_key]
            except KeyError:
                if miss == 'Exit':
                   raise CifError('Import frame %s not found in %s' % (target_key,full_uri))
                else: continue
            # now import appropriately
            mode = import_ref.get("mode",'Contents').lower()
            if target_key in self and mode=='full':  #so blockname will be duplicated
                if dupl == 'Exit':
                    raise CifError('Import frame %s already in dictionary' % target_key)
                elif dupl == 'Ignore':
                    continue
            if mode == 'contents':   #merge attributes only
                self[parent_block].merge(import_target)
            elif mode =="full":
                # Do the syntactic merge
                syntactic_head = self[self.get_parent(parent_block)] #root frame if no nesting
                from_cat_head = import_target['_name.object_id']
                child_frames = import_from.ddlm_all_children(from_cat_head)
                 # Check for Head merging Head
                if self[parent_block].get('_definition.class','Datum')=='Head' and \
                   import_target.get('_definition.class','Datum')=='Head':
                      head_to_head = True
                else:
                      head_to_head = False
                      child_frames.remove(from_cat_head)
                # As we are in syntax land, we call the CifFile methods
                child_blocks = list([import_from.block_id_table[a.lower()] for a in child_frames])
                child_blocks = super(CifDic,import_from).makebc(child_blocks)
                # Prune out any datablocks that have identical definitions
                from_defs = dict([(a,child_blocks[a].get('_definition.id','').lower()) for a in child_blocks.keys()])
                double_defs = list([b for b in from_defs.items() if self.has_key(b[1])])
                print ('Definitions for %s superseded' % repr(double_defs))
                for b in double_defs:
                    del child_blocks[b[0]]
                super(CifDic,self).merge_fast(child_blocks,parent=syntactic_head)      #
                print('Syntactic merge of %s (%d defs) in %s mode, now have %d defs' % (target_key,len(child_frames),
                   mode,len(self)))
                # Now the semantic merge
                # First expand our definition <-> blockname tree
                self.create_def_block_table()
                merging_cat = self[parent_block]['_name.object_id']      #new parent
                if head_to_head:
                    child_frames = self.ddlm_immediate_children(from_cat_head)    #old children
                    #the new parent is the importing category for all old children
                    for f in child_frames:
                        self[f].overwrite = True
                        self[f]['_name.category_id'] = merging_cat
                        self[f].overwrite = False
                    # remove the old head
                    del self[from_cat_head]
                    print('Semantic merge: %d defs reparented from %s to %s' % (len(child_frames),from_cat_head,merging_cat))
                else:  #imported category is only child
                    from_frame = import_from[target_key]['_definition.id'] #so we can find it
                    child_frame = [d for d in self.keys() if self[d]['_definition.id']==from_frame][0]
                    self[child_frame]['_name.category_id'] = merging_cat
                    print('Semantic merge: category for %s : now %s' % (from_frame,merging_cat))
            # it will never happen again...
            del self[parent_block]["_import.get"]

    def resolve_path(self,file_loc):
        url_comps = urlparse(file_loc)
        if url_comps[0]: return file_loc    #already full URI
        new_url = urljoin(self.my_uri,file_loc)
        #print("Transformed %s to %s for import " % (file_loc,new_url))
        return new_url



    def create_def_block_table(self):
        """ Create an internal table matching definition to block id """
        proto_table = [(super(CifDic,self).__getitem__(a),a) for a in super(CifDic,self).keys()]
        # now get the actual ids instead of blocks
        proto_table = list([(a[0].get(self.cat_id_spec,a[0].get(self.def_id_spec,a[1])),a[1]) for a in proto_table])
        # remove non-definitions
        if self.diclang != "DDL1":
            top_blocks = list([a[0].lower() for a in self.get_roots()])
        else:
            top_blocks = ["on_this_dictionary"]
        # catch dodgy duplicates
        uniques = set([a[0] for a in proto_table])
        if len(uniques)<len(proto_table):
            def_names = list([a[0] for a in proto_table])
            dodgy = [a for a in def_names if def_names.count(a)>1]
            raise CifError('Duplicate definitions in dictionary:' + repr(dodgy))
        self.block_id_table = dict([(a[0].lower(),a[1].lower()) for a in proto_table if a[1].lower() not in top_blocks])
        
    def __getitem__(self,key):
        """Access a datablock by definition id, after the lookup has been created"""
        try:
            return super(CifDic,self).__getitem__(self.block_id_table[key.lower()])
        except AttributeError:   #block_id_table not present yet
            return super(CifDic,self).__getitem__(key)
        except KeyError: # key is missing
            # print(Definition for %s not found, reverting to CifFile' % key)
            return super(CifDic,self).__getitem__(key)

    def __setitem__(self,key,value):
        """Add a new definition block"""
        super(CifDic,self).__setitem__(key,value)
        try:
            self.block_id_table[value['_definition.id']]=key
        except AttributeError:   #does not exist yet
            pass

    def __delitem__(self,key):
        """Remove a definition"""
        try:
            super(CifDic,self).__delitem__(self.block_id_table[key.lower()])
            del self.block_id_table[key.lower()]
        except (AttributeError,KeyError):   #block_id_table not present yet
            super(CifDic,self).__delitem__(key)
            return
        # fix other datastructures
        # cat_obj table
        
    def keys(self):
        """Return all definitions"""
        try:
            return self.block_id_table.keys()
        except AttributeError:
            return super(CifDic,self).keys()

    def has_key(self,key):
        return key in self

    def __contains__(self,key):
        try:
            return key.lower() in self.block_id_table
        except AttributeError:
            return super(CifDic,self).__contains__(key)
            
    def items(self):
        """Return (key,value) pairs"""
        return list([(a,self[a]) for a in self.keys()])

    def unlock(self):
        """Allow overwriting of all definitions in this collection"""
        for a in self.keys():
            self[a].overwrite=True

    def lock(self):
        """Disallow changes in definitions"""
        for a in self.keys():
            self[a].overwrite=False

    def rename(self,oldname,newname,blockname_as_well=True):
        """Change a _definition.id from oldname to newname, and if `blockname_as_well` is True,
        change the underlying blockname too."""
        if blockname_as_well:
            super(CifDic,self).rename(self.block_id_table[oldname.lower()],newname)        
            self.block_id_table[newname.lower()]=newname
            if oldname.lower() in self.block_id_table: #not removed
               del self.block_id_table[oldname.lower()]
        else:
            self.block_id_table[newname.lower()]=self.block_id_table[oldname.lower()]
            del self.block_id_table[oldname.lower()]
            return
                                                 
    def get_root_category(self):
        """Get the single 'Head' category of this dictionary"""
        root_cats = [r for r in self.keys() if self[r].get('_definition.class','Datum')=='Head']
        if len(root_cats)>1 or len(root_cats)==0:
            raise CifError("Cannot determine a unique Head category, got" % repr(root_cats))
        return root_cats[0]

    def ddlm_immediate_children(self,catname):
        """Return a list of datanames for the immediate children of catname.  These are
        semantic children (i.e. based on _name.category_id), not structural children as
        in the case of StarFile.get_immediate_children"""
                                                 
        straight_children = [a for a in self.keys() if self[a].get('_name.category_id','').lower() == catname.lower()]
        return list(straight_children)

    def ddlm_all_children(self,catname):
        """Return a list of all children, including the `catname`"""
        all_children = self.ddlm_immediate_children(catname)
        cat_children = [a for a in all_children if self[a].get('_definition.scope','Item') == 'Category']
        for c in cat_children:
            all_children.remove(c)
            all_children += self.ddlm_all_children(c)
        return all_children + [catname]

    def is_semantic_child(self,parent,maybe_child):
        """Return true if `maybe_child` is a child of `parent`"""
        all_children = self.ddlm_all_children(parent)
        return maybe_child in all_children

    def ddlm_danglers(self):
        """Return a list of definitions that do not have a category defined
        for them, or are children of an unattached category"""
        top_block = self.get_root_category()
        connected = set(self.ddlm_all_children(top_block))
        all_keys = set(self.keys())
        unconnected = all_keys - connected
        return list(unconnected)

    def get_ddlm_parent(self,itemname):
        """Get the parent category of itemname"""
        parent = self[itemname].get('_name.category_id','')
        if parent == '':  # use the top block by default
            raise CifError("%s has no parent" % itemname)
        return parent

    def expand_category_opt(self,name_list):
        """Return a list of all non-category items in a category or return the name
           if the name is not a category"""
        new_list = []
        for name in name_list:
          if self.get(name,{}).get('_definition.scope','Item') == 'Category':
            new_list += self.expand_category_opt([a for a in self.keys() if \
                     self[a].get('_name.category_id','').lower() == name.lower()])
          else:
            new_list.append(name)
        return new_list

    def get_categories(self):
        """Return a list of category names"""
        return list([c for c in self.keys() if self[c].get("_definition.scope")=='Category'])

    def names_in_cat(self,cat,names_only=False):
        names = [a for a in self.keys() if self[a].get('_name.category_id','').lower()==cat.lower()]
        if not names_only:
            return list([a for a in names if self[a].get('_definition.scope','Item')=='Item'])
        else:
            return list([self[a]["_name.object_id"] for a in names])

                           

    def create_alias_table(self):
        """Populate an alias table that we can look up when searching for a dataname"""
        all_aliases = [a for a in self.keys() if '_alias.definition_id' in self[a]]
        self.alias_table = dict([[a,self[a]['_alias.definition_id']] for a in all_aliases])

    def create_cat_obj_table(self):
        """Populate a table indexed by (cat,obj) and returning the correct dataname"""
        base_table = dict([((self[a].get('_name.category_id','').lower(),self[a].get('_name.object_id','').lower()),[self[a].get('_definition.id','')]) \
                           for a in self.keys() if self[a].get('_definition.scope','Item')=='Item'])
        loopable = self.get_loopable_cats() 
        loopers = [self.ddlm_immediate_children(a) for a in loopable]
        print('Loopable cats:' + repr(loopable))
        loop_children = [[b for b in a if b.lower() in loopable ] for a in loopers]
        expand_list = dict([(a,b) for a,b in zip(loopable,loop_children) if len(b)>0])
        print("Expansion list:" + repr(expand_list))
        extra_table = {}   #for debugging we keep it separate from base_table until the end
        def expand_base_table(parent_cat,child_cats):
            extra_names = []
            # first deal with all the child categories
            for child_cat in child_cats:
              nn = []
              if child_cat in expand_list:  # a nested category: grab its names
                nn = expand_base_table(child_cat,expand_list[child_cat])
                # store child names
                extra_names += nn
              # add all child names to the table
              child_names = [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                             for n in self.names_in_cat(child_cat) if self[n].get('_type.purpose','') != 'Key']
              child_names += extra_names
              extra_table.update(dict([((parent_cat,obj),[name]) for obj,name in child_names if (parent_cat,name) not in extra_table]))
            # and the repeated ones get appended instead
            repeats = [a for a in child_names if a in extra_table]
            for obj,name in repeats:
                extra_table[(parent_cat,obj)] += [name]
            # and finally, add our own names to the return list
            child_names += [(self[n]['_name.object_id'].lower(),self[n]['_definition.id']) \
                            for n in self.names_in_cat(parent_cat) if self[n].get('_type.purpose','')!='Key']
            return child_names
        [expand_base_table(parent,child) for parent,child in expand_list.items()]
        print('Expansion cat/obj values: ' + repr(extra_table))
        # append repeated ones
        non_repeats = dict([a for a in extra_table.items() if a[0] not in base_table])
        repeats = [a for a in extra_table.keys() if a in base_table]
        base_table.update(non_repeats)
        for k in repeats:
            base_table[k] += extra_table[k]
        self.cat_obj_lookup_table = base_table
        self.loop_expand_list = expand_list

    def get_loopable_cats(self):
        """A short utility function which returns a list of looped categories. This
        is preferred to a fixed attribute as that fixed attribute would need to be
        updated after any edits"""
        return [a.lower() for a in self.keys() if self[a].get('_definition.class','')=='Loop']

