Merge branch 'ghini-1.1' of github.com:Ghini/ghini.desktop into ghini…

…-1.1

Conflicts:
	bauble/images/bauble_logo.png
	bauble/images/icon.svg

README.rst

@@ -4,6 +4,7 @@ Ghini
 .. image:: https://travis-ci.org/Ghini/ghini.desktop.svg
 .. image:: https://img.shields.io/pypi/v/bauble.svg
 .. image:: https://coveralls.io/repos/Ghini/ghini.desktop/badge.svg?branch=master&service=github
+  :target: https://coveralls.io/github/Ghini/ghini.desktop?branch=master
 
 .. image:: https://hosted.weblate.org/widgets/bauble/es/svg-badge.svg
 .. image:: https://hosted.weblate.org/widgets/bauble/pt_BR/svg-badge.svg

bauble/bauble.glade

@@ -159,7 +159,7 @@
                       <object class="GtkImage" id="image4">
                         <property name="visible">True</property>
                         <property name="can_focus">False</property>
-                        <property name="icon_name">go-previous</property>
+                        <property name="stock">gtk-go-back</property>
                       </object>
                     </child>
                   </object>

bauble/db.py

@@ -131,6 +131,9 @@ def after_delete(self, mapper, connection, instance):
         self._add('delete', mapper, instance)
 
 
+registered_tables = {}
+
+
 class MapperBase(DeclarativeMeta):
     """
     MapperBase adds the id, _created and _last_updated columns to all
@@ -151,6 +154,7 @@ def __init__(cls, classname, bases, dict_):
                                           default=sa.func.now(),
                                           onupdate=sa.func.now())
             cls.__mapper_args__ = {'extension': HistoryExtension()}
+            registered_tables[dict_['__tablename__']] = cls
         if 'top_level_count' not in dict_:
             cls.top_level_count = lambda x: {classname: 1}
         if 'search_view_markup_pair' not in dict_:
@@ -494,7 +498,7 @@ def __getattr__(self, name):
                     return n.note
         if result == []:
             # if nothing was found, do not break the proxy.
-            return Base.__getattr__(self, name)
+            return self.__getattribute__(name)
         if is_dict:
             return dict(result)
         return result

bauble/plugins/abcd/__init__.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # Copyright (c) 2005,2006,2007,2008,2009 Brett Adams <brett@belizebotanic.org>
-# Copyright (c) 2012-2015 Mario Frasca <mario@anche.no>
+# Copyright (c) 2012-2016 Mario Frasca <mario@anche.no>
 #
 # This file is part of bauble.classic.
 #
@@ -17,29 +17,23 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with bauble.classic. If not, see <http://www.gnu.org/licenses/>.
-# -*- coding: utf-8 -*-
 #
 #
 # ABCD import/exporter
 #
 
 import os
-import csv
 
 import gtk
 
-from sqlalchemy import *
-from sqlalchemy.orm import *
-
-import bauble
 import bauble.db as db
-from bauble.error import check, CheckConditionError
+from bauble.error import check
 import bauble.paths as paths
 import bauble.utils as utils
 import bauble.pluginmgr as pluginmgr
-from bauble.plugins.plants.species_model import Species
 from bauble.plugins.garden.plant import Plant
-from bauble.plugins.garden.accession import Accession
+from bauble.i18n import _
+from bauble import prefs
 
 # NOTE: see biocase provider software for reading and writing ABCD data
 # files, already downloaded software to desktop
@@ -60,6 +54,7 @@
 # we could have a special case just for generating labels
 #
 
+
 def validate_xml(root):
     """
     Validate root against ABCD 2.06 schema
@@ -68,19 +63,20 @@ def validate_xml(root):
     :returns: True or False depending if root validates correctly
     """
     schema_file = os.path.join(paths.lib_dir(), 'plugins',
-            'abcd','abcd_2.06.xsd')
+                               'abcd', 'abcd_2.06.xsd')
     xmlschema_doc = etree.parse(schema_file)
     abcd_schema = etree.XMLSchema(xmlschema_doc)
     return abcd_schema.validate(root)
 
