def test_diel_migration(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_diel_migration")
num_steps = 168
num_particles = 4
start_time = datetime(2013,4,1,0, tzinfo=pytz.utc)
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/diel_suncycles.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=60.68, longitude=-146.42, depth=self.start_depth, start=start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=2, time_method='nearest')
output_path = os.path.join(self.output_path, "test_diel_migration")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "test_diel_migration.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_interp(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_interp")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_interp")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_interp.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
def test_timechunk_greater_than_timestep(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_timechunk_greater_than_timestep")
# 6 days
num_steps = 10
num_particles = 2
models = [self.transport]
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=2)
cache_path = os.path.join(self.cache_path,
"test_timechunk_greater_than_timestep.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
bathy=self.bathy_file,
cache=cache_path)
def test_run_from_polygon(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_polygon")
models = [self.transport]
poly = Point(self.start_lon, self.start_lat,
self.start_depth).buffer(0.001)
model = ModelController(geometry=poly,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(
os.path.dirname(__file__), "..",
"paegan/transport/_cache/test_run_from_polygon.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def test_bad_dataset(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_bad_dataset")
models = [self.transport]
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4,
time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_bad_dataset.nc")
with raises(DataControllerError):
model.run("http://asascience.com/thisisnotadataset.nc",
cache=cache_path)
def test_start_on_land(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_start_on_land")
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = ModelController(latitude=start_lat,
longitude=start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4,
time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_start_on_land.nc")
with raises(ModelError):
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def test_quick_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_quick_settlement")
num_steps = 24
num_particles = 4
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_quick_settle.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=12, horiz_chunk=2, time_method='nearest')
output_path = os.path.join(self.output_path, "test_quick_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline','Pickle']
cache_path = os.path.join(self.cache_path, "test_quick_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_nearest(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_nearest")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_nearest.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_multiple_files_without_cache(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_multiple_files_without_cache")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=datetime(2014, 1, 2, 0), step=self.time_step, nstep=self.num_steps, npart=self.num_particles,
models=models, use_bathymetry=False, use_shoreline=True, time_chunk=10, horiz_chunk=4)
model.run("/data/lm/tests/pws_das_2014*.nc", bathy=self.bathy_file, caching=False, output_formats = ['NetCDF'], output_path=os.path.join(self.output_path, "test_run_from_multiple_files_without_cache"))
def test_bad_dataset(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_bad_dataset")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_bad_dataset.nc")
with raises(DataControllerError):
model.run("http://asascience.com/thisisnotadataset.nc", cache=cache_path)
def test_run_from_point_with_wfs(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point_with_wfs")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, shoreline_path='http://geo.asascience.com/geoserver/shorelines/ows', shoreline_feature='shorelines:10m_land_polygons')
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_polygon(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_polygon")
models = [self.transport]
poly = Point(self.start_lon, self.start_lat, self.start_depth).buffer(0.001)
model = ModelController(geometry=poly, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(os.path.dirname(__file__), "..", "paegan/transport/_cache/test_run_from_polygon.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_point(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_timechunk_greater_than_timestep(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_timechunk_greater_than_timestep")
# 6 days
num_steps = 10
num_particles = 2
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=2)
cache_path = os.path.join(self.cache_path, "test_timechunk_greater_than_timestep.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path)
def test_start_on_land(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_start_on_land")
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = ModelController(latitude=start_lat, longitude=start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_start_on_land.nc")
with raises(ModelError):
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_diel_migration(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_diel_migration")
num_steps = 168
num_particles = 4
start_time = datetime(2013, 4, 1, 0, tzinfo=pytz.utc)
# Behavior
behavior_config = open(
os.path.normpath(
os.path.join(os.path.dirname(__file__),
"./resources/files/diel_suncycles.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=60.68,
longitude=-146.42,
depth=self.start_depth,
start=start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=2,
time_method='nearest')
output_path = os.path.join(self.output_path, "test_diel_migration")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
cache_path = os.path.join(self.cache_path, "test_diel_migration.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
def test_interp(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_interp")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_interp")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=self.num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_interp.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def run(self, hydrodatasets, **kwargs):
_wind_path = kwargs.get("winddataset", None)
num_particles = 1
models = [Transport(horizDisp=0., vertDisp=0.)]
if self._wind_model != None:
models.append(WindForcing())
for drifter in self.drifters:
start_location4d = drifter.locations[0]
start_time = start_location4d.time
start_lat = start_location4d.latitude
start_lon = start_location4d.longitude
start_depth = start_location4d.depth
time_step = self.time_step
num_steps = self.num_steps
model = ModelController(latitude=start_lat, longitude=start_lon,
depth=start_depth, start=start_time, step=time_step,
nstep=num_steps, npart=num_particles, models=models,
use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=10)
for hydromodel in hydrodatasets:
model.run(hydromodel, wind=_wind_path)
drifter.add_virtual_drifter(model.particles[0])
def test_run_from_point(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def run(run_id):
# Sleep to give the Run object enough time to save
time.sleep(10)
with app.app_context():
from paegan.logger import logger
job = get_current_job()
output_path = os.path.join(current_app.config['OUTPUT_PATH'], run_id)
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
cache_path = os.path.join(current_app.config['CACHE_PATH'], run_id)
shutil.rmtree(cache_path, ignore_errors=True)
os.makedirs(cache_path)
temp_animation_path = os.path.join(current_app.config['OUTPUT_PATH'], "temp_images_" + run_id)
shutil.rmtree(temp_animation_path, ignore_errors=True)
os.makedirs(temp_animation_path)
# Set up Logger
queue = multiprocessing.Queue(-1)
f, log_file = tempfile.mkstemp(dir=cache_path, prefix=run_id, suffix=".log")
os.close(f)
# Close any existing handlers
(hand.close() for hand in logger.handlers)
# Remove any existing handlers
logger.handlers = []
logger.setLevel(logging.PROGRESS)
handler = MultiProcessingLogHandler(log_file, queue)
handler.setLevel(logging.PROGRESS)
formatter = logging.Formatter('[%(asctime)s] - %(levelname)s - %(name)s - %(processName)s - %(message)s')
handler.setFormatter(formatter)
logger.addHandler(handler)
