Merge branch 'feature/Remove_postgres_from_docker-compose' into 'develop'

Feature/remove postgres from docker compose

See merge request VR-Group/in-situ-pipeline/access-node!5

access_node/__main__.py

@@ -16,126 +16,20 @@ def ConnectToDatabase(postgres_username, postgres_password, port):
 	return psycopg2.connect(database="postgres", user=postgres_username,
                        password=postgres_password, host="database", port=str(port))
 
-def SetupNestTables(postgres_username, postgres_password, port):
-	con = ConnectToDatabase(postgres_username, postgres_password, port)
-	print("Database connection opened successfully!")
-
-	cur = con.cursor()
-	cur.execute("DROP TABLE IF EXISTS nest_simulation_node CASCADE")
-	cur.execute("DROP TABLE IF EXISTS nest_multimeter CASCADE")
-	cur.execute("DROP TABLE IF EXISTS nest_neuron CASCADE")
-	cur.execute("DROP TABLE IF EXISTS nest_neuron_multimeter CASCADE")
-
-
-	cur.execute('''
-	  CREATE TABLE nest_simulation_node (
-        id                      SERIAL PRIMARY KEY NOT NULL UNIQUE,
-        address                 VARCHAR(50),
-        current_simulation_time FLOAT
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE nest_multimeter (
-        id         INT PRIMARY KEY NOT NULL UNIQUE,
-        attributes VARCHAR(50) ARRAY
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE nest_neuron (
-        id                 INT PRIMARY KEY NOT NULL UNIQUE,
-        simulation_node_id INT,  
-        population_id      INT,
-		position           FLOAT[],
-        FOREIGN KEY (simulation_node_id) REFERENCES nest_simulation_node (id)
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE nest_neuron_multimeter (
-        neuron_id     INT NOT NULL,
-        multimeter_id INT NOT NULL,
-        PRIMARY KEY (neuron_id,multimeter_id),
-        FOREIGN KEY (neuron_id) REFERENCES nest_neuron (id),
-        FOREIGN KEY (multimeter_id) REFERENCES nest_multimeter (id)
-	  );''')
-
-	con.commit()
-	con.close()
-	print("Nest tables created successfully!\n")
-
-def SetupArborTables(postgres_username, postgres_password, port):
-	con = ConnectToDatabase(postgres_username, postgres_password, port)
-	print("Database connection opened successfully!")
-	cur = con.cursor()
-	cur.execute("DROP TABLE IF EXISTS arbor_probe CASCADE")
-	cur.execute("DROP TABLE IF EXISTS arbor_cell CASCADE")
-	cur.execute("DROP TABLE IF EXISTS arbor_simulation_node CASCADE")
-	cur.execute("DROP TABLE IF EXISTS arbor_attribute CASCADE")
-
-	cur.execute('''
-	  CREATE TABLE arbor_simulation_node (
-        id                       INT PRIMARY KEY NOT NULL UNIQUE,
-        address                  VARCHAR(50),
-        current_simulation_time  FLOAT
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE arbor_cell (
-        id INT PRIMARY KEY NOT NULL UNIQUE
-	  );
-	  ''')
-
-	cur.execute('''
-	  CREATE TABLE cell_property (
-        cell_id  INT NOT NULL,
-		property VARCHAR(50) NOT NULL,
-		PRIMARY KEY (cell_id, property),
-		FOREIGN KEY (cell_id) REFERENCES arbor_cell (id),
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE arbor_attribute (
-        id   INT PRIMARY KEY NOT NULL UNIQUE,
-        name VARCHAR(50) NOT NULL,
-	  );''')
-
-	cur.execute('''
-	  CREATE TABLE arbor_probe (
-        id                 INT PRIMARY KEY NOT NULL UNIQUE,
-        cell_id            INT NOT NULL,  
-        segment_id 		   INT NOT NULL,
-		position   		   FLOAT,
-		attribute_id	   INT NOT NULL,
-		simulation_node_id INT,
-        FOREIGN KEY (simulation_node_id) REFERENCES arbor_simulation_node (id),
-		FOREIGN KEY (cell_id) REFERENCES arbor_cell (id),
-		FOREIGN KEY (attribute_id) REFERENCES arbor_attribute (id)
-	  );''')
-
-	
-
-	con.commit()
-	con.close()
-	print("Arbor tables created successfully!\n")
-
 
 def main():
-	# Connect to the Database and initalize basic Table structure
-	SetupNestTables('postgres', 'docker', 5432)
-	#SetupArborTables('postgres', 'docker', 5432)
-
 	# Wait for simulation nodes to post to database
 	time.sleep(5)
 
-
 	# get simulation nodes
-	con = ConnectToDatabase('postgres', 'docker', 5432)
+	con = ConnectToDatabase('postgres', 'postgres', 5432)
 	cur = con.cursor()
 	# NEST
 	cur.execute("SELECT address FROM nest_simulation_node")
 	nodes.nest_simulation_nodes = [i[0] for i in cur.fetchall()]
 	# Arbor
-	#cur.execute("SELECT address FROM nest_simulation_node")
-	#nodes.nest_simulation_nodes = [i[0] for i in cur.fetchall()]
+	cur.execute("SELECT address FROM nest_simulation_node")
+	nodes.arbor_simulation_nodes = [i[0] for i in cur.fetchall()]
 	con.close()
 
 

access_node/controllers/arbor_controller.py

@@ -16,7 +16,7 @@ import numpy as np
 
 def connect_to_database():
     return psycopg2.connect(database="postgres", user="postgres",
-                       password="docker", host="database", port="5432")
+                       password="postgres", host="database", port="5432")
 
 
 def arbor_get_attributes():  # noqa: E501

access_node/controllers/nest_controller.py

@@ -16,7 +16,7 @@ import numpy as np
 
 def connect_to_database():
     return psycopg2.connect(database="postgres", user="postgres",
-                       password="docker", host="database", port="5432")
+                       password="postgres", host="database", port="5432")
 
 
 def nest_get_gids():  # noqa: E501
@@ -304,7 +304,7 @@ def nest_get_spikes_by_population(population_id, _from=None, to=None, offset=Non
     spikes = Spikes([], [])
     for node in nodes.nest_simulation_nodes:
         response = requests.get(
-            node+'/population/'+population_id+'/spikes', params={"from": _from, "to": to}).json()
+            node+'/population/$'+str(population_id)+'/spikes', params={"from": _from, "to": to}).json()
         for x in range(len(response['simulation_times'])):
             spikes.simulation_times.append(response['simulation_times'][x])
             spikes.gids.append(response['gids'][x])