def test_uri(RE, hw):
bad_meta_config1 = {'uri': 'mongodb://localhost',
'host': 'localhost',
'database': 'mds_database_placholder'}
bad_meta_config2 = {'uri': 'mongodb://localhost',
'port': 27017,
'database': 'mds_database_placholder'}
meta_config = {'uri': 'mongodb://localhost',
'database': 'mds_database_placholder'}
asset_config = {'uri': 'mongodb://localhost',
'database': 'assets_database_placeholder'}
config = copy.deepcopy(EXAMPLE)
config['metadatastore']['config'] = bad_meta_config1
config['assets']['config'] = asset_config
with pytest.raises(InvalidConfig):
broker = Broker.from_config(config)
config['metadatastore']['config'] = bad_meta_config2
with pytest.raises(InvalidConfig):
broker = Broker.from_config(config)
config['metadatastore']['config'] = meta_config
broker = Broker.from_config(config)
RE.subscribe(broker.insert)
uid, = get_uids(RE(count([hw.det])))
run = broker[uid]
config['api_version'] = 0
broker = Broker.from_config(config)
def test_handler_registration():
db = Broker.from_config(EXAMPLE)
assert 'AD_HDF5' in db.reg.handler_reg # builtin
assert 'FOO' in db.reg.handler_reg # specified by config
db = Broker.from_config(EXAMPLE, auto_register=False)
assert 'AD_HDF5' not in db.reg.handler_reg # builtin
assert 'FOO' in db.reg.handler_reg # specified by config
def test_temp_config():
c = temp_config()
db = Broker.from_config(c)
uid = str(uuid.uuid4())
db.insert('start', {'uid': uid, 'time': 0})
db.insert('stop', {'uid': str(uuid.uuid4()), 'time': 1, 'run_start': uid})
db[-1]
def build_sqlite_backed_broker(request):
"""Uses mongoquery + sqlite -- no pymongo or mongo server anywhere"""
config = temp_config()
tempdir = config['metadatastore']['config']['directory']
def cleanup():
shutil.rmtree(tempdir)
request.addfinalizer(cleanup)
return Broker.from_config(config)
def test_transforms(RE, hw):
transforms = {'transforms':
{'start': 'databroker.tests.test_v2.transform.transform',
'stop': 'databroker.tests.test_v2.transform.transform',
'resource': 'databroker.tests.test_v2.transform.transform',
'descriptor': 'databroker.tests.test_v2.transform.transform'}}
config = {**EXAMPLE, **transforms}
broker = Broker.from_config(config)
RE.subscribe(broker.insert)
uid, = get_uids(RE(count([hw.det])))
run = broker[uid]
for name, doc in run.documents(fill='false'):
if name in {'start', 'stop', 'resource', 'descriptor'}:
assert doc.get('test_key') == 'test_value'
def test_from_config():
broker = Broker.from_config(EXAMPLE)
config = broker.get_config()
print(config)
# we explicitly test for parts we know should be accepted
mds_example = EXAMPLE['metadatastore']['config']
reg_example = EXAMPLE['assets']['config']
root_map_example = EXAMPLE['root_map']
mds_config = config['metadatastore']
reg_config = config['assets']
root_map_config = config['root_map']
assert mds_example == mds_config
assert reg_example == reg_config
assert root_map_example == root_map_config
def build_sim_db(sim_db_dir=None):
if not sim_db_dir:
sim_db_dir = tempfile.mkdtemp()
config = {
'metadatastore': {
'module': 'databroker.headersource.sqlite',
'class': 'MDS',
'config': {
'directory': sim_db_dir,
'timezone': 'US/Eastern'
}
},
'assets': {
'module': 'databroker.assets.sqlite',
'class': 'Registry',
'config': {
'dbpath': os.path.join(sim_db_dir, 'assets.sqlite')
}
}
}
return sim_db_dir, Broker.from_config(config)
def db_all(request):
'''Provide a function level scoped metadatastore instance talking to
temporary database on localhost:27017 with focus on v1.
