- fix

.emacs-prj

@@ -1,4 +1,4 @@
-; -*- lisp -*-
+r; -*- lisp -*-
 ;
 ; project settings for Bauble
 ;
@@ -8,4 +8,5 @@
 ;(setq org-agenda-files (list (expand-file-name (concat bauble-root "/org/bauble.org"))))
 (add-to-list org-agenda-files (expand-file-name (concat bauble-root "/org/bauble.org")))
 (setq tags-file-name (concat bauble-root "/TAGS"))
-(setenv "PYLINTRC" (concat bauble-root ".pylintrc"))
+(setenv "PYLINTRC" (concat bauble-root ".pylintrc"))
+(define-key run-project ("\C-pr")

bauble/db.py

@@ -1,9 +1,13 @@
+#  Copyright (c) 2005,2006,2007,2008  Brett Adams <brett@belizebotanic.org>
+#  This is free software, see GNU General Public License v2 for details.
 
 import traceback
 
 from bauble.i18n import _
 import bauble.error as error
 
+SQLALCHEMY_DEBUG = False
+
 try:
     import sqlalchemy as sa
     parts = sa.__version__.split('.')
@@ -27,6 +31,14 @@
 from bauble.utils.log import debug
 
 
+if SQLALCHEMY_DEBUG:
+    import logging
+    global engine
+    logging.basicConfig()
+    logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
+    logging.getLogger('sqlalchemy.orm.unitofwork').setLevel(logging.DEBUG)
+
+
 class MapperBase(DeclarativeMeta):
     """
     MapperBase adds the id, _created and _last_updated columns to all tables.
@@ -35,7 +47,7 @@ class MapperBase(DeclarativeMeta):
     def __init__(cls, classname, bases, dict_):
         #print >>sys.stderr, dict_
         if '__tablename__' in dict_:
-            seqname = '%s_seq_id' % dict_['__tablename__']
+            seqname = '%s_id_seq' % dict_['__tablename__']
             dict_['id'] = sa.Column('id', sa.Integer, sa.Sequence(seqname),
                                     primary_key=True)
             dict_['_created'] = sa.Column('_created', DateTime(True),
@@ -79,8 +91,9 @@ def open(uri, verify=True, show_error_dialogs=False):
     import bauble
     global engine
     new_engine = None
-    new_engine = sa.create_engine(uri)
-    new_engine.contextual_connect()
+    new_engine = sa.create_engine(uri, echo=SQLALCHEMY_DEBUG)
+    #new_engine.contextual_connect()
+    new_engine.connect()#.close()
     def _bind():
         """bind metadata to engine and create sessionmaker """
         global Session, engine
@@ -95,7 +108,7 @@ def _bind():
     elif new_engine is None:
         return None
 
-    _verify_connection(new_engine, show_error_dialogs)
+    #_verify_connection(new_engine, show_error_dialogs)
     _bind()
     return engine
 
@@ -128,15 +141,43 @@ def create(import_defaults=True):
     import bauble.pluginmgr as pluginmgr
     from bauble.task import TaskQuitting
     import datetime
-    #transaction = engine.contextual_connect().begin()
+    connection = engine.contextual_connect()
+    transaction = connection.begin()
     session = Session()
     try:
-        # TODO: here we are creating all the tables in the metadata whether
-        # they are in the registry or not, we should really only be creating
-        # those tables in the registry
-        metadata.drop_all(checkfirst=True)
-        metadata.create_all()
-##       debug('dropped and created')
+        # create fresh plugin registry seperate since
+        # pluginmgr.install() will be changing it
+        #debug('dropping and creating plugin registry')
+        from bauble.pluginmgr import PluginRegistry
+        #connection = None
+        #PluginRegistry.__table__.drop(bind=connection, checkfirst=True)
+        PluginRegistry.__table__.drop(bind=connection, checkfirst=True)
+        #debug(' - d')
+        PluginRegistry.__table__.create(bind=connection)
+        #PluginRegistry.__table__.create()
+        #debug(' - c')
+    except Exception, e:
+        debug(e)
+        transaction.rollback()
+        #connection.close()
+        raise
+    else:
+        transaction.commit()
+
+    connection = engine.contextual_connect()
+    transaction = connection.begin()
+    try:
+        # TODO: here we are dropping/creating all the tables in the
+        # metadata whether they are in the registry or not, we should
+        # really only be creating those tables from registered
+        # plugins, maybe with an uninstall() method on Plugin
+        #debug('drop all')
+        most_tables = metadata.sorted_tables
+        most_tables.remove(pluginmgr.PluginRegistry.__table__)
+        metadata.drop_all(bind=connection, tables=most_tables, checkfirst=True)
+        #debug(' -- dropped')
+        metadata.create_all(bind=connection, tables=most_tables)
+        #debug('dropped and created')
 
