Release candidate (#2298)

qiita_core/qiita_settings.py

@@ -1,14 +1,20 @@
 #!/usr/bin/env python
-from __future__ import division
-
 # -----------------------------------------------------------------------------
 # Copyright (c) 2014--, The Qiita Development Team.
 #
 # Distributed under the terms of the BSD 3-clause License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
+from __future__ import division
+
+from redis import Redis
 
 from qiita_core.configuration_manager import ConfigurationManager
 
 qiita_config = ConfigurationManager()
+
+r_client = Redis(host=qiita_config.redis_host,
+                 port=qiita_config.redis_port,
+                 password=qiita_config.redis_password,
+                 db=qiita_config.redis_db)

qiita_core/testing.py

@@ -9,7 +9,7 @@
 from json import loads
 from time import sleep
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_db.processing_job import ProcessingJob
 

qiita_core/util.py

@@ -11,9 +11,8 @@
 from os.path import dirname
 from git import Repo
 from git.exc import InvalidGitRepositoryError
-from moi import r_client
 
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_pet import __version__ as qiita_pet_lib_version
 import qiita_db as qdb
 

qiita_db/handlers/oauth2.py

@@ -14,7 +14,7 @@
 from traceback import format_exception
 
 from tornado.web import RequestHandler
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_core.exceptions import (IncorrectPasswordError, IncorrectEmailError,
                                    UnverifiedEmailError)

qiita_db/handlers/tests/oauthbase.py

@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 

qiita_db/handlers/tests/test_oauth2.py

@@ -8,7 +8,7 @@
 from unittest import main
 from json import loads
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 

qiita_db/meta_util.py

@@ -24,7 +24,6 @@
 # -----------------------------------------------------------------------------
 from __future__ import division
 
-from moi import r_client
 from os import stat, makedirs, rename
 from os.path import join, relpath, exists
 from time import strftime, localtime
@@ -38,7 +37,7 @@
 from tarfile import open as topen, TarInfo
 from hashlib import md5
 
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_core.configuration_manager import ConfigurationManager
 import qiita_db as qdb
 

qiita_db/test/test_meta_util.py

@@ -14,8 +14,7 @@
 
 import pandas as pd
 
-from moi import r_client
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_core.util import qiita_test_checker
 
 import qiita_db as qdb

qiita_pet/handlers/analysis_handlers/base_handlers.py

@@ -9,10 +9,9 @@
 from json import loads
 
 from tornado.web import authenticated
-from moi import r_client
 
 from qiita_core.util import execute_as_transaction
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.analysis_handlers import check_analysis_access
 from qiita_pet.handlers.util import to_int

qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py

@@ -10,9 +10,9 @@
 from json import loads, dumps
 
 from tornado.web import HTTPError
-from moi import r_client
 
 from qiita_core.util import qiita_test_checker
+from qiita_core.qiita_settings import r_client
 from qiita_core.testing import wait_for_processing_job
 from qiita_db.user import User
 from qiita_db.analysis import Analysis

qiita_pet/handlers/api_proxy/artifact.py

@@ -11,10 +11,9 @@
 
 from future.utils import viewitems
 from itertools import chain
-from moi import r_client
 
 from qiita_core.util import execute_as_transaction
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
 from qiita_ware.context import safe_submit
 from qiita_ware.dispatchable import copy_raw_data

qiita_pet/handlers/api_proxy/prep_template.py

@@ -12,9 +12,9 @@
 from json import loads, dumps
 
 from natsort import natsorted
-from moi import r_client
 
 from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import r_client
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
 from qiita_ware.context import safe_submit
 from qiita_ware.dispatchable import (

qiita_pet/handlers/api_proxy/sample_template.py

@@ -9,12 +9,12 @@
 from json import loads, dumps
 
 from natsort import natsorted
-from moi import r_client
 
+from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import r_client
 from qiita_db.metadata_template.sample_template import SampleTemplate
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.study import Study
-from qiita_core.util import execute_as_transaction
 from qiita_db.metadata_template.util import looks_like_qiime_mapping_file
 from qiita_db.exceptions import QiitaDBColumnError
 from qiita_db.user import User

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -13,10 +13,10 @@
 
 import pandas as pd
 import numpy.testing as npt
-from moi import r_client
 
 from qiita_core.util import qiita_test_checker
 from qiita_core.testing import wait_for_prep_information_job
+from qiita_core.qiita_settings import r_client
 from qiita_db.artifact import Artifact
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.study import Study

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -15,9 +15,9 @@
 
 import pandas as pd
 import numpy.testing as npt
-from moi import r_client
 
 from qiita_core.util import qiita_test_checker
+from qiita_core.qiita_settings import r_client
 from qiita_db.artifact import Artifact
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.ontology import Ontology

