def create_logger(self, log_level=logging.INFO):
daiquiri.setup(
outputs=(
daiquiri.output.File(
directory=self.settings.get('LOG_PATH'),
program_name=self.project_name,
),
daiquiri.output.STDOUT,
)
)
daiquiri.getLogger(program_name=self.project_name).logger.level = log_level
self.logger = daiquiri.getLogger(
program_name=self.project_name, log_level=log_level
)
def setup_logging(verbose=0):
global logging
progname = basename(sys.argv[0])
daiquiri.setup(
level=(logging.ERROR - 10*verbose),
program_name=progname)
logging = daiquiri.getLogger(progname)
import webinterface.queue as queue
from webinterface.common import templates
from webinterface.common import get_user_information
###################################################################################
## Helper classes
###################################################################################
daiquiri.setup(
level=logging.INFO,
outputs=(daiquiri.output.Stream(
formatter=daiquiri.formatter.ColorFormatter(
fmt="%(color)s%(levelname)-8.8s "
"%(name)s: %(message)s%(color_stop)s")), ),
)
logger = daiquiri.getLogger("webgui")
class ExtendedUser(SimpleUser):
def __init__(self, username: str, is_admin: False) -> None:
self.username = username
self.admin_status = is_admin
@property
def is_admin(self) -> bool:
return self.admin_status
class SessionAuthBackend(AuthenticationBackend):
async def authenticate(self, request):
import click
import daiquiri
import fixtures
import pbr.version
import pkg_resources
import psutil
from pifpaf import util
LOG = daiquiri.getLogger("pifpaf")
def _format_multiple_exceptions(e, debug=False):
valid_excs = []
# NOTE(sileht): Why do I not use this ? :
# excs = list(e.args)
# Because it raises SystemExit(2) on python3 !!?!?
excs = []
for i in range(len(e.args)):
excs.append(e.args[i])
while excs:
(etype, value, tb) = excs.pop(0)
if (etype == fixtures.MultipleExceptions):
excs.extend(value.args)
elif (etype == fixtures.SetupError):
modelID = ''
sampleZ = None
daiquiri.setup(
level=logging.INFO,
outputs=(
daiquiri.output.Stream(sys.stdout),
daiquiri.output.File(
'./logs/logs.log',
level=logging.INFO,
formatter=daiquiri.formatter.ColorFormatter(
fmt=
"\n###### %(asctime)s [%(levelname)s] %(name)s -> %(message)s ######\n"
)),
))
logger = daiquiri.getLogger(__name__, propagate=False)
logger.info('Parte la pipeline su dataset {} e modello {}'.format(
datasetID, modelID))
if sampleZ:
logger.info('La run è una prova con un sample n={}'.format(sampleZ))
class ETL(luigi.Task):
dataset_id = luigi.Parameter(default=datasetID)
path_dataset = luigi.Parameter(default=r'')
def requires(self):
return []
async def _extract_pulls_from_stream(
self, installation: context.Installation) -> PullsToConsume:
messages: typing.List[typing.Tuple[
T_MessageID, T_MessagePayload]] = await self.redis_stream.xrange(
installation.stream_name, count=config.STREAM_MAX_BATCH)
LOG.debug(
"read stream",
stream_name=installation.stream_name,
messages_count=len(messages),
)
statsd.histogram("engine.streams.size", len(messages))
statsd.gauge("engine.streams.max_size", config.STREAM_MAX_BATCH)
# TODO(sileht): Put this cache in Repository context
opened_pulls_by_repo: typing.Dict[
github_types.GitHubRepositoryName,
typing.List[github_types.GitHubPullRequest], ] = {}
# Groups stream by pull request
pulls: PullsToConsume = PullsToConsume(collections.OrderedDict())
for message_id, message in messages:
data = msgpack.unpackb(message[b"event"], raw=False)
repo_name = github_types.GitHubRepositoryName(data["repo"])
repo_id = github_types.GitHubRepositoryIdType(data["repo_id"])
source = typing.cast(context.T_PayloadEventSource, data["source"])
if data["pull_number"] is not None:
key = (
repo_name,
repo_id,
github_types.GitHubPullRequestNumber(data["pull_number"]),
)
group = pulls.setdefault(key, ([], []))
group[0].append(message_id)
group[1].append(source)
else:
logger = daiquiri.getLogger(
__name__,
gh_repo=repo_name,
gh_owner=installation.owner_login,
source=source,
)
if repo_name not in opened_pulls_by_repo:
try:
opened_pulls_by_repo[repo_name] = [
p async for p in installation.client.items(
f"/repos/{installation.owner_login}/{repo_name}/pulls"
)
]
except Exception as e:
if exceptions.should_be_ignored(e):
opened_pulls_by_repo[repo_name] = []
else:
raise
converted_messages = await self._convert_event_to_messages(
installation,
repo_id,
repo_name,
source,
opened_pulls_by_repo[repo_name],
)
logger.debug("event unpacked into %s messages",
len(converted_messages))
messages.extend(converted_messages)
deleted = await self.redis_stream.xdel(
installation.stream_name, message_id)
if deleted != 1:
