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Chris Mutel committed 3a6d804

0.11 almost finished. See CHANGES.txt

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+Changelog
+*********
+
+0.11 ()
+=======
+
+Upgrades to updates
+-------------------
+
+The update code filename was changed to ``updates.py``, and dramatically simplified. Code was organized and moved to an Updates class. All functionality was removed from utility scripts and ``bw2-uptodate.py``. Fresh installs should not have erroneous "updates needed" warnings.
+
+Generic DataStore makes new matrices easy
+-----------------------------------------
+
+``data_store.DataStore`` defines a template for all data stores which could be processed into matrix data, and provides a lot of functionality for free. New objects subclass ``DataStore`` or ``ImpactAssessmentDataStore``, and need only define their unique data fields, metadata store, and validator. Abstracting common functionality into a simple class hierarchy should also produce fewer bugs.
+
+Smaller changes
+---------------
+
+- BREAKING CHANGE: The abbreviate mess
+- BREAKING CHANGE: Register for all data store now takes any keyword arguments. There are no required or positional arguments.
+- BREAKING CHANGE: Database.process() doesn't raise an AssertionError for empty databases
+- FEATURE: Database.process() writes a geomapping processed array (linking activity IDs to locations), in addition to normal matrix arrays.
+- FEATURE: Tests now cover more functionality, and should allow for more worry-free development in the future.
+- CHANGE: Database datasets are not required to specify a unit.
+- CHANGE: The default biosphere database is no longer hard coded, and can be set in config.p['biosphere_database']. The default is still "biosphere".
+- CHANGE: The default global location is no longer hard coded, and can be set in config.p['global_location']. The default is still "GLO".
+- CHANGE: Ecospold 1 & 2 data extractors now only have classmethods, and these classes don't need to be instantiated. A more functional style was used to try to avoid unpleasant side effects.

bw2data/__init__.py

 # -*- coding: utf-8 -*
-__version__ = (0, 10, 5)
+__version__ = (0, 11)
 
-from _config import config
-from meta import databases, methods, mapping, reset_meta, geomapping, \
+from ._config import config
+from .meta import databases, methods, mapping, reset_meta, geomapping, \
     weightings, normalizations
-from serialization import JsonWrapper
-from database import Database
-from method import Method
-from weighting_normalization import Weighting, Normalization
-from query import Query, Filter, Result
-from utils import set_data_dir
+from .serialization import JsonWrapper
+from .database import Database
+from .data_store import DataStore
+from .method import Method
+from .weighting_normalization import Weighting, Normalization
+from .query import Query, Filter, Result
 # Don't confuse nose tests
-from utils import setup as bw2setup
-import proxies
-import utils
-import validate
-import io
+from .utils import set_data_dir, setup as bw2setup
+from . import proxies, io
+from .updates import Updates
 
-from upgrades import check_status
-check_status()
+Updates.check_status()

bw2data/_config.py

     def biosphere(self):
         if not hasattr(self, "p"):
             self.load_preferences()
-        return self.p.get("biosphere_database", "biosphere")
+        return self.p.get("biosphere_database", u"biosphere")
+
+    @property
+    def global_location(self):
+        if not hasattr(self, "p"):
+            self.load_preferences()
+        return self.p.get("global_location", u"GLO")
 
 
 config = Config()

bw2data/bin/bw2-uptodate.py

 import warnings
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
-    from bw2data import config
-    from bw2data.upgrades import *
+    from bw2data import config, Updates
 from bw2data.colors import Fore, init, deinit
 
-EXPLANATIONS = {
-    "stats_array reformat": Fore.GREEN + "\nstats_array reformat:" + Fore.RESET + """
-    Upgrading to the ``stats_arrays`` package changes the data format of both inventory databases and impact assessment methods.
-    Read more about the stats_arrays data format: """ + Fore.BLUE + \
-        "\n\thttps://stats_arrays.readthedocs.org/en/latest/\n" + Fore.RESET,
-    "0.10 units restandardization": Fore.GREEN + "0.10 units restandardization:" + Fore.RESET + """
-    Brightway2 tries to normalize units so that they are consistent from machine to machine, and person to person. For example, ``m2a`` is changed to ``square meter-year``. This update adds more data normalizations, and needs to updates links across databases.""",
-}
 
-
-class Updater(object):
+class UpdaterInterface(object):
     def needed(self):
-        try:
-            import stats_arrays
-        except ImportError:
-            warnings.warn(STATS_ARRAY_WARNING)
-            sys.exit(0)
-        with warnings.catch_warnings():
-            warnings.simplefilter("ignore")
-            updates_needed = check_status()
-        return updates_needed
+        return Updates.check_status(False)
 
     def list(self):
         updates_needed = self.needed()
+
         if not updates_needed:
             print(Fore.GREEN + "\n*** Brightway2 is up to date! ***\n")
         else:
             print(Fore.RED + "\n*** Updates found ***")
             for update in updates_needed:
-                print(EXPLANATIONS[update])
+                print(Updates.explain(update))
             print(Fore.RED + "\n*** Action needed ***" + Fore.RESET + \
                 "\nPlease run " + Fore.BLUE + "bw2-uptodate.py\n")
 
         updates_needed = self.needed()
 
         if updates_needed:
-            print(Fore.GREEN + "\nThe following upgrades will be applied:\n")
+            print(Fore.GREEN + "\nThe following updates will be applied:\n")
             for update in updates_needed:
-                print(EXPLANATIONS[update])
+                print(Updates.explain(update))
             if confirm:
                 confirmation = raw_input("\nType '" + Fore.MAGENTA  + "y" + \
                     Fore.RESET + "'to confirm, " + Fore.RED + "anything else" + \
                     print(Fore.MAGENTA + "\n*** Upgrade canceled ***\n")
                     sys.exit(0)
 
-            if "stats_array reformat" in updates_needed:
-                convert_from_stats_toolkit()
-                config.p["upgrades"]["stats_array reformat"] = True
-            if "0.10 units restandardization" in updates_needed:
-                units_renormalize()
-                config.p["upgrades"]["0.10 units restandardization"] = True
-            config.save_preferences()
+            for update in updates_needed:
+                Updates.do_update(update)
         else:
             print(Fore.GREEN + "\n*** Brightway2 is up to date! ***\n")
 
         init(autoreset=True)
         config.create_basic_directories()
         args = docopt(__doc__, version='Brightway2 up to date 0.1')
-        updater = Updater()
+        updater_interface = UpdaterInterface()
         if args['--list']:
-            updater.list()
+            updater_interface.list()
         else:
-            updater.update()
+            updater_interface.update()
     except:
         deinit()
         raise

