diff --git a/access_node/__main__.py b/access_node/__main__.py
index b701c9fd1784a4b2b5746d6d2637d087e4d12fe1..39dfd78630800656f150cabfcd7b98e173cd13b2 100644
--- a/access_node/__main__.py
+++ b/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()
diff --git a/access_node/controllers/arbor_controller.py b/access_node/controllers/arbor_controller.py
index 4b8115a2c70cbc7f269f31510a1b33ee4e1086e1..00a4ac4273c0d12a9f829bac53b3cb61d930e19a 100644
--- a/access_node/controllers/arbor_controller.py
+++ b/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
diff --git a/access_node/controllers/nest_controller.py b/access_node/controllers/nest_controller.py
index c183e09d07f6a4e42f0b3015895ce44fec5ea9c6..ffd4aa0e8f52a0839f13f043f09597eef52261c1 100644
--- a/access_node/controllers/nest_controller.py
+++ b/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])