From d2e5ba1d70d476adbcbf0d7880452780506fc7d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20M=C3=BCller?= <j.mueller@vr.rwth-aachen.de>
Date: Tue, 3 Mar 2020 17:21:28 +0100
Subject: [PATCH] Implement most of NEST Database functionallity
(get_neuron_properties is stil missing)
---
access_node/__main__.py | 14 +++--
access_node/controllers/nest_controller.py | 67 ++++++++++++++++++----
requirements.txt | 3 +-
3 files changed, 69 insertions(+), 15 deletions(-)
diff --git a/access_node/__main__.py b/access_node/__main__.py
index 6ef62f1..4336dd4 100644
--- a/access_node/__main__.py
+++ b/access_node/__main__.py
@@ -18,22 +18,28 @@ def SetupDB(postgres_username, postgres_password, port):
print("Database connection opened successfully!")
cur = con.cursor()
- cur.execute('''CREATE TABLE IF NOT EXISTS SIMULATION_NODES (
+ 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 INT PRIMARY KEY NOT NULL UNIQUE,
ADDRESS VARCHAR(25),
CURRENT_SIM_TIME FLOAT);''')
- cur.execute('''CREATE TABLE IF NOT EXISTS MULTIMETERS (
+ cur.execute('''CREATE TABLE MULTIMETERS (
MULTIMETER_ID INT PRIMARY KEY NOT NULL UNIQUE,
ATTRIBUTE CHAR(50) );''')
- cur.execute('''CREATE TABLE IF NOT EXISTS GIDS (
+ 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 IF NOT EXISTS MULT_PER_GID(
+ cur.execute('''CREATE TABLE MULT_PER_GID(
GID INT NOT NULL,
MULTIMETER_ID INT NOT NULL,
PRIMARY KEY (GID,MULTIMETER_ID),
diff --git a/access_node/controllers/nest_controller.py b/access_node/controllers/nest_controller.py
index 8c5affe..53600ab 100644
--- a/access_node/controllers/nest_controller.py
+++ b/access_node/controllers/nest_controller.py
@@ -10,6 +10,8 @@ from access_node import util
from access_node.models.nodes import nodes
import requests
+import psycopg2
+import numpy as np
def nest_get_gids(): # noqa: E501
"""Retrieves the list of all GID.
@@ -19,7 +21,13 @@ def nest_get_gids(): # noqa: E501
:rtype: List[int]
"""
- gids = requests.get(nodes.info_node+'/nest/gids').json()
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
+ cur = con.cursor()
+ cur.execute("SELECT GID FROM GIDS")
+ gids = [i[0] for i in cur.fetchall()]
+ con.close()
return gids
@@ -33,8 +41,13 @@ def nest_get_gids_in_population(population_id): # noqa: E501
:rtype: List[int]
"""
- gids = requests.get(nodes.info_node+'/nest/population/$' +
- str(population_id)+'/gids').json()
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
+ cur = con.cursor()
+ cur.execute("SELECT GID FROM GIDS WHERE GIDS.POPULATION_ID ="+str(population_id))
+ gids = [i[0] for i in cur.fetchall()]
+ con.close()
return gids
@@ -46,8 +59,24 @@ def nest_get_multimeter_info(): # noqa: E501
:rtype: MultimeterInfo
"""
- multimeter_info = requests.get(nodes.info_node+'/nest/multimeter_info').json()
- return multimeter_info
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+ cur = con.cursor()
+ cur.execute("SELECT MULTIMETER_ID FROM MULTIMETERS")
+ ids = cur.fetchall()
+ cur.execute("SELECT regexp_replace(ATTRIBUTE, '\s+$', '') FROM (SELECT * FROM MULTIMETERS) AS MULT_INFO;")
+ attributes = cur.fetchall()
+ mult_info = np.hstack((ids, attributes)).tolist()
+ gids = []
+ for id in ids:
+ cur.execute("SELECT GID FROM MULT_PER_GID WHERE MULTIMETER_ID = %s", (id,))
+ gids.append([i[0] for i in cur.fetchall()])
+
+ for i in range(len(gids)):
+ mult_info[i].append(gids[i])
+
+ con.close()
+ return mult_info.tolist()
def nest_get_multimeter_measurements(multimeter_id, attribute, _from=None, to=None, gids=None, offset=None, limit=None): # noqa: E501
@@ -134,8 +163,16 @@ def nest_get_neuron_properties(gids=None): # noqa: E501
:rtype: List[NestNeuronProperties]
"""
- properties = requests.get(nodes.info_node+'/nest/neuron_properties').json()
- return properties
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
+ cur = con.cursor()
+ # TODO HANDLE gids=None
+
+
+
+ con.close()
+ return "Not Implemented yet"
def nest_get_populations(): # noqa: E501
@@ -146,7 +183,12 @@ def nest_get_populations(): # noqa: E501
:rtype: List[int]
"""
- populations = requests.get(nodes.info_node+'/nest/populations').json()
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
+ cur = con.cursor()
+ cur.execute("SELECT DISTINCT (POPULATION_ID) FROM GIDS")
+ populations = populations = [i[0] for i in cur.fetchall()]
return populations
@@ -158,8 +200,13 @@ def nest_get_simulation_time_info(): # noqa: E501
:rtype: SimulationTimeInfo
"""
- time_info = requests.get(nodes.info_node+'/nest/simulation_time_info').json()
- return time_info
+ con = psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
+ cur = con.cursor()
+ cur.execute("SELECT MAX(CURRENT_SIM_TIME) FROM SIMULATION_NODES")
+ time = cur.fetchall()[0][0]
+ return time
def nest_get_spikes(_from=None, to=None, gids=None, offset=None, limit=None): # noqa: E501
diff --git a/requirements.txt b/requirements.txt
index 8fefc1e..76172a2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,4 +3,5 @@ python_dateutil == 2.6.0
setuptools >= 21.0.0
requests
flask_cors
-psycopg2-binary
\ No newline at end of file
+psycopg2-binary
+numpy
\ No newline at end of file
--
GitLab