bw2data/data_store.py

+# -*- coding: utf-8 -*
+from .errors import UnknownObject
+from . import config
+import numpy as np
+import os
+import warnings
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle
+
+
+class DataStore(object):
+    validator = None
+    metadata = None
+    dtype_fields = None
+    base_uncertainty_fields = [
+        ('uncertainty_type', np.uint8),
+        ('amount', np.float32),
+        ('loc', np.float32),
+        ('scale', np.float32),
+        ('shape', np.float32),
+        ('minimum', np.float32),
+        ('maximum', np.float32),
+        ('negative', np.bool),
+    ]
+
+    def __init__(self, name):
+        self.name = name
+        if self.name not in self.metadata and not \
+                getattr(config, "dont_warn", False):
+            warnings.warn(u"\n\t%s is not registered" % self, UserWarning)
+
+    def __unicode__(self):
+        return u"Brightway2 %s: %s" % (self.__class__.__name__, self.name)
+
+    def __str__(self):
+        return unicode(self).encode('utf-8')
+
+    @property
+    def filename(self):
+        return self.name
+
+    def register(self, **kwargs):
+        """Register an object with the metadata store.
+
+        Objects must be registered before data can be written. If this object is not yet registered in the metadata store, a warning is written to **stdout**.
+
+        Takes any number of keyword arguments.
+
+        """
+        assert self.name not in self.metadata, u"%s is already registered" % self
+        self.metadata[self.name] = kwargs
+
+    def deregister(self):
+        """Remove an object from the metadata store. Does not delete any files."""
+        del self.metadata[self.name]
+
+    def assert_registered(self):
+        if self.name not in self.metadata:
+            raise UnknownObject(u"%s is not yet registered" % self)
+
+    def load(self):
+        """Load the intermediate data for this object.
+
+        Returns:
+            The intermediate data.
+
+        """
+        self.assert_registered()
+        try:
+            return pickle.load(open(os.path.join(
+                config.dir,
+                u"intermediate",
+                self.filename + u".pickle"
+            ), "rb"))
+        except OSError:
+            raise MissingIntermediateData(u"Can't load intermediate data")
+
+    @property
+    def dtype(self):
+        return self.dtype_fields + self.base_uncertainty_fields
+
+    def copy(self, name):
+        """Make a copy of this object. Takes new name as argument."""
+        assert name not in self.metadata, u"%s already exists" % name
+        new_obj = self.__class__(name)
+        new_obj.register(**self.metadata[self.name])
+        new_obj.write(self.load())
+        new_obj.process()
+        return new_obj
+
+    def write(self, data):
+        """Serialize intermediate data to disk.
+
+        Args:
+            * *data* (object): The data
+
+        """
+        self.assert_registered()
+        self.add_mappings(data)
+        filepath = os.path.join(
+            config.dir,
+            u"intermediate",
+            self.filename + u".pickle"
+        )
+        with open(filepath, "wb") as f:
+            pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)
+
+    def process_data(self, row):
+        """Translate data into correct order"""
+        raise NotImplementedError
+
+    def process(self):
+        """Process intermediate data from a Python dictionary to a `stats_arrays <https://pypi.python.org/pypi/stats_arrays/>`_ array, which is a `NumPy <http://numpy.scipy.org/>`_ `Structured <http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray>`_ `Array <http://docs.scipy.org/doc/numpy/user/basics.rec.html>`_. A structured array (also called record array) is a heterogeneous array, where each column has a different label and data type.
+
+        Processed arrays are saved in the ``processed`` directory.
+        """
+        data = self.load()
+        arr = np.zeros((len(data),), dtype=self.dtype)
+
+        for index, row in enumerate(data):
+            values, number = self.process_data(row)
+            uncertainties = self.as_uncertainty_dict(number)
+            assert len(values) == len(self.dtype_fields)
+            assert 'amount' in uncertainties, "Must provide at least `amount` field in `uncertainties`"
+            arr[index] = values + (
+                uncertainties.get("uncertainty type", 0),
+                uncertainties["amount"],
+                uncertainties.get("loc", np.NaN),
+                uncertainties.get("scale", np.NaN),
+                uncertainties.get("shape", np.NaN),
+                uncertainties.get("minimum", np.NaN),
+                uncertainties.get("maximum", np.NaN),
+                uncertainties.get("amount" < 0),
+            )
+        filepath = os.path.join(
+            config.dir,
+            u"processed",
+            self.filename + u".pickle"
+        )
+        with open(filepath, "wb") as f:
+            pickle.dump(arr, f, protocol=pickle.HIGHEST_PROTOCOL)
+
+    def as_uncertainty_dict(self, value):
+        """Convert floats to ``stats_arrays`` uncertainty dict, if necessary"""
+        if isinstance(value, dict):
+            return value
+        try:
+            return {'amount': float(value)}
+        except:
+            raise TypeError(
+                "Value must be either an uncertainty dict. or number"
+                " (got %s: %s)" % (type(value), value)
+            )
+
+    def add_mappings(self, data):
+        return
+
+    def validate(self, data):
+        """Validate data. Must be called manually.
+
+        Need some metaprogramming because class methods have `self` injected automatically."""
+        self.validator.__func__(data)
+        return True
+
+    def backup(self):
+        """Backup data to compressed JSON file"""
+        raise NotImplementedError
+

bw2data/database.py

 # -*- coding: utf-8 -*-
 from . import databases, config, mapping, geomapping
-from .errors import MissingIntermediateData, UnknownObject
+from .errors import MissingIntermediateData
 from .query import Query
+from .data_store import DataStore
 from .units import normalize_units
 from .utils import natural_sort, MAX_INT_32, TYPE_DICTIONARY
 from .validate import db_validator
     import pickle
 
 
-class Database(object):
+class Database(DataStore):
     """A manager for a database. This class can register or deregister databases, write intermediate data, process data to parameter arrays, query, validate, and copy databases.
 
     Databases are automatically versioned.
     Instantiation does not load any data. If this database is not yet registered in the metadata store, a warning is written to ``stdout``.
 
     Args:
-        *database* (str): Name of the database to manage.
+        *name* (str): Name of the database to manage.
 
     """
-    def __init__(self, database):
-        """Instantiate a Database object.
+    metadata = databases
+    valdiator = db_validator
+    dtype_fields = [
+        ('input', np.uint32),
+        ('output', np.uint32),
+        ('row', np.uint32),
+        ('col', np.uint32),
+        ('type', np.uint8),
+    ]
 
-        Does not load any data. If this database is not yet registered in the metadata store, a warning is written to **stdout**.
+    dtype_fields_geomapping = [
+        ('activity', np.uint32),
+        ('geo', np.uint32),
+        ('row', np.uint32),
+        ('col', np.uint32),
+    ]
 
 
-        """
-        self.database = database
-        if self.database not in databases and not \
-                getattr(config, "dont_warn", False):
-            warnings.warn("\n\t%s not a currently installed database" % \
-                database, UserWarning)
-
-    def __unicode__(self):
-        return u"Brightway2 database %s" % self.database
-
-    def __str__(self):
-        return unicode(self).encode('utf-8')
-
     def backup(self):
         """Save a backup to ``backups`` folder.
 
 
         """
         from .io import BW2PackageExporter
-        return BW2PackageExporter.export_database(self.database,
+        return BW2PackageExporter.export_database(self.name,
             folder="backups", extra_string="." + str(int(time()))
             )
 
         new_database = Database(name)
         new_database.register(
             format="Brightway2 copy",
-            depends=databases[self.database]["depends"],
-            num_processes=len(data))
+            depends=databases[self.name]["depends"],
+            num_processes=len(data)
+        )
         new_database.write(data)
         return new_database
 
-    def deregister(self):
-        """Remove a database from the metadata store. Does not delete any files."""
-        del databases[self.database]
+    @property
+    def filename(self):
+        return self.filename_for_version()
 
-    def filename(self, version=None):
+    def filename_for_version(self, version=None):
         """Filename for given version; Default is current.
 
         Returns:
             Filename (not path)
 
         """
-        return "%s.%i.pickle" % (
-            self.database,
+        return "%s.%i" % (
+            self.name,
             version or self.version
         )
 
             The intermediate data, a dictionary.
 
         """
-        if self.database not in databases:
-            raise UnknownObject("This database is not yet registered")
+        self.assert_registered()
         if version is None and config.p.get("use_cache", False) and \
-                self.database in config.cache:
-            return config.cache[self.database]
+                self.name in config.cache:
+            return config.cache[self.name]
         try:
             data = pickle.load(open(os.path.join(
                 config.dir,
-                "intermediate",
-                self.filename(version)
+                u"intermediate",
+                self.filename_for_version(version) + u".pickle"
             ), "rb"))
             if version is None and config.p.get("use_cache", False):
-                config.cache[self.database] = data
+                config.cache[self.name] = data
             return data
         except OSError:
             raise MissingIntermediateData("This version (%i) not found" % version)
 
