diff --git a/access_node/__main__.py b/access_node/__main__.py
index 932a1d48aa9a43c6be843514622a5b9a1878daa9..9a7c5679c74b45fb99f73276b283e2e74fac2ce7 100644
--- a/access_node/__main__.py
+++ b/access_node/__main__.py
@@ -21,33 +21,41 @@ def SetupNestTables(postgres_username, postgres_password, port):
print("Database connection opened successfully!")
cur = con.cursor()
- cur.execute("DROP TABLE IF EXISTS SIMULATION_NODES CASCADE")
- cur.execute("DROP TABLE IF EXISTS MULTIMETERS CASCADE")
- cur.execute("DROP TABLE IF EXISTS GIDS CASCADE")
- cur.execute("DROP TABLE IF EXISTS MULT_PER_GID CASCADE")
-
-
- cur.execute('''CREATE TABLE SIMULATION_NODES (
- NODE_ID SERIAL PRIMARY KEY NOT NULL UNIQUE,
- ADDRESS VARCHAR(50),
- CURRENT_SIM_TIME FLOAT);''')
-
- cur.execute('''CREATE TABLE MULTIMETERS (
- MULTIMETER_ID INT PRIMARY KEY NOT NULL UNIQUE,
- ATTRIBUTE VARCHAR(50) );''')
-
- cur.execute('''CREATE TABLE GIDS (
- GID INT PRIMARY KEY NOT NULL UNIQUE,
- NODE_ID INT,
- POPULATION_ID INT,
- FOREIGN KEY (NODE_ID) REFERENCES SIMULATION_NODES (NODE_ID));''')
-
- cur.execute('''CREATE TABLE MULT_PER_GID(
- GID INT NOT NULL,
- MULTIMETER_ID INT NOT NULL,
- PRIMARY KEY (GID,MULTIMETER_ID),
- FOREIGN KEY (GID) REFERENCES GIDS (GID),
- FOREIGN KEY (MULTIMETER_ID) REFERENCES MULTIMETERS (MULTIMETER_ID));''')
+ 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,
+ attribute VARCHAR(50)
+ );''')
+
+ cur.execute('''
+ CREATE TABLE nest_neuron (
+ id INT PRIMARY KEY NOT NULL UNIQUE,
+ simulation_node_id INT,
+ population_id INT,
+ 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()
@@ -57,42 +65,50 @@ 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 PROBES CASCADE")
- cur.execute("DROP TABLE IF EXISTS CELLS CASCADE")
- cur.execute("DROP TABLE IF EXISTS ARBOR_SIMULATION_NODES CASCADE")
- cur.execute("DROP TABLE IF EXISTS ATTRIBUTES CASCADE")
-
- cur.execute('''CREATE TABLE ARBOR_SIMULATION_NODES (
- NODE_ID INT PRIMARY KEY NOT NULL UNIQUE,
- ADDRESS VARCHAR(50),
- CURRENT_SIM_TIME FLOAT);''')
-
- cur.execute('''CREATE TABLE CELLS (
- CELL_ID INT PRIMARY KEY NOT NULL UNIQUE
- );''')
-
- cur.execute('''CREATE TABLE CELL_PROPERTIES (
- CELL_ID INT NOT NULL,
- PROPERTY VARCHAR(50) NOT NULL,
- PRIMARY KEY (CELL_ID, PROPERTY),
- FOREIGN KEY (CELL_ID) REFERENCES CELLS (CELL_ID),
- );''')
-
- cur.execute('''CREATE TABLE ATTRIBUTES (
- ATTRIBUTE_ID INT PRIMARY KEY NOT NULL UNIQUE,
- NAME VARCHAR(50) NOT NULL,
- );''')
-
- cur.execute('''CREATE TABLE PROBES (
- 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,
- NODE_ID INT,
- FOREIGN KEY (NODE_ID) REFERENCES ARBOR_SIMULATION_NODES (NODE_ID),
- FOREIGN KEY (CELL_ID) REFERENCES CELLS (CELL_ID),
- FOREIGN KEY (ATTRIBUTE_ID) REFERENCES ATTRIBUTES (ATTRIBUTE_ID));''')
+ 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)
+ );''')
@@ -114,10 +130,10 @@ def main():
con = ConnectToDatabase('postgres', 'docker', 5432)
cur = con.cursor()
# NEST
- cur.execute("SELECT ADDRESS FROM SIMULATION_NODES")
+ 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 SIMULATION_NODES")
+ #cur.execute("SELECT address FROM nest_simulation_node")
#nodes.nest_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 4a74cee84c871a0ae1ad2d987a0b649b4bb5baed..4b8115a2c70cbc7f269f31510a1b33ee4e1086e1 100644
--- a/access_node/controllers/arbor_controller.py
+++ b/access_node/controllers/arbor_controller.py
@@ -30,7 +30,7 @@ def arbor_get_attributes(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT NAME FROM ATTRIBUTES")
+ cur.execute("SELECT name FROM arbor_attribute")
attributes = [i[0] for i in cur.fetchall()]
con.close()
@@ -48,7 +48,7 @@ def arbor_get_cell_ids(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT CELL_ID FROM CELLS")
+ cur.execute("SELECT id FROM arbor_cell")
cell_ids = [i[0] for i in cur.fetchall()]
con.close()
@@ -69,9 +69,9 @@ def arbor_get_cell_properties(cell_ids=None): # noqa: E501
cur = con.cursor()
if cell_ids == None:
- cur.execute("SELECT CELL_ID, PROPERTY FROM CELL_PROPERTIES")