# FIXME(sileht): During shutdown, heroku may have already started
# another worker that have already take the lead of this stream_name
# This can create duplicate events in the streams but that should not
# be a big deal as the engine will not been ran by the worker that's
# shutdowning.
contents = await self.redis_stream.xrange(
installation.stream_name,
start=message_id,
end=message_id)
if contents:
logger.error(
"message `%s` have not been deleted has expected, "
"(result: %s), content of current message id: %s",
message_id,
deleted,
contents,
)
return pulls
"""geo3dfeatures package
"""
import logging
import daiquiri
__version__ = "0.4.0"
daiquiri.setup(
level=logging.INFO,
outputs=(daiquiri.output.Stream(
formatter=daiquiri.formatter.ColorFormatter(fmt=(
"%(color)s[%(asctime)s] %(module)s.%(funcName)s "
"(%(levelname)s) -%(color_stop)s %(message)s"),
datefmt="%H:%M:%S")), ),
)
logger = daiquiri.getLogger("root")
import logging
import common.monitor as monitor
import daiquiri
logger = daiquiri.getLogger("rule_evaluation")
safe_eval_cmds = {"float": float, "int": int, "str": str}
def replace_tags(rule, tags):
"""Replaces all tags with format @tagname@ in the given rule string with
the corresponding values from the currently processed series (stored
in the second argument)."""
# Run the substitue operation manually instead of using
# the standard string function to enforce that the values
# read from the tags are treated as strings by default
tags_found = []
i = 0
while i < len(rule):
opening = rule.find("@", i)
if opening < 0:
break
closing = rule.find("@", opening + 1)
if closing < 0:
break
tagstring = rule[opening + 1:closing]
if tagstring in tags:
tags_found.append(tagstring)
i = closing + 1
for tag in tags_found:
from cliff import command
from cliff import commandmanager
from cliff import lister
import daiquiri
import fixtures
import pbr.version
import pkg_resources
import six
LOG = daiquiri.getLogger("pifpaf")
def _format_multiple_exceptions(e, debug=False):
valid_excs = []
excs = list(e.args)
while excs:
(etype, value, tb) = excs.pop(0)
if (etype == fixtures.MultipleExceptions):
excs.extend(value.args)
elif (etype == fixtures.SetupError):
continue
else:
valid_excs.append((etype, value, tb))
if len(valid_excs) == 1:
def get_logger(self, name='crontab_log'):
logger = daiquiri.getLogger(name)
return logger
# App-specific includes
import common.monitor as monitor
from common.constants import mercure_defs
###################################################################################
## Configuration and initialization
###################################################################################
daiquiri.setup(
level=logging.INFO,
outputs=(daiquiri.output.Stream(
formatter=daiquiri.formatter.ColorFormatter(
fmt="%(color)s%(levelname)-8.8s "
"%(name)s: %(message)s%(color_stop)s")), ),
)
logger = daiquiri.getLogger("bookkeeper")
bookkeeper_config = Config("configuration/bookkeeper.env")
BOOKKEEPER_PORT = bookkeeper_config("PORT", cast=int, default=8080)
BOOKKEEPER_HOST = bookkeeper_config("HOST", default="0.0.0.0")
DATABASE_URL = bookkeeper_config("DATABASE_URL",
default="postgresql://mercure@localhost")
database = databases.Database(DATABASE_URL)
app = Starlette(debug=True)
###################################################################################
## Definition of database tables
###################################################################################
metadata = sqlalchemy.MetaData()
from pathlib import Path
import uuid
import json
import shutil
import daiquiri
import socket
from datetime import datetime
# App-specific includes
import common.config as config
import common.rule_evaluation as rule_evaluation
import common.monitor as monitor
import common.helper as helper
from common.constants import mercure_defs, mercure_names, mercure_sections, mercure_rule, mercure_config, mercure_options, mercure_actions
logger = daiquiri.getLogger("generate_taskfile")
def compose_task(uid, uid_type, triggered_rules, tags_list, target):
task_json = {}
task_json.update(add_info(uid, uid_type, triggered_rules, tags_list))
task_json.update(add_dispatching(triggered_rules, tags_list, target))
task_json.update(add_processing(triggered_rules, tags_list))
return task_json
def add_processing(applied_rule, tags_list):
process_section = {}
process_section[mercure_sections.PROCESS] = {}
if (config.mercure[mercure_config.RULES][applied_rule].get(
Model for PASTA State of Health events
:Author:
servilla
:Created:
3/18/18
"""
import daiquiri
from sqlalchemy import Column, Integer, String, DateTime, ForeignKey, desc, asc
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import sessionmaker
from soh.config import Config
logger = daiquiri.getLogger('soh_db.py: ' + __name__)
Base = declarative_base()
class SohEvent(Base):
__tablename__ = 'soh_event'
event_id = Column(Integer(), primary_key=True, autoincrement=True)
timestamp = Column(DateTime(), nullable=False)
class SohAssert(Base):
__tablename__ = 'soh_assert'
assert_id = Column(Integer(), primary_key=True, autoincrement=True)
:Author:
servilla
:Created:
3/7/18
"""
import base64
import daiquiri
from flask_login import UserMixin
import requests
from webapp import login
from webapp.config import Config