    def create_cat_key_table(self):
        """Create a utility table with a list of keys applicable to each category. A key is
        a compound key, that is, it is a list"""
        self.cat_key_table = dict([(c,[listify(self[c].get("_category_key.name",
            [self[c].get("_category.key_id")]))]) for c in self.get_loopable_cats()])
        def collect_keys(parent_cat,child_cats):
                kk = []
                for child_cat in child_cats:
                    if child_cat in self.loop_expand_list:
                        kk += collect_keys(child_cat)
                    # add these keys to our list
                    kk += [listify(self[child_cat].get('_category_key.name',[self[child_cat].get('_category.key_id')]))]
                self.cat_key_table[parent_cat] = self.cat_key_table[parent_cat] + kk
                return kk
        for k,v in self.loop_expand_list.items():
            collect_keys(k,v)
        print('Keys for categories' + repr(self.cat_key_table))

    def add_type_info(self):
        if "_item_type_list.construct" in self.master_block:
            types = self.master_block["_item_type_list.code"]
            prim_types = self.master_block["_item_type_list.primitive_code"]
            constructs = list([a + "$" for a in self.master_block["_item_type_list.construct"]])
            # add in \r wherever we see \n, and change \{ to \\{
            def regex_fiddle(mm_regex):
                brack_match = r"((.*\[.+)(\\{)(.*\].*))"
                ret_match = r"((.*\[.+)(\\n)(.*\].*))"
                fixed_regexp = mm_regex[:]  #copy
                # fix the brackets
                bm = re.match(brack_match,mm_regex)
                if bm != None:
                    fixed_regexp = bm.expand(r"\2\\\\{\4")
                # fix missing \r
                rm = re.match(ret_match,fixed_regexp)
                if rm != None:
                    fixed_regexp = rm.expand(r"\2\3\\r\4")
                #print("Regexp %s becomes %s" % (mm_regex,fixed_regexp))
                return fixed_regexp
            constructs = map(regex_fiddle,constructs)
            for typecode,construct in zip(types,constructs):
                self.typedic[typecode] = re.compile(construct,re.MULTILINE|re.DOTALL)
            # now make a primitive <-> type construct mapping
            for typecode,primtype in zip(types,prim_types):
                self.primdic[typecode] = primtype

    def add_category_info(self,full=True):
        if self.diclang == "DDLm":
            catblocks = [c for c in self.keys() if self[c].get('_definition.scope')=='Category']
            looped_cats = [a for a in catblocks if self[a].get('_definition.class','Set') == 'Loop']
            self.parent_lookup = {}
            for one_cat in looped_cats:
                parent_cat = one_cat
                parent_def = self[parent_cat]
                next_up = parent_def['_name.category_id'].lower()
                while next_up in self and self[next_up].get('_definition.class','Set') == 'Loop':
                    parent_def = self[next_up]
                    parent_cat = next_up
                    next_up = parent_def['_name.category_id'].lower()
                self.parent_lookup[one_cat] = parent_cat

            if full:
                self.key_equivs = {}
                for one_cat in looped_cats:   #follow them up
                    lower_keys = listify(self[one_cat]['_category_key.name'])
                    start_keys = lower_keys[:]
                    while len(lower_keys)>0:
                        this_cat = self[lower_keys[0]]['_name.category_id']
                        parent = [a for a in looped_cats if self[this_cat]['_name.category_id'].lower()==a]
                        #print(Processing %s, keys %s, parent %s" % (this_cat,repr(lower_keys),repr(parent)))
                        if len(parent)>1:
                            raise CifError("Category %s has more than one parent: %s" % (one_cat,repr(parent)))
                        if len(parent)==0: break
                        parent = parent[0]
                        parent_keys = listify(self[parent]['_category_key.name'])
                        linked_keys = [self[l]["_name.linked_item_id"] for l in lower_keys]
                        # sanity check
                        if set(parent_keys) != set(linked_keys):
                            raise CifError("Parent keys and linked keys are different! %s/%s" % (parent_keys,linked_keys))
                            # now add in our information
                        for parent,child in zip(linked_keys,start_keys):
                            self.key_equivs[child] = self.key_equivs.get(child,[])+[parent]
                        lower_keys = linked_keys  #preserves order of start keys

        else:
            self.parent_lookup = {}
            self.key_equivs = {}

    def change_category_name(self,oldname,newname):
        self.unlock()
        """Change the category name from [[oldname]] to [[newname]]"""
        if oldname not in self:
            raise KeyError('Cannot rename non-existent category %s to %s' % (oldname,newname))
        if newname in self:
            raise KeyError('Cannot rename %s to %s as %s already exists' % (oldname,newname,oldname))
        child_defs = self.ddlm_immediate_children(oldname)
        self.rename(oldname,newname)   #NB no name integrity checks
        self[newname]['_name.object_id']=newname
        self[newname]['_definition.id']=newname
        for child_def in child_defs:
            self[child_def]['_name.category_id'] = newname
            if self[child_def].get('_definition.scope','Item')=='Item':
                newid = self.create_catobj_name(newname,self[child_def]['_name.object_id'])
                self[child_def]['_definition.id']=newid
                self.rename(child_def,newid[1:])  #no underscore at the beginning
        self.lock()

    def create_catobj_name(self,cat,obj):
        """Combine category and object in approved fashion to create id"""
        return ('_'+cat+'.'+obj)

    def change_category(self,itemname,catname):
        """Move itemname into catname, return new handle"""
        defid = self[itemname]
        if defid['_name.category_id'].lower()==catname.lower():
            print('Already in category, no change')
            return itemname
        if catname not in self:    #don't have it
            print('No such category %s' % catname)
            return itemname
        self.unlock()
        objid = defid['_name.object_id']
        defid['_name.category_id'] = catname
        newid = itemname # stays the same for categories
        if defid.get('_definition.scope','Item') == 'Item':
            newid = self.create_catobj_name(catname,objid)
            defid['_definition.id']= newid
            self.rename(itemname,newid)
        self.set_parent(catname,newid)
        self.lock()
        return newid

    def change_name(self,one_def,newobj):
        """Change the object_id of one_def to newobj. This is not used for
        categories, but can be used for dictionaries"""
        if '_dictionary.title' not in self[one_def]:  #a dictionary block
            newid = self.create_catobj_name(self[one_def]['_name.category_id'],newobj)
            self.unlock()
            self.rename(one_def,newid)
            self[newid]['_definition.id']=newid
            self[newid]['_name.object_id']=newobj
        else:
            self.unlock()
            newid = newobj
            self.rename(one_def,newobj)
            self[newid]['_dictionary.title'] = newid
        self.lock()
        return newid

    # Note that our semantic parent is given by catparent, but our syntactic parent is
    # always just the root block
    def add_category(self,catname,catparent=None,is_loop=True,allow_dangler=False):
        """Add a new category to the dictionary with name [[catname]].
           If [[catparent]] is None, the category will be a child of
           the topmost 'Head' category or else the top data block. If
           [[is_loop]] is false, a Set category is created. If [[allow_dangler]]
           is true, the parent category does not have to exist."""
        if catname in self:
            raise CifError('Attempt to add existing category %s' % catname)
        self.unlock()
        syntactic_root = self.get_roots()[0][0]
        if catparent is None:
            semantic_root = [a for a in self.keys() if self[a].get('_definition.class',None)=='Head']
            if len(semantic_root)>0:
                semantic_root = semantic_root[0]
            else:
                semantic_root = syntactic_root
        else:
            semantic_root = catparent
        realname = super(CifDic,self).NewBlock(catname,parent=syntactic_root)
        self.block_id_table[catname.lower()]=realname
        self[catname]['_name.object_id'] = catname
        if not allow_dangler or catparent is None:
            self[catname]['_name.category_id'] = self[semantic_root]['_name.object_id']
        else:
            self[catname]['_name.category_id'] = catparent
        self[catname]['_definition.id'] = catname
        self[catname]['_definition.scope'] = 'Category'
        if is_loop:
            self[catname]['_definition.class'] = 'Loop'
        else:
            self[catname]['_definition.class'] = 'Set'
        self[catname]['_description.text'] = 'No definition provided'
        self.lock()
        return catname

    def add_definition(self,itemname,catparent,def_text='PLEASE DEFINE ME',allow_dangler=False):
        """Add itemname to category [[catparent]]. If itemname contains periods,
        all text before the final period is ignored. If [[allow_dangler]] is True,
        no check for a parent category is made."""
        self.unlock()
        if '.' in itemname:
            objname = itemname.split('.')[-1]
        else:
            objname = itemname
        objname = objname.strip('_')
        if not allow_dangler and (catparent not in self or self[catparent]['_definition.scope']!='Category'):
            raise CifError('No category %s in dictionary' % catparent)
        fullname = '_'+catparent.lower()+'.'+objname
        print('New name: %s' % fullname)
        syntactic_root = self.get_roots()[0][0]
        realname = super(CifDic,self).NewBlock(fullname, fix=False, parent=syntactic_root) #low-level change
        # update our dictionary structures
        self.block_id_table[fullname]=realname
        self[fullname]['_definition.id']=fullname
        self[fullname]['_name.object_id']=objname
        self[fullname]['_name.category_id']=catparent
        self[fullname]['_definition.class']='Datum'
        self[fullname]['_description.text']=def_text
        
    def remove_definition(self,defname):
        """Remove a definition from the dictionary."""
        if defname not in self:
            return
        if self[defname].get('_definition.scope')=='Category':
            children = self.ddlm_immediate_children(defname)
            [self.remove_definition(a) for a in children]
            cat_id = self[defname]['_definition.id'].lower()
        del self[defname]

    def get_cat_obj(self,name):
        """Return (cat,obj) tuple. [[name]] must contain only a single period"""
        cat,obj = name.split('.')
        return (cat.strip('_'),obj)

    def get_name_by_cat_obj(self,category,object,give_default=False):
        """Return the dataname corresponding to the given category and object"""
        if category[0] == '_':    #accidentally left in
           true_cat = category[1:].lower()
        else:
           true_cat = category.lower()
        try:
            return self.cat_obj_lookup_table[(true_cat,object.lower())][0]
        except KeyError:
            if give_default:
               return '_'+true_cat+'.'+object
        raise KeyError('No such category,object in the dictionary: %s %s' % (true_cat,object))


    def WriteOut(self,**kwargs):
        myblockorder = self.get_full_child_list()
        self.set_grammar(self.grammar)
        self.standard = 'Dic'
        return super(CifDic,self).WriteOut(blockorder = myblockorder,**kwargs)

    def get_full_child_list(self):
        """Return a list of definition blocks in order parent-child-child-child-parent-child..."""
        top_block = self.get_roots()[0][0]
        root_cat = [a for a in self.keys() if self[a].get('_definition.class','Datum')=='Head']
        if len(root_cat) == 1:
            all_names = [top_block] + self.recurse_child_list(root_cat[0])
            unrooted = self.ddlm_danglers()
            double_names =  set(unrooted).intersection(set(all_names))
            if len(double_names)>0:
                raise CifError('Names are children of internal and external categories:%s' % repr(double_names))
            remaining = unrooted[:]
            for no_root in unrooted:
                if self[no_root].get('_definition.scope','Item')=='Category':
                    all_names += [no_root]
                    remaining.remove(no_root)
                    these_children = [n for n in unrooted if self[n]['_name.category_id'].lower()==no_root.lower()]
                    all_names += these_children
                    [remaining.remove(n) for n in these_children]
            # now sort by category
            ext_cats = set([self[r].get('_name.category_id',self.cat_from_name(r)).lower() for r in remaining])
            for e in ext_cats:
                cat_items = [r for r in remaining if self[r].get('_name.category_id',self.cat_from_name(r)).lower() == e]
                [remaining.remove(n) for n in cat_items]
                all_names += cat_items
            if len(remaining)>0:
                print('WARNING: following items do not seem to belong to a category??')
                print(repr(remaining))
                all_names += remaining
            print('Final block order: ' + repr(all_names))
            return all_names
        raise ValueError('Dictionary contains no/multiple Head categories, please print as plain CIF instead')

    def cat_from_name(self,one_name):
        """Guess the category from the name. This should be used only when this is not important semantic information,
        for example, when printing out"""
        (cat,obj) = one_name.split(".")
        if cat[0] == "_": cat = cat[1:]
        return cat

