Merge branch 'master' of https://github.com/biocore/qiita into delete-raw-data

Author: antgonza

qiita_core/configuration_manager.py

@@ -10,11 +10,12 @@
 from os.path import join, dirname, abspath, isdir
 from os import environ
 from future import standard_library
-with standard_library.hooks():
-    from configparser import ConfigParser
 
 from .exceptions import MissingConfigSection
 
+with standard_library.hooks():
+    from configparser import ConfigParser
+
 
 class ConfigurationManager(object):
     """Holds the QIITA configuration

qiita_core/util.py

@@ -7,14 +7,15 @@
 # -----------------------------------------------------------------------------
 from smtplib import SMTP, SMTP_SSL, SMTPException
 from future import standard_library
-with standard_library.hooks():
-    from email.mime.multipart import MIMEMultipart
-    from email.mime.text import MIMEText
 
 from qiita_core.qiita_settings import qiita_config
 from qiita_db.sql_connection import SQLConnectionHandler
 from qiita_db.environment_manager import reset_test_database
 
+with standard_library.hooks():
+    from email.mime.multipart import MIMEMultipart
+    from email.mime.text import MIMEText
+
 
 def send_email(to, subject, body):
     # create email

qiita_db/commands.py

@@ -14,8 +14,6 @@
 from future.utils import viewitems
 from collections import defaultdict
 from shutil import move
-with standard_library.hooks():
-    from configparser import ConfigParser
 
 from .study import Study, StudyPerson
 from .user import User
@@ -28,6 +26,10 @@
                          ProcessedSortmernaParams)
 from .sql_connection import SQLConnectionHandler
 
+with standard_library.hooks():
+    from configparser import ConfigParser
+
+
 SUPPORTED_PARAMS = ['preprocessed_sequence_illumina_params',
                     'preprocessed_sequence_454_params',
                     'processed_params_sortmerna']
@@ -51,7 +53,10 @@ def load_study_from_cmd(owner, title, info):
     config.readfp(info)
 
     optional = dict(config.items('optional'))
-    get_optional = lambda name: optional.get(name, None)
+
+    def get_optional(name):
+        return optional.get(name, None)
+
     get_required = partial(config.get, 'required')
     required_fields = ['timeseries_type_id', 'mixs_compliant',
                        'portal_type_id', 'reprocess', 'study_alias',

qiita_db/environment_manager.py

@@ -5,6 +5,9 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
+
+from qiita_db.ontology import Ontology
+from qiita_db.util import convert_to_id
 from os.path import abspath, dirname, join, exists, basename, splitext
 from functools import partial
 from os import mkdir
@@ -13,16 +16,16 @@
 
 from future import standard_library
 from future.utils import viewitems
-with standard_library.hooks():
-    from urllib.request import urlretrieve
-from natsort import natsorted
 
 from qiita_core.exceptions import QiitaEnvironmentError
 from qiita_core.qiita_settings import qiita_config
 from .sql_connection import SQLConnectionHandler
 from .reference import Reference
-from qiita_db.ontology import Ontology
-from qiita_db.util import convert_to_id
+from natsort import natsorted
+
+with standard_library.hooks():
+    from urllib.request import urlretrieve
+
 
 get_support_file = partial(join, join(dirname(abspath(__file__)),
                                       'support_files'))

qiita_db/metadata_template.py

@@ -388,7 +388,13 @@ def __getitem__(self, key):
         if key in self._get_categories(conn_handler):
             # It's possible that the key is asking for one of the *_id columns
             # that we have to do the translation
-            handler = lambda x: x
+            def handler(x):
+                return x
+
+            # prevent flake8 from complaining about the function not being
+            # used and a redefinition happening in the next few lines
+            handler(None)
+
             if key in self._md_template.translate_cols_dict.values():
                 handler = (
                     lambda x: self._md_template.str_cols_handlers[key][x])

qiita_db/test/test_commands.py

@@ -14,8 +14,6 @@
 from future.utils.six import StringIO
 from future import standard_library
 from functools import partial
-with standard_library.hooks():
-    import configparser
 
 from qiita_db.commands import (load_study_from_cmd, load_raw_data_cmd,
                                load_sample_template_from_cmd,
@@ -33,6 +31,9 @@
 from qiita_core.util import qiita_test_checker
 from qiita_ware.processing_pipeline import generate_demux_file
 
+with standard_library.hooks():
+    import configparser
+
 
 @qiita_test_checker()
 class TestMakeStudyFromCmd(TestCase):

qiita_db/util.py

@@ -661,9 +661,9 @@ def insert_filepaths(filepaths, obj_id, table, filepath_table, conn_handler,
             for old_fp, new_fp in zip(filepaths, new_filepaths):
                     move(old_fp[0], new_fp[0])
 
-        str_to_id = lambda x: (x if isinstance(x, (int, long))
-                               else convert_to_id(x, "filepath_type",
-                                                  conn_handler))
+        def str_to_id(x):
+            return (x if isinstance(x, (int, long))
+                    else convert_to_id(x, "filepath_type", conn_handler))
         paths_w_checksum = [(relpath(path, base_fp), str_to_id(id),
                             compute_checksum(path))
                             for path, id in new_filepaths]

qiita_pet/handlers/compute.py

@@ -51,7 +51,8 @@ def post(self):
         else:
             check_access(self.current_user, study, raise_error=True)
 
-        _split = lambda x: x.split(',') if x else []
+        def _split(x):
+            return x.split(',') if x else []
         filepaths, fps = [], []
         fps.append((_split(barcodes_str), 'raw_barcodes'))
         fps.append((_split(fasta_str), 'raw_fasta'))

qiita_pet/handlers/study_handlers/description_handlers.py

@@ -523,7 +523,8 @@ def display_template(self, study, user, msg, msg_level, top_tab=None,
 
         # set variable holding if we have all prep templates or not
         if available_prep_templates:
-            _test = lambda item: not item
+            def _test(item):
+                return not item
             prep_templates = all(
                 [_test(val) for val in viewvalues(available_prep_templates)])
         else:

qiita_ware/wrapper.py

@@ -1,14 +1,5 @@
 from __future__ import division
 
-__author__ = "Jose Antonio Navas Molina"
-__copyright__ = "Copyright 2011, The QIIME project"
-__credits__ = ["Jose Antonio Navas Molina"]
-__license__ = "BSD"
-__version__ = "1.8.0-dev"
-__maintainer__ = "Jose Navas Antonio Molina"
-# Taken from pull request #1616 in qiime, with permission from Jose
-# Permission was also given to release this code under the BSD licence
-
 from shutil import rmtree
 from os import remove
 from sys import stderr