allows config.txt to specify path to umls_tables

cliner/features_dir/umls_dir/create_sqliteDB.py

@@ -4,34 +4,46 @@
 import sys
 import os
 
+features_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+if features_dir not in sys.path:
+    sys.path.append(features_dir)
+
+
+# find where umls tables are located
+from read_config import enabled_modules
+enabled = enabled_modules()
+umls_tables = enabled['UMLS']
+
+
+
 def create_db():
 
     print "\ncreating umls.db"
     #connect to the .db file we are creating.
-    db_path = os.path.join(os.environ['CLINER_DIR'],'umls_tables/umls.db')
+    db_path = os.path.join(umls_tables, 'umls.db')
     conn = sqlite3.connect( db_path )
     conn.text_factory = str
 
     print "opening files"
     #load data in files.
     try:
-        mrsty_path = os.path.join(os.environ['CLINER_DIR'],'umls_tables/MRSTY.RRF')
+        mrsty_path = os.path.join(umls_tables, 'MRSTY.RRF')
         MRSTY_TABLE_FILE = open( mrsty_path, "r" )
     except IOError:
         print "\nNo file to use for creating MRSTY.RRF table\n"
         conn.close()
         sys.exit()
 
     try:
-        mrcon_path = os.path.join(os.environ['CLINER_DIR'],'umls_tables/MRCONSO.RRF')
+        mrcon_path = os.path.join(umls_tables, 'MRCONSO.RRF')
         MRCON_TABLE_FILE = open( mrcon_path , "r" )
     except IOError:
         print "\nNo file to use for creating MRCONSO.RRF table\n"
         conn.close()
         sys.exit()
 
     try:
-        mrrel_path = os.path.join(os.environ['CLINER_DIR'],'umls_tables/MRREL.RRF')
+        mrrel_path = os.path.join(umls_tables, 'MRREL.RRF')
         MRREL_TABLE_FILE = open( mrrel_path , "r" )
     except IOError:
         print "\nNo file to use for creating MRREL.RRF table\n"

cliner/features_dir/umls_dir/create_trie.py

@@ -3,6 +3,17 @@
 import sys
 import os
 
+features_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+if features_dir not in sys.path:
+    sys.path.append(features_dir)
+
+# find where umls tables are located
+from read_config import enabled_modules
+enabled = enabled_modules()
+umls_tables = enabled['UMLS']
+
+
+
 def create_trie():
 
     """
@@ -12,16 +23,11 @@ def create_trie():
 
     @return  A trie object
     """
-
     # Is trie already built & pickled?
-    prefix = os.environ['CLINER_DIR']
-    filename = os.path.join( prefix, 'umls_tables/umls-concept.trie' )
+    filename = os.path.join(umls_tables, 'umls-concept.trie')
     try:
-
         t = marisa_trie.Trie().load(filename)
-
         return t
-
     except IOError:
         pass
 
@@ -31,7 +37,7 @@ def create_trie():
     #load data in files.
     print "opening file"
     try:
-        mrcon_path = os.path.join(os.environ['CLINER_DIR'],'umls_tables/MRCONSO.RRF')
+        mrcon_path = os.path.join(umls_tables, 'MRCONSO.RRF')
         MRCON_TABLE = open( mrcon_path , "r" )
     except IOError:
         print "\nNo file to use for creating MRCON table\n"

cliner/features_dir/umls_dir/interface_umls.py

@@ -9,10 +9,22 @@
 import sqlite3
 import create_sqliteDB
 import os
+import sys
 
 import create_trie
 
 
+features_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+if features_dir not in sys.path:
+    sys.path.append(features_dir)
+
+
+# find where umls tables are located
+from read_config import enabled_modules
+enabled = enabled_modules()
+umls_tables = enabled['UMLS']
+
+
 
 
 ############################################
@@ -23,12 +35,10 @@
 #connect to UMLS database
 def SQLConnect():
     #try to connect to the sqlite database.
-    db_path = os.path.join( os.environ['CLINER_DIR'], "umls_tables/umls.db")
-    if( os.path.isfile( db_path ) ):
-        print "\ndb exists"
-    else:
-        # Database does not exit. Make one.
-        print "\ndb doesn't exist"
+    # if database does not exit. Make one.
+    db_path = os.path.join(umls_tables, "umls.db")
+    if not os.path.isfile(db_path):
+        print "\n\tdb doesn't exist (creating one now)\n"
         create_sqliteDB.create_db()
 
     db = sqlite3.connect( db_path )

cliner/features_dir/umls_dir/umls_cache.py

@@ -2,29 +2,47 @@
 import sys
 import os
 
-sys.path.append((os.environ["CLINER_DIR"] + "/cliner/features_dir"))
+import atexit
+
+
+features_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+if features_dir not in sys.path:
+    sys.path.append(features_dir)
+
+# find where umls tables are located
+from read_config import enabled_modules
+enabled = enabled_modules()
+umls_tables = enabled['UMLS']
+
 
+sys.path.append((os.environ["CLINER_DIR"] + "/cliner/features_dir"))
 from utilities import load_pickled_obj
 
+
 class UmlsCache:
+
+    # static class variables
+    filename = None
+    cache = None
+
     def __init__(self):
         try:
-            prefix = os.environ['CLINER_DIR']
-            self.filename = os.path.join( prefix, 'umls_tables/umls_cache' )
-
-            self.cache = load_pickled_obj(self.filename)
+            UmlsCache.filename = os.path.join(umls_tables, 'umls_cache')
+            UmlsCache.cache = load_pickled_obj(UmlsCache.filename)
 
         except IOError:
-            self.cache = {}
+            UmlsCache.cache = {}
 
-    def has_key( self , string ):
-        return self.cache.has_key( string )
+    def has_key(self , string):
+        return UmlsCache.cache.has_key( string )
 
-    def add_map( self , string, mapping ):
-        self.cache[string] = mapping
+    def add_map(self , string, mapping):
+        UmlsCache.cache[string] = mapping
 
-    def get_map( self , string ):
-        return self.cache[string]
+    def get_map(self , string):
+        return UmlsCache.cache[string]
 
-    def __del__(self):
-        pickle.dump( self.cache, open( self.filename, "wb" ) )
+    @staticmethod
+    @atexit.register
+    def destructor():
+        pickle.dump(UmlsCache.cache, open(UmlsCache.filename,"wb"))