    def recurse_child_list(self,parentname):
        """Recursively expand the logical child list of [[parentname]]"""
        final_list = [parentname]
        child_blocks = [a for a in self.child_table.keys() if self[a].get('_name.category_id','').lower() == parentname.lower()]
        child_blocks.sort()    #we love alphabetical order
        child_items = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Item']
        final_list += child_items
        child_cats = [a for a in child_blocks if self[a].get('_definition.scope','Item') == 'Category']
        for child_cat in child_cats:
            final_list += self.recurse_child_list(child_cat)
        return final_list



    def get_key_pack(self,category,value,data):
        keyname = self[category][self.unique_spec]
        onepack = data.GetPackKey(keyname,value)
        return onepack

    def get_number_with_esd(numstring):
        import string
        numb_re = '((-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?))([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|(\?)|(\.)'
        our_match = re.match(numb_re,numstring)
        if our_match:
            a,base_num,b,c,dad,dbd,esd,exp,q,dot = our_match.groups()
            # print("Debug: {} -> {!r}".format(numstring, our_match.groups()))
        else:
            return None,None
        if dot or q: return None,None     #a dot or question mark
        if exp:          #has exponent
           exp = exp.replace("d","e")     # mop up old fashioned numbers
           exp = exp.replace("D","e")
           base_num = base_num + exp
        # print("Debug: have %s for base_num from %s" % (base_num,numstring))
        base_num = float(base_num)
        # work out esd, if present.
        if esd:
            esd = float(esd[1:-1])    # no brackets
            if dad:                   # decimal point + digits
                esd = esd * (10 ** (-1* len(dad)))
            if exp:
                esd = esd * (10 ** (float(exp[1:])))
        return base_num,esd

    def getmaxmin(self,rangeexp):
        regexp = '(-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?)([eEdD][+-]?[0-9]+)?)*'
        regexp = regexp + ":" + regexp
        regexp = re.match(regexp,rangeexp)
        try:
            minimum = regexp.group(1)
            maximum = regexp.group(7)
        except AttributeError:
            print("Can't match %s" % rangeexp)
        if minimum == None: minimum = "."
        else: minimum = float(minimum)
        if maximum == None: maximum = "."
        else: maximum = float(maximum)
        return maximum,minimum

    def initialise_drel(self):
        """Parse drel functions and prepare data structures in dictionary"""
        self.ddlm_parse_valid() #extract validity information from data block
        self.transform_drel()   #parse the drel functions
        self.add_drel_funcs()   #put the drel functions into the namespace

    def transform_drel(self):
        from .drel import drel_ast_yacc
        from .drel import py_from_ast
        import traceback
        parser = drel_ast_yacc.parser
        lexer = drel_ast_yacc.lexer
        my_namespace = self.keys()
        my_namespace = dict(zip(my_namespace,my_namespace))
        # we provide a table of loopable categories {cat_name:((key1,key2..),[item_name,...]),...})
        loopable_cats = self.get_loopable_cats()
        loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
        loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
        cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
        loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
        # parser.listable_items = [a for a in self.keys() if "*" in self[a].get("_type.dimension","")]
        derivable_list = [a for a in self.keys() if "_method.expression" in self[a] \
                              and self[a].get("_name.category_id","")!= "function"]
        for derivable in derivable_list:
            target_id = derivable
            # reset the list of visible names for parser
            special_ids = [dict(zip(self.keys(),self.keys()))]
            print("Target id: %s" % derivable)
            drel_exprs = self[derivable]["_method.expression"]
            drel_purposes = self[derivable]["_method.purpose"]
            all_methods = []
            if not isinstance(drel_exprs,list):
                drel_exprs = [drel_exprs]
                drel_purposes = [drel_purposes]
            for drel_purpose,drel_expr in zip(drel_purposes,drel_exprs):
                if drel_purpose != 'Evaluation':
                    continue
                drel_expr = "\n".join(drel_expr.splitlines())
                # print("Transforming %s" % drel_expr)
                # List categories are treated differently...
                try:
                    meth_ast = parser.parse(drel_expr+"\n",lexer=lexer)
                except:
                    print('Syntax error in method for %s; leaving as is' % derivable)
                    a,b = sys.exc_info()[:2]
                    print((repr(a),repr(b)))
                    print(traceback.print_tb(sys.exc_info()[-1],None,sys.stdout))
                    # reset the lexer
                    lexer.begin('INITIAL')
                    continue
                # Construct the python method
                cat_meth = False
                if self[derivable].get('_definition.scope','Item') == 'Category':
                    cat_meth = True
                pyth_meth = py_from_ast.make_python_function(meth_ast,"pyfunc",target_id,
                                                                           loopable=loop_info,
                                                             cif_dic = self,cat_meth=cat_meth)
                all_methods.append(pyth_meth)
            if len(all_methods)>0:
                save_overwrite = self[derivable].overwrite
                self[derivable].overwrite = True
                self[derivable]["_method.py_expression"] = all_methods
                self[derivable].overwrite = save_overwrite
            #print("Final result:\n " + repr(self[derivable]["_method.py_expression"]))

    def add_drel_funcs(self):
        from .drel import drel_ast_yacc
        from .drel import py_from_ast
        funclist = [a for a in self.keys() if self[a].get("_name.category_id","")=='function']
        funcnames = [(self[a]["_name.object_id"],
                      getattr(self[a].GetKeyedPacket("_method.purpose","Evaluation"),"_method.expression")) for a in funclist]
        # create executable python code...
        parser = drel_ast_yacc.parser
        # we provide a table of loopable categories {cat_name:(key,[item_name,...]),...})
        loopable_cats = self.get_loopable_cats()
        loop_keys = [listify(self[a]["_category_key.name"]) for a in loopable_cats]
        loop_keys = [[self[a]['_name.object_id'] for a in b] for b in loop_keys]
        cat_names = [self.names_in_cat(a,names_only=True) for a in loopable_cats]
        loop_info = dict(zip(loopable_cats,zip(loop_keys,cat_names)))
        for funcname,funcbody in funcnames:
            newline_body = "\n".join(funcbody.splitlines())
            parser.target_id = funcname
            res_ast = parser.parse(newline_body)
            py_function = py_from_ast.make_python_function(res_ast,None,targetname=funcname,func_def=True,loopable=loop_info,cif_dic = self)
            #print('dREL library function ->\n' + py_function)
            global_table = globals()
            exec(py_function, global_table)    #add to namespace
        #print('Globals after dREL functions added:' + repr(globals()))
        self.ddlm_functions = globals()  #for outside access

    @track_recursion
    def derive_item(self,start_key,cifdata,store_value = False,allow_defaults=True):
        key = start_key   #starting value
        result = None     #success is a non-None value
        default_result = False #we have not used a default value
        # check for aliases
        # check for an older form of a new value
        found_it = [k for k in self.alias_table.get(key,[]) if k in cifdata]
        if len(found_it)>0:
            corrected_type = self.change_type(key,cifdata[found_it[0]])
            return corrected_type
        # now do the reverse check - any alternative form
        alias_name = [a for a in self.alias_table.items() if key in a[1]]
        print('Aliases for %s: %s' % (key,repr(alias_name)))
        if len(alias_name)==1:
            key = alias_name[0][0]   #actual definition name
            if key in cifdata: return self.change_type(key,cifdata[key])
            found_it = [k for k in alias_name[0][1] if k in cifdata]
            if len(found_it)>0:
                return self.change_type(key,cifdata[found_it[0]])
        elif len(alias_name)>1:
            raise CifError('Dictionary error: dataname alias appears in different definitions: ' + repr(alias_name))

        the_category = self[key]["_name.category_id"]
        cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
        has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
        # store any default value in case we have a problem
        def_val = self[key].get("_enumeration.default","")
        def_index_val = self[key].get("_enumeration.def_index_id","")
        if len(has_cat_names)==0: # try category method
            cat_result = {}
            pulled_from_cats = [k for k in self.keys() if '_category_construct_local.components' in self[k]]
            pulled_from_cats = [(k,[
                                  self[n]['_name.category_id'] for n in self[k]['_category_construct_local.components']]
                               ) for k in pulled_from_cats]
            pulled_to_cats = [k[0] for k in pulled_from_cats if the_category in k[1]]
            if '_category_construct_local.type' in self[the_category]:
                print("**Now constructing category %s using DDLm attributes**" % the_category)
                try:
                    cat_result = self.construct_category(the_category,cifdata,store_value=True)
                except (CifRecursionError,StarFile.StarDerivationError):
                    print('** Failed to construct category %s (error)' % the_category)
            # Trying a pull-back when the category is partially populated
            # will not work, hence we test that cat_result has no keys
            if len(pulled_to_cats)>0 and len(cat_result)==0:
                print("**Now populating category %s from pulled-back category %s" % (the_category,repr(pulled_to_cats)))
                try:
                    cat_result = self.push_from_pullback(the_category,pulled_to_cats,cifdata,store_value=True)
                except (CifRecursionError,StarFile.StarDerivationError):
                    print('** Failed to construct category %s from pullback information (error)' % the_category)
            if '_method.py_expression' in self[the_category] and key not in cat_result:
                print("**Now applying category method for %s in search of %s**" % (the_category,key))
                cat_result = self.derive_item(the_category,cifdata,store_value=True)
            print("**Tried pullbacks, obtained for %s " % the_category + repr(cat_result))
            # do we now have our value?
            if key in cat_result:
                return cat_result[key]

        # Recalculate in case it actually worked
        has_cat_names = [a for a in cat_names if cifdata.has_key_or_alias(a)]
        the_funcs = self[key].get('_method.py_expression',"")
        if the_funcs:   #attempt to calculate it
            #global_table = globals()
            #global_table.update(self.ddlm_functions)
            for one_func in the_funcs:
                print('Executing function for %s:' % key)
                #print(one_func)
                exec(one_func, globals())  #will access dREL functions, puts "pyfunc" in scope
                # print('in following global environment: ' + repr(global_table))
                stored_setting = cifdata.provide_value
                cifdata.provide_value = True
                try:
                    result = pyfunc(cifdata)
                except CifRecursionError as s:
                    print(s)
                    result = None
                except StarFile.StarDerivationError as s:
                    print(s)
                    result = None
                finally:
                    cifdata.provide_value = stored_setting
                if result is not None:
                    break
                #print("Function returned {!r}".format(result))

        if result is None and allow_defaults:   # try defaults
            if def_val:
                result = self.change_type(key,def_val)
                default_result = True
            elif def_index_val:            #derive a default value
                index_vals = self[key]["_enumeration_default.index"]
                val_to_index = cifdata[def_index_val]     #what we are keying on
                if self[def_index_val]['_type.contents'] in ['Code','Name','Tag']:
                    lcase_comp = True
                    index_vals = [a.lower() for a in index_vals]
                # Handle loops
                if isinstance(val_to_index,list):
                    if lcase_comp:
                        val_to_index = [a.lower() for a in val_to_index]
                    keypos = [index_vals.index(a) for a in val_to_index]
                    result = [self[key]["_enumeration_default.value"][a]  for a in keypos]
                else:
                    if lcase_comp:
                        val_to_index = val_to_index.lower()
                    keypos = index_vals.index(val_to_index)   #value error if no such value available
                    result = self[key]["_enumeration_default.value"][keypos]
                    default_result = True   #flag that it must be extended
                result = self.change_type(key,result)
                print("Indexed on %s to get %s for %s" % (def_index_val,repr(result),repr(val_to_index)))

        # read it in
        if result is None:   #can't do anything else
            print('Warning: no way of deriving item %s, allow_defaults is %s' % (key,repr(allow_defaults)))
            raise StarFile.StarDerivationError(start_key)
        is_looped = False
        if self[the_category].get('_definition.class','Set')=='Loop':
            is_looped = True
            if len(has_cat_names)>0:   #this category already exists
                if result is None or default_result: #need to create a list of values
                    loop_len = len(cifdata[has_cat_names[0]])
                    out_result = [result]*loop_len
                    result = out_result
            else:   #nothing exists in this category, we can't store this at all
                print('Resetting result %s for %s to null list as category is empty' % (key,result))
                result = []