'''
db_name1 = "mds_testing_disposable_{}".format(str(uuid.uuid4()))
db_name2 = "mds_testing_disposable_{}".format(str(uuid.uuid4()))
test_config = {
'metadatastore': {
'module': 'databroker.headersource.mongo',
'class': 'MDS',
'config': {
'host': 'localhost',
'port': 27017,
'database': db_name1,
'timezone': 'US/Eastern'
}
},
'assets': {
'module': 'databroker.assets.mongo',
'class': 'Registry',
'config': {
'host': 'localhost',
'port': 27017,
'database': db_name2
}
}
}
db = Broker.from_config(test_config)
def delete_dm():
print("DROPPING DB")
db.mds._connection.drop_database(db_name1)
db.mds._connection.drop_database(db_name2)
request.addfinalizer(delete_dm)
return db
def run_server(
folder,
outbound_proxy_address=glbl_dict["outbound_proxy_address"],
prefix=None,
handlers=None,
):
"""Start up the portable databroker server
Parameters
----------
folder : str
The location where to save the portable databrokers
outbound_proxy_address : str, optional
The address and port of the zmq proxy. Defaults to
``glbl_dict["outbound_proxy_address"]``
prefix : bytes or list of bytes, optional
The Publisher channels to listen to. Defaults to
``[b"an", b"raw"]``
handlers : dict
The map between handler specs and handler classes, defaults to
the map used by the experimental databroker if possible
"""
# TODO: convert to bytestrings if needed
# TODO: maybe separate this into different processes?
# TODO: support multiple locations for folders
if prefix is None:
prefix = [b"an", b"raw"]
d = RemoteDispatcher(outbound_proxy_address, prefix=prefix)
portable_folder = folder
portable_configs = {}
for folder_name in ["an", "raw"]:
fn = os.path.join(portable_folder, folder_name)
os.makedirs(fn, exist_ok=True)
# if the path doesn't exist then make the databrokers
with open(os.path.join(portable_folder, f"{folder_name}.yml"),
"w") as f:
f.write(portable_template.format(folder_name))
print(portable_template.format(folder_name))
print(fn)
portable_configs[folder_name] = yaml.load(
io.StringIO(portable_template.format(fn)))
os.makedirs(os.path.join(fn, "data"), exist_ok=True)
# TODO: add more files here, eg. a databroker readme/tutorial
with open(os.path.join(portable_folder, "db_load.py"), "w") as f:
f.write(load_script)
an_broker = Broker.from_config(portable_configs["an"])
an_source = Stream()
zed = an_source.Store(
os.path.join(
portable_configs["an"]["metadatastore"]["config"]["directory"],
"data",
),
NpyWriter,
)
zed.starsink(an_broker.insert)
raw_broker = Broker.from_config(portable_configs["raw"])
if handlers is None:
handlers = raw_broker.reg.handler_reg
raw_source = Stream()
raw_source.starmap(
ExportCallback(
os.path.join(
portable_configs["raw"]["metadatastore"]["config"]
["directory"],
"data",
),
handler_reg=handlers,
)).starsink(raw_broker.insert)
rr = RunRouter([
lambda x: (lambda *nd: raw_source.emit(nd))
if x.get("analysis_stage", "") == "raw" else None
] + [
lambda x: (lambda *nd: an_source.emit(nd))
if x.get("analysis_stage", None) == "pdf" else None,
lambda x: (lambda *nd: an_source.emit(nd))
if x.get("analysis_stage", None) == "integration" else None,
])
d.subscribe(rr)
print("Starting Portable DB Server")
d.start()
def run_server(
folder,
outbound_proxy_address=glbl_dict["outbound_proxy_address"],
prefix=None,
handlers=None,
):
"""Start up the portable databroker server
Parameters
----------
folder : str
The location where to save the portable databrokers
outbound_proxy_address : str, optional
The address and port of the zmq proxy. Defaults to
``glbl_dict["outbound_proxy_address"]``
prefix : bytes or list of bytes, optional
The Publisher channels to listen to. Defaults to
``[b"an", b"raw"]``
handlers : dict
The map between handler specs and handler classes, defaults to
the map used by the experimental databroker if possible
"""
