Globals straighten-up.

* Move `env` to lakeusperior package
* Make `env` a global module again
* Add `thread_env` only for thread-local vars
* Add `config` read-only property of AppGlobals

conftest.py

@@ -1,11 +1,8 @@
-import sys
-
 import pytest
 
-sys.path.append('.')
+from lakesuperior import env
 from lakesuperior.config_parser import test_config
 from lakesuperior.globals import AppGlobals
-from lakesuperior.env import env
 
 env.config = test_config
 env.app_globals = AppGlobals(test_config)

docs/apidoc/lakesuperior.rst

@@ -34,7 +34,7 @@ lakesuperior\.config\_parser module
 lakesuperior\.env module
 ------------------------
 
-.. automodule:: lakesuperior.env
+.. automodule:: lakesuperior
     :members:
     :undoc-members:
     :show-inheritance:

docs/usage.rst

@@ -125,9 +125,9 @@ Or, to specify an alternative configuration::
 
     >>> from lakesuperior.config_parser import parse_config
     >>> from lakesuperior.globals import AppGlobals
-    >>> env.config, test_config = parse_config('/my/custom/config_dir')
+    >>> config, test_config = parse_config('/my/custom/config_dir')
     Reading configuration at /my/custom/config_dir
-    >>> env.app_globals = AppGlobals(env.config)
+    >>> env.app_globals = AppGlobals(config)
 
 Create and replace resources
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lakesuperior/__init__.py

@@ -0,0 +1,49 @@
+import threading
+
+from os import path
+
+basedir = path.dirname(path.realpath(__file__))
+"""
+Base directory for the module.
+
+This can be used by modules looking for configuration and data files to be
+referenced or copied with a known path relative to the package root.
+
+:rtype: str
+"""
+
+class Env:
+    pass
+
+env = Env()
+"""
+A pox on "globals are evil".
+
+All-purpose bucket for storing global variables. Different environments
+(e.g. webapp, test suite) put the appropriate value in it.
+The most important values to be stored are app_conf (either from
+lakesuperior.config_parser.config or lakesuperior.config_parser.test_config)
+and app_globals (obtained by an instance of lakesuperior.globals.AppGlobals).
+
+e.g.::
+
+    >>> from lakesuperior.config_parser import config
+    >>> from lakesuperior.globals import AppGlobals
+    >>> from lakesuperior import env
+    >>> env.app_globals = AppGlobals(config)
+
+This is automated in non-test environments by importing
+`lakesuperior.env_setup`.
+
+:rtype: Object
+"""
+
+thread_env = threading.local()
+"""
+Thread-local environment.
+
+This is used to store thread-specific variables such as start/end request
+timestamps.
+
+:rtype: threading.local
+"""

lakesuperior/api/admin.py

@@ -1,7 +1,7 @@
 import logging
 
+from lakesuperior import env
 from lakesuperior.config_parser import parse_config
-from lakesuperior.env import env
 from lakesuperior.globals import AppGlobals
 from lakesuperior.migrator import Migrator
 from lakesuperior.store.ldp_nr.default_layout import DefaultLayout as FileLayout
@@ -55,8 +55,7 @@ def integrity_check(config_dir=None):
     be added and triggered by different argument flags.
     """
     if config_dir:
-        env.config = parse_config(config_dir)[0]
-        env.app_globals = AppGlobals(env.config)
+        env.app_globals = AppGlobals(parse_config(config_dir)[0])
     else:
         import lakesuperior.env_setup
     with TxnManager(env.app_globals.rdfly.store):

lakesuperior/api/query.py

@@ -2,9 +2,9 @@ import logging
 
 from io import BytesIO
 
+from lakesuperior import env
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
 from lakesuperior.dictionaries.namespaces import ns_mgr as nsm
-from lakesuperior.env import env
 from lakesuperior.store.ldp_rs.lmdb_store import LmdbStore, TxnManager
 
 