        # now try to insert the new information into the right place
        # find if items of this category already appear...
        # Never cache empty values
        if not (isinstance(result,list) and len(result)==0) and\
          store_value:
            if self[key].get("_definition.scope","Item")=='Item':
                if is_looped:
                    result = self.store_new_looped_value(key,cifdata,result,default_result)
                else:
                    result = self.store_new_unlooped_value(key,cifdata,result)
            else:
                self.store_new_cat_values(cifdata,result,the_category)
        return result

    def store_new_looped_value(self,key,cifdata,result,default_result):
          """Store a looped value from the dREL system into a CifFile"""
          # try to change any matrices etc. to lists
          the_category = self[key]["_name.category_id"]
          out_result = result
          if result is not None and not default_result:
                  # find any numpy arrays
                  def conv_from_numpy(one_elem):
                      if not hasattr(one_elem,'dtype'):
                         if isinstance(one_elem,(list,tuple)):
                            return StarFile.StarList([conv_from_numpy(a) for a in one_elem])
                         return one_elem
                      if one_elem.size > 1:   #so is not a float
                         return StarFile.StarList([conv_from_numpy(a) for a in one_elem.tolist()])
                      else:
                          try:
                            return one_elem.item(0)
                          except:
                            return one_elem
                  out_result = [conv_from_numpy(a) for a in result]
          # so out_result now contains a value suitable for storage
          cat_names = [a for a in self.keys() if self[a].get("_name.category_id",None)==the_category]
          has_cat_names = [a for a in cat_names if a in cifdata]
          print('Adding {}, found pre-existing names: '.format(key) + repr(has_cat_names))
          if len(has_cat_names)>0:   #this category already exists
              cifdata[key] = out_result      #lengths must match or else!!
              cifdata.AddLoopName(has_cat_names[0],key)
          else:
              cifdata[key] = out_result
              cifdata.CreateLoop([key])
          print('Loop info:' + repr(cifdata.loops))
          return out_result

    def store_new_unlooped_value(self,key,cifdata,result):
          """Store a single value from the dREL system"""
          if result is not None and hasattr(result,'dtype'):
              if result.size > 1:
                  out_result = StarFile.StarList(result.tolist())
                  cifdata[key] = out_result
              else:
                  cifdata[key] = result.item(0)
          else:
              cifdata[key] = result
          return result

    def construct_category(self,category,cifdata,store_value=True):
        """Construct a category using DDLm attributes"""
        con_type = self[category].get('_category_construct_local.type',None)
        if con_type == None:
            return {}
        if con_type == 'Pullback' or con_type == 'Filter':
            morphisms  = self[category]['_category_construct_local.components']
            morph_values = [cifdata[a] for a in morphisms] # the mapped values for each cat
            cats = [self[a]['_name.category_id'] for a in morphisms]
            cat_keys = [self[a]['_category.key_id'] for a in cats]
            cat_values = [list(cifdata[a]) for a in cat_keys] #the category key values for each cat
            if con_type == 'Filter':
                int_filter = self[category].get('_category_construct_local.integer_filter',None)
                text_filter = self[category].get('_category_construct_local.text_filter',None)
                if int_filter is not None:
                    morph_values.append([int(a) for a in int_filter])
                if text_filter is not None:
                    morph_values.append(text_filter)
                cat_values.append(range(len(morph_values[-1])))
            # create the mathematical product filtered by equality of dataname values
            pullback_ids = [(x,y) for x in cat_values[0] for y in cat_values[1] \
                            if morph_values[0][cat_values[0].index(x)]==morph_values[1][cat_values[1].index(y)]]
            # now prepare for return
            if len(pullback_ids)==0:
                return {}
            newids = self[category]['_category_construct_local.new_ids']
            fullnewids = [self.cat_obj_lookup_table[(category,n)][0] for n in newids]
            if con_type == 'Pullback':
                final_results = {fullnewids[0]:[x[0] for x in pullback_ids],fullnewids[1]:[x[1] for x in pullback_ids]}
                final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
                final_results.update(self.duplicate_datanames(cifdata,cats[1],category,key_vals = final_results[fullnewids[1]],skip_names=newids))
            elif con_type == 'Filter':   #simple filter
                final_results = {fullnewids[0]:[x[0] for x in pullback_ids]}
                final_results.update(self.duplicate_datanames(cifdata,cats[0],category,key_vals = final_results[fullnewids[0]],skip_names=newids))
            if store_value:
                self.store_new_cat_values(cifdata,final_results,category)
            return final_results

    def push_from_pullback(self,target_category,source_categories,cifdata,store_value=True):
        """Each of the categories in source_categories are pullbacks that include
        the target_category"""
        target_key = self[target_category]['_category.key_id']
        result = {target_key:[]}
        first_time = True
        # for each source category, determine which element goes to the target
        for sc in source_categories:
            components = self[sc]['_category_construct_local.components']
            comp_cats = [self[c]['_name.category_id'] for c in components]
            new_ids = self[sc]['_category_construct_local.new_ids']
            source_ids = [self.cat_obj_lookup_table[(sc,n)][0] for n in new_ids]
            if len(components) == 2:  # not a filter
                element_pos = comp_cats.index(target_category)
                old_id = source_ids[element_pos]
                print('Using %s to populate %s' % (old_id,target_key))
                result[target_key].extend(cifdata[old_id])
                # project through all identical names
                extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids+[target_key])
                # we only include keys that are common to all categories
                if first_time:
                    result.update(extra_result)
                else:
                    for k in extra_result.keys():
                        if k in result:
                            print('Updating %s: was %s' % (k,repr(result[k])))
                            result[k].extend(extra_result[k])
            else:
                extra_result = self.duplicate_datanames(cifdata,sc,target_category,skip_names=new_ids)
                if len(extra_result)>0 or source_ids[0] in cifdata:  #something is present
                    result[target_key].extend(cifdata[source_ids[0]])
                    for k in extra_result.keys():
                        if k in result:
                            print('Reverse filter: Updating %s: was %s' % (k,repr(result[k])))
                            result[k].extend(extra_result[k])
                        else:
                            result[k]=extra_result[k]
    # Bonus derivation if there is a singleton filter
                    if self[sc]['_category_construct_local.type'] == 'Filter':
                        int_filter = self[sc].get('_category_construct_local.integer_filter',None)
                        text_filter = self[sc].get('_category_construct_local.text_filter',None)
                        if int_filter is not None:
                            filter_values = int_filter
                        else:
                            filter_values = text_filter
                        if len(filter_values)==1:    #a singleton
                            extra_dataname = self[sc]['_category_construct_local.components'][0]
                            if int_filter is not None:
                                new_value = [int(filter_values[0])] * len(cifdata[source_ids[0]])
                            else:
                                new_value = filter_values * len(cifdata[source_ids[0]])
                            if extra_dataname not in result:
                                result[extra_dataname] = new_value
                            else:
                                result[extra_dataname].extend(new_value)
                    else:
                        raise ValueError('Unexpected category construct type' + self[sc]['_category_construct_local.type'])
            first_time = False
        # check for sanity - all dataname lengths must be identical
        datalen = len(set([len(a) for a in result.values()]))
        if datalen != 1:
            raise AssertionError('Failed to construct equal-length category items,'+ repr(result))
        if store_value:
            print('Now storing ' + repr(result))
            self.store_new_cat_values(cifdata,result,target_category)
        return result

    def duplicate_datanames(self,cifdata,from_category,to_category,key_vals=None,skip_names=[]):
        """Copy across datanames for which the from_category key equals [[key_vals]]"""
        result = {}
        s_names_in_cat = set(self.names_in_cat(from_category,names_only=True))
        t_names_in_cat = set(self.names_in_cat(to_category,names_only=True))
        can_project = s_names_in_cat & t_names_in_cat
        can_project -= set(skip_names)  #already dealt with
        source_key = self[from_category]['_category.key_id']
        print('Source dataname set: ' + repr(s_names_in_cat))
        print('Target dataname set: ' + repr(t_names_in_cat))
        print('Projecting through following datanames from %s to %s' % (from_category,to_category) + repr(can_project))
        for project_name in can_project:
            full_from_name = self.cat_obj_lookup_table[(from_category.lower(),project_name.lower())][0]
            full_to_name = self.cat_obj_lookup_table[(to_category.lower(),project_name.lower())][0]
            if key_vals is None:
                try:
                    result[full_to_name] = cifdata[full_from_name]
                except StarFile.StarDerivationError:
                    pass
            else:
                all_key_vals = cifdata[source_key]
                filter_pos = [all_key_vals.index(a) for a in key_vals]
                try:
                    all_data_vals = cifdata[full_from_name]
                except StarFile.StarDerivationError:
                    pass
                result[full_to_name] = [all_data_vals[i] for i in filter_pos]
        return result

    def store_new_cat_values(self,cifdata,result,the_category):
        """Store the values in [[result]] into [[cifdata]]"""
        the_key = [a for a in result.keys() if self[a].get('_type.purpose','')=='Key']
        double_names = [a for a in result.keys() if a in cifdata]
        if len(double_names)>0:
            already_present = [a for a in self.names_in_cat(the_category) if a in cifdata]
            if set(already_present) != set(result.keys()):
                print("Category %s not updated, mismatched datanames: %s" % (the_category, repr(set(already_present)^set(result.keys()))))
                return
            #check key values
            old_keys = set(cifdata[the_key])
            common_keys = old_keys & set(result[the_key])
            if len(common_keys)>0:
                print("Category %s not updated, key values in common:" % (common_keys))
                return
            #extend result values with old values
            for one_name,one_value in result.items():
                result[one_name].extend(cifdata[one_name])
        for one_name, one_value in result.items():
            try:
                self.store_new_looped_value(one_name,cifdata,one_value,False)
            except StarFile.StarError:
                print('%s: Not replacing %s with calculated %s' % (one_name,repr(cifdata[one_name]),repr(one_value)))
        #put the key as the first item
        print('Fixing item order for {}'.format(repr(the_key)))
        for one_key in the_key:  #should only be one
            cifdata.ChangeItemOrder(one_key,0)


    def generate_default_packet(self,catname,catkey,keyvalue):
        """Return a StarPacket with items from ``catname`` and a key value
        of ``keyvalue``"""
        newpack = StarPacket()
        for na in self.names_in_cat(catname):
            def_val = self[na].get("_enumeration.default","")
            if def_val:
                final_val = self.change_type(na,def_val)
                newpack.extend(final_val)
                setattr(newpack,na,final_val)
        if len(newpack)>0:
            newpack.extend(keyvalue)
            setattr(newpack,catkey,keyvalue)
        return newpack


    def switch_numpy(self,to_val):
        pass

    def change_type(self,itemname,inval):
        import numpy
        if inval == "?": return inval
        change_function = convert_type(self[itemname])
        if isinstance(inval,list) and not isinstance(inval,StarFile.StarList):   #from a loop
            newval = list([change_function(a) for a in inval])
        else:
            newval = change_function(inval)
        return newval

    def install_validation_functions(self):
        """Install the DDL-appropriate validation checks"""
        if self.diclang != 'DDLm':
          self.item_validation_funs = [
            self.validate_item_type,
            self.validate_item_esd,
            self.validate_item_enum,   # functions which check conformance
            self.validate_enum_range,
            self.validate_looping]
          self.loop_validation_funs = [
            self.validate_loop_membership,
            self.validate_loop_key,
            self.validate_loop_references]    # functions checking loop values
          self.global_validation_funs = [
            self.validate_exclusion,
            self.validate_parent,
            self.validate_child,
            self.validate_dependents,
            self.validate_uniqueness] # where we need to look at other values
          self.block_validation_funs = [  # where only a full block will do
            self.validate_mandatory_category]
          self.global_remove_validation_funs = [
            self.validate_remove_parent_child] # removal is quicker with special checks
        elif self.diclang == 'DDLm':
            self.item_validation_funs = [
                self.validate_item_enum,
                self.validate_item_esd_ddlm,
                ]
            self.loop_validation_funs = [
                self.validate_looping_ddlm,
                self.validate_loop_key_ddlm,
                self.validate_loop_membership
                ]
            self.global_validation_funs = []
            self.block_validation_funs = [
                self.check_mandatory_items,
                self.check_prohibited_items
                ]
            self.global_remove_validation_funs = []
        self.optimize = False        # default value
        self.done_parents = []
        self.done_children = []
        self.done_keys = []