logger = daiquiri.getLogger('user.py: ' + __name__)
class User(UserMixin):
def __init__(self, auth_token=None):
self._auth_token = auth_token
@staticmethod
def authenticate(user_dn=None, password=None):
auth_token = None
r = requests.get(Config.AUTH_URL, auth=(user_dn, password))
if r.status_code == requests.codes.ok:
auth_token = r.cookies['auth-token']
return auth_token
def get_id(self):
import shutil
import time
from datetime import datetime
from pathlib import Path
from shlex import split
from subprocess import CalledProcessError, run
import daiquiri
from common.monitor import s_events, send_series_event, send_event, h_events, severity
from dispatch.retry import increase_retry
from dispatch.status import is_ready_for_sending
from common.constants import mercure_names
logger = daiquiri.getLogger("send")
DCMSEND_ERROR_CODES = {
1: "EXITCODE_COMMANDLINE_SYNTAX_ERROR",
21: "EXITCODE_NO_INPUT_FILES",
22: "EXITCODE_INVALID_INPUT_FILE",
23: "EXITCODE_NO_VALID_INPUT_FILES",
43: "EXITCODE_CANNOT_WRITE_REPORT_FILE",
60: "EXITCODE_CANNOT_INITIALIZE_NETWORK",
61: "EXITCODE_CANNOT_NEGOTIATE_ASSOCIATION",
62: "EXITCODE_CANNOT_SEND_REQUEST",
65: "EXITCODE_CANNOT_ADD_PRESENTATION_CONTEXT",
}
def _create_command(target_info, folder):
# coding: utf-8
"""Flask Web Application for Jitenshea (Bicycle-sharing data)
"""
import daiquiri
import logging
from flask import Flask, render_template, abort
daiquiri.setup(level=logging.INFO)
logger = daiquiri.getLogger("jitenshea-webapp")
app = Flask(__name__)
app.config['ERROR_404_HELP'] = False
app.config['SWAGGER_UI_DOC_EXPANSION'] = 'list'
CITIES = ['bordeaux', 'lyon']
def check_city(city):
if city not in CITIES:
abort(404, "City {} not found".format(city))
@app.route('/')
def index():
return render_template("index.html")
@app.route('/doc/')
def _loop(self, max_iter=None):
if not self._SILENCE_LOGGER: # pragma: no cover don't want to clutter tests
logger = daiquiri.getLogger(self._name)
logger.info('Starting {}'.format(self._name))
# fleming and dateutil have arguments that just differ by ending in an "s"
fleming_kwargs = self._every_kwargs
relative_delta_kwargs = {}
# build the relative delta kwargs
for k, v in self._every_kwargs.items():
relative_delta_kwargs[k + 's'] = v
# if a starting time was given use the floored second of that time as the previous time
if self._starting is not None:
previous_time = fleming.floor(self._starting, second=1)
# otherwise use the interval floored value of now as the previous time
else:
previous_time = fleming.floor(datetime.datetime.now(),
**fleming_kwargs)
# keep track of iterations
n_iter = 0
# this is the infinite loop that runs the cron. It will only be stopped when the
# process is killed by its monitor.
while True:
n_iter += 1
if max_iter is not None and n_iter > max_iter:
break
# everything is run in a try block so errors can be explicitly handled
try:
# push forward the previous/next times
next_time = previous_time + relativedelta(
**relative_delta_kwargs)
previous_time = next_time
# get the current time
now = datetime.datetime.now()
# if our job ran longer than an interval, we will need to catch up
if next_time < now:
continue
# sleep until the computed time to run the function
sleep_seconds = (next_time - now).total_seconds()
time.sleep(sleep_seconds)
# See what time it is on wakeup
timestamp = datetime.datetime.now()
# If passed until date, break out of here
if self._until is not None and timestamp > self._until:
break
# If not inhibited, run the function
if self._is_uninhibited(timestamp):
self._log('Running {}'.format(self._name))
self._func(*self._func_args, **self._func_kwargs)
except KeyboardInterrupt: # pragma: no cover
pass
except: # noqa
# only raise the error if not in robust mode.
if self._robust:
s = 'Error in tab\n' + traceback.format_exc()
logger = daiquiri.getLogger(self._name)
logger.error(s)
else:
raise
self._log('Finishing {}'.format(self._name))
from werkzeug.utils import secure_filename
from deeposlandia import utils
from deeposlandia.inference import predict
MODELS = ('feature_detection', 'semantic_segmentation')
DATASETS = ('mapillary', 'shapes')
ALLOWED_EXTENSIONS = set(['png', 'jpg', 'jpeg'])
PROJECT_FOLDER = '/tmp/deeposlandia'
UPLOAD_FOLDER = os.path.join(PROJECT_FOLDER, 'uploads/')
PREDICT_FOLDER = os.path.join(PROJECT_FOLDER, 'predicted/')
os.makedirs(UPLOAD_FOLDER, exist_ok=True)
os.makedirs(PREDICT_FOLDER, exist_ok=True)
daiquiri.setup(level=logging.INFO)
logger = daiquiri.getLogger("deeposlandia-webapp")
app = Flask(__name__)
app.config['ERROR_404_HELP'] = False
app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
def check_model(model):
"""Check if `model` is valid, *i.e.* equal to `feature_detection` or
`semantic_segmentation`
Parameters
----------
model : str
String to verify
"""
def _log(self, msg):
if self._verbose and not self._SILENCE_LOGGER: # pragma: no cover
logger = daiquiri.getLogger(self._name)
logger.info(msg)
import daiquiri
from datetime import datetime
from collections import OrderedDict
from pathlib import Path
from typing import List, Union
from IPython import get_ipython
from IPython.core.display import display, Javascript
from ipykernel.comm import Comm
logger = daiquiri.getLogger()
Jupyter = get_ipython()
"""Current InteractiveShell instance."""