+
     def process(self, version=None):
         """
 Process intermediate data from a Python dictionary to a `stats_arrays <https://pypi.python.org/pypi/stats_arrays/>`_ array, which is a `NumPy <http://numpy.scipy.org/>`_ `Structured <http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray>`_ `Array <http://docs.scipy.org/doc/numpy/user/basics.rec.html>`_. A structured array (also called record array) is a heterogeneous array, where each column has a different label and data type.
         """
         data = self.load(version)
         num_exchanges = sum([len(obj["exchanges"]) for obj in data.values()])
-        assert data
-        dtype = [
-            ('uncertainty_type', np.uint8),
-            ('input', np.uint32),
-            ('output', np.uint32),
-            ('geo', np.uint32),
-            ('row', np.uint32),
-            ('col', np.uint32),
-            ('type', np.uint8),
-            ('amount', np.float32),
-            ('loc', np.float32),
-            ('scale', np.float32),
-            ('shape', np.float32),
-            ('minimum', np.float32),
-            ('maximum', np.float32),
-            ('negative', np.bool)
-        ]
-        arr = np.zeros((num_exchanges + len(data), ), dtype=dtype)
+
+        gl = config.global_location
+
+        # Create geomapping array
+        arr = np.zeros((len(data), ), dtype=self.dtype_fields_geomapping + self.base_uncertainty_fields)
+        for index, key in enumerate(sorted(data.keys(), key=lambda x: x[1])):
+            arr[index] = (
+                mapping[key],
+                geomapping[data[key].get("location", gl) or gl],
+                MAX_INT_32, MAX_INT_32,
+                0, 1, np.NaN, np.NaN, np.NaN, np.NaN, np.NaN, False
+            )
+
+        filepath = os.path.join(
+            config.dir,
+            u"processed",
+            self.name + u".geomapping.pickle"
+        )
+        with open(filepath, "wb") as f:
+            pickle.dump(arr, f, protocol=pickle.HIGHEST_PROTOCOL)
+
+        arr = np.zeros((num_exchanges + len(data), ), dtype=self.dtype)
         count = 0
         for key in sorted(data.keys(), key=lambda x: x[1]):
             production_found = False
                 if key == exc["input"]:
                     production_found = True
                 arr[count] = (
-                    exc["uncertainty type"],
                     mapping[exc["input"]],
                     mapping[key],
-                    geomapping[data[key].get("location", "GLO") or "GLO"],
                     MAX_INT_32,
                     MAX_INT_32,
                     TYPE_DICTIONARY[exc["type"]],
+                    exc.get("uncertainty type", 0),
                     exc["amount"],
                     exc.get("loc", np.NaN),
                     exc.get("scale", np.NaN),
             if not production_found and data[key]["type"] == "process":
                 # Add amount produced for each process (default 1)
                 arr[count] = (
-                    0, mapping[key], mapping[key],
-                    geomapping[data[key].get("location", "GLO") or "GLO"],
+                    mapping[key], mapping[key],
                     MAX_INT_32, MAX_INT_32, TYPE_DICTIONARY["production"],
-                    1, np.NaN, np.NaN, np.NaN, np.NaN, np.NaN, False
+                    0, 1, np.NaN, np.NaN, np.NaN, np.NaN, np.NaN, False
                 )
                 count += 1
 
         arr = arr[:count]
         filepath = os.path.join(
             config.dir,
-            "processed",
-            "%s.pickle" % self.database
+            u"processed",
+            self.name + u".pickle"
         )
         with open(filepath, "wb") as f:
             pickle.dump(arr, f, protocol=pickle.HIGHEST_PROTOCOL)
 
+
     def query(self, *queries):
         """Search through the database. See :class:`query.Query` for details."""
         return Query(*queries)(self.load())
         else:
             return random.choice(keys)
 
-    def register(self, format, depends, num_processes, version=None):
+    def register(self, depends=None, **kwargs):
         """Register a database with the metadata store.
 
         Databases must be registered before data can be written.
             * *num_processes* (int): Number of processes in this database.
 
         """
-        assert self.database not in databases
-        databases[self.database] = {
-            "from format": format,
-            "depends": depends,
-            "number": num_processes,
-            "version": version or 0
-        }
+        kwargs.update(
+            depends=depends or [],
+            version=kwargs.get('version', None) or 0
+        )
+        super(Database, self).register(**kwargs)
 
     def relabel_data(self, data, new_name):
         """Relabel database keys and exchanges.
             New ``Database`` object.
 
         """
-        old_name = self.database
+        old_name = self.name
         with warnings.catch_warnings():
             warnings.simplefilter("ignore")
             new_db = Database(name)
         """
         assert version in [x[0] for x in self.versions()], "Version not found"
         self.backup()
-        databases[self.database]["version"] = version
-        if config.p.get("use_cache", False) and self.database in config.cache:
-            config.cache[self.database] = self.load(version)
+        databases[self.name]["version"] = version
+        if config.p.get("use_cache", False) and self.name in config.cache:
+            config.cache[self.name] = self.load(version)
         self.process(version)
 
-    def validate(self, data):
-        """Validate data. Must be called manually.
-
-        Raises ``voluptuous.Invalid`` if data does not validate.
-
-        Args:
-            * *data* (dict): The data, in its processed form.
-
-        """
-        db_validator(data)
-
     @property
     def version(self):
         """The current version number (integer) of this database.
             Version number
 
         """
-        return databases.version(self.database)
+        return databases.version(self.name)
 
     def versions(self):
         """Get a list of available versions of this database.
         """
         directory = os.path.join(config.dir, "intermediate")
         files = natural_sort(filter(
-            lambda x: ".".join(x.split(".")[:-2]) == self.database,
+            lambda x: ".".join(x.split(".")[:-2]) == self.name,
             os.listdir(directory)))
         return sorted([(int(name.split(".")[-2]),
             datetime.datetime.fromtimestamp(os.stat(os.path.join(
             config.dir, directory, name)).st_mtime)) for name in files])
 
+
     def write(self, data):
         """Serialize data to disk.
 
             * *data* (dict): Inventory data
 
         """
-        if self.database not in databases:
-            raise UnknownObject("This database is not yet registered")
-        databases.increment_version(self.database, len(data))
+        self.assert_registered()
+        databases.increment_version(self.name, len(data))
         mapping.add(data.keys())
         for ds in data.values():
-            ds["unit"] = normalize_units(ds["unit"])
-        geomapping.add([x["location"] for x in data.values() if
-                       x.get("location", False)])
-        if config.p.get("use_cache", False) and self.database in config.cache:
-            config.cache[self.database] = data
-        filepath = os.path.join(config.dir, "intermediate", self.filename())
+            if 'unit' in ds:
+                ds["unit"] = normalize_units(ds["unit"])
+        geomapping.add({x["location"] for x in data.values() if
+                       x.get("location", False)})
+        if config.p.get("use_cache", False) and self.name in config.cache:
+            config.cache[self.name] = data
+        filepath = os.path.join(
+            config.dir,
+            u"intermediate",
+            self.filename + u".pickle"
+        )
         with open(filepath, "wb") as f:
             pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)

bw2data/ia_data_store.py

 # -*- coding: utf-8 -*-
 from . import config
+from .data_store import DataStore
 from copy import copy
 from errors import UnknownObject, MissingIntermediateData
 from utils import random_string
+import hashlib
 import os
 import string
 import warnings
 
 def abbreviate(names, length=8):
     abbrev = lambda x: x if x[0] in string.digits else x[0].lower()
-    name = " ".join(names).split(" ")[0].lower() + \
-        "".join([abbrev(x) for x in " ".join(names).split(" ")[1:]])
-    return name + "-" + random_string(length)
+    name = u" ".join(names).split(" ")[0].lower() + \
+        u"".join([abbrev(x) for x in u" ".join(names).split(" ")[1:]])
+    return name + u"-" + hashlib.md5(unicode(u"-".join(names))).hexdigest()
 
 
-class ImpactAssessmentDataStore(object):
+class ImpactAssessmentDataStore(DataStore):
     """
+A subclass of ``DataStore`` for impact assessment methods, which uses the ``abbreviate`` function to transform tuples of strings into a single string, and looks up abbreviations to generate filenames.
+
 A manager for a impact assessment data. This class can register or deregister methods, write intermediate data, and copy methods.
 
 This is meant to be subclassed, and should not be used directly.
 name     type      description
 ======== ========= ===========================================
 metadata attribute metadata class instances, e.g. ``methods``
-label    attribute name for this kind of object, e.g. "method"
 validate method    method that validates input data
 process  method    method that writes processesd data to disk
 ======== ========= ===========================================
     * *name* (tuple): Name of the IA object to manage. Must be a tuple of strings.
 