+ cur.execute("SELECT cell_id, property FROM cell_property")
else:
- cur.execute("SELECT CELL_ID, PROPERTY FROM CELL_PROPERTIES WHERE CELL_PROPERTIES.CELL_ID IN %s", (tuple(cell_ids),))
+ cur.execute("SELECT cell_id, property FROM cell_property WHERE cell_property.cell_id IN %s", (tuple(cell_ids),))
properties = np.array(cur.fetchall())
cell_ids = np.unique(properties[:,0])
@@ -159,20 +159,20 @@ def arbor_get_probes(attribute=None): # noqa: E501
if attribute == None:
cur.execute('''SELECT
- PROBES.PROBE_ID,
- PROBES.CELL_ID,
- PROBES.SEGMENT_ID,
- PROBES.POSITION,
- FROM PROBES''')
+ arbor_probe.id,
+ arbor_probe.cell_id,
+ arbor_probe.segment_id,
+ arbor_probe.position,
+ FROM arbor_probe''')
else:
cur.execute('''SELECT
- PROBES.PROBE_ID,
- PROBES.CELL_ID,
- PROBES.SEGMENT_ID,
- PROBES.POSITION,
- FROM PROBES INNER JOIN ATTRIBUTES
- ON PROBES.ATTRIBUTE_ID = ATTRIBUTES.ATTRIBUTE_ID
- WHERE ATTRIBUTES.NAME = %s''', (attribute,))
+ arbor_probe.id,
+ arbor_probe.cell_id,
+ arbor_probe.segment_id,
+ arbor_probe.position,
+ FROM arbor_probe INNER JOIN arbor_attribute
+ ON arbor_probe.attribute_id = arbor_attribute.id
+ WHERE arbor_attribute.name = %s''', (attribute,))
probes = np.array(cur.fetchall())
con.close()
@@ -191,7 +191,7 @@ def arbor_get_simulation_time_info(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT MIN(CURRENT_SIM_TIME) FROM ARBOR_SIMULATION_NODES")
+ cur.execute("SELECT MIN(current_simulation_time) FROM arbor_simulation_node")
current_time = cur.fetchall()[0][0]
con.close()
diff --git a/access_node/controllers/nest_controller.py b/access_node/controllers/nest_controller.py
index 6b8f1b86214cfad2729719414b6268c0c4a64c15..95a2934df78dd6ddab6aef92f4efe425c2c3c592 100644
--- a/access_node/controllers/nest_controller.py
+++ b/access_node/controllers/nest_controller.py
@@ -30,7 +30,7 @@ def nest_get_gids(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT GID FROM GIDS")
+ cur.execute("SELECT id FROM nest_neuron")
gids = [i[0] for i in cur.fetchall()]
con.close()
@@ -50,7 +50,7 @@ def nest_get_gids_in_population(population_id): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT GID FROM GIDS WHERE GIDS.POPULATION_ID ="+str(population_id))
+ cur.execute("SELECT id FROM nest_neuron WHERE nest_neuron.population_id ="+str(population_id))
gids = [i[0] for i in cur.fetchall()]
con.close()
@@ -68,13 +68,13 @@ def nest_get_multimeter_info(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- ur.execute("SELECT * FROM MULTIMETERS;")
+ ur.execute("SELECT * FROM nest_multimeter;")
attributes = np.array(cur.fetchall())
gids = []
for id in attributes[:,0]:
- cur.execute("SELECT GID FROM MULT_PER_GID WHERE MULTIMETER_ID = %s", (id,))
+ cur.execute("SELECT id FROM nest_neuron_multimeter WHERE id = %s", (id,))
gids.append([i[0] for i in cur.fetchall()])
mult_info = []
@@ -175,15 +175,15 @@ def nest_get_neuron_properties(gids=None): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("Select * FROM GIDS LIMIT 0")
+ cur.execute("Select * FROM nest_neuron LIMIT 0")
colnames = np.array([desc[0] for desc in cur.description])
# column 1 and 2 contain the Node_id/Population_id and thus are removed
colnames = np.delete(colnames, [1,2])
if gids == None:
- cur.execute("Select * FROM GIDS")
+ cur.execute("Select * FROM nest_neuron")
else:
- cur.execute("Select * FROM GIDS WHERE GID IN %s", (tuple(gids),))
+ cur.execute("Select * FROM nest_neuron WHERE id IN %s", (tuple(gids),))
con.close()
@@ -212,7 +212,7 @@ def nest_get_populations(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT DISTINCT (POPULATION_ID) FROM GIDS")
+ cur.execute("SELECT DISTINCT (population_id) FROM nest_neuron")
populations = [i[0] for i in cur.fetchall()]
con.close()
@@ -230,7 +230,7 @@ def nest_get_simulation_time_info(): # noqa: E501
con = connect_to_database()
cur = con.cursor()
- cur.execute("SELECT MIN(CURRENT_SIM_TIME) FROM SIMULATION_NODES")
+ cur.execute("SELECT MIN(current_simulation_time) FROM nest_simulation_node")
current_time = cur.fetchall()[0][0]
con.close()