_is_notebook = Jupyter and Jupyter.has_trait('kernel')
class CommError(Exception):
"""Base class for Comm related exceptions."""
def __init__(self, *args, **kwargs):
msg = ". ".join([*args[:1], "HINT: Try reloading <F5> the window."])
args = msg, *args[1:]
super().__init__(*args, **kwargs)
def main(
ctx, verbose, api_key, service_account,
config_file, level, export, outputs
):
"""
"""
Log(verbose).initialize()
logger = daiquiri.getLogger(ctx.command.name, subsystem="MAIN")
logger.info(
"================ {0} =================".format(
ctx.command.name
)
)
# --config-file
fn_config = os.path.expanduser(config_file)
logger.debug(
"Configuration file =====> {0}".format(fn_config)
)
if os.path.exists(fn_config):
ctx.default_map = CONTEXT_SETTINGS['default_map']
logger.debug(
"Context with default map =====> {0}".format(
json.dumps(ctx.default_map)
)
)
else:
logger.critical(
"Configuration file {0} is not available!".format(
fn_config
)
)
raise click.Abort()
try:
pass
except KeyError as e:
logger.debug("Error =====> {0}".format(
e.message
))
raise
scopes = []
for wapor_data_key in ctx.default_map.keys():
if wapor_data_key.startswith("google."):
scopes.append(ctx.default_map[wapor_data_key]["scope"])
if wapor_data_key == "gee_workspace_base":
ee_workspace_base = ctx.default_map[wapor_data_key]
if wapor_data_key == "gee_workspace_project":
ee_workspace_wapor = ctx.default_map[wapor_data_key]
logger.debug("Scopes =====> {0}".format(scopes))
# --credential-file
credentials = os.path.expanduser(service_account)
logger.debug(
"Credential file =====> {0}".format(credentials)
)
if os.path.exists(credentials):
logger.info(
"Authenticate with Service Account {0}".format(credentials)
)
auth = Initialize(
CredentialConfigFile(credentials).get_sa_credentials(scopes)
)
elif api_key:
logger.info(
"Authenticate with Api Key {0}".format(api_key)
)
auth = Initialize(api_key)
else:
logger.info(
"Neither Api Key nor Service Account has been provided!\
Please check the default Service Account file {0}".format(
credentials
)
)
raise click.Abort()
ctx.obj = {
'auth': auth,
'EE_WORKSPACE_BASE': ee_workspace_base,
'EE_WORKSPACE_WAPOR': os.path.join(
ee_workspace_base,
ee_workspace_wapor
),
'level': level,
'verbose': verbose,
'export': export,
'outputs': outputs
}
model_has_complex_texttypes)
from webapp.buttons import *
from webapp.home.exceptions import *
from webapp.pages import *
from webapp.home.views import process_up_button, process_down_button, get_help, get_helps
from metapype.eml import names
from metapype.model.node import Node
from webapp.home.intellectual_rights import (INTELLECTUAL_RIGHTS_CC0,
INTELLECTUAL_RIGHTS_CC_BY)
from webapp.home.views import set_current_page, get_keywords
logger = daiquiri.getLogger('views: ' + __name__)
res_bp = Blueprint('res', __name__, template_folder='templates')
def log_error(msg):
if current_user and hasattr(current_user, 'get_username'):
logger.error(msg, USER=current_user.get_username())
else:
logger.error(msg)
def log_info(msg):
if current_user and hasattr(current_user, 'get_username'):
logger.info(msg, USER=current_user.get_username())
else:
logger.info(msg)
def common(ctx, year, temporal_resolution, input_component, area_code, nodatavalue):
"""
YEAR 2009|2010|...|2018|2019\n
TEMPORAL_RESOLUTION A\n
INPUT_COMPONENT E|T|I|AETI|NPP\n
AREA_CODE: NA|BKA|AWA|KOG|ODN|ZAN\n
NODATAVALUE: 255|-9999\n
example general annual: wapor -l L1 common -- 2016 A E (255)\n
example area code general annual: wapor -l L3 common -- 2016 A E BKA (255)\n
example AETI annual: wapor -l L1 common -- 2016 A AETI (-9999)\n
example area code AETI annual: wapor -l L3 common -- 2016 A AETI BKA (-9999)\n
"""
Log(ctx.obj["verbose"]).initialize()
logger = daiquiri.getLogger(ctx.command.name, subsystem="COMMON")
logger.info(
"================ {0} {1} calculation =================".format(
ctx.command.name,
temporal_resolution
)
)
from algorithms.common import Common
kwargs = {
"year": year,
"temporal_resolution": temporal_resolution,
"component": input_component,
"area_code": area_code,
"nodatavalue": nodatavalue
}
context = ctx.obj.copy()
context.update(kwargs)
# Use class Name to express wapor name convention over GEE
src_image_coll = CommonName(**context).src_collection()
# L1_E_D, L1_T_D, L1_I_D
# L3_E_D, L3_T_D, L3_I_D
logger.debug(
"src_image_coll variable =====> {0}".format(src_image_coll)
)
dst_image_coll = CommonName(**context).dst_collection()
# L1_E_A, L1_T_A, L1_I_A
# L3_E_A, L3_T_A, L3_I_A
logger.debug(
"dst_image_coll variable =====> {0}".format(dst_image_coll)
)
dst_asset_coll = CommonName(**context).dst_assetcollection_id()