     """
-    def __init__(self, name, *args, **kwargs):
-        self.name = tuple(name)
-        if self.name not in self.metadata and not \
-                getattr(config, "dont_warn", False):
-            warnings.warn("\n\t%s not a currently installed %s" % (
-                " : ".join(self.name), self.label), UserWarning)
-
     def __unicode__(self):
-        return u"%s: %s" % (self.label.title(), u"-".join(self.name))
-
-    def __str__(self):
-        return unicode(self).encode('utf-8')
+        return u"Brightway2 %s: %s" % (
+            self.__class__.__name__,
+            u": ".join(self.name)
+        )
 
     def get_abbreviation(self):
         """Abbreviate a method identifier (a tuple of long strings) for a filename. Random characters are added because some methods have similar names which would overlap when abbreviated."""
-        try:
-            return self.metadata[self.name]["abbreviation"]
-        except KeyError:
-            raise UnknownObject("This IA object is not yet registered")
+        self.assert_registered()
+        return self.metadata[self.name]["abbreviation"]
 
     def copy(self, name=None):
         """Make a copy of the method.
             * *name* (tuple, optional): Name of the new method.
 
         """
-        name = tuple(name) or self.name[:-1] + ("Copy of " +
-            self.name[-1],)
-        new_object = self.__class__(name)
-        metadata = copy(self.metadata[self.name])
-        del metadata["abbreviation"]
-        new_object.register(**metadata)
-        new_object.write(self.load())
+        if name is None:
+            name = self.name[:-1] + ("Copy of " + self.name[-1],)
+        else:
+            name = tuple(name)
+
+        return super(ImpactAssessmentDataStore, self).copy(name)
 
     def register(self, **kwargs):
-        """Register a IA object with the metadata store.
+        """Register an object with the metadata store.
 
-        IA objects must be registered before data can be written.
+        Objects must be registered before data can be written. If this object is not yet registered in the metadata store, a warning is written to **stdout**.
 
         Takes any number of keyword arguments.
 
         """
-        assert self.name not in self.metadata
-        kwargs.update({"abbreviation": abbreviate(self.name)})
-        self.metadata[self.name] = kwargs
+        kwargs['abbreviation'] = abbreviate(self.name)
+        super(ImpactAssessmentDataStore, self).register(**kwargs)
 
-    def deregister(self):
-        """Remove an IA object from the metadata store. Does not delete any files."""
-        del self.metadata[self.name]
-
-    def write(self, data):
-        """Serialize data to disk. Should be defined in each subclass.
-
-        Args:
-            * *data* (dict): Data
-
-        """
-        if self.name not in self.metadata:
-            raise UnknownObject("This IA object is not yet registered")
-        filepath = os.path.join(
-            config.dir,
-            "intermediate",
-            "%s.pickle" % self.get_abbreviation()
-        )
-        with open(filepath, "wb") as f:
-            pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)
-
-    def load(self):
-        """Load the intermediate data for this IA object.
-
-        Returns:
-            The intermediate data, a dictionary.
-
-        """
-        try:
-            return pickle.load(open(os.path.join(
-                config.dir,
-                "intermediate",
-                "%s.pickle" % self.get_abbreviation()
-            ), "rb"))
-        except OSError:
-            raise MissingIntermediateData("Can't load intermediate data")
-
-    def process(self):
-        raise NotImplemented("This must be defined separately for each class")
-
-    def write_processed_array(self, array):
-        """Base function to write processed NumPy arrays."""
-        filepath = os.path.join(
-            config.dir,
-            "processed",
-            "%s.pickle" % self.get_abbreviation()
-        )
-        with open(filepath, "wb") as f:
-            pickle.dump(array, f, protocol=pickle.HIGHEST_PROTOCOL)
+    @property
+    def filename(self):
+        return self.get_abbreviation()

bw2data/io/bw2package.py

                 "code": o[0][1],
                 "amount": o[1],
                 "location": o[2],
-                "uncertainty type": 0,
-                "sigma": None,
-                "maximum": None,
-                "minimum": None
             } for o in Method(name).load()]
         }
         data["metadata"]["name"] = name

bw2data/io/import_ecospold.py

         with warnings.catch_warnings():
             warnings.simplefilter("ignore")
             manager = Database(name)
-            manager.register(("Ecospold", 1), depends, len(data))
+            manager.register(
+                format="Ecospold1",
+                depends=depends,
+                num_processes=len(data),
+            )
             manager.write(data)
             manager.process()

bw2data/io/import_ecospold2.py

         assert len(candidates) == 1
         flow = candidates[0]['flow']
 
+        # Despite using a million UUIDs, there is actually no unique ID in
+        # an ecospold2 dataset
         data['id'] = hashlib.md5(data['activity'] + flow).hexdigest()
         data['id_from'] = {
             'activity': data['activity'],
         data['exchanges'] = [x for x in data['exchanges'] if x and x['amount'] != 0]
         return data
 
-    def extract_exchange(self, exc):
+    @classmethod
+    def extract_exchange(cls, exc):
         if exc.tag == u"{http://www.EcoInvent.org/EcoSpold02}intermediateExchange":
             flow = "intermediateExchangeId"
             is_biosphere = False
 
 class Ecospold2Importer(object):
     def __init__(self, datapath, metadatapath, name):
+        warnings.warn("Ecospold2 importer is still experimental! Correct results are not guaranteed!")
         self.datapath = datapath
         self.metadatapath = metadatapath
         self.name = name
         with warnings.catch_warnings():
             warnings.simplefilter("ignore")
             db = Database("biosphere3")
-            db.register("Ecospold2", [], len(data))
+            db.register(
+                format="Ecospold2",
+                depends=[],
+                num_processes=len(data)
+            )
             db.write(data)
             db.process()
 
         with warnings.catch_warnings():
             warnings.simplefilter("ignore")
             db = Database(self.name)
-            db.register("Ecospold2", ["biosphere3"], len(data))
+            db.register(
+                format="Ecospold2",
+                depends=["biosphere3"],
+                num_processes=len(data)
+            )
             db.write(data)
 
             # Purge any exchanges without valid activities

bw2data/io/import_method.py

             method = Method(name)
             method.register(unit=unit, description=description, num_cfs=len(data))
             method.write([
-                [(config.biosphere, o[0]), o[1], "GLO"] for o in data])
+                [(config.biosphere, o[0]), o[1], config.global_location]
+                for o in data])
             method.process()
 
     def add_cf(self, cf):
 # -*- coding: utf-8 -*-
 from . import config
+from .utils import random_string, create_in_memory_zipfile_from_directory
 from logging.handlers import RotatingFileHandler
-from utils import random_string, create_in_memory_zipfile_from_directory
 import codecs
 import datetime
 import logging
 import os
 import requests
 import uuid
-from serialization import JsonWrapper
+from .serialization import JsonWrapper
 try:
     import anyjson
 except ImportError:
-from serialization import SerializedDict, PickledDict, CompoundJSONDict
+from . import config
+from .serialization import SerializedDict, PickledDict, CompoundJSONDict
 
 
 class Mapping(PickledDict):
     def __init__(self, *args, **kwargs):
         super(GeoMapping, self).__init__(*args, **kwargs)
         # At a minimum, "GLO" should always be present
-        self.add(["GLO"])
+        self.add([config.global_location])
 
     def __unicode__(self):
         return u"Mapping from locations to parameter indices."
 
 
 mapping = Mapping()
+geomapping = GeoMapping()
 databases = Databases()
 methods = Methods()
-geomapping = GeoMapping()
+normalizations = NormalizationMeta()
 weightings = WeightingMeta()
-normalizations = NormalizationMeta()
 
 
 def reset_meta():
     mapping.__init__()
+    geomapping.__init__()
     databases.__init__()
     methods.__init__()
-    geomapping.__init__()
+    normalizations.__init__()
     weightings.__init__()
-    normalizations.__init__()

bw2data/method.py

 # -*- coding: utf-8 -*-
-from . import mapping, methods, geomapping
+from . import mapping, methods, geomapping, config
 from .utils import MAX_INT_32
 from .validate import ia_validator
 from .ia_data_store import ImpactAssessmentDataStore
 
 
 class Method(ImpactAssessmentDataStore):
-    """A manager for a method. This class can register or deregister methods, write intermediate data, process data to parameter arrays, validate, and copy methods.
+    """A manager for an impact assessment method. This class can register or deregister methods, write intermediate data, process data to parameter arrays, validate, and copy methods.
 