    def validate_item_type(self,item_name,item_value):
        def mymatch(m,a):
            res = m.match(a)
            if res != None: return res.group()
            else: return ""
        target_type = self[item_name].get(self.type_spec)
        if target_type == None:          # e.g. a category definition
            return {"result":True}                  # not restricted in any way
        matchexpr = self.typedic[target_type]
        item_values = listify(item_value)
        #for item in item_values:
            #print("Type match " + item_name + " " + item + ":",)
        #skip dots and question marks
        check_all = [a for a in item_values if a !="." and a != "?"]
        check_all = [a for a in check_all if mymatch(matchexpr,a) != a]
        if len(check_all)>0: return {"result":False,"bad_values":check_all}
        else: return {"result":True}

    def decide(self,result_list):
        """Construct the return list"""
        if len(result_list)==0:
               return {"result":True}
        else:
               return {"result":False,"bad_values":result_list}

    def validate_item_container(self, item_name,item_value):
        container_type = self[item_name]['_type.container']
        item_values = listify(item_value)
        if container_type == 'Single':
           okcheck = [a for a in item_values if not isinstance(a,(int,float,long,unicode))]
           return decide(okcheck)
        if container_type in ('Multiple','List'):
           okcheck = [a for a in item_values if not isinstance(a,StarList)]
           return decide(okcheck)
        if container_type == 'Array':    #A list with numerical values
           okcheck = [a for a in item_values if not isinstance(a,StarList)]
           first_check = decide(okcheck)
           if not first_check['result']: return first_check
           #num_check = [a for a in item_values if len([b for b in a if not isinstance

    def validate_item_esd(self,item_name,item_value):
        if self[item_name].get(self.primitive_type) != 'numb':
            return {"result":None}
        can_esd = self[item_name].get(self.esd_spec,"none") == "esd"
        if can_esd: return {"result":True}         #must be OK!
        item_values = listify(item_value)
        check_all = list([a for a in item_values if get_number_with_esd(a)[1] != None])
        if len(check_all)>0: return {"result":False,"bad_values":check_all}
        return {"result":True}

    def validate_item_esd_ddlm(self,item_name,item_value):
        if self[item_name].get('self.primitive_type') not in \
        ['Count','Index','Integer','Real','Imag','Complex','Binary','Hexadecimal','Octal']:
            return {"result":None}
        can_esd = True
        if self[item_name].get('_type.purpose') != 'Measurand':
            can_esd = False
        item_values = listify(item_value)
        check_all = [get_number_with_esd(a)[1] for a in item_values]
        check_all = [v for v in check_all if (can_esd and v == None) or \
                 (not can_esd and v != None)]
        if len(check_all)>0: return {"result":False,"bad_values":check_all}
        return {"result":True}

    def validate_enum_range(self,item_name,item_value):
        if "_item_range.minimum" not in self[item_name] and \
           "_item_range.maximum" not in self[item_name]:
            return {"result":None}
        minvals = self[item_name].get("_item_range.minimum",default = ["."])
        maxvals = self[item_name].get("_item_range.maximum",default = ["."])
        def makefloat(a):
            if a == ".": return a
            else: return float(a)
        maxvals = map(makefloat, maxvals)
        minvals = map(makefloat, minvals)
        rangelist = list(zip(minvals,maxvals))
        item_values = listify(item_value)
        def map_check(rangelist,item_value):
            if item_value == "?" or item_value == ".": return True
            iv,esd = get_number_with_esd(item_value)
            if iv==None: return None  #shouldn't happen as is numb type
            for lower,upper in rangelist:
                #check the minima
                if lower == ".": lower = iv - 1
                if upper == ".": upper = iv + 1
                if iv > lower and iv < upper: return True
                if upper == lower and iv == upper: return True
            # debug
            # print("Value %s fails range check %d < x < %d" % (item_value,lower,upper))
            return False
        check_all = [a for a in item_values if map_check(rangelist,a) != True]
        if len(check_all)>0: return {"result":False,"bad_values":check_all}
        else: return {"result":True}

    def validate_item_enum(self,item_name,item_value):
        try:
            enum_list = self[item_name][self.enum_spec][:]
        except KeyError:
            return {"result":None}
        enum_list.append(".")   #default value
        enum_list.append("?")   #unknown
        item_values = listify(item_value)
        #print("Enum check: {!r} in {!r}".format(item_values, enum_list))
        check_all = [a for a in item_values if a not in enum_list]
        if len(check_all)>0: return {"result":False,"bad_values":check_all}
        else: return {"result":True}

    def validate_looping(self,item_name,item_value):
        try:
            must_loop = self[item_name][self.must_loop_spec]
        except KeyError:
            return {"result":None}
        if must_loop == 'yes' and isinstance(item_value,(unicode,str)): # not looped
            return {"result":False}      #this could be triggered
        if must_loop == 'no' and not isinstance(item_value,(unicode,str)):
            return {"result":False}
        return {"result":True}

    def validate_looping_ddlm(self,loop_names):
        """Check that all names are loopable"""
        truly_loopy = self.get_final_cats(loop_names)
        if len(truly_loopy)<len(loop_names):  #some are bad
            categories = [(a,self[a][self.cat_spec].lower()) for a in loop_names]
            not_looped = [a[0] for a in categories if a[1] not in self.parent_lookup.keys()]
            return {"result":False,"bad_items":not_looped}
        return {"result":True}


    def validate_loop_membership(self,loop_names):
        final_cat = self.get_final_cats(loop_names)
        bad_items =  [a for a in final_cat if a != final_cat[0]]
        if len(bad_items)>0:
            return {"result":False,"bad_items":bad_items}
        else: return {"result":True}

    def get_final_cats(self,loop_names):
        """Return a list of the uppermost parent categories for the loop_names. Names
        that are not from loopable categories are ignored."""
        try:
            categories = [self[a][self.cat_spec].lower() for a in loop_names]
        except KeyError:       #category is mandatory
            raise ValidCifError( "%s missing from dictionary %s for item in loop containing %s" % (self.cat_spec,self.dicname,loop_names[0]))
        truly_looped = [a for a in categories if a in self.parent_lookup.keys()]
        return [self.parent_lookup[a] for a in truly_looped]

    def validate_loop_key(self,loop_names):
        category = self[loop_names[0]][self.cat_spec]
        # find any unique values which must be present 
        key_spec = self[category].get(self.key_spec,[])
        for names_to_check in key_spec:
            if isinstance(names_to_check,unicode):   #only one
                names_to_check = [names_to_check]
            for loop_key in names_to_check:
                if loop_key not in loop_names:
                    #is this one of those dang implicit items?
                    if self[loop_key].get(self.must_exist_spec,None) == "implicit":
                        continue          #it is virtually there...
                    alternates = self.get_alternates(loop_key)
                    if alternates == []:
                        return {"result":False,"bad_items":loop_key}
                    for alt_names in alternates:
                        alt = [a for a in alt_names if a in loop_names]
                        if len(alt) == 0:
                            return {"result":False,"bad_items":loop_key}  # no alternates
        return {"result":True}

    def validate_loop_key_ddlm(self,loop_names):
        """Make sure at least one of the necessary keys are available"""
        final_cats = self.get_final_cats(loop_names)
        if len(final_cats)>0:
            poss_keys = self.cat_key_table[final_cats[0]]
            found_keys = [a for a in poss_keys if a in loop_names]
            if len(found_keys)>0:
                return {"result":True}
            else:
                return {"result":False,"bad_items":poss_keys}
        else:
            return {"result":True}

    def validate_loop_references(self,loop_names):
        must_haves = [self[a].get(self.list_ref_spec,None) for a in loop_names]
        must_haves = [a for a in must_haves if a != None]
        # build a flat list.  For efficiency we don't remove duplicates,as
        # we expect no more than the order of 10 or 20 looped names.
        def flat_func(a,b):
            if isinstance(b,unicode):
               a.append(b)       #single name
            else:
               a.extend(b)       #list of names
            return a
        flat_mh = []
        [flat_func(flat_mh,a) for a in must_haves]
        group_mh = filter(lambda a:a[-1]=="_",flat_mh)
        single_mh = filter(lambda a:a[-1]!="_",flat_mh)
        res = [a for a in single_mh if a not in loop_names]
        def check_gr(s_item, name_list):
            nl = map(lambda a:a[:len(s_item)],name_list)
            if s_item in nl: return True
            return False
        res_g = [a for a in group_mh if check_gr(a,loop_names)]
        if len(res) == 0 and len(res_g) == 0: return {"result":True}
        # construct alternate list
        alternates = map(lambda a: (a,self.get_alternates(a)),res)
        alternates = [a for a in alternates if a[1] != []]
        # next line purely for error reporting
        missing_alts = [a[0] for a in alternates if a[1] == []]
        if len(alternates) != len(res):
           return {"result":False,"bad_items":missing_alts}   #short cut; at least one
                                                       #doesn't have an altern
        #loop over alternates
        for orig_name,alt_names in alternates:
             alt = [a for a in alt_names if a in loop_names]
             if len(alt) == 0: return {"result":False,"bad_items":orig_name}# no alternates
        return {"result":True}        #found alternates

    def get_alternates(self,main_name,exclusive_only=False):
        alternates = self[main_name].get(self.related_func,None)
        alt_names = []
        if alternates != None:
            alt_names =  self[main_name].get(self.related_item,None)
            if isinstance(alt_names,unicode):
                alt_names = [alt_names]
                alternates = [alternates]
            together = zip(alt_names,alternates)
            if exclusive_only:
                alt_names = [a for a in together if a[1]=="alternate_exclusive" \
                                             or a[1]=="replace"]
            else:
                alt_names = [a for a in together if a[1]=="alternate" or a[1]=="replace"]
            alt_names = list([a[0] for a in alt_names])
        # now do the alias thing
        alias_names = listify(self[main_name].get("_item_aliases.alias_name",[]))
        alt_names.extend(alias_names)
        # print("Alternates for {}: {!r}".format(main_name, alt_names))
        return alt_names


    def validate_exclusion(self,item_name,item_value,whole_block,provisional_items={},globals={}):
       alternates = [a.lower() for a in self.get_alternates(item_name,exclusive_only=True)]
       item_name_list = [a.lower() for a in whole_block.keys()]
       item_name_list.extend([a.lower() for a in provisional_items.keys()])
       bad = [a for a in alternates if a in item_name_list]
       if len(bad)>0:
           print("Bad: %s, alternates %s" % (repr(bad),repr(alternates)))
           return {"result":False,"bad_items":bad}
       else: return {"result":True}

    # validate that parent exists and contains matching values
    def validate_parent(self,item_name,item_value,whole_block,provisional_items={},globals={}):
        parent_item = self[item_name].get(self.parent_spec)
        if not parent_item: return {"result":None}   #no parent specified
        if isinstance(parent_item,list):
            parent_item = parent_item[0]
        if self.optimize:
            if parent_item in self.done_parents:
                return {"result":None}
            else:
                self.done_parents.append(parent_item)
                print("Done parents %s" % repr(self.done_parents))
        # initialise parent/child values
        if isinstance(item_value,unicode):
            child_values = [item_value]
        else: child_values = item_value[:]    #copy for safety
        # track down the parent
        # print("Looking for {} parent item {} in {!r}".format(item_name, parent_item, whole_block))
        # if globals contains the parent values, we are doing a DDL2 dictionary, and so
        # we have collected all parent values into the global block - so no need to search
        # for them elsewhere.
        # print("Looking for {!r}".format(parent_item))
        parent_values = globals.get(parent_item)
        if not parent_values:
            parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
        if not parent_values:
            # go for alternates
            namespace = whole_block.keys()
            namespace.extend(provisional_items.keys())
            namespace.extend(globals.keys())
            alt_names = filter_present(self.get_alternates(parent_item),namespace)
            if len(alt_names) == 0:
                if len([a for a in child_values if a != "." and a != "?"])>0:
                    return {"result":False,"parent":parent_item}#no parent available -> error
                else:
                    return {"result":None}       #maybe True is more appropriate??
            parent_item = alt_names[0]           #should never be more than one??
            parent_values = provisional_items.get(parent_item,whole_block.get(parent_item))
            if not parent_values:   # check global block
                parent_values = globals.get(parent_item)
        if isinstance(parent_values,unicode):
            parent_values = [parent_values]
        #print("Checking parent %s against %s, values %r/%r" % (parent_item,
        #                                          item_name, parent_values, child_values))
        missing = self.check_parent_child(parent_values,child_values)
        if len(missing) > 0:
            return {"result":False,"bad_values":missing,"parent":parent_item}
        return {"result":True}

    def validate_child(self,item_name,item_value,whole_block,provisional_items={},globals={}):
        try:
            child_items = self[item_name][self.child_spec][:]  #copy
        except KeyError:
            return {"result":None}    #not relevant
        # special case for dictionaries  -> we check parents of children only
        if item_name in globals:  #dictionary so skip
            return {"result":None}
        if isinstance(child_items,unicode): # only one child
            child_items = [child_items]
        if isinstance(item_value,unicode): # single value
            parent_values = [item_value]
        else: parent_values = item_value[:]
        # expand child list with list of alternates
        for child_item in child_items[:]:
            child_items.extend(self.get_alternates(child_item))
        # now loop over the children
        for child_item in child_items:
            if self.optimize:
                if child_item in self.done_children:
                    return {"result":None}
                else:
                    self.done_children.append(child_item)
                    print("Done children %s" % repr(self.done_children))
            if child_item in provisional_items:
                child_values = provisional_items[child_item][:]
            elif child_item in whole_block:
                child_values = whole_block[child_item][:]
            else:  continue
            if isinstance(child_values,unicode):
                child_values = [child_values]
                # print("Checking child %s against %s, values %r/%r" % (child_item,
                #       item_name, child_values, parent_values))
            missing = self.check_parent_child(parent_values,child_values)
            if len(missing)>0:
                return {"result":False,"bad_values":missing,"child":child_item}
        return {"result":True}       #could mean that no child items present