# projects/fao_wapor/L1_E_A
# projects/fao_wapor/L3_E_A
logger.debug(
"dst_asset_coll variable =====> {0}".format(dst_asset_coll)
)
dst_asset_image = CommonName(**context).dst_image()
# L1_E_16
# L3_E_16_BKA
logger.debug(
"dst_asset_image variable =====> {0}".format(dst_asset_image)
)
dst_asset_id = CommonName(**context).dst_asset_id()
# projects/fao_wapor/L1_E_A/L1_E_16
# projects/fao_wapor/L3_E_A/L3_E_16_BKA
logger.debug(
"dst_asset_id variable =====> {0}".format(dst_asset_id)
)
kwargs.update(
{
"src_coll": os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll
),
"dst_coll": dst_image_coll,
"dst_asset_coll": dst_asset_coll,
"dst_asset": dst_asset_id,
"to_asset": context["export"],
"intermediate_outputs": context["outputs"]
}
)
logger.debug(
"Input kwargs dictionary for Common process is =====> \n{0}".format(
json.dumps(kwargs)
)
)
# create the instance of the common script class
proc = Common(**kwargs)
# run the process and return the task id
result = proc.process_annual()
if result["errors"]:
raise click.ClickException(
"Commad execution has produced:\n{0}".format(
json.dumps(result)
)
)
else:
click.echo(
json.dumps(result)
)
async def _consume_pulls(
self,
installation: context.Installation,
pulls: PullsToConsume,
) -> None:
LOG.debug("stream contains %d pulls",
len(pulls),
stream_name=installation.stream_name)
for (repo, repo_id, pull_number), (message_ids,
sources) in pulls.items():
statsd.histogram("engine.streams.batch-size", len(sources))
for source in sources:
if "timestamp" in source:
statsd.histogram(
"engine.streams.events.latency",
(datetime.datetime.utcnow() -
datetime.datetime.fromisoformat(
source["timestamp"])).total_seconds(),
)
logger = daiquiri.getLogger(
__name__,
gh_repo=repo,
gh_owner=installation.owner_login,
gh_pull=pull_number,
)
attempts_key = f"pull~{installation.owner_login}~{repo}~{pull_number}"
try:
async with self._translate_exception_to_retries(
installation.stream_name, attempts_key):
await run_engine(installation, repo_id, repo, pull_number,
sources)
await self.redis_stream.hdel("attempts", attempts_key)
await self.redis_stream.execute_command(
"XDEL", installation.stream_name, *message_ids)
except IgnoredException:
await self.redis_stream.execute_command(
"XDEL", installation.stream_name, *message_ids)
logger.debug("failed to process pull request, ignoring",
exc_info=True)
except MaxPullRetry as e:
await self.redis_stream.execute_command(
"XDEL", installation.stream_name, *message_ids)
logger.error(
"failed to process pull request, abandoning",
attempts=e.attempts,
exc_info=True,
)
except PullRetry as e:
logger.info(
"failed to process pull request, retrying",
attempts=e.attempts,
exc_info=True,
)
except StreamRetry:
raise
except StreamUnused:
raise
except vcr_errors_CannotOverwriteExistingCassetteException:
raise
except Exception:
# Ignore it, it will retried later
logger.error("failed to process pull request", exc_info=True)
def aeti(ctx, year, temporal_resolution, input_component, area_code, dekad):
"""
YEAR 2009|2010|...|2018|2019\n
TEMPORAL_RESOLUTION D (DEKADAL)\n
INPUT_COMPONENT AETI\n
AREA_CODE: NA|BKA|AWA|KOG|ODN|ZAN\n
DEKAD: 01|02|...|36\n
example whole dekads: wapor -l L1 aeti -- 2016 D AETI\n
example single dekad: wapor -l L1 aeti -- 2016 D AETI NA 01\n
example area code whole dekads: wapor -l L3 aeti -- 2016 D AETI BKA\n
example area code single dekad: wapor -l L3 aeti -- 2016 D AETI BKA 01\n
"""
Log(ctx.obj["verbose"]).initialize()
logger = daiquiri.getLogger(ctx.command.name, subsystem="AETI")
logger.info(
"================ {0} {1} calculation =================".format(
ctx.command.name,
temporal_resolution
)
)
from algorithms.aeti import AETI
kwargs = {
"year": year,
"temporal_resolution": temporal_resolution,
"component": input_component, # AETI
"area_code": area_code,
"dekad": dekad
}
context = ctx.obj.copy()
context.update(kwargs)
# Use class AETIName to express wapor name convention over GEE
src_image_coll = AETIName(**context).src_collection()
# L1_E_D, L1_T_D, L1_I_D
logger.debug(
"src_image_coll variable =====> {0}".format(src_image_coll)
)
dst_image_coll = AETIName(**context).dst_collection()
# L1_AETI_D
logger.debug(
"dst_image_coll variable =====> {0}".format(dst_image_coll)
)
dst_asset_coll = AETIName(**context).dst_assetcollection_id()
# projects/fao_wapor/L1_AETI_D
logger.debug(
"dst_asset_coll variable =====> {0}".format(dst_asset_coll)
)
dst_asset_images = AETIName(**context).dst_images()
# [L1_AETI_1601,...,L1_AETI_1636]
# [L3_AETI_1601_BKA,...,L3_AETI_1636_BKA]
logger.debug(
"dst_asset_images variable =====> {0}".format(dst_asset_images)