+
 # TODO: this function needs to be renamed since we now check an object in
 # the list is an Accession them we use the accession data as the UnitID, else
 # we treat it as a Plant...using plants is necessary for things like making
 # labels but most likely accessions are wanted if we're exchanging data, the
 # only problem is that accessions don't keep status, like dead, etc.
 
 def verify_institution(institution):
-    test = lambda x: x != '' and x != None
+    test = lambda x: x != '' and x is not None
     return test(institution.name) and \
         test(institution.technical_contact) and \
         test(institution.email) and test(institution.contact) and \
@@ -102,7 +98,7 @@ def ABCDElement(parent, name, text=None, attrib=None):
     if attrib is None:
         attrib = {}
     el = SubElement(parent, '{%s}%s' % (namespaces['abcd'], name),
-                   nsmap=namespaces, attrib=attrib)
+                    nsmap=namespaces, attrib=attrib)
     el.text = text
     return el
 
@@ -174,7 +170,6 @@ def get_InformalNameString(self):
         pass
 
 
-
 def create_abcd(decorated_objects, authors=True, validate=True):
     """
     :param objects: a list/tuple of objects that implement the ABCDDecorator
@@ -187,8 +182,8 @@ def create_abcd(decorated_objects, authors=True, validate=True):
     import bauble.plugins.garden.institution as institution
     inst = institution.Institution()
     if not verify_institution(inst):
-        msg = _('Some or all of the information about your institution or ' \
-                'business is not complete. Please make sure that the ' \
+        msg = _('Some or all of the information about your institution or '
+                'business is not complete. Please make sure that the '
                 'Name, Technical Contact, Email, Contact and Institution '
                 'Code fields are filled in.')
         utils.message_dialog(msg)
@@ -213,7 +208,7 @@ def create_abcd(decorated_objects, authors=True, validate=True):
 
     # TODO: need to get the localized language
     representation = ABCDElement(description, 'Representation',
-                                    attrib={'language': 'en'})
+                                 attrib={'language': 'en'})
     revision = ABCDElement(metadata, 'RevisionData')
     ABCDElement(revision, 'DateModified', text='2001-03-01T00:00:00')
     title = ABCDElement(representation, 'Title', text='TheTitle')
@@ -249,12 +244,12 @@ def create_abcd(decorated_objects, authors=True, validate=True):
 
         scientific_name = ABCDElement(taxon_identified, 'ScientificName')
         ABCDElement(scientific_name, 'FullScientificNameString',
-                       text=obj.get_FullScientificNameString(authors))
+                    text=obj.get_FullScientificNameString(authors))
 
         name_atomised = ABCDElement(scientific_name, 'NameAtomised')
         botanical = ABCDElement(name_atomised, 'Botanical')
         ABCDElement(botanical, 'GenusOrMonomial',
-                       text=obj.get_GenusOrMonomial())
+                    text=obj.get_GenusOrMonomial())
         ABCDElement(botanical, 'FirstEpithet', text=obj.get_FirstEpithet())
         author_team = obj.get_AuthorTeam()
         if author_team is not None:
@@ -270,7 +265,7 @@ def create_abcd(decorated_objects, authors=True, validate=True):
             result = ABCDElement(identification, 'Result')
             taxon_identified = ABCDElement(result, 'TaxonIdentified')
             ABCDElement(taxon_identified, 'InformalNameString',
-                           text=vernacular_name)
+                        text=vernacular_name)
 
         # add all the extra non standard elements
         obj.extra_elements(unit)
@@ -290,22 +285,21 @@ def create_abcd(decorated_objects, authors=True, validate=True):
     return ElementTree(datasets)
 
 
-
 class ABCDExporter(object):
     """
     Export Plants to an ABCD file.
     """
 
     def start(self, filename=None, plants=None):
-        if filename == None: # no filename, ask the user
+        if filename is None:  # no filename, ask the user
             d = gtk.FileChooserDialog(_("Choose a file to export to..."), None,
                                       gtk.FILE_CHOOSER_ACTION_SAVE,
                                       (gtk.STOCK_OK, gtk.RESPONSE_ACCEPT,
                                        gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
             response = d.run()
             filename = d.get_filename()
             d.destroy()
-            if response != gtk.RESPONSE_ACCEPT or filename == None:
+            if response != gtk.RESPONSE_ACCEPT or filename is None:
                 return
 