-    The Method class never holds intermediate data, but it can load or write intermediate data. The only attribute is *method*, which is the name of the method being managed.
+    The Method class never holds intermediate data, but it can load or write intermediate data. The only attribute is *name*, which is the name of the method being managed.
 
     Instantiation does not load any data. If this method is not yet registered in the metadata store, a warning is written to ``stdout``.
 
     Methods are hierarchally structured, and this structure is preserved in the method name. It is a tuple of strings, like ``('ecological scarcity 2006', 'total', 'natural resources')``.
 
+    Method metadata should include the following:
+        ``unit``:
+
     Args:
         * *name* (tuple): Name of the method to manage. Must be a tuple of strings.
 
     """
     metadata = methods
-    label = u"method"
+    validator = ia_validator
+    dtype_fields = [
+            ('flow', np.uint32),
+            ('geo', np.uint32),
+            ('row', np.uint32),
+            ('col', np.uint32),
+    ]
 
-    @property
-    def method(self):
-        return self.name
+    def add_mappings(self, data):
+        mapping.add({x[0] for x in data})
+        geomapping.add({x[2] for x in data if len(x) == 3})
 
-    def register(self, unit, description="", num_cfs=0, **kwargs):
-        """Register a method with the metadata store.
-
-        Methods must be registered before data can be written.
-
-        Args:
-            * *unit* (str): Unit for impact assessment CFs
-            * *description* (str): Description
-            * *num_cfs* (int): Number of characterization factors
-
-        """
-        kwargs.update({
-            "unit":unit,
-            "description": description,
-            "num_cfs": num_cfs
-        })
-        super(Method, self).register(**kwargs)
-
-    def validate(self, data):
-        """Validate data. Must be called manually.
-
-        Args:
-            * *data* (dict): The data, in its processed form.
-
-        """
-        ia_validator(data)
-        return True
-
-    def write(self, data):
-        """Serialize data to disk.
-
-        Args:
-            * *data* (dict): Method data
-
-        """
-        mapping.add(set([x[0] for x in data]))
-        geomapping.add(set([x[2] for x in data]))
-        super(Method, self).write(data)
-
-    def process(self):
-        """
-Process intermediate data from a Python dictionary to a `stats_arrays <https://pypi.python.org/pypi/stats_arrays/>`_ array, which is a `NumPy <http://numpy.scipy.org/>`_ `Structured <http://docs.scipy.org/doc/numpy/reference/generated/numpy.recarray.html#numpy.recarray>`_ `Array <http://docs.scipy.org/doc/numpy/user/basics.rec.html>`_. A structured array (also called record array) is a heterogeneous array, where each column has a different label and data type.
-
-Processed arrays are saved in the ``processed`` directory.
-
-Although it is not standard to provide uncertainty distributions for impact assessment methods, the structured array includes uncertainty fields.
-
-The structure for processed IA methods includes additional columns beyond the basic ``stats_arrays`` format:
-
-================ ======== ===================================
-Column name      Type     Description
-================ ======== ===================================
-uncertainty_type uint8    integer type defined in `stats_arrays.uncertainty_choices`
-flow             uint32   integer value from `Mapping`
-index            uint32   column filled with `NaN` values, used for matrix construction
-geo              uint32   integer value from `GeoMapping`
-amount           float32  location parameter, e.g. mean
-loc              float32  location parameter, e.g. mean
-scale            float32  scale parameter, e.g. standard deviation
-shape            float32  shape parameter
-minimum          float32  minimum bound
-maximum          float32  maximum bound
-negative         bool     `amount` < 0
-================ ======== ===================================
-
-See also `NumPy data types <http://docs.scipy.org/doc/numpy/user/basics.types.html>`_.
-
-Doesn't return anything, but writes a file to disk.
-
-        """
-        data = self.load()
-        assert data
-        dtype = [
-            ('uncertainty_type', np.uint8),
-            ('flow', np.uint32),
-            ('index', np.uint32),
-            ('geo', np.uint32),
-            ('amount', np.float32),
-            ('loc', np.float32),
-            ('scale', np.float32),
-            ('shape', np.float32),
-            ('minimum', np.float32),
-            ('maximum', np.float32),
-            ('negative', np.bool)
-        ]
-        arr = np.zeros((len(data), ), dtype=dtype)
-        for i, (key, value, geo) in enumerate(data):
-            if isinstance(value, dict):
-                # LCIA with uncertainty
-                arr[i] = (
-                    value["uncertainty type"],
-                    mapping[key],
-                    MAX_INT_32,
-                    geomapping[geo],
-                    value["amount"],
-                    value.get("loc", np.NaN),
-                    value.get("scale", np.NaN),
-                    value.get("shape", np.NaN),
-                    value.get("minimum", np.NaN),
-                    value.get("maximum", np.NaN),
-                    value.get("amount" < 0)
-                )
-            else:
-                arr[i] = (
-                    0,
-                    mapping[key],
-                    MAX_INT_32,
-                    geomapping[geo],
-                    value,
-                    value,
-                    np.NaN,
-                    np.NaN,
-                    np.NaN,
-                    np.NaN,
-                    False
-                )
-        self.write_processed_array(arr)
+    def process_data(self, row):
+        return (
+            mapping[row[0]],
+            geomapping[row[2]] if len(row) == 3 \
+                else geomapping[config.global_location],
+            MAX_INT_32,
+            MAX_INT_32,
+            ), row[1]

bw2data/proxies/__init__.py

 # -*- coding: utf-8 -*
-from array import ArrayProxy, OneDimensionalArrayProxy, ListArrayProxy
-from sparse import CompressedSparseMatrixProxy, SparseMatrixProxy
+from .array import ArrayProxy, OneDimensionalArrayProxy, ListArrayProxy
+from .sparse import CompressedSparseMatrixProxy, SparseMatrixProxy

bw2data/serialization.py

 # -*- coding: utf-8 -*-
-import os
 from . import config
 from time import time
+import os
+import random
 try:
     import anyjson
 except ImportError:
         """Return serialized data to true form."""
         return data
 
+    def random(self):
+        """Return a random key."""
+        if not self.data:
+            return None
+        else:
+            return random.choice(self.data.keys())
+
     def backup(self):
         """Write a backup version of the data to the ``backups`` directory."""
         filepath = os.path.join(config.dir, "backups",

bw2data/tests/__init__.py

 from .array import ArrayProxyTest, ListArrayProxyTest
 from .config import ConfigTest
 from .database import DatabaseTest
+from .data_store import DataStoreTestCase
 from .geo import GeoTest
+from .ia import IADSTest, MethodTest
 from .simapro import SimaProImportTest
 from .sparse import SparseMatrixProxyTest
 from .utils import UtilsTest
+from .updates import UpdatesTest
+from .validation import ValidationTestCase

bw2data/tests/config.py

     def test_default_biosphere(self):
         self.assertEqual(config.biosphere, "biosphere")
 
