Merge branch 'Nature' of https://github.com/neurosynth/ACE into Nature

Author: adelavega

ace/database.py

@@ -210,10 +210,12 @@ class Activation(Base):
     p_value = Column(String(100))
 
     missing_source = Column(Boolean, default=False)
+    is_valid = Column(Boolean, default=True)  # Added to track validation status
 
     def __init__(self):
         self.problems = []
         self.columns = {}
+        self.is_valid = True
 
     def set_coords(self, x, y, z):
         new_xyz = []
@@ -238,29 +240,30 @@ def add_col(self, key, val):
     # Depending on config, either excludes peak, or allows it through
     # but flags potential problems for later inspection.
     def validate(self):
+        valid = True
 
         for c in [self.x, self.y, self.z]:
             if c == '' or c is None:
-                logger.debug('Missing x, y, or z coordinate information: [%s, %s, %s]' % tuple(
-                    [str(e) for e in [self.x, self.y, self.z]]))
-                return False
+                msg = 'Missing x, y, or z coordinate information: [%s, %s, %s]'
+                logger.debug(msg % tuple([str(e) for e in [self.x, self.y, self.z]]))
+                valid = False
+                break
             try:
                 if abs(c) >= 100:
-                    logger.debug(
-                        'Invalid coordinates: at least one dimension (x,y,z) >= 100.')
-                    return False
-            except:
-                print(c)
-                print(sys.exc_info()[0])
+                    logger.debug('Invalid coordinates: at least one dimension (x,y,z) >= 100.')
+                    valid = False
+                    break
+            except Exception as ex:
+                logger.error("Error validating coordinate: %s" % str(ex))
                 raise
 
-        sorted_xyz = sorted([abs(self.x), abs(self.y), abs(self.z)])
-        if sorted_xyz[0] == 0 and sorted_xyz[1] == 0:
-            logger.debug(
-                "At least two dimensions have value == 0; coordinate is probably not real.")
-            return False
+        if valid:
+            sorted_xyz = sorted([abs(self.x), abs(self.y), abs(self.z)])
+            if sorted_xyz[0] == 0 and sorted_xyz[1] == 0:
+                logger.debug("At least two dimensions have value 0; coordinate is probably not real.")
+                valid = False
 
-        return True
+        self.is_valid = valid
 
 class NeurovaultLink(Base):