)
dst_asset_ids = AETIName(**context).dst_asset_ids()
# [projects/fao_wapor/L1_AETI_D/L1_AETI_1601,...,
# ,...,projects/fao_wapor/L1_AETI_D/L1_AETI_1636]
# [projects/fao_wapor/L3_AETI_D/L3_AETI_1601_BKA,...,
# ,...,projects/fao_wapor/L3_AETI_D/L3_AETI_1636_BKA]
logger.debug(
"dst_asset_ids variable =====> {0}".format(dst_asset_ids)
)
if "AETI" in dst_image_coll:
if context["temporal_resolution"] in [
tr.dekadal.value,
tr.short_dekadal.value
]:
# projects/fao_wapor/L1_E_D
e = os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll[0]
)
# projects/fao_wapor/L1_T_D
t = os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll[1]
)
# projects/fao_wapor/L1_I_D
i = os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll[2]
)
colls = {"collI": i, "collE": e, "collT": t}
kwargs.update(colls)
kwargs.update(
{
"dst_coll": dst_image_coll,
"dst_asset_coll": dst_asset_coll,
"dst_assets": dst_asset_ids,
"to_asset": context["export"],
"intermediate_outputs": context["outputs"]
}
)
logger.debug(
"Input kwargs dictionary for AETI process is =====> \n{0}".format(
json.dumps(kwargs)
)
)
# Create Marmee object instance with specific inputs for AETI and filter
aeti = AETI(**kwargs)
# Run the process for dekadal
try:
# run the process and return the task id
result = aeti.process_dekadal()
if result["errors"]:
raise click.ClickException(
"Commad execution has produced:\n{0}".format(
json.dumps(result)
)
)
else:
click.echo(
json.dumps(result)
)
except Exception as e:
raise
elif context["temporal_resolution"] in [
tr.annual.value,
tr.short_annual.value
]:
pass
# Run the process for annual
try:
pass
aeti.process_annual()
except Exception as e:
raise
else:
raise ValueError("Not allowed for wapor annual or dekadal.")
else:
raise ValueError("Wrong value for algorithm not being AETI")
#!/usr/bin/env python3
import requests
import click
import logging
import daiquiri
daiquiri.setup(level=logging.INFO)
_LOGGER = daiquiri.getLogger(__name__)
DOCKERHUB_ORGANIZATION = 'radanalyticsio'
DOCKERHUB_API_URL = 'https://hub.docker.com/'
THOTH_ANALYZER_NAME = 'fridex/thoth-package-extract'
def list_dockerhub_images(dockerhub_user: str, dockerhub_password: str,
organization: str) -> list:
"""List images on docker hub in the given organization."""
response = requests.post(DOCKERHUB_API_URL + '/v2/users/login/',
json={
'username': dockerhub_user,
'password': dockerhub_password
})
response.raise_for_status()
token = response.json()['token']
# TODO: pagination
response = requests.get(DOCKERHUB_API_URL +
f'/v2/repositories/{organization}',
headers={'Authorization': f'JWT {token}'},
def AGBP(ctx, year, temporal_resolution, input_component, nodatavalue):
"""
YEAR 2009|2010|...|2018|2019\n
TEMPORAL_RESOLUTION A (ANNUAL)\n
INPUT_COMPONENT NPP\n
NODATAVALUE -9999\n
example annual: wapor -l L1 agbp -- 2016 A NPP (-9999)\n
"""
Log(ctx.obj["verbose"]).initialize()
logger = daiquiri.getLogger(ctx.command.name, subsystem="AGBP")
logger.info(
"================ {0} {1} calculation =================".format(
ctx.command.name,
temporal_resolution
)
)
from algorithms.agbp import AGBP
kwargs = {
"year": year,
"temporal_resolution": temporal_resolution,
"component": input_component,
"nodatavalue": nodatavalue
}
context = ctx.obj.copy()
context.update(kwargs)
# Use class Name to express wapor name convention over GEE
src_image_coll = AGBPName(**context).src_collection()
# L1_NPP_D
logger.debug(
"AGBP src_image_coll variable =====> {0}".format(src_image_coll)
)
dst_image_coll = AGBPName(**context).dst_collection()
# L1_AGBP_A
logger.debug(
"AGBP dst_image_coll variable =====> {0}".format(dst_image_coll)
)
dst_asset_coll = AGBPName(**context).dst_assetcollection_id()
# projects/fao_wapor/L1_AGBP_A
logger.debug(
"AGBP dst_asset_coll variable =====> {0}".format(dst_asset_coll)
)
dst_asset_image = AGBPName(**context).dst_image()
# L1_AGBP_16
logger.debug(
"AGBP dst_asset_image variable =====> {0}".format(dst_asset_image)
)
dst_asset_id = AGBPName(**context).dst_asset_id()
# projects/fao_wapor/L1_AGBP_A/L1_AGBP_16
logger.debug(
"AGBP dst_asset_id variable =====> {0}".format(dst_asset_id)
)
kwargs.update(
{
"src_coll": os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll
),
"dst_coll": dst_image_coll,
"dst_asset_coll": dst_asset_coll,
"dst_asset": dst_asset_id,
"to_asset": context["export"],
"intermediate_outputs": context["outputs"]
}
)
logger.debug(
"Input kwargs dictionary for AGBP process is =====> \n{0}".format(
json.dumps(kwargs)
)
)
# create the instance of the agbp script class
proc = AGBP(**kwargs)
# run the process and return the task id
result = proc.process_annual()