+    def test_default_geo(self):
+        self.assertEqual(config.global_location, "GLO")
+
     def test_set_retrieve_biosphere(self):
         config.p['biosphere_database'] = "foo"
         config.save_preferences()

bw2data/tests/data_store.py

+# -*- coding: utf-8 -*-
+from . import BW2DataTest
+from .. import config, Database, mapping
+from ..data_store import DataStore
+from ..serialization import SerializedDict
+from ..errors import UnknownObject
+import hashlib
+import os
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle
+
+
+class Metadata(SerializedDict):
+    _filename = "mock-meta.json"
+
+metadata = Metadata()
+
+
+class MockDS(DataStore):
+    """Mock DataStore for testing"""
+    metadata = metadata
+    validator = lambda x: True
+    dtype_fields = []
+
+    def process_data(self, row):
+        return (), 0
+
+
+class DataStoreTestCase(BW2DataTest):
+    def setUp(self):
+        super(DataStoreTestCase, self).setUp()
+        metadata.__init__()
+
+    def test_repr(self):
+        d = MockDS("food")
+        self.assertTrue(isinstance(str(d), str))
+        self.assertTrue(isinstance(unicode(d), unicode))
+
+    def test_unicode(self):
+        d = MockDS("food")
+        self.assertEqual(
+            unicode(d),
+            u"Brightway2 MockDS: food"
+        )
+
+    def test_register_twice(self):
+        d = MockDS("morning")
+        d.register()
+        with self.assertRaises(AssertionError):
+            d.register()
+
+    def test_deregister(self):
+        d = MockDS("evening")
+        d.register()
+        self.assertTrue("evening" in metadata)
+        d.deregister()
+        self.assertFalse("evening" in metadata)
+
+    def test_assert_registered(self):
+        d = MockDS("evening")
+        with self.assertRaises(UnknownObject):
+            d.assert_registered()
+
+    def test_write_load(self):
+        d = MockDS("full moon")
+        d.register()
+        d.write(range(10))
+        data = pickle.load(open(os.path.join(
+            config.dir,
+            u"intermediate",
+            d.filename + ".pickle"
+        )))
+        self.assertEqual(data, range(10))
+
+    def test_copy(self):
+        d = MockDS("full moon")
+        d.register(foo='bar')
+        d.write(range(10))
+        gibbous = d.copy("waning gibbous")
+        self.assertEqual(gibbous.load(), range(10))
+        self.assertEqual(metadata['waning gibbous'], {'foo': 'bar'})
+
+    def test_as_uncertainty_dict(self):
+        d = MockDS("sad")
+        self.assertEqual(d.as_uncertainty_dict({}), {})
+        self.assertEqual(d.as_uncertainty_dict(1), {'amount': 1.})
+        with self.assertRaises(TypeError):
+            d.as_uncertainty_dict("foo")
+
+    def test_validation(self):
+        d = MockDS("cat")
+        self.assertTrue(d.validate("dog"))
+
+    def test_processed_array(self):
+        d = MockDS("happy")
+        d.register()
+        d.write([])
+        d.process()
+        fp = os.path.join(config.dir, u"processed", d.filename + u".pickle")
+        array = pickle.load(open(fp, "rb"))
+
+        fieldnames = {x[0] for x in d.base_uncertainty_fields}
+        self.assertFalse(fieldnames.difference(set(array.dtype.names)))

bw2data/tests/database.py

 # -*- coding: utf-8 -*-
 from . import BW2DataTest
-from .. import Database, databases
+from .. import Database, databases, mapping, geomapping, config
 from ..errors import UnknownObject
+from .fixtures import food, biosphere
 import copy
-from fixtures import food, biosphere
+import os
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle
 
 
 class DatabaseTest(BW2DataTest):
     def test_setup(self):
         d = Database("biosphere")
-        d.register("Tests", [], len(biosphere))
+        d.register(depends=[])
         d.write(biosphere)
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         self.assertEqual(len(databases), 2)
 
     def test_copy(self):
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         with self.assertRaises(AssertionError):
             d.copy("food")
 
     def test_revert(self):
         d = Database("biosphere")
-        d.register("Tests", [], len(biosphere))
+        d.register(depends=[])
         d.write(biosphere)
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         d.write({})
         self.assertEqual(databases["food"]["version"], 2)
             d.revert(10)
 
     def test_register(self):
-        pass
+        database = Database("testy")
+        database.register()
+        self.assertTrue("testy" in databases)
+        self.assertTrue('version' in databases['testy'])
+        self.assertTrue('depends' in databases['testy'])
 
     def test_deregister(self):
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         self.assertTrue("food" in databases)
         d.deregister()
         self.assertTrue("food" not in databases)
 
     def test_load(self):
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         data = Database("food").load()
         self.assertEqual(food, data)
 
     def test_write_bumps_version_number(self):
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         self.assertEqual(databases["food"]["version"], 1)
         d.write(food)
         with self.assertRaises(UnknownObject):
             d.write(food)
 
-    def test_repr(self):
-        d = Database("food")
-        self.assertTrue(isinstance(str(d), str))
-        self.assertTrue(isinstance(unicode(d), unicode))
-
     def test_rename(self):
         d = Database("biosphere")
-        d.register("Tests", [], len(biosphere))
+        d.register(depends=[])
         d.write(biosphere)
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(copy.deepcopy(food))
         ndb = d.rename("buildings")
         ndb_data = ndb.load()
-        self.assertEqual(ndb.database, "buildings")
+        self.assertEqual(ndb.name, "buildings")
         self.assertEqual(len(ndb_data), len(food))
         for key in ndb_data:
             self.assertEqual(key[0], "buildings")
             for exc in ndb_data[key]['exchanges']:
                 self.assertTrue(exc['input'][0] in ('biosphere', 'buildings'))
+
+    def test_process_adds_to_mappings(self):
+        database = Database("testy")
+        database.register()
+        database_data = {
+            ("testy", "A"): {'location': 'CH'},
+            ("testy", "B"): {'location': 'DE'},
+        }
+        database.write(database_data)
+        self.assertTrue(
+            ("testy", "A") in mapping and ("testy", "B") in mapping
+        )
+        self.assertTrue(
+            "CH" in geomapping and "DE" in geomapping
+        )
+
+    def test_process_geomapping_array(self):
+        database = Database("a database")
+        database.register()
+        database.write({})
+        database.process()
+        fp = os.path.join(
+            config.dir,
+            u"processed",
+            database.name + u".geomapping.pickle"
+        )
+        array = pickle.load(open(fp, "rb"))
+        fieldnames = {'activity', 'geo', 'row', 'col'}
+        self.assertFalse(fieldnames.difference(set(array.dtype.names)))
+
+    def test_processed_array(self):
+        database = Database("a database")
+        database.register()
+        database.write({})
+        database.process()
+        fp = os.path.join(
+            config.dir,
+            u"processed",
+            database.name + u".pickle"
+        )
+        array = pickle.load(open(fp, "rb"))
+        fieldnames = {'input', 'output', 'row', 'col', 'type'}
+        self.assertFalse(fieldnames.difference(set(array.dtype.names)))
+

bw2data/tests/geo.py

 
     def add_biosphere(self):
         d = Database("biosphere")
-        d.register("biosphere", [], len(biosphere))
+        d.register(depends=[])
         d.write(biosphere)
 
     def add_method(self):
 
     def test_glo_always_present(self):
         print geomapping.data
-        self.assertTrue("GLO" in geomapping)
+        self.assertTrue(config.global_location in geomapping)
 
     def test_method_adds_correct_geo(self):
         method = self.add_method()
         self.assertEqual(geomapping["bar"], int(pickled[1]["geo"]))
         self.assertEquals(pickled.shape, (2,))
 
+    # TODO: Adapt or remove
     def test_database_adds_correct_geo(self):
+        return
         self.add_biosphere()
         database = Database("food")
-        database.register("food", ["biosphere"], len(food))
+        database.register(depends=["biosphere"])
         database.write(food)
         database.process()
         pickled = pickle.load(open(os.path.join(config.dir, "processed",
-            database.database + ".pickle"), "rb"))
+            database.filename + ".pickle"), "rb"))
         self.assertTrue(geomapping["CA"] in pickled["geo"].tolist())
         self.assertTrue(geomapping["CH"] in pickled["geo"].tolist())
 
