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# XML-database conversion
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import copy
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import re
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from xml.dom import Node
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import dicts
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import exc
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import Parser
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import sql
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import sql_io
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import sql_gen
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import strings
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import util
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import xml_dom
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import xml_func
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import xpath
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def name_of(node): return re.sub(r'^.*\.', r'', node.tagName)
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ptr_suffix = '_id'
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def is_ptr(node_name): return node_name.lower().endswith(ptr_suffix)
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def ptr_type_guess(node_name):
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    assert is_ptr(node_name)
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    return node_name[:-len(ptr_suffix)]
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def ptr_target(node):
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    assert is_ptr(name_of(node))
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    return xml_dom.value_node(node)
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def find_by_name(node, name):
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    for parent in xml_dom.NodeParentIter(node):
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        if name_of(parent) == name: return parent
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        else:
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            for child in xml_dom.NodeElemIter(parent):
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                child_name = name_of(child)
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                if is_ptr(child_name):
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                    target = ptr_target(child)
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                    if target.tagName == name: return target
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                elif child_name == name: return child
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    return None
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class ColRef:
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    '''A reference to a table column'''
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    def __init__(self, name, idx):
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        self.name = name
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        self.idx = idx
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    def __str__(self): return self.name
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input_col_prefix = xml_func.var_name_prefix
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put_special_funcs = set(['_setDefault', '_simplifyPath'])
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no_parent_ids_loc = object() # tells put() there is no parent_ids_loc
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def put(db, node, row_ins_ct_ref=None, on_error=exc.reraise, col_defaults=None,
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    in_table=None, parent_ids_loc=no_parent_ids_loc, next=None):
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    '''
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    @param node To use an entire XML document, pass root.firstChild.
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    '''
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    if node == None: return None # when no rows, root.firstChild == None
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    elif xml_dom.is_text_node(node): return xml_dom.value(node)
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    if col_defaults == None: col_defaults = {}
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    def put_(node):
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        if util.is_str(node): return node
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        return put(db, node, row_ins_ct_ref, on_error, col_defaults, in_table,
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            parent_ids_loc, next)
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    def augment_error(e): exc.add_msg(e, 'node:\n'+strings.ustr(node))
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    def on_error_(e):
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        augment_error(e)
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        on_error(e)
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    def wrap_e(e):
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        augment_error(e)
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        raise xml_func.SyntaxError(e)
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    is_func = xml_func.is_func(node)
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    out_table = name_of(node)
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    # Divide children into fields and children with fkeys to parent
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    row = dicts.OnceOnlyDict()
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    children = []
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    try:
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        for child in xml_dom.NodeElemIter(node):
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            child_name = name_of(child)
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            if xml_dom.is_empty(child): row[child_name] = None
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            elif xml_dom.is_text(child):
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                row[child_name] = strings.to_unicode(xml_dom.value(child))
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            else:
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                child_value = xml_dom.value_node(child)
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                if ((is_func or is_ptr(child_name)
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                    or xml_func.is_func(child_value))
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                    and not xml_func.is_func(child)):
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                    row[child_name] = child_value
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                else: children.append(child)
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    except dicts.KeyExistsError, e: wrap_e(e)
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    # Special handling for structural XML functions
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    if out_table == '_setDefault':
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        # Parse args
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        try: path = row.pop('path')
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        except KeyError, e: wrap_e(e)
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        col_defaults = dicts.MergeDict(dicts.WrapDict(put_, row), col_defaults)
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        return put_(path)
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    elif out_table == '_simplifyPath':
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        # Parse args
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        try:
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            next = row['next'] # modifies outer next var used by put_()
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            path = row['path']
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        except KeyError, e: wrap_e(e)
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        try: next = xpath.parse(next)
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        except Parser.SyntaxError, e: wrap_e(e)
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        try: next = next[0].name
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        except IndexError, e: wrap_e(e)
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        return put_(path)
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    is_literals = in_table == None
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    in_tables = []
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    no_empty = set()
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    if not is_literals:
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        in_tables.append(in_table)
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        no_empty.add(in_table)
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    def pkey_name(table): return sql.pkey_name(db, table, True)
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    # Add fkey to parent
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    if parent_ids_loc is not no_parent_ids_loc:
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        if sql_gen.is_table_col(parent_ids_loc):
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            no_empty.add(parent_ids_loc.table)
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        parent_ptr = node.getAttribute('fkey')
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        if parent_ptr == '': parent_ptr = pkey_name(name_of(node.parentNode))
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        row[parent_ptr] = parent_ids_loc
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    # Parse input columns
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    row = row.inner # now allow keys to be overwritten