# Progress stuff. Hokey!
progress_deque = collections.deque(maxlen=1)
progress_handler = ProgressHandler(progress_deque)
progress_handler.setLevel(logging.PROGRESS)
logger.addHandler(progress_handler)
e = threading.Event()
def save_progress():
while e.wait(5) is not True:
try:
record = progress_deque.pop()
if record == StopIteration:
break
job.meta["updated"] = record[0]
if record is not None and record[1] >= 0:
job.meta["progress"] = record[1]
if isinstance(record[2], unicode) or isinstance(record[2], str):
job.meta["message"] = record[2]
job.save()
except IndexError:
pass
except Exception:
raise
return
t = threading.Thread(name="ProgressUpdater", target=save_progress)
t.daemon = True
t.start()
model = None
try:
logger.progress((0, "Configuring model"))
run = db.Run.find_one( { '_id' : ObjectId(run_id) } )
if run is None:
return "Failed to locate run %s. May have been deleted while task was in the queue?" % run_id
geometry = loads(run['geometry'])
start_depth = run['release_depth']
num_particles = run['particles']
time_step = run['timestep']
num_steps = int(math.ceil((run['duration'] * 24 * 60 * 60) / time_step))
start_time = run['start'].replace(tzinfo = pytz.utc)
shoreline_path = run['shoreline_path'] or app.config.get("SHORE_PATH")
shoreline_feat = run['shoreline_feature']
# Set up output directory/bucket for run
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
# Setup Models
models = []
if run['cached_behavior'] is not None and run['cached_behavior'].get('results', None) is not None:
behavior_data = run['cached_behavior']['results'][0]
l = LarvaBehavior(data=behavior_data)
models.append(l)
models.append(Transport(horizDisp=run['horiz_dispersion'], vertDisp=run['vert_dispersion']))
# Setup ModelController
model = ModelController(geometry=geometry, depth=start_depth, start=start_time, step=time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=run['time_chunk'], horiz_chunk=run['horiz_chunk'], time_method=run['time_method'], shoreline_path=shoreline_path, shoreline_feature=shoreline_feat, reverse_distance=1500)
# Run the model
cache_file = os.path.join(cache_path, run_id + ".nc.cache")
bathy_file = current_app.config['BATHY_PATH']
model.run(run['hydro_path'], output_path=output_path, bathy=bathy_file, output_formats=output_formats, cache=cache_file, remove_cache=False, caching=run['caching'])
# Skip creating movie output_path
"""
from paegan.viz.trajectory import CFTrajectory
logger.info("Creating animation...")
for filename in os.listdir(output_path):
if os.path.splitext(filename)[1][1:] == "nc":
# Found netCDF file
netcdf_file = os.path.join(output_path,filename)
traj = CFTrajectory(netcdf_file)
success = traj.plot_animate(os.path.join(output_path,'animation.avi'), temp_folder=temp_animation_path, bathy=app.config['BATHY_PATH'])
if not success:
logger.info("Could not create animation")
else:
logger.info("Animation saved")
"""
job.meta["outcome"] = "success"
job.save()
return "Successfully ran %s" % run_id
except Exception as exception:
logger.warn("Run FAILED, cleaning up and uploading log.")
logger.warn(exception.message)
job.meta["outcome"] = "failed"
job.save()
raise
finally:
logger.progress((99, "Processing output files"))
# Close the handler so we can upload the log file without a file lock
(hand.close() for hand in logger.handlers)
queue.put(StopIteration)
# Break out of the progress loop
e.set()
t.join()
# Move logfile to output directory
shutil.move(log_file, os.path.join(output_path, 'model.log'))
# Move cachefile to output directory if we made one
if run['caching']:
shutil.move(cache_file, output_path)
output_files = []
for filename in os.listdir(output_path):
outfile = os.path.join(output_path, filename)
output_files.append(outfile)
result_files = []
base_access_url = current_app.config.get('NON_S3_OUTPUT_URL', None)
# Handle results and cleanup
if current_app.config['USE_S3'] is True:
base_access_url = urljoin("http://%s.s3.amazonaws.com/output/" % current_app.config['S3_BUCKET'], run_id)
# Upload results to S3 and remove the local copies
conn = S3Connection()
bucket = conn.get_bucket(current_app.config['S3_BUCKET'])
for outfile in output_files:
# Don't upload the cache file
if os.path.basename(outfile) == os.path.basename(cache_file):
continue
# Upload the outfile with the same as the run name
_, ext = os.path.splitext(outfile)
new_filename = slugify(unicode(run['name'])) + ext
k = Key(bucket)
k.key = "output/%s/%s" % (run_id, new_filename)
k.set_contents_from_filename(outfile)
k.set_acl('public-read')
result_files.append(base_access_url + "/" + new_filename)
os.remove(outfile)
shutil.rmtree(output_path, ignore_errors=True)
else:
for outfile in output_files:
result_files.append(urljoin(base_access_url, run_id) + "/" + os.path.basename(outfile))
shutil.rmtree(temp_animation_path, ignore_errors=True)
# Set output fields
run.output = result_files
run.ended = datetime.utcnow()
run.compute()
run.save()
# Cleanup
logger.removeHandler(handler)
del formatter
del handler
del logger
del model
queue.close()
job.meta["message"] = "Complete"
job.save()