    #a generic checker: all child vals should appear in parent_vals
    def check_parent_child(self,parent_vals,child_vals):
        # shield ourselves from dots and question marks
        pv = parent_vals[:]
        pv.extend([".","?"])
        res =  [a for a in child_vals if a not in pv]
        #print("Missing: %s" % res)
        return res

    def validate_remove_parent_child(self,item_name,whole_block):
        try:
            child_items = self[item_name][self.child_spec]
        except KeyError:
            return {"result":None}
        if isinstance(child_items,unicode): # only one child
            child_items = [child_items]
        for child_item in child_items:
            if child_item in whole_block:
                return {"result":False,"child":child_item}
        return {"result":True}

    def validate_dependents(self,item_name,item_value,whole_block,prov={},globals={}):
        try:
            dep_items = self[item_name][self.dep_spec][:]
        except KeyError:
            return {"result":None}    #not relevant
        if isinstance(dep_items,unicode):
            dep_items = [dep_items]
        actual_names = whole_block.keys()
        actual_names.extend(prov.keys())
        actual_names.extend(globals.keys())
        missing = [a for a in dep_items if a not in actual_names]
        if len(missing) > 0:
            alternates = map(lambda a:[self.get_alternates(a),a],missing)
            # compact way to get a list of alternative items which are
            # present
            have_check = [(filter_present(b[0],actual_names),
                                       b[1]) for b in alternates]
            have_check = list([a for a in have_check if len(a[0])==0])
            if len(have_check) > 0:
                have_check = [a[1] for a in have_check]
                return {"result":False,"bad_items":have_check}
        return {"result":True}

    def validate_uniqueness(self,item_name,item_value,whole_block,provisional_items={},
                                                                  globals={}):
        category = self[item_name].get(self.cat_spec)
        if category == None:
            print("No category found for %s" % item_name)
            return {"result":None}
        # print("Category {!r} for item {}".format(category, item_name))
        # we make a copy in the following as we will be removing stuff later!
        unique_i = self[category].get("_category_key.name",[])[:]
        if isinstance(unique_i,unicode):
            unique_i = [unique_i]
        if item_name not in unique_i:       #no need to verify
            return {"result":None}
        if isinstance(item_value,unicode):  #not looped
            return {"result":None}
        # print("Checking %s -> %s -> %s ->Unique: %r" % (item_name,category,catentry, unique_i))
        # check that we can't optimize by not doing this check
        if self.optimize:
            if unique_i in self.done_keys:
                return {"result":None}
            else:
                self.done_keys.append(unique_i)
        val_list = []
        # get the matching data from any other data items
        unique_i.remove(item_name)
        other_data = []
        if len(unique_i) > 0:            # i.e. do have others to think about
           for other_name in unique_i:
           # we look for the value first in the provisional dict, then the main block
           # the logic being that anything in the provisional dict overrides the
           # main block
               if other_name in provisional_items:
                   other_data.append(provisional_items[other_name])
               elif other_name in whole_block:
                   other_data.append(whole_block[other_name])
               elif self[other_name].get(self.must_exist_spec)=="implicit":
                   other_data.append([item_name]*len(item_value))  #placeholder
               else:
                   return {"result":False,"bad_items":other_name}#missing data name
        # ok, so we go through all of our values
        # this works by comparing lists of strings to one other, and
        # so could be fooled if you think that '1.' and '1' are
        # identical
        for i in range(len(item_value)):
            #print("Value no. %d" % i, end=" ")
            this_entry = item_value[i]
            for j in range(len(other_data)):
                this_entry = " ".join([this_entry,other_data[j][i]])
            #print("Looking for {!r} in {!r}: ".format(this_entry, val_list))
            if this_entry in val_list:
                return {"result":False,"bad_values":this_entry}
            val_list.append(this_entry)
        return {"result":True}


    def validate_mandatory_category(self,whole_block):
        mand_cats = [self[a]['_category.id'] for a in self.keys() if self[a].get("_category.mandatory_code","no")=="yes"]
        if len(mand_cats) == 0:
            return {"result":True}
        # print("Mandatory categories - {!r}".format(mand_cats)
        # find which categories each of our datanames belongs to
        all_cats = [self[a].get(self.cat_spec) for a in whole_block.keys()]
        missing = set(mand_cats) - set(all_cats)
        if len(missing) > 0:
            return {"result":False,"bad_items":repr(missing)}
        return {"result":True}

    def check_mandatory_items(self,whole_block,default_scope='Item'):
        """Return an error if any mandatory items are missing"""
        if len(self.scopes_mandatory)== 0: return {"result":True}
        if default_scope == 'Datablock':
            return {"result":True}     #is a data file
        scope = whole_block.get('_definition.scope',default_scope)
        if '_dictionary.title' in whole_block:
           scope = 'Dictionary'
        missing = list([a for a in self.scopes_mandatory[scope] if a not in whole_block])
        if len(missing)==0:
            return {"result":True}
        else:
            return {"result":False,"bad_items":missing}

    def check_prohibited_items(self,whole_block,default_scope='Item'):
        """Return an error if any prohibited items are present"""
        if len(self.scopes_naughty)== 0: return {"result":True}
        if default_scope == 'Datablock':
            return {"result":True}     #is a data file
        scope = whole_block.get('_definition.scope',default_scope)
        if '_dictionary.title' in whole_block:
           scope = 'Dictionary'
        present = list([a for a in self.scopes_naughty[scope] if a in whole_block])
        if len(present)==0:
            return {"result":True}
        else:
            return {"result":False,"bad_items":present}


    def run_item_validation(self,item_name,item_value):
        return {item_name:list([(f.__name__,f(item_name,item_value)) for f in self.item_validation_funs])}

    def run_loop_validation(self,loop_names):
        return {loop_names[0]:list([(f.__name__,f(loop_names)) for f in self.loop_validation_funs])}

    def run_global_validation(self,item_name,item_value,data_block,provisional_items={},globals={}):
        results = list([(f.__name__,f(item_name,item_value,data_block,provisional_items,globals)) for f in self.global_validation_funs])
        return {item_name:results}

    def run_block_validation(self,whole_block,block_scope='Item'):
        results = list([(f.__name__,f(whole_block)) for f in self.block_validation_funs])
        # fix up the return values
        return {"whole_block":results}

    def optimize_on(self):
        self.optimize = True
        self.done_keys = []
        self.done_children = []
        self.done_parents = []

    def optimize_off(self):
        self.optimize = False
        self.done_keys = []
        self.done_children = []
        self.done_parents = []



class ValidCifBlock(CifBlock):
    """A `CifBlock` that is valid with respect to a given CIF dictionary.  Methods
    of `CifBlock` are overridden where necessary to disallow addition of invalid items to the
    `CifBlock`.

    ## Initialisation

    * `dic` is a `CifDic` object to be used for validation.

    """
    def __init__(self,dic = None, diclist=[], mergemode = "replace",*args,**kwords):
        CifBlock.__init__(self,*args,**kwords)
        if dic and diclist:
            print("Warning: diclist argument ignored when initialising ValidCifBlock")
        if isinstance(dic,CifDic):
            self.fulldic = dic
        else:
            raise TypeError( "ValidCifBlock passed non-CifDic type in dic argument")
        if len(diclist)==0 and not dic:
            raise ValidCifError( "At least one dictionary must be specified")
        if diclist and not dic:
            self.fulldic = merge_dic(diclist,mergemode)
        if not self.run_data_checks()[0]:
            raise ValidCifError( self.report())

    def run_data_checks(self,verbose=False):
        self.v_result = {}
        self.fulldic.optimize_on()
        for dataname in self.keys():
            update_value(self.v_result,self.fulldic.run_item_validation(dataname,self[dataname]))
            update_value(self.v_result,self.fulldic.run_global_validation(dataname,self[dataname],self))
        for loop_names in self.loops.values():
            update_value(self.v_result,self.fulldic.run_loop_validation(loop_names))
        # now run block-level checks
        update_value(self.v_result,self.fulldic.run_block_validation(self))
        # return false and list of baddies if anything didn't match
        self.fulldic.optimize_off()
        all_keys = list(self.v_result.keys()) #dictionary will change
        for test_key in all_keys:
            #print("%s: %r" % (test_key, self.v_result[test_key]))
            self.v_result[test_key] = [a for a in self.v_result[test_key] if a[1]["result"]==False]
            if len(self.v_result[test_key]) == 0:
                del self.v_result[test_key]
        isvalid = len(self.v_result)==0
        #if not isvalid:
        #    print("Baddies: {!r}".format(self.v_result))
        return isvalid,self.v_result

    def single_item_check(self,item_name,item_value):
        #self.match_single_item(item_name)
        if item_name not in self.fulldic:
            result = {item_name:[]}
        else:
            result = self.fulldic.run_item_validation(item_name,item_value)
        baddies = list([a for a in result[item_name] if a[1]["result"]==False])
        # if even one false one is found, this should trigger
        isvalid = (len(baddies) == 0)
        # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
        return isvalid,baddies

    def loop_item_check(self,loop_names):
        in_dic_names = list([a for a in loop_names if a in self.fulldic])
        if len(in_dic_names)==0:
            result = {loop_names[0]:[]}
        else:
            result = self.fulldic.run_loop_validation(in_dic_names)
        baddies = list([a for a in result[in_dic_names[0]] if a[1]["result"]==False])
        # if even one false one is found, this should trigger
        isvalid = (len(baddies) == 0)
        # if not isvalid: print("Failures for {}: {!r}".format(loop_names, baddies))
        return isvalid,baddies

    def global_item_check(self,item_name,item_value,provisional_items={}):
        if item_name not in self.fulldic:
            result = {item_name:[]}
        else:
            result = self.fulldic.run_global_validation(item_name,
               item_value,self,provisional_items = provisional_items)
        baddies = list([a for a in result[item_name] if a[1]["result"] is False])
        # if even one false one is found, this should trigger
        isvalid = (len(baddies) == 0)
        # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
        return isvalid,baddies

    def remove_global_item_check(self,item_name):
        if item_name not in self.fulldic:
            result = {item_name:[]}
        else:
            result = self.fulldic.run_remove_global_validation(item_name,self,False)
        baddies = list([a for a in result[item_name] if a[1]["result"]==False])
        # if even one false one is found, this should trigger
        isvalid = (len(baddies) == 0)
        # if not isvalid: print("Failures for {}: {!r}".format(item_name, baddies))
        return isvalid,baddies