# TODO: convert to bytestrings if needed
# TODO: maybe separate this into different processes?
# TODO: support multiple locations for folders
if prefix is None:
prefix = [b"an", b"raw"]
d = RemoteDispatcher(outbound_proxy_address, prefix=prefix)
portable_folder = folder
portable_configs = {}
for folder_name in ["an", "raw"]:
fn = os.path.join(portable_folder, folder_name)
os.makedirs(fn, exist_ok=True)
# if the path doesn't exist then make the databrokers
with open(
os.path.join(portable_folder, f"{folder_name}.yml"), "w"
) as f:
f.write(portable_template.format(folder_name))
print(portable_template.format(folder_name))
print(fn)
portable_configs[folder_name] = yaml.load(
io.StringIO(portable_template.format(fn))
)
os.makedirs(os.path.join(fn, "data"), exist_ok=True)
# TODO: add more files here, eg. a databroker readme/tutorial
with open(os.path.join(portable_folder, "db_load.py"), "w") as f:
f.write(load_script)
an_broker = Broker.from_config(portable_configs["an"])
an_source = Stream()
zed = an_source.Store(
os.path.join(
portable_configs["an"]["metadatastore"]["config"]["directory"],
"data",
),
NpyWriter,
)
zed.starsink(an_broker.insert)
raw_broker = Broker.from_config(portable_configs["raw"])
if handlers is None:
handlers = raw_broker.reg.handler_reg
raw_source = Stream()
raw_source.starmap(
ExportCallback(
os.path.join(
portable_configs["raw"]["metadatastore"]["config"][
"directory"
],
"data",
),
handler_reg=handlers,
)
).starsink(raw_broker.insert)
rr = RunRouter(
[
lambda x: (lambda *nd: raw_source.emit(nd))
if x.get("analysis_stage", "") == "raw"
else None
]
+ [
lambda x: (lambda *nd: an_source.emit(nd))
if x.get("analysis_stage", None) == "pdf"
else None,
lambda x: (lambda *nd: an_source.emit(nd))
if x.get("analysis_stage", None) == "integration"
else None,
]
)
d.subscribe(rr)
print("Starting Portable DB Server")
d.start()
def test_root_map():
db = Broker.from_config(EXAMPLE)
assert 'foo' in db.reg.root_map
assert db.reg.root_map['foo'] == EXAMPLE['root_map']['foo']
assert db.reg.root_map['boo'] == EXAMPLE['root_map']['boo']
from ophyd.sim import det4, motor1, motor2, motor3
from bluesky import RunEngine
from bluesky.callbacks.best_effort import BestEffortCallback
from databroker.tests.utils import temp_config
from databroker import Broker
# db setup
config = temp_config()
tempdir = config['metadatastore']['config']['directory']
def cleanup():
shutil.rmtree(tempdir)
db = Broker.from_config(config)
RE = RunEngine({})
# subscribe BEC
bec = BestEffortCallback()
RE.subscribe(bec)
RE.subscribe(db.insert)
# move motor to a reproducible location
RE(mov(motor1, 0))
RE(mov(motor2, 0))
RE(relative_outer_product_scan([det4], motor1, -1, 0, 10, motor2, -2,
0, 20, True))
def test_from_config():
broker = Broker.from_config(EXAMPLE)
config = broker.get_config()
assert EXAMPLE == config
def test_auto_register():
db_auto = Broker.from_config(temp_config())
db_manual = Broker.from_config(temp_config(), auto_register=False)
assert db_auto.reg.handler_reg
assert not db_manual.reg.handler_reg
def main():
server = "otz"
otz_config = {
"description": "heavyweight shared database",
"metadatastore": {
"module": "databroker.headersource.mongo",
"class": "MDS",
"config": {
"host": server,
"port": 27017,
"database": "metadatastore-production-v1",
"timezone": "US/Central"
}
},
"assets": {
"module": "databroker.assets.mongo",
"class": "Registry",
"config": {
"host": server,
"port": 27017,
"database": "filestore-production-v1"
}
}
}
otz_db = Broker.from_config(otz_config)
tbl = pyRestTable.Table()
tbl.labels = "beamline uid plan_name".split()
headers = otz_db(since='2018-09-01', until='2018-11-06')
for h in headers:
row = (h.start["beamline_id"], h.start["login_id"],
h.start["plan_name"])
tbl.addRow(row)
print(tbl)
tbl = pyRestTable.Table()
tbl.labels = "date/time # uid plan_name".split()