         if plants:
@@ -314,27 +308,26 @@ def start(self, filename=None, plants=None):
             nplants = db.Session().query(Plant).count()
 
         if nplants > 3000:
-            msg = _('You are exporting %(nplants)s plants to ABCD format.  ' \
-                    'Exporting this many plants may take several minutes.  '\
+            msg = _('You are exporting %(nplants)s plants to ABCD format.  '
+                    'Exporting this many plants may take several minutes.  '
                     '\n\n<i>Would you like to continue?</i>') \
-                    % ({'nplants': nplants})
+                % ({'nplants': nplants})
             if not utils.yes_no_dialog(msg):
                 return
         self.run(filename, plants)
 
-
     def run(self, filename, plants=None):
-        if filename == None:
+        if filename is None:
             raise ValueError("filename can not be None")
 
         if os.path.exists(filename) and not os.path.isfile(filename):
-            raise ValueError("%s exists and is not a a regular file" \
-                                 % filename)
+            raise ValueError("%s exists and is not a a regular file"
+                             % filename)
 
         # if plants is None then export all plants, this could be huge
         # TODO: do something about this, like list the number of plants
         # to be returned and make sure this is what the user wants
-        if plants == None:
+        if plants is None:
             plants = db.Session().query(Plant).all()
 
         # TODO: move PlantABCDAdapter, AccessionABCDAdapter and
@@ -350,6 +343,8 @@ def run(self, filename, plants=None):
         if not validate_xml(data):
             msg = _("The ABCD file was created but failed to validate "
                     "correctly against the ABCD standard.")
+            if prefs.testing:
+                raise ValueError(msg)
             utils.message_dialog(msg, gtk.MESSAGE_WARNING)
 
 
@@ -369,7 +364,7 @@ class ABCDImexPlugin(pluginmgr.Plugin):
 
 try:
     import lxml.etree as etree
-    import lxml._elementpath # put this here sp py2exe picks it up
+    import lxml._elementpath  # put this here sp py2exe picks it up
     from lxml.etree import Element, SubElement, ElementTree
 except ImportError:
     utils.message_dialog(_('The <i>lxml</i> package is required for the '

bauble/plugins/garden/accession.py

@@ -1181,7 +1181,7 @@ def sp_get_completions(text):
                 query = self.presenter().session.query(Species).join('genus').\
                     filter(utils.ilike(Genus.genus, '%s%%' % text)).\
                     filter(Species.id != self.model.id).\
-                    order_by(Species.sp)
+                    order_by(Species.epithet)
                 return query
 
             def sp_cell_data_func(col, cell, model, treeiter, data=None):
@@ -1775,7 +1775,7 @@ def sp_get_completions(text):
                 and_(Species.genus_id == Genus.id,
                      or_(ilike(Genus.genus, '%s%%' % text),
                          ilike(Genus.genus, '%s%%' % genus)))).\
-                order_by(Species.sp)
+                order_by(Species.epithet)
 
         def on_select(value):
             logger.debug('on select: %s' % value)
@@ -1910,7 +1910,7 @@ def refresh_id_qual_rank_combo(self):
         active = None
         if self.model.id_qual_rank == 'genus':
             active = it
-        it = model.append([str(species.sp), u'sp'])
+        it = model.append([str(species.epithet), u'sp'])
         if self.model.id_qual_rank == u'sp':
             active = it
 

bauble/plugins/garden/plant.py

@@ -450,6 +450,7 @@ class Plant(db.Base, db.Serializable, db.DefiningPictures, db.WithNotes):
 
     # columns
     code = Column(Unicode(6), nullable=False)
+    date_planted = Column(types.Date, nullable=True, default=None)
 
     @validates('code')
     def validate_stripping(self, key, value):
@@ -670,6 +671,7 @@ def restore_state(self):
 class PlantEditorPresenter(GenericEditorPresenter):
 
     widget_to_field_map = {'plant_code_entry': 'code',
+                           'plant_date_entry': 'date_planted',
                            'plant_acc_entry': 'accession',
                            'plant_loc_comboentry': 'location',
                            'plant_acc_type_combo': 'acc_type',

bauble/plugins/garden/source.py

@@ -263,7 +263,7 @@ class Collection(db.Base):
     # ITF2 - F18 - Collection Notes
     notes = Column(UnicodeText)
 