    def AddToLoop(self,dataname,loopdata):
        # single item checks
        paired_data = loopdata.items()
        for name,value in paired_data:
            valid,problems = self.single_item_check(name,value)
            self.report_if_invalid(valid,problems)
        # loop item checks; merge with current loop
        found = 0
        for aloop in self.block["loops"]:
            if dataname in aloop:
                loopnames = aloop.keys()
                for new_name in loopdata.keys():
                    if new_name not in loopnames: loopnames.append(new_name)
                valid,problems = self.looped_item_check(loopnames)
                self.report_if_invalid(valid,problems)
        prov_dict = loopdata.copy()
        for name,value in paired_data:
            del prov_dict[name]   # remove temporarily
            valid,problems = self.global_item_check(name,value,prov_dict)
            prov_dict[name] = value  # add back in
            self.report_if_invalid(valid,problems)
        CifBlock.AddToLoop(self,dataname,loopdata)

    def AddCifItem(self,data):
        if isinstance(data[0],(unicode,str)):   # single item
            valid,problems = self.single_item_check(data[0],data[1])
            self.report_if_invalid(valid,problems,data[0])
            valid,problems = self.global_item_check(data[0],data[1])
            self.report_if_invalid(valid,problems,data[0])
        elif isinstance(data[0],tuple) or isinstance(data[0],list):
            paired_data = list(zip(data[0],data[1]))
            for name,value in paired_data:
                valid,problems = self.single_item_check(name,value)
                self.report_if_invalid(valid,problems,name)
            valid,problems = self.loop_item_check(data[0])
            self.report_if_invalid(valid,problems,data[0])
            prov_dict = {}            # for storing temporary items
            for name,value in paired_data: prov_dict[name]=value
            for name,value in paired_data:
                del prov_dict[name]   # remove temporarily
                valid,problems = self.global_item_check(name,value,prov_dict)
                prov_dict[name] = value  # add back in
                self.report_if_invalid(valid,problems,name)
        else:
            raise ValueError("Programming error: AddCifItem passed non-tuple,non-string item")
        super(ValidCifBlock,self).AddCifItem(data)

    def AddItem(self,key,value,**kwargs):
        """Set value of dataname `key` to `value` after checking for conformance with CIF dictionary"""
        valid,problems = self.single_item_check(key,value)
        self.report_if_invalid(valid,problems,key)
        valid,problems = self.global_item_check(key,value)
        self.report_if_invalid(valid,problems,key)
        super(ValidCifBlock,self).AddItem(key,value,**kwargs)

    # utility function
    def report_if_invalid(self,valid,bad_list,data_name):
        if not valid:
            bad_tests = [a[0] for a in bad_list]
            error_string = ",".join(bad_tests)
            error_string = repr(data_name) + " fails following validity checks: "  + error_string
            raise ValidCifError( error_string)

    def __delitem__(self,key):
        # we don't need to run single item checks; we do need to run loop and
        # global checks.
        if key in self:
            try:
                loop_items = self.GetLoop(key)
            except TypeError:
                loop_items = []
            if loop_items:             #need to check loop conformance
                loop_names = [a[0] for a in loop_items if a[0] != key]
                valid,problems = self.loop_item_check(loop_names)
                self.report_if_invalid(valid,problems)
            valid,problems = self.remove_global_item_check(key)
            self.report_if_invalid(valid,problems)
        self.RemoveCifItem(key)


    def report(self):
       outstr = StringIO()
       outstr.write( "Validation results\n")
       outstr.write( "------------------\n")
       print("%d invalid items found\n" % len(self.v_result))
       for item_name,val_func_list in self.v_result.items():
           outstr.write("%s fails following tests:\n" % item_name)
           for val_func in val_func_list:
               outstr.write("\t%s\n")
       return outstr.getvalue()


class ValidCifFile(CifFile):
    """A CIF file for which all datablocks are valid.  Argument `dic` to
    initialisation specifies a `CifDic` object to use for validation."""
    def __init__(self,dic=None,diclist=[],mergemode="replace",*args,**kwargs):
        if not diclist and not dic and not hasattr(self,'bigdic'):
            raise ValidCifError( "At least one dictionary is required to create a ValidCifFile object")
        if not dic and diclist:     #merge here for speed
            self.bigdic = merge_dic(diclist,mergemode)
        elif dic and not diclist:
            self.bigdic = dic
        CifFile.__init__(self,*args,**kwargs)
        for blockname in self.keys():
            self.dictionary[blockname]=ValidCifBlock(data=self.dictionary[blockname],dic=self.bigdic)

    def NewBlock(self,blockname,blockcontents,**kwargs):
        CifFile.NewBlock(self,blockname,blockcontents,**kwargs)
        # dictionary[blockname] is now a CifBlock object.  We
        # turn it into a ValidCifBlock object
        self.dictionary[blockname] = ValidCifBlock(dic=self.bigdic,
                                         data=self.dictionary[blockname])


class ValidationResult:
    """Represents validation result. It is initialised with """
    def __init__(self,results):
        """results is return value of validate function"""
        self.valid_result, self.no_matches = results

    def report(self,use_html):
        """Return string with human-readable description of validation result"""
        return validate_report((self.valid_result, self.no_matches),use_html)

    def is_valid(self,block_name=None):
        """Return True for valid CIF file, otherwise False"""
        if block_name is not None:
            block_names = [block_name]
        else:
            block_names = self.valid_result.iterkeys()
        for block_name in block_names:
            if not self.valid_result[block_name] == (True,{}):
                valid = False
                break
            else:
                valid = True
        return valid

    def has_no_match_items(self,block_name=None):
        """Return true if some items are not found in dictionary"""
        if block_name is not None:
            block_names = [block_name]
        else:
            block_names = self.no_matches.iter_keys()
        for block_name in block_names:
            if self.no_matches[block_name]:
                has_no_match_items = True
                break
            else:
                has_no_match_items = False
        return has_no_match_items



def Validate(ciffile,dic = "", diclist=[],mergemode="replace",isdic=False):
    """Validate the `ciffile` conforms to the definitions in `CifDic` object `dic`, or if `dic` is missing,
    to the results of merging the `CifDic` objects in `diclist` according to `mergemode`.  Flag
    `isdic` indicates that `ciffile` is a CIF dictionary meaning that save frames should be
    accessed for validation and that mandatory_category should be interpreted differently for DDL2."""
    if not isinstance(ciffile,CifFile):
        check_file = CifFile(ciffile)
    else:
        check_file = ciffile
    if not dic:
        fulldic = merge_dic(diclist,mergemode)
    else:
        fulldic = dic
    no_matches = {}
    valid_result = {}
    if isdic:          #assume one block only
        check_file.scoping = 'instance' #only data blocks visible
        top_level = check_file.keys()[0]
        check_file.scoping = 'dictionary'   #all blocks visible
        # collect a list of parents for speed
        if fulldic.diclang == 'DDL2':
            poss_parents = fulldic.get_all("_item_linked.parent_name")
            for parent in poss_parents:
                curr_parent = listify(check_file.get(parent,[]))
                new_vals = check_file.get_all(parent)
                new_vals.extend(curr_parent)
                if len(new_vals)>0:
                    check_file[parent] = new_vals
                print("Added %s (len %d)" % (parent,len(check_file[parent])))
    # now run the validations
    for block in check_file.keys():
        if isdic and block == top_level:
           block_scope = 'Dictionary'
        elif isdic:
           block_scope = 'Item'
        else:
           block_scope = 'Datablock'
        no_matches[block] = [a for a in check_file[block].keys() if a not in fulldic]
        # remove non-matching items
        print("Not matched: " + repr(no_matches[block]))
        for nogood in no_matches[block]:
             del check_file[block][nogood]
        print("Validating block %s, scope %s" % (block,block_scope))
        valid_result[block] = run_data_checks(check_file[block],fulldic,block_scope=block_scope)
    return valid_result,no_matches

def validate_report(val_result,use_html=False):
    valid_result,no_matches = val_result
    outstr = StringIO()
    if use_html:
        outstr.write("<h2>Validation results</h2>")
    else:
        outstr.write( "Validation results\n")
        outstr.write( "------------------\n")
    if len(valid_result) > 10:
        suppress_valid = True         #don't clutter with valid messages
        if use_html:
           outstr.write("<p>For brevity, valid blocks are not reported in the output.</p>")
    else:
        suppress_valid = False
    for block in valid_result.keys():
        block_result = valid_result[block]
        if block_result[0]:
            out_line = "Block '%s' is VALID" % block
        else:
            out_line = "Block '%s' is INVALID" % block
        if use_html:
            if (block_result[0] and (not suppress_valid or len(no_matches[block])>0)) or not block_result[0]:
                outstr.write( "<h3>%s</h3><p>" % out_line)
        else:
                outstr.write( "\n %s\n" % out_line)
        if len(no_matches[block])!= 0:
            if use_html:
                outstr.write( "<p>The following items were not found in the dictionary")
                outstr.write(" (note that this does not invalidate the data block):</p>")
                outstr.write("<p><table>\n")
                [outstr.write("<tr><td>%s</td></tr>" % it) for it in no_matches[block]]
                outstr.write("</table>\n")
            else:
                outstr.write( "\n The following items were not found in the dictionary:\n")
                outstr.write("Note that this does not invalidate the data block\n")
                [outstr.write("%s\n" % it) for it in no_matches[block]]
        # now organise our results by type of error, not data item...
        error_type_dic = {}
        for error_item, error_list in block_result[1].items():
            for func_name,bad_result in error_list:
                bad_result.update({"item_name":error_item})
                try:
                    error_type_dic[func_name].append(bad_result)
                except KeyError:
                    error_type_dic[func_name] = [bad_result]
        # make a table of test name, test message
        info_table = {\
        'validate_item_type':\
            "The following data items had badly formed values",
        'validate_item_esd':\
            "The following data items should not have esds appended",
        'validate_enum_range':\
            "The following data items have values outside permitted range",
        'validate_item_enum':\
            "The following data items have values outside permitted set",
        'validate_looping':\
            "The following data items violate looping constraints",
        'validate_loop_membership':\
            "The following looped data names are of different categories to the first looped data name",
        'validate_loop_key':\
            "A required dataname for this category is missing from the loop\n containing the dataname",
        'validate_loop_key_ddlm':\
            "A loop key is missing for the category containing the dataname",
        'validate_loop_references':\
            "A dataname required by the item is missing from the loop",
        'validate_parent':\
            "A parent dataname is missing or contains different values",
        'validate_child':\
            "A child dataname contains different values to the parent",
        'validate_uniqueness':\
            "One or more data items do not take unique values",
        'validate_dependents':\
            "A dataname required by the item is missing from the data block",
        'validate_exclusion': \
            "Both dataname and exclusive alternates or aliases are present in data block",
        'validate_mandatory_category':\
            "A required category is missing from this block",
        'check_mandatory_items':\
            "A required data attribute is missing from this block",
        'check_prohibited_items':\
            "A prohibited data attribute is present in this block"}

        for test_name,test_results in error_type_dic.items():
           if use_html:
               outstr.write(html_error_report(test_name,info_table[test_name],test_results))
           else:
               outstr.write(error_report(test_name,info_table[test_name],test_results))
               outstr.write("\n\n")
    return outstr.getvalue()

# A function to lay out a single error report.  We are passed
# the name of the error (one of our validation functions), the
# explanation to print out, and a dictionary with the error
# information.  We print no more than 50 characters of the item

def error_report(error_name,error_explanation,error_dics):
   retstring = "\n\n " + error_explanation + ":\n\n"
   headstring = "%-32s" % "Item name"
   bodystring = ""
   if "bad_values" in error_dics[0]:
      headstring += "%-20s" % "Bad value(s)"
   if "bad_items" in error_dics[0]:
      headstring += "%-20s" % "Bad dataname(s)"
   if "child" in error_dics[0]:
      headstring += "%-20s" % "Child"
   if "parent" in error_dics[0]:
      headstring += "%-20s" % "Parent"
   headstring +="\n"
   for error in error_dics:
      bodystring += "\n%-32s" % error["item_name"]
      if "bad_values" in error:
          out_vals = [repr(a)[:50] for a in error["bad_values"]]
          bodystring += "%-20s" % out_vals
      if "bad_items" in error:
          bodystring += "%-20s" % repr(error["bad_items"])
      if "child" in error:
          bodystring += "%-20s" % repr(error["child"])
      if "parent" in error:
          bodystring += "%-20s" % repr(error["parent"])
   return retstring + headstring + bodystring