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

@@ -11,9 +11,8 @@
 from time import sleep
 from json import loads, dumps
 
-from moi import r_client
-
 from qiita_core.util import qiita_test_checker
+from qiita_core.qiita_settings import r_client
 import qiita_db as qdb
 from qiita_pet.handlers.api_proxy.sample_template import (
     sample_template_summary_get_req, sample_template_post_req,

qiita_pet/handlers/artifact_handlers/base_handlers.py

@@ -10,9 +10,8 @@
 from json import dumps
 
 from tornado.web import authenticated, StaticFileHandler
-from moi import r_client
 
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import safe_execution
 from qiita_pet.exceptions import QiitaHTTPError

qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py

@@ -13,9 +13,8 @@
 from json import loads
 
 from tornado.web import HTTPError
-from moi import r_client
 
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_core.testing import wait_for_prep_information_job
 from qiita_core.util import qiita_test_checker
 from qiita_db.user import User

qiita_pet/handlers/auth_handlers.py

@@ -9,10 +9,8 @@
 from tornado.escape import url_escape, json_encode
 from tornado.web import HTTPError
 
-from moi import r_client
-
 from qiita_pet.handlers.base_handlers import BaseHandler
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_core.util import send_email, execute_as_transaction
 from qiita_core.exceptions import (IncorrectPasswordError, IncorrectEmailError,
                                    UnverifiedEmailError)

qiita_pet/handlers/stats.py

@@ -10,11 +10,10 @@
 
 from random import choice
 
-from moi import r_client
 from tornado.gen import coroutine, Task
 
 from qiita_core.util import execute_as_transaction
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_db.study import Study
 from .base_handlers import BaseHandler
 

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -13,18 +13,17 @@
 from tornado.web import authenticated, HTTPError
 from tornado.gen import coroutine, Task
 from pyparsing import ParseException
-from moi import r_client
 
+from qiita_core.exceptions import IncompetentQiitaDeveloperError
+from qiita_core.util import execute_as_transaction
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_db.artifact import Artifact
 from qiita_db.user import User
 from qiita_db.study import Study
 from qiita_db.search import QiitaStudySearch
 from qiita_db.logger import LogEntry
 from qiita_db.exceptions import QiitaDBIncompatibleDatatypeError
 from qiita_db.util import (add_message, generate_study_list)
-from qiita_core.exceptions import IncompetentQiitaDeveloperError
-from qiita_core.util import execute_as_transaction
-from qiita_core.qiita_settings import qiita_config
 from qiita_pet.util import EBI_LINKIFIER
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.util import (

qiita_pet/handlers/study_handlers/tests/test_listing_handlers.py

@@ -9,10 +9,9 @@
 from json import loads
 
 from mock import Mock
-from moi import r_client
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_db.artifact import Artifact
 from qiita_db.study import Study
 from qiita_db.user import User

qiita_pet/handlers/study_handlers/tests/test_sample_template.py

@@ -9,7 +9,7 @@
 from json import loads
 from time import sleep
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 from qiita_pet.handlers.study_handlers.sample_template import (

qiita_pet/handlers/websocket_handlers.py

@@ -17,7 +17,7 @@
 from tornado.gen import engine, Task
 from future.utils import viewvalues
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_db.artifact import Artifact
 from qiita_core.util import execute_as_transaction

qiita_pet/templates/sitebase.html

@@ -1,5 +1,4 @@
-{% from moi import r_client %}
-{% from qiita_core.qiita_settings import qiita_config %}
+{% from qiita_core.qiita_settings import qiita_config, r_client %}
 {% from qiita_core.util import get_qiita_version, get_release_info %}
 {% from qiita_pet import allowed_min_browser_versions %}
 {% from qiita_pet.portal import portal_styling %}

qiita_pet/test/rest/test_base.py

@@ -5,7 +5,7 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 

qiita_pet/test/test_user_handlers.py

@@ -8,7 +8,7 @@
 
 from unittest import main
 
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 

qiita_ware/context.py

@@ -12,7 +12,7 @@
 from time import sleep
 
 from IPython.parallel import Client
-from moi import r_client
+from qiita_core.qiita_settings import r_client
 
 from .exceptions import ComputeError
 
@@ -206,7 +206,7 @@ def _deposit_payload(redis_deets, payload):
         class function does not work.
         """
         from json import dumps
-        from moi import r_client
+        from qiita_core.qiita_settings import r_client
 
         job_id = redis_deets['job_id']
         pubsub = redis_deets['pubsub']

scripts/qiita

@@ -22,10 +22,9 @@ import click
 import tornado.httpserver
 import tornado.ioloop
 from psycopg2 import OperationalError
-from moi import r_client
 
 import qiita_db as qdb
-from qiita_core.qiita_settings import qiita_config
+from qiita_core.qiita_settings import qiita_config, r_client
 from qiita_ware.ebi import EBISubmission
 from qiita_ware.commands import submit_EBI as _submit_EBI
 from qiita_ware.context import system_call, ComputeError

scripts/qiita-env

@@ -128,8 +128,8 @@ def test(runner):
 def job_details(job):
     """Pretty print moi job details"""
     from json import loads
-    from moi import r_client
     from redis.exceptions import ResponseError
+    from qiita_core.qiita_settings import r_client
 
     try:
         data = r_client.get(job)