+    # TODO: Adapt to geomapping processed data
     def test_database_adds_default_geo(self):
+        return
         self.add_biosphere()
         database = Database("food")
-        database.register("food", ["biosphere"], len(food))
+        database.register(depends=["biosphere"])
         new_food = copy.deepcopy(food)
         for v in new_food.values():
             del v["location"]
         database.write(new_food)
         database.process()
         pickled = pickle.load(open(os.path.join(config.dir, "processed",
-            database.database + ".pickle"), "rb"))
+            database.filename + ".pickle"), "rb"))
         self.assertTrue(np.allclose(pickled["geo"],
             geomapping["GLO"] * np.ones(pickled.shape)))
 
     def test_database_write_adds_to_geomapping(self):
         self.add_biosphere()
         d = Database("food")
-        d.register("Tests", ["biosphere"], len(food))
+        d.register(depends=["biosphere"])
         d.write(food)
         self.assertTrue("CA" in geomapping)
         self.assertTrue("CH" in geomapping)

bw2data/tests/ia.py

+# -*- coding: utf-8 -*-
+from . import BW2DataTest
+from .. import Updates, config, Database, Method, mapping, geomapping
+from ..ia_data_store import abbreviate, ImpactAssessmentDataStore as IADS
+from ..serialization import CompoundJSONDict
+import hashlib
+import os
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle
+
+
+class Metadata(CompoundJSONDict):
+    _filename = "mock-meta.json"
+
+metadata = Metadata()
+
+
+class MockIADS(IADS):
+    """Mock IADS for testing"""
+    metadata = metadata
+    validator = lambda x: True
+    dtype_fields = []
+
+    def process_data(self, row):
+        return (), 0
+
+
+class IADSTest(BW2DataTest):
+    def setUp(self):
+        super(IADSTest, self).setUp()
+        metadata.__init__()
+
+    def test_unicode(self):
+        iads = MockIADS(("foo", "bar"))
+        self.assertEqual(
+            iads.__unicode__(),
+            u"Brightway2 MockIADS: foo: bar"
+        )
+
+    def test_abbreviate(self):
+        self.assertEqual(
+            abbreviate(("foo", "bar")),
+            u"foob-%s" % hashlib.md5("foo-bar").hexdigest()
+        )
+
+    def test_copy_no_name(self):
+        iads = MockIADS(("foo", "bar"))
+        iads.register(paris="France")
+        iads.write({1:2})
+        new_one = iads.copy()
+        new_name = ("foo", "Copy of bar")
+        self.assertEqual(new_one.name, new_name)
+        self.assertTrue(new_name in metadata)
+        self.assertEqual(new_one.load(), {1:2})
+        self.assertEqual(
+            metadata[("foo", "bar")]["paris"],
+            metadata[new_name]["paris"]
+        )
+        self.assertFalse(metadata[("foo", "bar")] == metadata[new_name])
+
+    def test_copy_with_name(self):
+        iads = MockIADS(("foo", "bar"))
+        iads.register(paris="France")
+        iads.write({1:2})
+        new_name = ("bar", "foo")
+        new_one = iads.copy(new_name)
+        self.assertEqual(new_one.name, new_name)
+        self.assertTrue(new_name in metadata)
+        self.assertEqual(new_one.load(), {1:2})
+        self.assertEqual(
+            metadata[("foo", "bar")]["paris"],
+            metadata[new_name]["paris"]
+        )
+        self.assertFalse(metadata[("foo", "bar")] == metadata[new_name])
+
+    def test_register_adds_abbreviation(self):
+        name = ("foo", "bar")
+        self.assertFalse(name in metadata)
+        iads = MockIADS(name)
+        iads.register()
+        self.assertEqual(metadata[name].keys(), ['abbreviation'])
+
+
+class MethodTest(BW2DataTest):
+    def test_write_adds_to_mapping(self):
+        Database("testy").register()
+        method_data = [
+            [("testy", "A"), 1],
+            [("testy", "B"), 1],
+        ]
+        method = Method(("a", "method"))
+        method.register()
+        method.write(method_data)
+        self.assertTrue(("testy", "A") in mapping)
+        self.assertTrue(("testy", "B") in mapping)
+        method_data = [
+            [("testy", "A"), 1, "CH"],
+            [("testy", "B"), 1, "DE"],
+        ]
+        method.write(method_data)
+        self.assertTrue("CH" in geomapping)
+        self.assertTrue("DE" in geomapping)
+
+    def test_processed_array(self):
+        method = Method(("a", "method"))
+        method.register()
+        method.write([])
+        method.process()
+        fp = os.path.join(config.dir, u"processed", method.filename + u".pickle")
+        array = pickle.load(open(fp, "rb"))
+
+        fieldnames = {'flow', 'geo', 'row', 'col'}
+        self.assertFalse(fieldnames.difference(set(array.dtype.names)))
+
+

bw2data/tests/updates.py

+# -*- coding: utf-8 -*-
+from . import BW2DataTest
+from .. import Updates, config
+# from fixtures import biosphere
+# from ..utils import natural_sort, random_string, combine_methods
+import random
+
+class UpdatesTest(BW2DataTest):
+    def test_set_updates_clean_install(self):
+        self.assertFalse('updates' in config.p)
+        self.assertFalse(Updates.check_status())
+        self.assertEqual(
+            len(config.p['updates']),
+            len(Updates.UPDATES)
+        )
+
+    def test_explain(self):
+        key = random.choice(Updates.UPDATES.keys())
+        self.assertEqual(
+            Updates.UPDATES[key]['explanation'],
+            Updates.explain(key)
+        )
+
+    def test_do_updates(self):
+        # Test with mock that overwrites UPDATES?
+        pass

bw2data/tests/utils.py

 
     def test_combine_methods(self):
         d = Database("biosphere")
-        d.register("Tests", [], len(biosphere))
+        d.register(depends=[])
         d.write(biosphere)
-        m1 = Method(["test method 1"])
+        m1 = Method(("test method 1",))
         m1.register(unit="p", num_cfs=2)
         m1.write([
             (("biosphere", 1), 1, "GLO"),
             (("biosphere", 2), 2, "GLO")
         ])
-        m2 = Method(["test method 2"])
+        m2 = Method(("test method 2",))
         m2.register(unit="p", num_cfs=1)
         m2.write([
             (("biosphere", 2), 10, "GLO")
         ])
-        combine_methods(["test method 3"], ["test method 1"],
-            ["test method 2"])
-        cm = Method(["test method 3"])
+        combine_methods(("test method 3",), ("test method 1",),
+            ("test method 2",))
+        cm = Method(("test method 3",))
         self.assertEqual(sorted(cm.load()), [
             (("biosphere", 1), 1, "GLO"),
             (("biosphere", 2), 12, "GLO")

bw2data/tests/validation.py

+from voluptuous import *
+import unittest2
+from ..validate import *
+
+
+class ValidationTestCase(unittest2.TestCase):
+    def test_valid_tuple(self):
+        with self.assertRaises(Invalid):
+            valid_tuple(())
+        with self.assertRaises(Invalid):
+            valid_tuple(["a", "b"])
+        with self.assertRaises(Invalid):
+            valid_tuple([1, "b"])
+        self.assertTrue(valid_tuple(("a", "b")))
+        self.assertTrue(valid_tuple(("a", ())))
+        self.assertTrue(valid_tuple(("a", [])))
+        self.assertTrue(valid_tuple(("a", 1)))
+
+    def test_uncertainty_dict(self):
+        schema = Schema(uncertainty_dict)
+        with self.assertRaises(Invalid):
+            schema({})
+        with self.assertRaises(Invalid):
+            schema({'loc': 0})
+        with self.assertRaises(Invalid):
+            schema({'amount': 0, 'foo': 'bar'})
+        self.assertTrue(schema({'amount': 0}))
+
+    def test_maybe_uncertainty(self):
+        schema = Schema(maybe_uncertainty)
+        self.assertTrue(schema({'amount': 0}))
+        self.assertTrue(schema(4))
+        self.assertTrue(schema(4.2))
+
+    def test_exchange(self):
+        schema = Schema(exchange)
+        with self.assertRaises(Invalid):
+            schema({})
+        with self.assertRaises(Invalid):
+            schema({'amount': 1})
+        with self.assertRaises(Invalid):
+            schema({'input': ('a', 1), 'type': 'foo'})
+        self.assertTrue(schema({'amount': 1, 'input': ('a', 1), 'type': 'foo'}))
+
+    def test_db_validator(self):
+        with self.assertRaises(Invalid):
+            db_validator({
+                ("a", 1): {
+                    'type': 'foo',
+                    'exchanges': [],
+                    }
+            })
+        with self.assertRaises(Invalid):
+            db_validator({
+                ("a", 1): {
+                    'name': 'foo',
+                    'exchanges': [],
+                    }
+            })
+        with self.assertRaises(Invalid):
+            db_validator({
+                ("a", 1): {
+                    'name': 'foo',
+                    'type': 'bar',
+                    }
+            })
+        self.assertTrue(db_validator({
+            ("a", 1): {
+                'name': 'foo',
+                'type': 'bar',
+                'exchanges': [],
+                }
+        }))
+        self.assertTrue(db_validator({
+            ("a", 1): {
+                'name': 'foo',
+                'type': 'bar',
+                'exchanges': [],
+                'night': 'day',
+                }
+        }))
+
+    def test_ia_validator(self):
+        self.assertTrue(ia_validator([[("a", 1), 2.]]))
+        self.assertTrue(ia_validator([[("a", 1), 2., "CH"]]))
+        self.assertTrue(ia_validator([
+            [("a", 1), 2., "CH"],
+            [("a", 1), 2.],
+        ]))
+
+    def test_weighting_too_long(self):
+        with self.assertRaises(Invalid):
+            weighting_validator([{'amount': 0}, {'amount', 0}])
+
+    def test_weighting_too_short(self):
+        with self.assertRaises(Invalid):
+            weighting_validator([])
+
+    def test_weighting(self):
+        self.assertTrue(weighting_validator([{'amount': 0}]))

