adding a sql query to get all products and reactants with the reactio…

…n and its type

etc/translate_mcm.py

@@ -1,12 +1,42 @@
 import sqlite3
 import re
+from tabulate import tabulate
+
+counted = """
+WITH ReactantCounts AS (
+    SELECT ReactionID, GROUP_CONCAT(CAST(count AS TEXT) || ' ' || Species) AS ReactantSpecies
+    FROM (
+        SELECT ReactionID, Species, COUNT(*) as count
+        FROM Reactants
+        GROUP BY ReactionID, Species
+    )
+    GROUP BY ReactionID
+),
+ProductCounts AS (
+    SELECT ReactionID, GROUP_CONCAT(CAST(count AS TEXT) || ' ' || Species) AS ProductSpecies
+    FROM (
+        SELECT ReactionID, Species, COUNT(*) as count
+        FROM Products
+        GROUP BY ReactionID, Species
+    )
+    GROUP BY ReactionID
+)
+SELECT r.ReactionID, r.Rate, rates.RateType,
+       rc.ReactantSpecies, pc.ProductSpecies
+FROM Reactions r
+INNER JOIN Rates rates ON r.Rate = rates.Rate
+LEFT JOIN ReactantCounts rc ON r.ReactionID = rc.ReactionID
+LEFT JOIN ProductCounts pc ON r.ReactionID = pc.ReactionID
+WHERE r.Mechanism = 'MCM'
+GROUP BY r.ReactionID, r.Rate, rates.RateType;
+"""
 
 statements = {
-    "number_of_reactions": "SELECT COUNT(DISTINCT ReactioNID) FROM Reactions WHERE Mechanism = 'MCM';",
+    "number_of_reactions": "SELECT COUNT(DISTINCT ReactionID) FROM Reactions WHERE Mechanism = 'MCM';",
     "number_of_rate_constants": "SELECT COUNT(DISTINCT RATE) FROM Reactions INNER JOIN Rates USING(Rate) WHERE Mechanism = 'MCM';",
     "rate_types": "SELECT RateType, COUNT(*) FROM Rates GROUP BY RateType;",
-    "reactions_with_rate_types": "SELECT r.ReactionID, r.Rate, rates.RateType FROM Reactions r INNER JOIN Rates rates ON r.Rate = rates.Rate;",
-    "get_reactants_and_products_per_reaction": "SELECT r.ReactionID, r.Rate, GROUP_CONCAT(reactants.Species, ', ') AS ReactantSpecies, GROUP_CONCAT(products.Species, ', ') AS ProductSpecies FROM Reactions r LEFT JOIN Reactants reactants ON r.ReactionID = reactants.ReactionID LEFT JOIN Products products ON r.ReactionID = products.ReactionID WHERE r.Mechanism = 'MCM' GROUP BY r.ReactionID;"
+    "mcm_reactions_with_rate_type": "SELECT rates.RateType, COUNT(*) FROM Reactions r INNER JOIN Rates rates ON r.Rate = rates.Rate WHERE MEchanism = 'MCM' GROUP BY rates.RateType;",
+    "counted": counted
 }
 
 def get_count(cursor, stmt):
@@ -22,10 +52,19 @@ def get_all(cursor, stmt):
 def translate_mcm():
     conn = sqlite3.connect('data/mcm.db')
     cursor = conn.cursor()
-    print(get_count(cursor, statements["number_of_reactions"]))
-    print(get_count(cursor, statements["number_of_rate_constants"]))
-    print(get_all(cursor, statements["rate_types"]))
-    print(get_all(cursor, statements["reactions_with_rate_types"])[:10])
-    print(get_all(cursor, statements["get_reactants_and_products_per_reaction"])[:10])
+    total_number_of_mcm_reactions = get_count(cursor, statements["number_of_reactions"])
+
+    number_of_rate_types = get_all(cursor, statements["mcm_reactions_with_rate_type"])
+    number_of_rate_types = [(('Null' if rate_type is None else rate_type), count) for rate_type, count in number_of_rate_types]
+    total_number_of_rate_types = sum([x[1] for x in number_of_rate_types])
+
+    assert(total_number_of_mcm_reactions == total_number_of_rate_types)
+    print(tabulate(number_of_rate_types, headers=['Rate Type', 'Count'], tablefmt='github'))
+
+    reactions = get_all(cursor, statements["counted"])
+    assert(len(reactions) == total_number_of_mcm_reactions)
+
+    for reaction in reactions[:15]:
+        print(reaction)
 
 translate_mcm()