#  This lays out an HTML error report

def html_error_report(error_name,error_explanation,error_dics,annotate=[]):
   retstring = "<h4>" + error_explanation + ":</h4>"
   retstring = retstring + "<table cellpadding=5><tr>"
   headstring = "<th>Item name</th>"
   bodystring = ""
   if "bad_values" in error_dics[0]:
      headstring += "<th>Bad value(s)</th>"
   if "bad_items" in error_dics[0]:
      headstring += "<th>Bad dataname(s)</th>"
   if "child" in error_dics[0]:
      headstring += "<th>Child</th>"
   if "parent" in error_dics[0]:
      headstring += "<th>Parent</th>"
   headstring +="</tr>\n"
   for error in error_dics:
      bodystring += "<tr><td><tt>%s</tt></td>" % error["item_name"]
      if "bad_values" in error:
          bodystring += "<td>%s</td>" % error["bad_values"]
      if "bad_items" in error:
          bodystring += "<td><tt>%s</tt></td>" % error["bad_items"]
      if "child" in error:
          bodystring += "<td><tt>%s</tt></td>" % error["child"]
      if "parent" in error:
          bodystring += "<td><tt>%s</tt></td>" % error["parent"]
      bodystring += "</tr>\n"
   return retstring + headstring + bodystring + "</table>\n"

def run_data_checks(check_block,fulldic,block_scope='Item'):
    v_result = {}
    for key in check_block.keys():
        update_value(v_result, fulldic.run_item_validation(key,check_block[key]))
        update_value(v_result, fulldic.run_global_validation(key,check_block[key],check_block))
    for loopnames in check_block.loops.values():
        update_value(v_result, fulldic.run_loop_validation(loopnames))
    update_value(v_result,fulldic.run_block_validation(check_block,block_scope=block_scope))
    # return false and list of baddies if anything didn't match
    all_keys = list(v_result.keys())
    for test_key in all_keys:
        v_result[test_key] = [a for a in v_result[test_key] if a[1]["result"]==False]
        if len(v_result[test_key]) == 0:
            del v_result[test_key]
    # if even one false one is found, this should trigger
    # print("Baddies: {!r}".format(v_result))
    isvalid = len(v_result)==0
    return isvalid,v_result


def get_number_with_esd(numstring):
    import string
    numb_re = '((-?(([0-9]*[.]([0-9]+))|([0-9]+)[.]?))([(][0-9]+[)])?([eEdD][+-]?[0-9]+)?)|(\?)|(\.)'
    our_match = re.match(numb_re,numstring)
    if our_match:
        a,base_num,b,c,dad,dbd,esd,exp,q,dot = our_match.groups()
        # print("Debug: {} -> {!r}".format(numstring, our_match.groups()))
    else:
        return None,None
    if dot or q: return None,None     #a dot or question mark
    if exp:          #has exponent
       exp = exp.replace("d","e")     # mop up old fashioned numbers
       exp = exp.replace("D","e")
       base_num = base_num + exp
    # print("Debug: have %s for base_num from %s" % (base_num,numstring))
    base_num = float(base_num)
    # work out esd, if present.
    if esd:
        esd = float(esd[1:-1])    # no brackets
        if dad:                   # decimal point + digits
            esd = esd * (10 ** (-1* len(dad)))
        if exp:
            esd = esd * (10 ** (float(exp[1:])))
    return base_num,esd

def float_with_esd(inval):
    if isinstance(inval,unicode):
        j = inval.find("(")
        if j>=0:  return float(inval[:j])
    return float(inval)



def convert_type(definition):
    """Convert value to have the type given by definition"""
    #extract the actual required type information
    container = definition['_type.container']
    dimension = definition.get('_type.dimension',StarFile.StarList([]))
    structure = interpret_structure(definition['_type.contents'])
    if container == 'Single':   #a single value to convert
        return convert_single_value(structure)
    elif container == 'List':   #lots of the same value
        return convert_list_values(structure,dimension)
    elif container == 'Multiple': #no idea
        return None
    elif container in ('Array','Matrix'): #numpy array
        return convert_matrix_values(structure)
    return lambda a:a    #unable to convert

def convert_single_value(type_spec):
    """Convert a single item according to type_spec"""
    if type_spec == 'Real':
        return float_with_esd
    if type_spec in ('Count','Integer','Index','Binary','Hexadecimal','Octal'):
        return int
    if type_spec == 'Complex':
        return complex
    if type_spec == 'Imag':
        return lambda a:complex(0,a)
    if type_spec in ('Code','Name','Tag'):  #case-insensitive -> lowercase
        return lambda a:a.lower()
    return lambda a:a   #can't do anything numeric

#def convert_list_values(structure,dimension):
#    """Convert the values according to the element
#       structure given in [[structure]]"""
#    if isinstance(structure,(unicode,str)):   #simple repetition
#        func_def =  "element_convert = convert_single_value('%s')" % structure
#    else:
#        func_def =       "def element_convert(element):\n"
#        func_def +=      "   final_val = []\n"
#        for pos_no in range(len(structure)):
#            func_def +=  "   final_val.append("
#            type_spec = structure[pos_no]
#            if type_spec == 'Real':
#                cf = "float_with_esd("
#            elif type_spec in ('Count','Integer','Index','Binary','Hexadecimal','Octal'):
#                cf = 'int('
#            elif type_spec == 'Complex':
#                cf = 'complex('
#            elif type_spec == 'Imag':
#                cf = 'complex(0,'
#            elif type_spec in ('Code','Name','Tag'):
#                cf = '('
#            else: cf = ''
#            func_def += cf
#            func_def += "element[%d]" % pos_no
#            if "(" in cf: func_def +=")"
#            if type_spec in ('Code','Name','Tag'):
#                func_def +=".lower()"
#            func_def +=")\n"  # close append
#        func_def +=      "   return final_val\n"
#    print(func_def)
#    exec(func_def, globals()) #(re)defines element_convert in global namespace
#    if len(dimension)> 0 and int(dimension[0]) != 1:
#        return lambda a: list(map(element_convert,a))
#    else: return element_convert
#
#def convert_matrix_values(valtype):
#    """Convert a dREL String or Float valued List structure to a numpy matrix structure"""
#    # first convert to numpy array, then let numpy do the work
#    try: import numpy
#    except:
#        return lambda a:a   #cannot do it
#    func_def =     "def matrix_convert(a):\n"
#    func_def +=    "    import numpy\n"
#    func_def +=    "    p = numpy.array(a)\n"
#    if valtype == 'Real':
#        func_def+= "    return p.astype('float')\n"
#    elif valtype == 'Integer':
#        func_def +="    return p.astype('int')\n"
#    elif valtype == 'Complex':
#        func_def +="    return p.astype('complex')\n"
#    else:
#        raise ValueError('Unknown matrix value type')
#    exec(func_def,globals())  #matrix convert is defined
#    return matrix_convert

def interpret_structure(struc_spec):
    """Interpret a DDLm structure specification"""
    from . import TypeContentsParser as t
    p = t.TypeParser(t.TypeParserScanner(struc_spec))
    return getattr(p,"input")()


# A utility function to append to item values rather than replace them
def update_value(base_dict,new_items):
    for new_key in new_items.keys():
        if new_key in base_dict:
            base_dict[new_key].extend(new_items[new_key])
        else:
            base_dict[new_key] = new_items[new_key]

#Transpose the list of lists passed to us
def transpose(base_list):
    new_lofl = []
    full_length = len(base_list)
    opt_range = range(full_length)
    for i in range(len(base_list[0])):
       new_packet = []
       for j in opt_range:
          new_packet.append(base_list[j][i])
       new_lofl.append(new_packet)
    return new_lofl

# listify strings - used surprisingly often
def listify(item):
    if isinstance(item,(unicode,str)): return [item]
    else: return item

# given a list of search items, return a list of items
# actually contained in the given data block
def filter_present(namelist,datablocknames):
    return [a for a in namelist if a in datablocknames]

# Make an item immutable, used if we want a list to be a key
def make_immutable(values):
    """Turn list of StarList values into a list of immutable items"""
    if not isinstance(values[0],StarList):
        return values
    else:
        return [tuple(a) for a in values]

# merge ddl dictionaries.  We should be passed filenames or CifFile
# objects
def merge_dic(diclist,mergemode="replace",ddlspec=None):
    dic_as_cif_list = []
    for dic in diclist:
        if not isinstance(dic,CifFile) and \
           not isinstance(dic,(unicode,str)):
               raise TypeError("Require list of CifFile names/objects for dictionary merging")
        if not isinstance(dic,CifFile): dic_as_cif_list.append(CifFile(dic))
        else: dic_as_cif_list.append(dic)
    # we now merge left to right
    basedic = dic_as_cif_list[0]
    if "on_this_dictionary" in basedic:   #DDL1 style only
        for dic in dic_as_cif_list[1:]:
           basedic.merge(dic,mode=mergemode,match_att=["_name"])
    elif len(basedic.keys()) == 1:                     #One block: DDL2/m style
        old_block = basedic[basedic.keys()[0]]
        for dic in dic_as_cif_list[1:]:
           new_block = dic[dic.keys()[0]]
           basedic.merge(dic,mode=mergemode,
                         single_block=[basedic.keys()[0],dic.keys()[0]],
                         match_att=["_item.name"],match_function=find_parent)
    return CifDic(basedic)

def find_parent(ddl2_def):
    if "_item.name" not in ddl2_def:
       return None
    if isinstance(ddl2_def["_item.name"],unicode):
        return ddl2_def["_item.name"]
    if "_item_linked.child_name" not in ddl2_def:
        raise CifError("Asked to find parent in block with no child_names")
    if "_item_linked.parent_name" not in ddl2_def:
        raise CifError("Asked to find parent in block with no parent_names")
    result = list([a for a in ddl2_def["_item.name"] if a not in ddl2_def["_item_linked.child_name"]])
    if len(result)>1 or len(result)==0:
        raise CifError("Unable to find single unique parent data item")
    return result[0]


def ReadCif(filename,grammar='auto',scantype='standard',scoping='instance',standard='CIF'):
    """ Read in a CIF file, returning a `CifFile` object.

    * `filename` may be a URL, a file
    path on the local system, or any object with a `read` method.

    * `grammar` chooses the CIF grammar variant. `1.0` is the original 1992 grammar and `1.1`
    is identical except for the exclusion of square brackets as the first characters in
    undelimited datanames. `2.0` will read files in the CIF2.0 standard, and `STAR2` will
    read files according to the STAR2 publication.  If grammar is `None`, autodetection
    will be attempted in the order `2.0`, `1.1` and `1.0`. This will always succeed for
    properly-formed CIF2.0 files.  Note that only Unicode characters in the basic multilingual
    plane are recognised (this will be fixed when PyCIFRW is ported to Python 3).

    * `scantype` can be `standard` or `flex`.  `standard` provides pure Python parsing at the
    cost of a factor of 10 or so in speed.  `flex` will tokenise the input CIF file using
    fast C routines, but is not available for CIF2/STAR2 files.  Note that running PyCIFRW in
    Jython uses native Java regular expressions
    to provide a speedup regardless of this argument (and does not yet support CIF2).

    * `scoping` is only relevant where nested save frames are expected (STAR2 only).
    `instance` scoping makes nested save frames
    invisible outside their hierarchy, allowing duplicate save frame names in separate
    hierarchies. `dictionary` scoping makes all save frames within a data block visible to each
    other, thereby restricting all save frames to have unique names.
    Currently the only recognised value for `standard` is `CIF`, which when set enforces a
    maximum length of 75 characters for datanames and has no other effect. """

    finalcif = CifFile(scoping=scoping,standard=standard)
    return StarFile.ReadStar(filename,prepared=finalcif,grammar=grammar,scantype=scantype)
    #return StarFile.StarFile(filename,maxlength,scantype=scantype,grammar=grammar,**kwargs)

class CifLoopBlock(StarFile.LoopBlock):
    def __init__(self,data=(),**kwargs):
        super(CifLoopBlock,self).__init__(data,**kwargs)

#No documentation flags