view seg2matrix/CGData/BaseTable.py @ 37:e81019e3ac99

Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format

from CGData import CGObjectBase

import csv
import types

class TableRow(object):
    def __init__(self):
        pass
        
    def __str__(self):
        return "<" + ",".join( "%s=%s" % (col, getattr(self,col)) for col in self.__format__['columnOrder']) + ">"

class InvalidFormat(Exception):
    def __init__(self, txt):
        Exception.__init__(self, txt)

class BaseTable(CGObjectBase):
    def __init__(self):
        super(BaseTable,self).__init__()        
        self.__row_class__ = type( "TableRow_" + self['cgformat']['name'], (TableRow,), dict(__format__=self.__format__) )        
        self.free()
    
    def free(self):
        self.firstKey = None
        self.secondKey = None
        self.groupKey = None
        self.loaded = False
        if 'primaryKey' in self['cgformat']:
            self.firstKey = self['cgformat']['primaryKey']
            setattr(self, self['cgformat']['primaryKey'] + "_map", {} )
            self.groupKey = False
        
        #setup the map for groupKeys
        if 'groupKey' in self['cgformat']:
            self.firstKey = self['cgformat']['groupKey']
            setattr(self, self['cgformat']['groupKey'] + "_map", {} )
            self.groupKey = True
        
        if 'secondaryKey' in self['cgformat']:
            self.secondKey = self['cgformat']['secondaryKey']
    
    def read(self, handle):
        cols = self['cgformat']['columnOrder']
        colType = {}
        for col in cols:
            if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'type' in self['cgformat']['columnDef'][col]:
                if self['cgformat']['columnDef'][col]['type'] == 'float':
                    colType[col] = float
                elif self['cgformat']['columnDef'][col]['type'] == 'int':
                    colType[col] = int
                else:
                    colType[col] = str
            else:
                colType[col] = str
                
        read = csv.reader(handle, delimiter="\t")

        storeMap = getattr(self, self.firstKey + "_map")
        comment = None
        if 'comment' in self['cgformat']:
            comment = self['cgformat']['comment']
        linenum = 0
        for row in read:
            linenum += 1
            r = self.__row_class__()
            if comment is None or not row[0].startswith(comment):
                for i, col in enumerate(cols):
                    isOptional = False
                    if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
                        isOptional = self['cgformat']['columnDef'][col]['optional']
                    if len(row) > i:
                        try:
                            setattr(r, col, colType[col](row[i]))
                        except ValueError:
                            raise ValueError( "col invalid type %s on line %d" % (row[i], linenum))
                    else:
                        if isOptional:
                            setattr(r, col, None)
                        else:
                            print row
                            raise InvalidFormat("missing colum " + col)
                            
                if not self.groupKey:
                    if self.secondKey is not None:
                        key1 = getattr(r, self.firstKey )                    
                        key2 = getattr(r, self.secondKey )
                        if key1 not in storeMap:
                            storeMap[key1] = {}
                        storeMap[key1][key2] = r
                    else:
                        storeMap[ getattr(r, self.firstKey ) ] = r
                else:
                    key1 = getattr(r, self.firstKey )
                    if self.secondKey is not None:
                        key2 = getattr(r, self.secondKey )
                        if key1 not in storeMap:
                            storeMap[key1] = {}
                        if key2 not in storeMap[key1]:
                            storeMap[key1][key2] = []
                        storeMap[key1][key2].append(r)
                    else:
                        if key1 not in storeMap:
                            storeMap[key1] = []
                        storeMap[key1].append(r)
        self.loaded = True
    
    """
    def __getattr__(self, item):
        if not self.loaded:
            self.load()

        if item == "get_" + self.firstKey + "_list":
            return self.__get_firstmap__().keys
        if item == "get_by_" + self.firstKey:
            return self.__get_firstmap__().__getitem__                
        if item == "get_" + self.firstKey + "_values":
            return self.__get_firstmap__().values      
        if item == "get_" + self.firstKey + "_map":
            return self.__get_firstmap__
        if item == "has_" + self.firstKey:
            return self.__get_firstmap__().__contains__
        raise AttributeError(item)
    """
        
    def get_key_list(self):
        """
        List keys
        """
        if not self.loaded:
            self.load()    
        return self.__get_firstmap__().keys()
    
    def get_by(self, key):
        """
        get by key
        """
        if not self.loaded:
            self.load()    
        return self.__get_firstmap__().__getitem__(key)
    
    def get_values(self):
        """
        get values
        """
        if not self.loaded:
            self.load()    
        return self.__get_firstmap__().values()
    
    def get_map(self):
        """
        get key map
        """
        if not self.loaded:
            self.load()
        return self.__get_firstmap__()
    
    def has_key(self, key):
        """
        Does the table have a key
        """
        if not self.loaded:
            self.load()
        return self.__get_firstmap__().__contains__(key)
        def __get_firstmap__(self):
            return getattr(self, self.firstKey + "_map")
    
    def init_blank(self):
        self.free()
        self['cgdata'] = { 'type' : self['cgformat']['name'] }
        self.loaded = True
    
    def insert(self, name, vals):
        storeMap = getattr(self, self.firstKey + "_map")
        cols = self['cgformat']['columnOrder']
        r = self.__row_class__()
        for col in cols:
            isOptional = False
            if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
                isOptional = self['cgformat']['columnDef'][col]['optional']
            if col in vals:
                setattr(r, col, vals[col])
            else:
                if isOptional:
                    setattr(r, col, None)
                else:
                    raise InvalidFormat("missing colum " + col)                            
                            
        if not self.groupKey:
            if self.secondKey is not None:
                key1 = getattr(r, self.firstKey )                    
                key2 = getattr(r, self.secondKey )
                if key1 not in storeMap:
                    storeMap[key1] = {}
                storeMap[key1][key2] = r
            else:
                storeMap[ getattr(r, self.firstKey ) ] = r
        else:
            key1 = getattr(r, self.firstKey )
            if self.secondKey is not None:
                key2 = getattr(r, self.secondKey )
                if key1 not in storeMap:
                    storeMap[key1] = {}
                if key2 not in storeMap[key1]:
                    storeMap[key1][key2] = []
                storeMap[key1][key2].append(r)
            else:
                if key1 not in storeMap:
                    storeMap[key1] = []
                storeMap[key1].append(r)
    
    def write(self, handle):
        writer = csv.writer(handle, delimiter="\t", lineterminator="\n")
        for row in self.row_iter():
            orow = []
            for col in self['cgformat']['columnOrder']:
                orow.append( getattr(row, col) )
            writer.writerow(orow)
        
    
    def row_iter(self):
        if not self.groupKey:
            keyMap = getattr(self, self.firstKey + "_map")
            for rowKey in keyMap:
                yield keyMap[rowKey]
        else:
            keyMap = getattr(self, self.firstKey + "_map")
            for rowKey in keyMap:
                for elem in keyMap[rowKey]:
                    yield elem
        
    def __get_firstmap__(self):
        return getattr(self, self.firstKey + "_map")