if result["errors"]:
raise click.ClickException(
"Commad execution has produced:\n{0}".format(
json.dumps(result)
)
)
else:
click.echo(
json.dumps(result)
)
from utils import cloud_constants as cc
import boto3
import botocore
import os
from pathlib import Path
import daiquiri
import logging
daiquiri.setup(level=logging.INFO)
_logger = daiquiri.getLogger(__name__)
_aws_key_id = cc.AWS_S3_ACCESS_KEY_ID or os.environ.get('AWS_S3_ACCESS_KEY_ID')
_aws_secret_key = cc.AWS_S3_SECRET_ACCESS_KEY or os.environ.get(
'AWS_S3_SECRET_ACCESS_KEY')
_aws_region = cc.AWS_S3_REGION or os.environ.get('AWS_S3_REGION', 'us-east-1')
session = boto3.session.Session(aws_access_key_id=_aws_key_id,
aws_secret_access_key=_aws_secret_key,
region_name=_aws_region)
S3_OBJ = session.resource(
's3',
config=botocore.client.Config(signature_version='s3v4'),
use_ssl=True)
def s3_download_folder(
s3_bucket_obj,
bucket_dir_prefix='',
download_path='./',
):
def GBWP(ctx, year, temporal_resolution, season, input_component, area_code, nodatavalue):
"""
YEAR 2009|2010|...|2018|2019\n
TEMPORAL_RESOLUTION A (ANNUAL) S (SEASONAL)\n
SEASON 1|2\n
INPUT_COMPONENT AGBP\n
AREA_CODE: NA|BKA|AWA|KOG|ODN|ZAN\n
NODATAVALUE -9999\n
example L1 annual: wapor -l L1 gbwp -- 2016 A -1 AGBP NA (-9999)\n
example L2 seasonal: wapor -l L2 gbwp -- 2016 S 1 AGBP NA (-9999)\n
example L3 seasonal: wapor -l L3 gbwp -- 2016 S 1 AGBP AWA (-9999)\n
"""
Log(ctx.obj["verbose"]).initialize()
logger = daiquiri.getLogger(ctx.command.name, subsystem="GBWP")
logger.info(
"================ {0} {1} calculation =================".format(
ctx.command.name,
temporal_resolution
)
)
from algorithms.gbwp import GBWP
kwargs = {
"year": year,
"temporal_resolution": temporal_resolution,
"season": season,
"component": input_component,
"area_code": area_code,
"nodatavalue": nodatavalue
}
context = ctx.obj.copy()
context.update(kwargs)
# Use class Name to express wapor name convention over GEE
src_image_coll = GBWPName(**context).src_collection()
# L1_AGBP_A | L2_AGBP_S | L3_AGBP_S
logger.debug(
"GBWP src_image_coll variable =====> {0}".format(src_image_coll)
)
dst_image_coll = GBWPName(**context).dst_collection()
# L1_GBWP_A | L2_GBWP_S | L3_GBWP_S
logger.debug(
"GBWP dst_image_coll variable =====> {0}".format(dst_image_coll)
)
dst_asset_coll = GBWPName(**context).dst_assetcollection_id()
# projects/fao-wapor/L1/L1_GBWP_A | projects/fao-wapor/L2/L2_GBWP_S
# | projects/fao-wapor/L3/L3_GBWP_S
logger.debug(
"GBWP dst_asset_coll variable =====> {0}".format(dst_asset_coll)
)
dst_asset_image = GBWPName(**context).dst_image()
# L1_GBWP_16 | L2_GBWP_16s1 | L3_GBWP_16s1_AWA
logger.debug(
"GBWP dst_asset_image variable =====> {0}".format(dst_asset_image)
)
dst_asset_id = GBWPName(**context).dst_asset_id()
# projects/fao-wapor/L1/L1_GBWP_A/L1_GBWP_16 |
# projects/fao-wapor/L2/L2_GBWP_S/L2_GBWP_16s1 |
# projects/fao-wapor/L3/L3_GBWP_S/L3_GBWP_16s1_AWA
logger.debug(
"GBWP dst_asset_id variable =====> {0}".format(dst_asset_id)
)
kwargs.update(
{
"src_coll": os.path.join(
os.path.join(
context["EE_WORKSPACE_WAPOR"],
context["level"]
),
src_image_coll
),
"dst_coll": dst_image_coll,
"dst_asset_coll": dst_asset_coll,
"dst_asset": dst_asset_id,
"to_asset": context["export"],
"intermediate_outputs": context["outputs"],
"level": context["level"]
}
)
logger.debug(
"Input kwargs dictionary for GBWP process is =====> \n{0}".format(
json.dumps(kwargs)
)
)
# create the instance of the gbwp script class
proc = GBWP(**kwargs)
# run the process and return the task id
if proc.config["season"] == '-1':
result = proc.process_annual()
else:
result = proc.process_seasonal()
if result["errors"]:
raise click.ClickException(
"Commad execution has produced:\n{0}".format(
json.dumps(result)
)
)
else:
click.echo(
json.dumps(result)
)
import asyncio
import dataclasses
import json
import daiquiri
import redis
from mergify_engine import check_api
from mergify_engine import context
from mergify_engine import exceptions
from mergify_engine import sub_utils
from mergify_engine import utils
from mergify_engine.actions.merge import helpers
from mergify_engine.clients import github
LOG = daiquiri.getLogger(__name__)
@dataclasses.dataclass
class Queue:
redis: redis.Redis
installation_id: int
owner: str
repo: str
ref: str
@property
def log(self):
return daiquiri.getLogger(__name__,
gh_owner=self.owner,
gh_repo=self.repo,
:Synopsis:
:Author:
servilla
:Created:
3/30/18
"""
from http import HTTPStatus
import aiohttp
import daiquiri
from soh.config import Config
logger = daiquiri.getLogger('audit.py: ' + __name__)