headers = otz_db(beamline_id='3-ID')
for h in headers:
t_float = h.start["time"]
dt = datetime.datetime.fromtimestamp(t_float)
row = [dt, h.start["scan_id"], h.start["uid"], h.start["plan_name"]]
tbl.addRow(row)
print(tbl)
# build a local sqlite database for testing
test_dir = "/tmp/bluesky"
if not os.path.exists(test_dir):
os.makedirs(test_dir)
test_config = {
"description": "lightweight personal database",
"metadatastore": {
"module": "databroker.headersource.sqlite",
"class": "MDS",
"config": {
"directory": test_dir,
"timezone": "US/Central"
}
},
"assets": {
"module": "databroker.assets.sqlite",
"class": "Registry",
"config": {
"dbpath": test_dir + "/database.sql"
}
}
}
test_db = Broker.from_config(test_config)
# test the export from otz using a local sqlite db
if os.path.exists(test_dir):
shutil.rmtree(test_dir)
os.makedirs(test_dir)
for h in otz_db.stream(headers):
tag, doc = h
print(tag)
if tag == "descriptor":
print(sorted(doc.data_keys.keys()))
elif tag == "event":
print(doc.seq_num)
test_db.insert(tag, doc)
if tag == "descriptor":
print(sorted(doc.data_keys.keys()))
elif tag == "event":
print(sorted(doc.data_keys.keys()))
def test_root_map():
db = Broker.from_config(EXAMPLE)
assert 'foo' in db.reg.root_map
assert db.reg.root_map['foo'] == 'bar'
assert db.reg.root_map['boo'] == 'far'
def test_auto_register():
db_auto = Broker.from_config(EXAMPLE)
db_manual = Broker.from_config(EXAMPLE, auto_register=False)
assert 'AD_HDF5' in db_auto.reg.handler_reg
assert 'AD_HDF5' not in db_manual.reg.handler_reg
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# PV names
self.pv_names = loadPV()
# ZMQ Ports
self.zmqSendPort = 5301
self.zmqRecvPort = 5201
try:
self.zmqSendSock = CONTEXT.socket(zmq.PUB)
self.zmqSendSock.bind("tcp://*:" + str(self.zmqSendPort))
except:
self.zmqSendSock = None
print("Failed to bind to socket : {}".format(self.zmqSendPort))
# MainWindow Title
self.setWindowTitle("DataViewer")
# Initialize
self._dragging = False
self._last_y_axis_type = 0
self._last_tab_index = 0
self.plot_type = 'measure'
self.start_timer = 0
self.settings = {}
self.settings['E0'] = 8333
self.settings['sdd'] = False
self.settings['ratio'] = 0.7
self.settings['plot_type'] = 'measure'
self.settings['blink'] = False
self.settings['scanCounts'] = 1
# DataBroker
self.dbv1 = Broker.from_config(config)
self.db = self.dbv1.v2
# Main QWidget
main_panel = qt.QWidget(self)
main_panel.setLayout(qt.QVBoxLayout())
self.setCentralWidget(main_panel)
# Status Widget
self.status = StatusWidget(self)
self.status.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Fixed)
# Intialize plot
self.plot = Plot1DCustom(self, 'mpl')
self.plot.getLegendsDockWidget().show()
self.plot.setBackgroundColor('#FCF9F6')
self.plot.setGraphXLabel("Energy [eV]")
self.plot.setGraphYLabel("Counts [Arbs.]")
self.plot.setDataMargins(0.01, 0.01, 0.01, 0.01)
# Layout
main_panel.layout().addWidget(self.status)
main_panel.layout().addWidget(self.plot)
# Adjust operation graph's margin(left, bottom, width height)
self.plot._backend.ax.set_position([0.1, 0.05, 0.83, 0.93])
self.plot._backend.ax2.set_position([0.1, 0.05, 0.83, 0.93])
# self.updatePlotThread = UpdatePlotThread(self)
# self.updatePlotThread.daemon = True
# self.updatePlotThread.start()
self.updatePlotThread = TestThread(self)
self.updatePlotThread.daemon = True
self.updatePlotThread.start()
# Upper pannel for safety
self.status.abortButton.clicked.connect(self.abortScan)
# Manage zoom history of plot
self.status.x_axis_type_combo_box.currentIndexChanged.connect(
self.clearZoomHistory)
self.status.y_axis_type_combo_box.currentIndexChanged.connect(
self.clearZoomHistory)
# Start ZMQ Recv Thread
self.zmqRecvThread = QThreadFuture(self.receiveZmq)
self.zmqRecvThread.start()
if self.status:
# RunEngine Notifier
self._dummyIndex = 0