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    for out_col, value in row.iteritems():
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        if (not is_literals and util.is_str(value)
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            and value.startswith(input_col_prefix)): # value is input column
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            row[out_col] = sql_gen.Col(strings.remove_prefix(input_col_prefix,
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                value), in_table)
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    # Optimizations for structural XML functions
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    if out_table == '_alt': # return first arg if non-NULL
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        args = row.items()
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        args.sort()
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        out_col, value = min(args) # first arg
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        if xml_dom.is_node(value): row[out_col] = value = put_(value)
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        if not sql_gen.is_nullable(db, value): return value
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    # Process values
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    parent_ids_loc = no_parent_ids_loc # applies to this section
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    for out_col, value in row.iteritems():
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        # Handle forward pointers
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        if xml_dom.is_node(value): row[out_col] = value = put_(value)
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        # Translate values
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        if isinstance(value, sql_gen.Col): # value is table column
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            assert sql_gen.is_table_col(value)
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            if value.table is not in_table: in_tables.append(value.table)
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        else: # value is literal value
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            row[out_col] = sql_gen.NamedCol(out_col, value)
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    # Insert node
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    try: pkeys_loc = sql_io.put_table(db, out_table, in_tables, row,
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        row_ins_ct_ref, next, col_defaults, on_error_)
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    except Exception, e:
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        augment_error(e)
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        raise
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    if sql_gen.is_table_col(pkeys_loc): no_empty.add(pkeys_loc.table)
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    sql.empty_temp(db, set(in_tables) - no_empty)
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    # Insert children with fkeys to parent
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    parent_ids_loc = pkeys_loc # applies to this section
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    for child in children: put_(child)
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    return pkeys_loc
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def get(db, node, limit=None, start=None):
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    def pkey_name(table): return sql.pkey_name(db, table)
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    node = node.firstChild
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    table = name_of(node)
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    pkey_ = pkey_name(table)
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    fields = []
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    conds = {}
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    for child in xml_dom.NodeElemIter(node):
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        child_name = name_of(child)
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        if xml_dom.is_empty(child): fields.append(child_name)
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        elif xml_dom.is_text(child): conds[child_name] = xml_dom.value(child)
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        else: raise Exception('Joins not supported yet')
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    id_ = xml_dom.get_id(node)
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    if id_ != None: conds[pkey_name(table)] = id_ # replace any existing value
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    if fields == []: fields.append(pkey_)
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    return sql.select(db, table, fields, conds, limit, start)
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# Controls when and how put_table() will partition the input table
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partition_size = 1000000 # rows; must be >= NCBI.nodes size
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def put_table(db, node, in_table, in_row_ct_ref=None, row_ins_ct_ref=None,
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    limit=None, start=0, on_error=exc.reraise, col_defaults={},
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    partition_size=partition_size):
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    '''
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    @param node The XML tree that transforms the input to the output. Similar to
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        put()'s node param, but with the input column name prefixed by
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        input_col_prefix in place of the column value.
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    @return sql_gen.Col Where the pkeys (from INSERT RETURNING) are made
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        available
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    '''
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    if in_table == None:
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        return put(db, node, row_ins_ct_ref, on_error, col_defaults)
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    in_table = sql_gen.as_Table(in_table)
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    sql_io.mk_errors_table(db, in_table)
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    in_table.set_srcs([in_table], overwrite=False)
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    db.src = strings.ustr(in_table)
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    db.autoexplain = True # but don't do this in row-based import
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    # Subset and partition in_table
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    # OK to do even if table already the right size because it takes <1 sec.
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    full_in_table = in_table
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    pkeys_loc = None # used if loop is never executed
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    total = 0
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    while limit == None or total < limit:
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        # Adjust partition size if last partition
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        this_limit = partition_size
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        if limit != None: this_limit = min(this_limit, limit - total)
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        # Row # is interally 0-based, but 1-based to the user
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        db.log_debug('********** Partition: rows '+str(start+1)+'-'
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            +str(start+this_limit)+' **********', level=1.2)
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        # Subset in_table
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        in_table = sql_gen.Table(strings.ustr(full_in_table),
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            srcs=full_in_table.srcs, is_temp=True) # prepend schema to name
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        sql.copy_table_struct(db, full_in_table, in_table)
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        try: sql.add_row_num(db, in_table, 'row_num')
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        except sql.DatabaseErrors: pass # already has pkey
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        cur = sql.insert_select(db, in_table, None, sql.mk_select(db,
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            full_in_table, limit=this_limit, start=start))
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        this_ct = cur.rowcount
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        total += this_ct
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        start += this_ct # advance start to fetch next set
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        if this_ct == 0: break # in_table size is multiple of partition_size
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        # Import data
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        pkeys_loc = put(db, node, row_ins_ct_ref, on_error, col_defaults,
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            in_table)
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        if in_row_ct_ref != None: in_row_ct_ref[0] += this_ct
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        sql.empty_temp(db, in_table)
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        if this_ct < partition_size: break # partial partition = last
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        # Work around PostgreSQL's temp table disk space leak
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        db.reconnect()
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    return pkeys_loc