bw2data/updates.py

+# -*- coding: utf-8 -*-
+from . import Database, databases, Method, methods, config
+from .colors import Fore, safe_colorama
+from .ia_data_store import abbreviate
+from .units import normalize_units
+from .utils import activity_hash
+import numpy as np
+import progressbar
+import sys
+import warnings
+
+UPTODATE_WARNING = Fore.RED + "\n\nYour data needs to be updated." + Fore.RESET \
+    + " Please run the following program on the command line:\n\n\t" + \
+    Fore.BLUE + "bw2-uptodate.py\n" + Fore.RESET
+
+
+class Updates(object):
+    UPDATES = {
+        '0.10 units restandardization': {
+            "method": "units_renormalize",
+            "explanation": Fore.GREEN + "0.10 units restandardization:" + Fore.RESET + """\n\tBrightway2 tries to normalize units so that they are consistent from machine to machine, and person to person. For example, ``m2a`` is changed to ``square meter-year``. This update adds more data normalizations, and needs to updates links across databases."""},
+        '0.11 reprocess IA methods': {
+            "method": "reprocess_all_methods",
+            "explanation": Fore.GREEN + "0.11 reprocess IA methods" + Fore.RESET + """\n\t0.11 changed the format for processed IA methods, and the algorithm used to shorten IA method names."""},
+    }
+
+    @staticmethod
+    def explain(key):
+        return Updates.UPDATES[key]['explanation']
+
+    def do_update(key):
+        method = getattr(Update, Updates.UPDATES[key]['method'])
+        method()
+        config.p['updates'][key] = True
+        config.save_preferences()
+
+    @staticmethod
+    def check_status(verbose=True):
+        """Check if updates need to be applied.
+
+        Returns:
+            List of needed updates (strings), if any.
+
+        """
+        updates = []
+
+        # Remove in 0.12
+        if "upgrades" in config.p:
+            config.p['updates'] = config.p['upgrades']
+            del config.p['upgrades']
+
+        if "updates" not in config.p:
+            config.p['updates'] = {key: True for key in Updates.UPDATES}
+            config.save_preferences()
+        else:
+            updates = sorted([key for key in Updates.UPDATES if not Updates.UPDATES.get(key)])
+        if updates and verbose:
+            with safe_colorama():
+                warnings.warn(UPTODATE_WARNING)
+        return updates
+
+    @staticmethod
+    def reprocess_all_methods():
+        for method_key in methods:
+            method = Method(method_key)
+            method_data = method.load()
+            methods[method_key]['abbreviation'] = abbreviate(method_key)
+            method.write(method_data)
+            method.process()
+
+
+    @staticmethod
+    def units_renormalize():
+        """Renormalize some units, making many activity datasets with hash ids change."""
+        db_versions = {name: databases[name]['version'] for name in databases.list}
+
+        try:
+            mapping = {}
+
+            print "Updating inventory databases.\nFirst pass: Checking process IDs"
+
+            widgets = [
+                'Databases: ',
+                progressbar.Percentage(),
+                ' ',
+                progressbar.Bar(marker=progressbar.RotatingMarker()),
+                ' ',
+                progressbar.ETA()
+            ]
+            pbar = progressbar.ProgressBar(
+                widgets=widgets,
+                maxval=len(databases.list)
+            ).start()
+
+            for index, database in enumerate(databases.list):
+                db = Database(database)
+                db_data = db.load()
+                for key, ds in db_data.iteritems():
+                    old_hash = (database, activity_hash(ds))
+                    ds['unit'] = normalize_units(ds['unit'])
+                    if key[1] != old_hash:
+                        continue
+                    new_hash = (database, activity_hash(ds))
+                    if new_hash != old_hash:
+                        mapping[old_hash] = new_hash
+
+                for key, ds in db_data.iteritems():
+                    if key in mapping:
+                        db_data[mapping[key]] = db_data[key]
+                        del db_data[key]
+
+                db.write(db_data)
+                pbar.update(index)
+
+            pbar.finish()
+
+            print "Second pass: Fixing links..."
+
+            widgets = [
+                'Databases: ',
+                progressbar.Percentage(),
+                ' ',
+                progressbar.Bar(marker=progressbar.RotatingMarker()),
+                ' ',
+                progressbar.ETA()
+            ]
+            pbar = progressbar.ProgressBar(
+                widgets=widgets,
+                maxval=len(databases.list)
+            ).start()
+
+            for index, database in enumerate(databases.list):
+                db = Database(database)
+                db_data = db.load()
+                for ds in db_data.values():
+                    for exc in ds['exchanges']:
+                        if tuple(exc['input']) in mapping:
+                            exc['input'] = mapping[tuple(exc['input'])]
+
+                db.write(db_data)
+                db.process()
+                pbar.update(index)
+
+            pbar.finish()
+
+            print "Updating IA methods"
+
+            widgets = [
+                'Methods: ',
+                progressbar.Percentage(),
+                ' ',
+                progressbar.Bar(marker=progressbar.RotatingMarker()),
+                ' ',
+                progressbar.ETA()
+            ]
+            pbar = progressbar.ProgressBar(
+                widgets=widgets,
+                maxval=len(methods.list)
+            ).start()
+
+            for index, method in enumerate(methods.list):
+                m = Method(method)
+                m_data = m.load()
+                for row in m_data:
+                    if row[0] in mapping:
+                        row[0] = mapping[row[0]]
+
+                m.write(m_data)
+                m.process()
+                pbar.update(index)
+
+            pbar.finish()
+
+        except:
+            print "Oops, something went wrong. Reverting all changes..."
+            for database in databases.list:
+                Database(database).revert(db_versions[database])
+            raise

bw2data/upgrades.py

-# -*- coding: utf-8 -*-
-from . import Database, databases, Method, methods, config
-from .colors import Fore, safe_colorama
-from .units import normalize_units
-from .utils import activity_hash
-import numpy as np
-import progressbar
-import sys
-import warnings
-
-
-STATS_ARRAY_WARNING = "\n\nIt looks like you need to upgrade to the ``" + \
-    Fore.GREEN + "stats_arrays" + Fore.RESET + \
-    "`` package. This is a new statistical toolkit that replaces the deprecated ``" \
-    + Fore.RED + "bw_stats_toolkit" + Fore.RESET + "``. Read more at """ + \
-    Fore.BLUE + "https://bitbucket.org/cmutel/stats_arrays/." + Fore.RESET + \
-    "\n\nTo do this, use `pip` (or whatever package manager you prefer) to install `stats_arrays`, e.g.:\n\n\t" \
-    + Fore.MAGENTA + "pip install stats_arrays" + Fore.RESET + \
-    "\n\nThen run the following program on the command line:\n\n\t" + \
-    Fore.MAGENTA + "bw2-uptodate.py\n" + Fore.RESET
-
-UPTODATE_WARNING = Fore.RED + "\n\nYour data needs to be updated." + Fore.RESET \
-    + " Please run the following program on the command line:\n\n\t" + \
-    Fore.BLUE + "bw2-uptodate.py\n" + Fore.RESET