self.notifyTimer = qt.QTimer()
self.notifyTimer.timeout.connect(self._notifyColor)
self.notifyTimer.start(1000)
# As a thread that monitors the DCM moving state, check the case
# that it is normally located but is displaying as moving
# self.checkDcmThread = CheckDcmThread()
# self.checkDcmThread.daemon = True
# self.checkDcmThread.start()
# Connections
self.status.num_of_history_spin_box.valueChanged.connect(
self.updatePlotThread.trigger)
self.status.x_axis_type_combo_box.currentIndexChanged.connect(
self.updatePlotThread.trigger)
self.status.y_axis_type_combo_box.currentIndexChanged.connect(
self.updatePlotThread.trigger)
self.status.derivativeCB.stateChanged.connect(
self.updatePlotThread.trigger)
# Check for dragging
self.plot.sigPlotSignal.connect(self.checkDragging)
# Initial query
self.sendZmq('ViewerInitialized')
def test_from_config():
Broker.from_config(EXAMPLE)
'database': 'metadatastore_production_v1',
'timezone': 'US/Eastern'
},
},
'assets': {
'module': 'databroker.assets.mongo',
'class': 'Registry',
'config': {
'host': 'xf16idc-ca',
'port': 27017,
'database': 'filestore',
},
},
}
db = Broker.from_config(db_config)
bec = None
#import bluesky
#from ophyd import *
#from ophyd.commands import *
def reload_macros(file='~/.ipython/profile_collection/startup/99-macros.py'):
ipy = get_ipython()
ipy.magic('run -i ' + file)
def is_ipython():
ip = True
if 'ipykernel' in sys.modules:
from bluesky import RunEngine
from bluesky.callbacks.best_effort import BestEffortCallback
from databroker.tests.utils import temp_config
from databroker import Broker
# db setup
config = temp_config()
tempdir = config['metadatastore']['config']['directory']
def cleanup():
shutil.rmtree(tempdir)
db = Broker.from_config(config)
RE = RunEngine({})
# subscribe BEC
bec = BestEffortCallback()
RE.subscribe(bec)
RE.subscribe(db.insert)
# move motor to a reproducible location
RE(mov(motor1, 0))
RE(mov(motor2, 0))
RE(
relative_outer_product_scan([det4], motor1, -1, 0, 10, motor2, -2, 0, 20,
True))
RE(outer_product_scan([det4], motor1, -1, 0, 10, motor2, -2, 0, 20, True))
def build_db_from_config():
config = get_db_config()
db = Broker.from_config(config)
return db
'''
Author: Jorge Diaz
Exercise 8
'''
import uuid
import humanize
import pandas as pd
import os
from databroker.tests.utils import temp_config
from databroker import Broker
# this will create a temporary databroker object with nothing in it
db = Broker.from_config(temp_config())
# These transformations are the transformations necessary
# to convert the hex values that come from the ADC's into units of Volts.
fc = 7.62939453125e-05
def adc2counts(x):
return ((int(x, 16) >> 8) - 0x40000) * fc \
if (int(x, 16) >> 8) > 0x1FFFF else (int(x, 16) >> 8)*fc
def enc2counts(x):
return int(x) if int(x) <= 0 else -(int(x) ^ 0xffffff - 1)
class PizzaBoxANHandler():
def __init__(self, resource_path, chunk_size=1024):
shutter_control=True,
auto_load_calib=True,
calib_config_name=glbl_dict["calib_config_name"],
# instrument config
det_image_field=glbl_dict["image_fields"],
all_folders=ALL_FOLDERS,
userscript_dir=USERSCRIPT_DIR,
_exclude_dir=[HOME_DIR, BLCONFIG_DIR, YAML_DIR],
archive_base_dir=ARCHIVE_BASE_DIR,
))
if glbl_dict["exp_broker_name"] == "xpd_sim_databroker":
with open(sim_db_config_path, "r") as f:
db_config = yaml.safe_load(f)
db_config["metadatastore"]["config"]["directory"] = db_config[
"metadatastore"]["config"]["directory"].format(**glbl_dict)
db_config["assets"]["config"]["dbpath"] = db_config["assets"]["config"][
"dbpath"].format(**glbl_dict)
glbl_dict["exp_db"] = Broker.from_config(db_config)
else:
glbl_dict["exp_db"] = Broker.named(glbl_dict["exp_broker_name"])
glbl_dict.update({
k: os.path.join(glbl_dict["base_dir"], glbl_dict[z])
for k, z in zip(
["home_dir", "blconfig_dir"],
["home_dir_name", "blconfig_dir_name"],
)
})