Source Code for Module biana.BianaObjects.ExternalEntity'

  1  """ 
  2      BIANA: Biologic Interactions and Network Analysis 
  3      Copyright (C) 2009  Javier Garcia-Garcia, Emre Guney, Baldo Oliva 
  4   
  5      This program is free software: you can redistribute it and/or modify 
  6      it under the terms of the GNU General Public License as published by 
  7      the Free Software Foundation, either version 3 of the License, or 
  8      (at your option) any later version. 
  9   
 10      This program is distributed in the hope that it will be useful, 
 11      but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
 13      GNU General Public License for more details. 
 14   
 15      You should have received a copy of the GNU General Public License 
 16      along with this program.  If not, see <http://www.gnu.org/licenses/>. 
 17   
 18  """ 
 19   
 20  import sys 
 21  import sets 
 22  import biana.biana_globals as BIANA_GLOBALS 
 23   
 24   
 25 -class ExternalEntity(object): 
 26      """ 
 27      This general object represents an entry in an external database 
 28   
 29      It can contain several attributes. 
 30      """ 
 31   
 32      # to remove 
 33      PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT = dict(BIANA_GLOBALS.PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT) 
 34   
 35   
 36 -    def __init__(self, source_database, type, id=None): 
 37          """ 
 38          "source_database" is the source database id wbere this entity is described 
 39   
 40          "type" indicates the type of externalEntity.It can be: 
 41                                'protein','gene','protein alignment','cluster','structure, SCOPElement' 
 42   
 43          "id" is the UNIQUE identifier in the database for this external entity 
 44          """ 
 45   
 46          type = type.lower() 
 47   
 48          self.id = id           # This value will be "None" if still not inserted in the database. It has been inserted in the database, it MUST be a numeric value 
 49          self.attributes = {} 
 50          self.sourceDatabase = source_database 
 51          self.type = type 
 52   
 53          return 
 54   
 55   
 56 -    def __str__(self): 
 57           
 58          string = "External Entity ID: %s\n" %self.id 
 59           
 60          for current_attribute in self.attributes: 
 61              string += "%s:\n\t%s\n" %(current_attribute, "\t".join(map(str,self.attributes[current_attribute]))) 
 62   
 63          #print string 
 64          return string 
 65   
 66   
 67   
 68 -    def __eq__(self, other): 
 69   
 70          return self.id==other.id 
 71   
 72   
 73   
 74 -    def get_id(self): 
 75          """ 
 76          Gets the UNIQUE identifier 
 77          """ 
 78          return self.id 
 79   
 80   
 81   
 82 -    def get_source_database(self): 
 83          """ 
 84          Gets the ExternalDatabase Object where this externalEntity is contained 
 85          """ 
 86          return self.sourceDatabase 
 87   
 88   
 89   
 90 -    def get_type(self): 
 91          """ 
 92          Gets a string representing the type of this externalEntity 
 93          """ 
 94          return self.type 
 95   
 96   
 97   
 98 -    def set_id(self, id_value): 
 99          if self.id is None: 
100              self.id = id_value 
101          else: 
102              raise ValueError("Cannot change identifier from externalEntity") 
103   
104   
105   
106 -    def add_attribute(self, externalEntityAttribute): 
107          """ 
108          Adds an attribute to this ExternalEntity Object 
109           
110          "externalEntityAttribute": A valid externalEntityAttribute Object. It cannot contain value None as its value 
111          """ 
112           
113          if externalEntityAttribute.value is None: 
114              sys.stderr.write("Attribute %s not added because it has None value\n" %(externalEntityAttribute.attribute_identifier)) 
115              return 
116   
117          self.attributes.setdefault(externalEntityAttribute.attribute_identifier.lower(),sets.Set([])).add(externalEntityAttribute) 
118   
119   
120   
121 -    def get_attribute(self, attribute_identifier): 
122          """ 
123          Returns a SET with the externalEntityAttribute objects corresponding to the attribute_identifier associated to this externalEntity. 
124   
125          If the externalEntity object does not contain any attribute of "attribute_identifier" type, it returns an empty list 
126          """ 
127   
128          try: 
129              return self.attributes[attribute_identifier.lower()] 
130          except KeyError: 
131              return sets.Set() 
132   
133           
134 -    def get_attributes_dict(self): 
135          """ 
136          Returns a dictionary with all the ExternalEntityAttributes associated to this externalEntity. 
137   
138          Keys correspond to "attribute_identifier" and values to a Set with all external entity objects 
139          """ 
140          return self.attributes 
141   
142   
143   
144 -    def isValidType(type, biana_database): 
145   
146          return type.lower() in biana_database.VALID_EXTERNAL_ENTITY_TYPES_DICT 
147   
148      isValidType = staticmethod(isValidType) 
149   
150   
151   
152 -    def get_valid_external_entity_types(biana_database): 
153           
154          return biana_database.VALID_EXTERNAL_ENTITY_TYPES_DICT.values() 
155   
156      get_valid_external_entity_types = staticmethod(get_valid_external_entity_types) 
157