         # TODO: clearing the insert menu probably shouldn't be here and should
         # probably be pushed into db.create, the problem is at the
@@ -153,33 +194,53 @@ def create(import_defaults=True):
 
         # fill in the bauble meta table and install all the plugins
         meta_table = meta.BaubleMeta.__table__
-        meta_table.insert().execute(name=meta.VERSION_KEY,
-                                    value=unicode(bauble.version))
-        meta_table.insert().execute(name=meta.CREATED_KEY,
+        meta_table.insert(bind=connection).execute(name=meta.VERSION_KEY,
+                                                 value=unicode(bauble.version))
+        meta_table.insert(bind=connection).execute(name=meta.CREATED_KEY,
                                         value=unicode(datetime.datetime.now()))
+
+    except (GeneratorExit, TaskQuitting), e:
+        # this is here in case the main windows is closed in the middle
+        # of a task
+        debug(e)
+#        debug('db.create(): rollback')
+        transaction.rollback()
+        #session.rollback()
+        raise
+    except Exception, e:
+        debug(e)
+        #debug('db.create(): rollback')
+        transaction.rollback()
+        raise
+    else:
+        transaction.commit()
+
+    connection = engine.contextual_connect()
+    transaction = connection.begin()
+    try:
         pluginmgr.install('all', import_defaults, force=True)
     except (GeneratorExit, TaskQuitting), e:
         # this is here in case the main windows is closed in the middle
         # of a task
         debug(e)
 #        debug('db.create(): rollback')
-        #transaction.rollback()
-        session.rollback()
+        transaction.rollback()
+        #session.rollback()
         raise
     except Exception, e:
         debug(e)
         #debug('db.create(): rollback')
-        #transaction.rollback()
-        session.rollback()
-        msg = _('Error creating tables.\n\n%s') % utils.xml_safe_utf8(e)
-        debug(traceback.format_exc())
-        utils.message_details_dialog(msg, traceback.format_exc(),
-                                     gtk.MESSAGE_ERROR)
+        transaction.rollback()
+        #session.rollback()
+#         msg = _('Error creating the database.\n\n%s') % utils.xml_safe_utf8(e)
+#         debug(traceback.format_exc())
+#         utils.message_details_dialog(msg, traceback.format_exc(),
+#                                      gtk.MESSAGE_ERROR)
         raise
     else:
 ##        debug('db.create(): committing')
-        session.commit()
-        #transaction.commit()
+        #session.commit()
+        transaction.commit()
 
 
 def _verify_connection(engine, show_error_dialogs=False):
@@ -260,9 +321,12 @@ def _verify_connection(engine, show_error_dialogs=False):
     try:
         major, minor, revision = result.value.split('.')
     except:
+        session.close()
         raise error.VersionError(result.value)
 
     if major != bauble.version_tuple[0] or minor != bauble.version_tuple[1]:
+        session.close()
         raise error.VersionError(result.value)
 
+    session.close()
     return True

bauble/plugins/plants/__init__.py

@@ -100,17 +100,16 @@ def install(cls, import_defaults=True):
         if not import_defaults:
             return
         path = os.path.join(paths.lib_dir(), "plugins", "plants", "default")
-        filenames = [os.path.join(path, f) for f in 'family.txt',
-                     'genus.txt', 'genus_synonym.txt', 'geography.txt']
+#         filenames = [os.path.join(path, f) for f in 'family.txt',
+#                      'genus.txt',
+#                      'genus_synonym.txt',
+#                      'geography.txt']
+        filenames = [os.path.join(path, 'genus_synonym.txt')]
         from bauble.plugins.imex.csv_ import CSVImporter
         csv = CSVImporter()
         import_error = False
         import_exc = None
-        try:
-            csv.start(filenames, metadata=db.metadata, force=True)
-        except Exception, e:
-            error(e)
-            raise
+        csv.start(filenames, metadata=db.metadata, force=True)
 
