Source Code for Module biana.BianaObjects.ExternalDatabase'

  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 time 
 21  import sets 
 22   
 23   
 24 -class ExternalDatabase(object): 
 25      """ 
 26      Class to represent an external database (any database giving biologic relevant information) 
 27      """ 
 28   
 29   
 30 -    def __init__(self, databaseName, databaseVersion, databaseFile, databaseDescription, defaultExternalEntityAttribute, databaseDate=None, externalDatabaseID=None, isPromiscuous=False): 
 31          """ 
 32          Initializes a ExternalDatabase Object 
 33   
 34          "databaseName" is the name for the external database (i.e. swissprot, IntAct, Reactome...) 
 35           
 36          "datavaseVersion" is the version of the database. The combination of databaseName and databaseVersion must be unique! 
 37   
 38          "databaseFile" is the parsed database file. If there are multiple files, it is an empty string 
 39   
 40          "databaseDescription" is a longer description of the database (for example, "public repository of interactions of ncbi", etc.) 
 41   
 42          "externalDatabaseID" is a unique identifier for the database. When parsing it should not be added, only when this information is persistent in the database 
 43   
 44          "defaultExternalEntityAttribute" is the default attribute type of the data an external database is providing 
 45   
 46          "databaseDate" Parsing date. If it is None, automatically assigns to current date to it 
 47          "isPromiscuous" Flag deciding whether database gives information that is going to be added to more than one user entiries 
 48          """ 
 49   
 50          self.databaseName = databaseName.lower() 
 51          self.databaseVersion = databaseVersion.lower() 
 52          self.databaseFile = databaseFile 
 53          self.databaseDescription = databaseDescription 
 54          self.defaultExternalEntityAttribute = defaultExternalEntityAttribute  
 55          self.isPromiscuous = isPromiscuous 
 56   
 57          self.externalDatabaseID = externalDatabaseID         # Only it is setted to a value when it is inserted or loaded from the database. If it is not loaded, it is None 
 58   
 59          if( databaseDate is None ): 
 60              date = time.localtime() 
 61              actual_date = "%s-%s-%s" %(date[0],date[1],date[2]) 
 62              self.databaseDate = actual_date 
 63          else: 
 64              self.databaseDate = databaseDate 
 65   
 66          self.valid_eE_attributes = sets.Set() 
 67          self.valid_eEr_attributes = sets.Set() 
 68          self.valid_eE_types = sets.Set() 
 69          self.valid_eEr_types = sets.Set() 
 70   
 71          self.parsing_time = None   # Parsing time is set to None by default 
 72   
 73 -    def add_valid_external_entity_attribute_type(self, attribute_identifier): 
 74          self.valid_eE_attributes.add(attribute_identifier.lower()) 
 75   
 76 -    def add_valid_external_entity_relation_attribute_type(self, attribute_identifier): 
 77          self.valid_eEr_attributes.add(attribute_identifier.lower()) 
 78   
 79 -    def add_valid_external_entity_type(self, eE_type): 
 80          self.valid_eE_types.add(eE_type.lower()) 
 81   
 82 -    def add_valid_external_entity_relation_type(self, eEr_type): 
 83          self.valid_eEr_types.add(eEr_type.lower()) 
 84   
 85 -    def get_valid_external_entity_attribute_type(self): 
 86          return self.valid_eE_attributes 
 87   
 88 -    def get_valid_external_entity_relation_attribute_type(self): 
 89          return self.valid_eEr_attributes 
 90   
 91 -    def get_valid_external_entity_type(self): 
 92          return self.valid_eE_types 
 93   
 94 -    def has_external_entity_type(self, eE_type): 
 95          """ 
 96          Checks if this external database contains external entities of the type "eE_type" 
 97          """ 
 98          return self.valid_eE_types.has_key(eE_type) 
 99   
100 -    def get_valid_external_entity_relation_type(self): 
101          return self.valid_eEr_types 
102   
103 -    def get_name(self): 
104          return self.databaseName 
105   
106 -    def get_version(self): 
107          return self.databaseVersion 
108   
109 -    def get_parsed_file(self): 
110          return self.databaseFile 
111   
112 -    def get_parsing_date(self): 
113          return self.databaseDate 
114   
115 -    def get_description(self): 
116          return self.databaseDescription 
117   
118 -    def get_default_eE_attribute(self): 
119          return self.defaultExternalEntityAttribute 
120   
121 -    def get_id(self): 
122          return self.externalDatabaseID 
123   
124 -    def set_id(self, externalDatabaseID): 
125          self.externalDatabaseID = externalDatabaseID 
126   
127 -    def set_parsing_time(self, time): 
128          self.parsing_time = time 
129   
130 -    def get_parsing_time(self): 
131          return self.parsing_time 
132   
133 -    def get_promiscuity(self): 
134          return self.isPromiscuous 
135   
136 -    def __str__(self): 
137          return "%s [%s]" %(self.databaseName,self.databaseVersion) 
138