lakesuperior/api/resource.py

@@ -13,7 +13,7 @@ from rdflib.namespace import XSD
 from lakesuperior.config_parser import config
 from lakesuperior.exceptions import (
         InvalidResourceError, ResourceNotExistsError, TombstoneError)
-from lakesuperior.env import env
+from lakesuperior import env, thread_env
 from lakesuperior.globals import RES_DELETED, RES_UPDATED
 from lakesuperior.model.ldp_factory import LDP_NR_TYPE, LdpFactory
 from lakesuperior.store.ldp_rs.lmdb_store import TxnManager
@@ -72,15 +72,16 @@ def transaction(write=False):
         def _wrapper(*args, **kwargs):
             # Mark transaction begin timestamp. This is used for create and
             # update timestamps on resources.
-            env.timestamp = arrow.utcnow()
-            env.timestamp_term = Literal(env.timestamp, datatype=XSD.dateTime)
+            thread_env.timestamp = arrow.utcnow()
+            thread_env.timestamp_term = Literal(
+                    thread_env.timestamp, datatype=XSD.dateTime)
             with TxnManager(env.app_globals.rdf_store, write=write) as txn:
                 ret = fn(*args, **kwargs)
             if len(env.app_globals.changelog):
                 job = Thread(target=_process_queue)
                 job.start()
-            delattr(env, 'timestamp')
-            delattr(env, 'timestamp_term')
+            delattr(thread_env, 'timestamp')
+            delattr(thread_env, 'timestamp_term')
             return ret
         return _wrapper
     return _transaction_deco

lakesuperior/endpoints/query.py

@@ -3,7 +3,7 @@ import logging
 from flask import Blueprint, current_app, request, render_template, send_file
 from rdflib.plugin import PluginException
 
-from lakesuperior.env import env
+from lakesuperior import env
 from lakesuperior.dictionaries.namespaces import ns_mgr as nsm
 from lakesuperior.api import query as query_api
 

lakesuperior/env.py

@@ -1,28 +0,0 @@
-import threading
-
-'''
-Global bucket for switching configuration. Different environments
-(e.g. webapp, test suite) put the appropriate value in it.
-The most important values to be stored are app_conf (either from
-lakesuperior.config_parser.config or lakesuperior.config_parser.test_config)
-and app_globals (obtained by an instance of lakesuperior.globals.AppGlobals).
-
-e.g.:
-
->>> from lakesuperior.config_parser import config
->>> from lakesuperior.globals import AppGlobals
->>> from lakesuperior.env import env
->>> env.config = config
->>> env.app_globals = AppGlobals(config)
-
-This is automated in non-test environments by importing
-`lakesuperior.env_setup`.
-'''
-class Env:
-    pass
-
-# NOTE: this can lead to race conditions in multi-thread operations competing
-# to set a timestamp.
-#env = Env()
-# NOTE: This should be thread-safe but is experimental.
-env = threading.local()

lakesuperior/env_setup.py

@@ -1,16 +1,15 @@
+from lakesuperior import env
 from lakesuperior.config_parser import config
 from lakesuperior.globals import AppGlobals
-from lakesuperior.env import env
 
 __doc__="""
 Default configuration.
 
 Import this module to initialize the configuration for a production setup::
 
-    >>>from lakesuperior import env_setup
+    >>> from lakesuperior import env_setup
 
 Will load the default configuration.
 """
 
-env.config = config
 env.app_globals = AppGlobals(config)

lakesuperior/globals.py

@@ -27,7 +27,7 @@ class AppGlobals:
 
     The variables are set on initialization by passing a configuration dict.
     Usually this is done when starting an application. The instance with the
-    loaded variables is then assigned to the :data:`lakesuperior.env.env`
+    loaded variables is then assigned to the :data:`lakesuperior.env`
     global variable.
 
     You can either load the default configuration::
@@ -36,20 +36,19 @@ class AppGlobals:
 
     Or set up an environment with a custom configuration::
 
-        >>>from lakesuperior.env import env
-        >>>from lakesuperior.app_globals import AppGlobals
-        >>>my_config = {'name': 'value', '...': '...'}
-        >>>env.config = my_config
-        >>>env.app_globals = AppGlobals(my_config)
+        >>> from lakesuperior import env
+        >>> from lakesuperior.app_globals import AppGlobals
+        >>> my_config = {'name': 'value', '...': '...'}
+        >>> env.app_globals = AppGlobals(my_config)
 
     """
-    def __init__(self, conf):
+    def __init__(self, config):
         """
         Generate global variables from configuration.
         """
         from lakesuperior.messaging.messenger import Messenger
 
-        app_conf = conf['application']
+        app_conf = config['application']
 
         # Initialize RDF layout.
         rdfly_mod_name = app_conf['store']['ldp_rs']['layout']
@@ -69,11 +68,26 @@ class AppGlobals:
         self._messenger  = Messenger(app_conf['messaging'])
 
         # Exposed globals.
+        self._config = config
         self._rdfly = rdfly_cls(app_conf['store']['ldp_rs'])
         self._nonrdfly = nonrdfly_cls(app_conf['store']['ldp_nr'])
         self._changelog = deque()
 