async def is_down(host=None):
url = 'http://' + host + ':8080/audit/docs/api'
assert_is_down = True
try:
async with aiohttp.ClientSession() as session:
async with session.get(url) as resp:
r = resp.status
assert_is_down = r != HTTPStatus.OK
if assert_is_down:
msg = f"{__file__}: Status code is {r}"
logger.warning(msg)
except Exception as e:
logger.error(e)
"""
import logging
import daiquiri
import numpy as np
import pandas as pd
from dateutil import parser
from workalendar.europe import France
from sklearn.cluster import KMeans
import xgboost as xgb
from jitenshea import config
daiquiri.setup(logging.INFO)
logger = daiquiri.getLogger("stats")
# French Calendar
cal = France()
SEED = 2018
np.random.seed(SEED)
CLUSTER_ACT_PATH_CSV ='jitenshea/data/cluster_activite.csv'
###################################
### CLUSTER ACTIVITE
###################################
def preprocess_data_for_clustering(df):
import glob
import itertools
import logging
import netrc
import operator
import os
import shutil
import subprocess
import sys
import tempfile
from urllib import parse
import daiquiri
import github
LOG = daiquiri.getLogger("git-pull-request")
def _run_shell_command(cmd, output=None, raise_on_error=True):
if output is True:
output = subprocess.PIPE
LOG.debug("running %s", cmd)
sub = subprocess.Popen(cmd, stdout=output, stderr=output)
out = sub.communicate()
if raise_on_error and sub.returncode:
raise RuntimeError("%s returned %d" % (cmd, sub.returncode))
if out[0] is not None:
return out[0].strip().decode()
# -*- coding: utf-8 -*-
import sys
import ssl
import socket
import logging
from http.server import HTTPServer
from socketserver import ThreadingMixIn
import daiquiri
daiquiri.setup(level=logging.DEBUG)
logger = daiquiri.getLogger()
from pyproxy import settings
class ThreadingHTTPServer(ThreadingMixIn, HTTPServer):
address_family = socket.AF_INET6
daemon_threads = True
def handle_error(self, request, client_address):
cls, e = sys.exc_info()[:2]
if cls in (socket.error, ssl.SSLError):
pass
else:
return HTTPServer.handle_error(self, request, client_address)
class ProxyFactory:
@staticmethod
def create(handler):
# handler.protocol_version = settings.PROTOCOL_VERSION
http_server = ThreadingHTTPServer((settings.HOST, settings.PORT), handler)
from pathlib import Path
import uuid
import json
import shutil
import daiquiri
# App-specific includes
import common.config as config
import common.rule_evaluation as rule_evaluation
import common.monitor as monitor
import common.helper as helper
import common.notification as notification
from common.constants import mercure_defs, mercure_names, mercure_actions, mercure_rule, mercure_config, mercure_options, mercure_folders, mercure_events
from routing.generate_taskfile import generate_taskfile_route, generate_taskfile_process, create_study_task, create_series_task_processing
logger = daiquiri.getLogger("route_series")
def route_series(series_UID):
"""Processes the series with the given series UID from the incoming folder."""
lock_file = Path(config.mercure[mercure_folders.INCOMING] + '/' +
str(series_UID) + mercure_names.LOCK)
if lock_file.exists():
# Series is locked, so another instance might be working on it
return
# Create lock file in the incoming folder and prevent other instances from working on this series
try:
lock = helper.FileLock(lock_file)
except:
from gnocchi import utils
OPTS = [
cfg.StrOpt('file_basepath',
default='/var/lib/gnocchi',
help='Path used to store gnocchi data files.'),
cfg.IntOpt('file_subdir_len',
default=2, min=0, max=32,
help='if > 0, this create a subdirectory for every N bytes'
'of the metric uuid')
]
ATTRGETTER_METHOD = operator.attrgetter("method")
LOG = daiquiri.getLogger(__name__)
# Python 2 compatibility
try:
FileNotFoundError
except NameError:
FileNotFoundError = None
class FileStorage(storage.StorageDriver):
WRITE_FULL = True
CFG_PREFIX = 'gnocchi-storage-config'
CFG_SUBDIR_LEN = 'subdir_len'
def __init__(self, conf):
super(FileStorage, self).__init__(conf)
"""
import pathlib
import shutil
import tempfile
from typing import Optional, List
import repobee_plug as plug
import daiquiri
import git
from repobee_sanitizer import _sanitize, _fileutils, _syntax, _format
PLUGIN_NAME = "sanitizer"
LOGGER = daiquiri.getLogger(__file__)
class EmptyCommitError(plug.PlugError):
pass
def check_repo_state(repo_root) -> Optional[str]:
try:
repo = git.Repo(repo_root)
except git.InvalidGitRepositoryError as exc:
raise plug.PlugError(f"Not a git repository: '{repo_root}'") from exc
message = ""
help_message = "\n\nUse --force to ingore this warning and sanitize anyway"
