diff --git a/access_node/controllers/arbor_controller.py b/access_node/controllers/arbor_controller.py
index a3a488c5eafe5952ee2512cdc5a4ac9b4916655c..aa3fe5b4a91017e01b9f0805f6a6fa2b6dea002e 100644
--- a/access_node/controllers/arbor_controller.py
+++ b/access_node/controllers/arbor_controller.py
@@ -10,6 +10,14 @@ from access_node import util
from access_node.models.nodes import nodes
import requests
+import psycopg2
+import numpy as np
+
+
+def connect_to_database():
+ return psycopg2.connect(database="postgres", user="postgres",
+ password="docker", host="database", port="5432")
+
def arbor_get_attributes(): # noqa: E501
"""Retrieves the list of all attributes.
@@ -19,7 +27,14 @@ def arbor_get_attributes(): # noqa: E501
:rtype: List[str]
"""
- return 'do some magic!'
+ con = connect_to_database()
+ cur = con.cursor()
+
+ cur.execute("SELECT NAME FROM ATTRIBUTES")
+ attributes = [i[0] for i in cur.fetchall()]
+
+ con.close()
+ return attributes
def arbor_get_cell_ids(): # noqa: E501
@@ -30,7 +45,13 @@ def arbor_get_cell_ids(): # noqa: E501
:rtype: List[int]
"""
- cell_ids = requests.get(nodes.info_node+'/arbor/cell_ids').json()
+ con = connect_to_database()
+ cur = con.cursor()
+
+ cur.execute("SELECT CELL_ID FROM CELLS")
+ cell_ids = [i[0] for i in cur.fetchall()]
+
+ con.close()
return cell_ids
@@ -44,7 +65,25 @@ def arbor_get_cell_properties(cell_ids=None): # noqa: E501
:rtype: List[ArborCellProperties]
"""
- cell_properties = requests.get(nodes.info_node+'/arbor/cell_properties').json()
+ con = connect_to_database()
+ cur = con.cursor()
+
+ if cell_ids == None:
+ cur.execute("SELECT CELL_ID, PROPERTY FROM CELL_PROPERTIES")
+ else:
+ cur.execute("SELECT CELL_ID, PROPERTY FROM CELL_PROPERTIES WHERE CELL_PROPERTIES.CELL_ID IN %s", (tuple(cell_ids),))
+
+ properties = np.array(cur.fetchall())
+ cell_ids = np.unique(properties[:,0])
+ cell_properties = []
+ for i in range(len(cell_ids)):
+ per_cell_properties = []
+ for prop in properties:
+ if prop[0] == cell_ids[i]:
+ per_cell_properties.append(prop)
+ cell_properties.append(ArborCellProperties(cell_ids[i], per_cell_properties))
+
+ con.close()
return cell_properties
@@ -68,26 +107,26 @@ def arbor_get_measurements(attribute, probe_ids=None, _from=None, to=None, offse
:rtype: ArborMeasurement
"""
- if measurement_point_ids == None:
- measurement_points = arbor_get_measurement_points()
- measurement_point_ids = []
- for point in measurement_points:
- measurement_point_ids.append(point.id)
+ if probe_ids == None:
+ probes = arbor_get_probes()
+ probe_ids = []
+ for probe in probes:
+ probe_ids.append(probe.id)
init = True
sim_times = []
measurement = ArborMeasurement([], [], [])
for node in nodes.arbor_simulation_nodes:
response = requests.get(
- 'http://'+node+'/arbor/measurements', params={"attribute": attribute, "measurement_point_ids": measurement_point_ids, "_from": _from, "to": to, "gids": gids}).json()
+ 'http://'+node+'/arbor/measurements', params={"attribute": attribute, "probe_ids": probe_ids, "_from": _from, "to": to}).json()
if init:
sim_times = response['simulation_times']
measurement = ArborMeasurement(
- sim_times, measurement_point_ids, [None for x in range(0, (len(sim_times)*len(measurement_point_ids)))])
+ sim_times, probe_ids, [None for x in range(0, (len(sim_times)*len(probe_ids)))])
init = False
- for x in range(len(response['measurement_point_ids'])):
- m_id = response['measurement_point_ids'][x]
- index = measurement.measurement_point_ids.index(m_id)
+ for x in range(len(response['probe_ids'])):
+ m_id = response['probe_ids'][x]
+ index = measurement.probe_ids.index(m_id)
index_offset = index * len(sim_times)
for y in range(len(sim_times)):
measurement.values[index_offset +
@@ -96,9 +135,9 @@ def arbor_get_measurements(attribute, probe_ids=None, _from=None, to=None, offse
# offset and limit
if (offset is None):
offset = 0
- if (limit is None or (limit + offset) > len(measurement.measurement_point_ids)):
- limit = len(measurement.measurement_point_ids) - offset
- measurement.measurement_point_ids = measurement.measurement_point_ids[offset:offset+limit]
+ if (limit is None or (limit + offset) > len(measurement.probe_ids)):
+ limit = len(measurement.probe_ids) - offset
+ measurement.probe_ids = measurement.probe_ids[offset:offset+limit]
measurement.values = measurement.values[offset *
len(sim_times):(offset+limit)*len(sim_times)]
@@ -115,8 +154,18 @@ def arbor_get_probes(attribute=None): # noqa: E501
:rtype: List[Probe]
"""
- probes = requests.get(nodes.info_node+'/arbor/probes').json()
- return probes
+ con = connect_to_database()
+ cur = con.cursor()
+
+ # TODO Multiple Attributes per Probe possible? - Complete this
+
+ if attribute == None:
+ cur.execute("SELECT PROBE_ID, CELL_ID, SEGMENT_ID, POSITION FROM PROBES")
+
+
+
+ con.close()
+ return
def arbor_get_simulation_time_info(): # noqa: E501
@@ -127,8 +176,17 @@ def arbor_get_simulation_time_info(): # noqa: E501
:rtype: SimulationTimeInfo
"""
- simulation_time_info = requests.get(nodes.info_node+'/arbor/simulation_time_info').json()
- return simulation_time_info
+ con = connect_to_database()
+ cur = con.cursor()
+
+ cur.execute("SELECT MIN(CURRENT_SIM_TIME) FROM ARBOR_SIMULATION_NODES")
+ current_time = cur.fetchall()[0][0]
+
+ con.close()
+
+ # TODO Add Start and End time when available
+ time_info = SimulationTimeInfo(current=current_time)
+ return time_info
def arbor_get_spikes(_from=None, to=None, cell_ids=None, segment_ids=None, offset=None, limit=None): # noqa: E501
@@ -154,7 +212,7 @@ def arbor_get_spikes(_from=None, to=None, cell_ids=None, segment_ids=None, offse
spikes = Spikes([], [])
for node in nodes.arbor_simulation_nodes:
response = requests.get(
- 'http://'+node+'/arbor/spikes', params={"from": _from, "to": to, "gids": gids}).json()
+ 'http://'+node+'/arbor/spikes', params={"from": _from, "to": to, "cell_ids": cell_ids, "segment_ids": segment_ids}).json()
for x in range(len(response['simulation_times'])):
spikes.simulation_times.append(response['simulation_times'][x])
spikes.gids.append(response['gids'][x])