 
+    @property
+    def config(self):
+        """
+        Global configuration.
+
+        This is a collection of all configuration options **except** for the
+        WSGI configuration which is initialized at a different time and is
+        stored under :data:`lakesuperior.env.wsgi_options`.
+
+        *TODO:* Update class reference when interface will be separated from
+        implementation.
+        """
+        return self._config
+
     @property
     def rdfly(self):
         """

lakesuperior/lsup_admin.py

@@ -5,9 +5,9 @@ import logging
 import os
 import sys
 
+from lakesuperior import env
 from lakesuperior.api import admin as admin_api
 from lakesuperior.config_parser import config
-from lakesuperior.env import env
 from lakesuperior.store.ldp_rs.lmdb_store import TxnManager
 
 logger = logging.getLogger(__name__)

lakesuperior/migrator.py

@@ -10,8 +10,8 @@ import yaml
 
 from rdflib import Graph, URIRef
 
+from lakesuperior import env, basedir
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
-from lakesuperior.env import env
 from lakesuperior.globals import AppGlobals, ROOT_UID
 from lakesuperior.config_parser import parse_config
 from lakesuperior.store.ldp_rs.lmdb_store import TxnManager
@@ -28,8 +28,7 @@ class StoreWrapper(ContextDecorator):
         self.store = store
 
     def __enter__(self):
-        self.store.open(
-                env.config['application']['store']['ldp_rs'])
+        self.store.open(env.app_globals.rdfly.config)
 
     def __exit__(self, *exc):
         self.store.close()
@@ -95,7 +94,6 @@ class Migrator:
         """
         # Set up repo folder structure and copy default configuration to
         # destination file.
-        cur_dir = path.dirname(path.dirname(path.abspath(__file__)))
         self.dbpath = '{}/data/ldprs_store'.format(dest)
         self.fpath = '{}/data/ldpnr_store'.format(dest)
         self.config_dir = '{}/etc'.format(dest)

lakesuperior/model/ldp_factory.py

@@ -7,11 +7,11 @@ from rdflib import Graph, parser, plugin, serializer
 from rdflib.resource import Resource
 from rdflib.namespace import RDF
 
+from lakesuperior import env
 from lakesuperior.model.ldpr import Ldpr
 from lakesuperior.model.ldp_nr import LdpNr
 from lakesuperior.model.ldp_rs import LdpRs, Ldpc, LdpDc, LdpIc
 from lakesuperior.config_parser import config
-from lakesuperior.env import env
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
 from lakesuperior.exceptions import (
         IncompatibleLdpTypeError, InvalidResourceError, ResourceExistsError,

lakesuperior/model/ldp_nr.py

@@ -6,7 +6,7 @@ from rdflib.namespace import RDF, XSD
 from rdflib.resource import Resource
 from rdflib.term import URIRef, Literal, Variable
 
-from lakesuperior.env import env
+from lakesuperior import env
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
 from lakesuperior.model.ldpr import Ldpr
 from lakesuperior.model.ldp_rs import LdpRs

lakesuperior/model/ldp_rs.py

@@ -2,7 +2,7 @@ import logging
 
 from rdflib import Graph
 
-from lakesuperior.env import env
+from lakesuperior import env
 from lakesuperior.globals import RES_UPDATED
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
 from lakesuperior.model.ldpr import Ldpr

lakesuperior/model/ldpr.py

@@ -10,7 +10,7 @@ import arrow
 from rdflib import Graph, URIRef, Literal
 from rdflib.namespace import RDF
 
-from lakesuperior.env import env
+from lakesuperior import env, thread_env
 from lakesuperior.globals import (
     RES_CREATED, RES_DELETED, RES_UPDATED, ROOT_UID)
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
@@ -411,7 +411,7 @@ class Ldpr(metaclass=ABCMeta):
         else:
             add_trp = {
                 (self.uri, RDF.type, nsc['fcsystem'].Tombstone),
-                (self.uri, nsc['fcrepo'].created, env.timestamp_term),
+                (self.uri, nsc['fcrepo'].created, thread_env.timestamp_term),
             }
 
         self.modify(RES_DELETED, remove_trp, add_trp)
@@ -432,7 +432,7 @@ class Ldpr(metaclass=ABCMeta):
         Remove all traces of a resource and versions.
         """
         logger.info('Purging resource {}'.format(self.uid))
-        refint = env.config['store']['ldp_rs']['referential_integrity']
+        refint = rdfly.config['referential_integrity']
         inbound = True if refint else inbound
         rdfly.forget_rsrc(self.uid, inbound)
 
@@ -692,7 +692,7 @@ class Ldpr(metaclass=ABCMeta):
 
         if (
                 ev_type is not None and
-                env.config['application'].get('messaging')):
+                env.app_globals.config['application'].get('messaging')):
             logger.debug('Enqueuing message for {}'.format(self.uid))
             self._enqueue_msg(ev_type, remove_trp, add_trp)
 