-    geography_id = Column(Integer, ForeignKey('geography.id'))
+    geography_id = Column(Integer, ForeignKey('gheography.id'))
     region = relation(Geography, uselist=False)
 
     source_id = Column(Integer, ForeignKey('source.id'), unique=True)

bauble/plugins/garden/test.py

@@ -180,10 +180,10 @@ def __init__(self, *args, **kwargs):
     def setUp(self):
         super(GardenTestCase, self).setUp()
         plants_test.setUp_data()
-        self.family = Family(family=u'Cactaceae')
-        self.genus = Genus(family=self.family, genus=u'Echinocactus')
-        self.species = Species(genus=self.genus, sp=u'grusonii')
-        self.sp2 = Species(genus=self.genus, sp=u'texelensis')
+        self.family = Family(epithet=u'Cactaceae')
+        self.genus = Genus(family=self.family, epithet=u'Echinocactus')
+        self.species = Species(genus=self.genus, epithet=u'grusonii')
+        self.sp2 = Species(genus=self.genus, epithet=u'texelensis')
         self.session.add_all([self.family, self.genus, self.species, self.sp2])
         self.session.commit()
 
@@ -884,7 +884,7 @@ def __init__(self, *args):
 
     def setUp(self):
         super(AccessionQualifiedTaxon, self).setUp()
-        self.sp3 = Species(genus=self.genus, sp=u'grusonii',
+        self.sp3 = Species(genus=self.genus, epithet=u'grusonii',
                            infrasp1_rank=u'var.', infrasp1=u'albispinus')
         self.session.add(self.sp3)
         self.session.commit()
@@ -1190,7 +1190,7 @@ def test_editor(self):
         """
         raise SkipTest('separate view from presenter, then test presenter')
         #donor = self.create(Donor, name=u'test')
-        sp2 = Species(genus=self.genus, sp=u'species')
+        sp2 = Species(genus=self.genus, epithet=u'species')
         sp2.synonyms.append(self.species)
         self.session.add(sp2)
         self.session.commit()

bauble/plugins/imex/csv_.py

@@ -350,11 +350,15 @@ def create_table(table):
 
             # import the tables one at a time, breaking every so often
             # so the GUI can update
+            from bauble.db import registered_tables
             for table, filename in reversed(sorted_tables):
                 if self.__cancel or self.__error:
                     break
+                klass = registered_tables.get(table.name)
+                klassname = klass and klass.__name__ or table.name
                 msg = _('importing %(table)s table from %(filename)s') \
-                    % {'table': table.name, 'filename': filename}
+                    % {'table': klassname,
+                       'filename': filename}
                 #log.info(msg)
                 bauble.task.set_message(msg)
                 yield  # allow progress bar update
@@ -542,20 +546,6 @@ def do_insert():
                                          traceback.format_exc(),
                                          type=gtk.MESSAGE_ERROR)
 
-# TODO: we don't use the progress dialog any more but we'll leave this
-# around to remind us when we support cancelling via the progress statusbar
-#
-#     def _cancel_import(self, *args):
-#         '''
-#         called by the progress dialog to cancel the current import
-#         '''
-#         msg = _('Are you sure you want to cancel importing?\n\n<i>All '
-#                 'changes so far will be rolled back.</i>')
-#         self.__pause = True
-#         if utils.yes_no_dialog(msg, parent=self.__progress_dialog):
-#             self.__cancel = True
-##         self.__pause = False
-
     def _get_filenames(self):
         def on_selection_changed(filechooser, data=None):
             """
@@ -586,8 +576,6 @@ def on_response(self, widget, response, data=None):
         logger.debug(response)
 
 
-# TODO: add support for exporting only specific tables
-
 class CSVExporter(object):
 
     def start(self, path=None):
@@ -613,10 +601,7 @@ def start(self, path=None):
             logger.debug(e)
 
     def __export_task(self, path):
-#        if not os.path.exists(path):
-#            raise ValueError("CSVExporter: path does not exist.\n" + path)
         filename_template = os.path.join(path, "%s.txt")
-#        timeout = tasklet.WaitForTimeout(12)
         steps_so_far = 0
         ntables = 0
         for table in db.metadata.sorted_tables: