ecoscape-utilities 0.0.37__tar.gz → 0.0.39__tar.gz

{ecoscape_utilities-0.0.37 → ecoscape_utilities-0.0.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ecoscape-utilities
-Version: 0.0.37
+Version: 0.0.39
 Summary: A collection of EcoScape utilities.
 Author-email: Luca de Alfaro <luca@ucsc.edu>, Coen Adler <ctadler@ucsc.edu>, Artie Nazarov <anazarov@ucsc.edu>, Natalia Ocampo-Peñuela <nocampop@ucsc.edu>, Jasmine Tai <cjtai@ucsc.edu>, Natalie Valett <nvalett@ucsc.edu>
 Project-URL: Homepage, https://github.com/ecoscape-earth/ecoscape-utilities

{ecoscape_utilities-0.0.37 → ecoscape_utilities-0.0.39}/ecoscape_utilities/ebird_db.py

@@ -11,6 +11,34 @@ from pyproj.crs import CRS
 
 from scgt import GeoTiff
 
+def expand_sqlite_query(query, params):
+    """
+    Expands an SQLite query string with named parameters from a dictionary.
+
+    Args:
+        query (str): The SQL query string with :variable placeholders.
+        params (dict): A dictionary mapping variable names to their values.
+
+    Returns:
+        str: The expanded SQL query string.
+    """
+    expanded_query = query
+    for key, value in params.items():
+        placeholder = f":{key}"
+        if isinstance(value, str):
+            # Escape any single quotes within the string
+            formatted_value = f"'{value.replace("'", "''")}'"
+        elif value is None:
+            formatted_value = 'NULL'
+        else:
+            # For integers, floats, and other types
+            formatted_value = str(value)
+        
+        expanded_query = expanded_query.replace(placeholder, formatted_value)
+        
+    return expanded_query
+    
+    
 """
 A module for interaction with a sqlite database. Contains functions for query execution, 
 and some common functionality we need to run on the DB
@@ -120,6 +148,7 @@ class EbirdObservations(Connection):
         query_string = " ".join(query_string)
         if verbose:
             print("Query:", query_string)
+            print("Expanded query:", expand_sqlite_query(query_string, d))
         squares_list = self.execute_query((query_string, d))
         return [sq[0] for sq in squares_list]
 
@@ -197,10 +226,13 @@ class EbirdObservations(Connection):
         # Adds breeding portion
         if breeding is not None:
             query_string.extend([
-                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
-                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
+                'and substr(checklist."OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr(checklist."OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
             d['br1'], d['br2'] = breeding
+        if min_time is not None:
+            query_string.append('and "checklist.DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
@@ -220,6 +252,7 @@ class EbirdObservations(Connection):
         query_string = " ".join(query_string)
         if verbose:
             print("Query:", query_string)
+            print("Expanded query:", expand_sqlite_query(query_string, d))
         r = self.execute_query((query_string, d))
         if r is None:
             num_birds = 0
@@ -237,7 +270,7 @@ class EbirdObservations(Connection):
         )
 
     def get_square_individual_checklists(self, square, bird,
-                          breeding=None, date_range=None,
+                          breeding=None, date_range=None, min_time=None,
                           lat_range=None, lng_range=None, max_dist=2,
                           verbose=False):
         """
@@ -270,6 +303,9 @@ class EbirdObservations(Connection):
                 'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
             d['br1'], d['br2'] = breeding
+        if min_time is not None:
+            query_string.append('and "DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         if date_range is not None:
             query_string.append('and "OBSERVATION DATE" >= :min_date')
             query_string.append('and "OBSERVATION DATE" <= :max_date')
@@ -301,14 +337,17 @@ class EbirdObservations(Connection):
         # Adds breeding portion
         if breeding is not None:
             query_string.extend([
-                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
-                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
+                'and substr(checklist."OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr(checklist."OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
             d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
             d["min_date"], d["max_date"] = date_range
+        if min_time is not None:
+            query_string.append('and checklist."DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         if lat_range is not None:
             query_string.append('and checklist."LATITUDE" >= :min_lat')
             query_string.append('and checklist."LATITUDE" <= :max_lat')
@@ -324,6 +363,7 @@ class EbirdObservations(Connection):
         query_string = " ".join(query_string)
         if verbose:
             print("Query:", query_string)
+            print("Expanded query:", expand_sqlite_query(query_string, d))
         rows = self.execute_query((query_string, d))
         counts = defaultdict(int)
         for r in rows:
@@ -331,7 +371,7 @@ class EbirdObservations(Connection):
         checklists_df["Count"] = checklists_df.apply(lambda row : counts[row["SAMPLING EVENT IDENTIFIER"]], axis=1)
         return checklists_df
 
-    def get_squares_with_bird(self, bird, max_dist=1, breeding=None,
+    def get_squares_with_bird(self, bird, max_dist=1, breeding=None, min_time=None,
                               date_range=None, lat_range=None, lng_range=None,
                               state=None, verbose=False):
         """Gets all the squares where a bird has been sighted.  This is used
@@ -364,6 +404,9 @@ class EbirdObservations(Connection):
                 'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
             d['br1'], d['br2'] = breeding
+        if min_time is not None:
+            query_string.append('and "DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
@@ -380,6 +423,7 @@ class EbirdObservations(Connection):
         query_string = " ".join(query_string)
         if verbose:
             print("Query:", query_string)
+            print("Expanded query:", expand_sqlite_query(query_string, d))
         r = self.execute_query((query_string, d))
         return [row[0] for row in r]
 

{ecoscape_utilities-0.0.37 → ecoscape_utilities-0.0.39}/ecoscape_utilities.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ecoscape-utilities
-Version: 0.0.37
+Version: 0.0.39
 Summary: A collection of EcoScape utilities.
 Author-email: Luca de Alfaro <luca@ucsc.edu>, Coen Adler <ctadler@ucsc.edu>, Artie Nazarov <anazarov@ucsc.edu>, Natalia Ocampo-Peñuela <nocampop@ucsc.edu>, Jasmine Tai <cjtai@ucsc.edu>, Natalie Valett <nvalett@ucsc.edu>
 Project-URL: Homepage, https://github.com/ecoscape-earth/ecoscape-utilities

{ecoscape_utilities-0.0.37 → ecoscape_utilities-0.0.39}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ecoscape-utilities"
-version = "0.0.37"
+version = "0.0.39"
 authors = [
   {name="Luca de Alfaro", email="luca@ucsc.edu"},
   {name="Coen Adler", email="ctadler@ucsc.edu"},