@@ -720,7 +720,7 @@ class Ldpr(metaclass=ABCMeta):
 
         env.app_globals.changelog.append((set(remove_trp), set(add_trp), {
             'ev_type': ev_type,
-            'timestamp': env.timestamp.format(),
+            'timestamp': thread_env.timestamp.format(),
             'rsrc_type': rsrc_type,
             'actor': actor,
         }))
@@ -769,7 +769,7 @@ class Ldpr(metaclass=ABCMeta):
         # Create and modify timestamp.
         if create:
             self.provided_imr.set((
-                self.uri, nsc['fcrepo'].created, env.timestamp_term))
+                self.uri, nsc['fcrepo'].created, thread_env.timestamp_term))
             self.provided_imr.set((
                 self.uri, nsc['fcrepo'].createdBy, self.DEFAULT_USER))
         else:
@@ -781,7 +781,7 @@ class Ldpr(metaclass=ABCMeta):
                     self.uri, nsc['fcrepo'].createdBy)))
 
         self.provided_imr.set((
-            self.uri, nsc['fcrepo'].lastModified, env.timestamp_term))
+            self.uri, nsc['fcrepo'].lastModified, thread_env.timestamp_term))
         self.provided_imr.set((
             self.uri, nsc['fcrepo'].lastModifiedBy, self.DEFAULT_USER))
 

lakesuperior/profiler.py

@@ -5,9 +5,9 @@ from werkzeug.contrib.profiler import ProfilerMiddleware
 # Environment must be set before importing the app factory function.
 import lakesuperior.env_setup
 
+from lakesuperior import env
 from lakesuperior.config_parser import config
 from lakesuperior.globals import AppGlobals
-from lakesuperior.env import env
 
 options = {
     'restrictions': [30],

lakesuperior/server.py

@@ -4,21 +4,20 @@ from logging.config import dictConfig
 # Environment must be set before importing the app factory function.
 import lakesuperior.env_setup
 
+from lakesuperior import env
 from lakesuperior.config_parser import config
 from lakesuperior.globals import AppGlobals
-from lakesuperior.env import env
 
 from lakesuperior.app import create_app
 
-dictConfig(env.config['logging'])
+dictConfig(env.app_globals.config['logging'])
 logger = logging.getLogger(__name__)
 
 logger.info('Graph store location: {}'.format(
-    env.config['application']['store']['ldp_rs']['location']))
-logger.info('Binary store location: {}'.format(
-    env.config['application']['store']['ldp_nr']['path']))
+    env.app_globals.rdfly.config['location']))
+logger.info('Binary store location: {}'.format(env.app_globals.nonrdfly.root))
 
-fcrepo = create_app(env.config['application'])
+fcrepo = create_app(env.app_globals.config['application'])
 
 if __name__ == "__main__":
     fcrepo.run(host='0.0.0.0')

lakesuperior/store/ldp_rs/lmdb_store.py

@@ -14,7 +14,7 @@ from rdflib import Graph, Namespace, URIRef, Variable
 from rdflib.graph import DATASET_DEFAULT_GRAPH_ID as RDFLIB_DEFAULT_GRAPH_URI
 from rdflib.store import Store, VALID_STORE, NO_STORE
 
-from lakesuperior.env import env
+from lakesuperior import env
 
 logger = logging.getLogger(__name__)
 

lakesuperior/store/ldp_rs/rsrc_centric_layout.py

@@ -13,13 +13,13 @@ from rdflib.query import ResultException
 from rdflib.resource import Resource
 from rdflib.store import Store
 
+from lakesuperior import env
 from lakesuperior.dictionaries.namespaces import ns_collection as nsc
 from lakesuperior.dictionaries.namespaces import ns_mgr as nsm
 from lakesuperior.dictionaries.srv_mgd_terms import  srv_mgd_subjects, \
         srv_mgd_predicates, srv_mgd_types
 from lakesuperior.exceptions import (InvalidResourceError,
         ResourceNotExistsError, TombstoneError, PathSegmentError)
-from lakesuperior.env import env
 from lakesuperior.store.ldp_rs.lmdb_store import TxnManager
 
 

lakesuperior/wsgi.py

@@ -5,8 +5,8 @@ from os import environ, makedirs, path
 
 import gunicorn.app.base
 
+from lakesuperior import env
 from lakesuperior.config_parser import default_config_dir
-from lakesuperior.env import env
 
 
 config_file = '{}/gunicorn.yml'.format(default_config_dir)