updated readme, made read_config check if paths are actually correct

README.rst

@@ -125,6 +125,10 @@ Good luck!
 
     **reference** http://www.nactem.ac.uk/tsujii/GENIA/tagger/
 
+    You must edit the file "$CLINER_DIR/config.txt" and change the line saying "GENIA  None" to "GENIA <path to genia executable>".
+
+    This command will do that: sed -i ``sed -i 's|GENIA.*|GENIA '<path of dir containing genia exe>/geniatagger'|g' $CLINER_DIR/config.txt``
+
 
 (3) UMLS tables
 
@@ -174,7 +178,9 @@ These are resources that require login credentials to access secure data, so we
 
     **Put these tables in the $CLINER_DIR/umls_tables directory.**
 
-    In order to tell CliNER that the tables are there, you must edit the file "$CLINER_DIR/config.txt" and change the line saying "UMLS  None" to "UMLS <path to dir containing tables>". This command will do that ``sed -i "s/UMLS  None/UMLS  example/umls_tables_dir/g" $CLINER_DIR/config.txt``
+    In order to tell CliNER that the tables are there, you must edit the file "$CLINER_DIR/config.txt" and change the line saying "UMLS  None" to "UMLS <path to dir containing tables>".
+
+    This command will do that: ``sed -i 's|UMLS.*|UMLS '<path of dir containing umls tables>'|g' $CLINER_DIR/config.txt``
 
     **The database will be built from the tables when CliNER is run for the first time.**
 

cliner/features_dir/read_config.py

@@ -10,7 +10,7 @@
 
 
 import os
-
+import sys
 
 def enabled_modules():
     """
@@ -42,6 +42,17 @@ def enabled_modules():
                 else:
                     specs[words[0]] = os.path.expandvars(words[1]).strip('\"').strip('\'')
 
+    # check if paths are actually valid
+    if specs["GENIA"] is not None:
+
+        if os.path.isfile(specs["GENIA"]) is False:
+            sys.exit("Invalid path to genia executable.")
+
+    if specs["UMLS"] is not None:
+
+        if os.path.isdir(specs["UMLS"]) is False:
+            sys.exit("Invalid path to directory containing UMLS database tables")
+
     return specs
 
 if __name__ == "__main__":

config.txt

@@ -1,2 +1,3 @@
 GENIA None
-UMLS None
+UMLS  None
+