 
 

bauble/plugins/report/template/__init__.py

@@ -82,7 +82,7 @@ def format(objs, **kwargs):
             utils.message_dialog(_('Could not open the report with the '\
                                    'default program. You can open the '\
                                    'file manually at %s') % filename)
-        return True
+        return report
 
 
 formatter_plugin = TemplateFormatterPlugin

bauble/plugins/report/template/test.py

@@ -1,4 +1,5 @@
 import os
+import sys
 
 from sqlalchemy import *
 from sqlalchemy.exc import *
@@ -14,7 +15,8 @@
 #import bauble.plugins.report as report_plugin
 from bauble.plugins.report import get_all_species, get_all_accessions, \
      get_all_plants
-from bauble.plugins.plants import Family, Genus, Species, VernacularName
+from bauble.plugins.plants import Family, Genus, Species, \
+    SpeciesDistribution, VernacularName, Geography
 from bauble.plugins.garden import Accession, Plant, Location
 from bauble.plugins.tag import tag_objects, Tag
 from bauble.plugins.report.template import TemplateFormatterPlugin
@@ -39,9 +41,14 @@ def setUp(self, *args):
                 for s in range(2):
                     sctr+=1
                     sp = Species(id=sctr, genus=genus, sp=u'sp%s' % sctr)
+                    # TODO: why doesn't this geography, species
+                    # distribution stuff seem to work
+                    geo = Geography(id=sctr, name=u'Mexico%s' % sctr)
+                    dist = SpeciesDistribution(geography_id=sctr)
+                    sp.distribution.append(dist)
                     vn = VernacularName(id=sctr, species=sp,
                                         name=u'name%s' % sctr)
-                    self.session.add_all([sp, vn])
+                    self.session.add_all([sp, geo, dist, vn])
                     for a in range(2):
                         actr+=1
                         acc = Accession(id=actr, species=sp, code=u'%s' % actr)
@@ -61,8 +68,10 @@ def tearDown(self, *args):
 
     def test_format(self):
         plants = self.session.query(Plant).all()
-        filename = os.path.join(os.path.dirname(__file__), 'test.html')
+        filename = os.path.join(os.path.dirname(__file__), 'labels.html')
         report = TemplateFormatterPlugin.format(plants, template=filename)
+        open('/tmp/testlabels.html', 'w').write(report)
+        #print >>sys.stderr, report
         # TODO: need to make some sort of assertion here
 
 

bauble/plugins/tag/__init__.py

@@ -447,8 +447,8 @@ def _reset_tags_menu():
     except:
         debug(traceback.format_exc())
         msg = _('Could not create the tags menus')
-        tb = utils.xml_safe_utf8(traceback.format_exc())
-        utils.message_details_dialog(msg, tb, gtk.MESSAGE_ERROR)
+        utils.message_details_dialog(msg, traceback.format_exc(),
+                                     gtk.MESSAGE_ERROR)
     #	raise
             #debug('** maybe the tags table hasn\'t been created yet')
 

bauble/task.py

@@ -122,7 +122,7 @@ def flush():
             #  pending tasks would be able to complete...on_error also
             #  shouldn't raise an exception
             #gobject.idle_add(on_error, e)
-            error(e)
+            #error(e)
             if on_error:
                 on_error(e)
 
@@ -149,7 +149,9 @@ def queue(task, on_quit, on_error, *args):
     Queue a new task
 
     :param task: the task to queue
-    :param callback: the function to call when the task is finished
+    :param on_quit: the function to call when the task is finished
+    :param on_error: the function to call when there is an error, this
+    method should not raise an exception or the other tasks will not complete
     :param args: the arguments to pass to the task
     """
     global _task_queue

test/itest.py

@@ -15,22 +15,33 @@
 import logging
 logging.basicConfig()
 
-uri = 'sqlite:///:memory:'
+#uri = 'sqlite:///:memory:'
+uri = 'postgres://admin:3riven&@ceiba/bbg'
 db.open(uri, False)
 pluginmgr.load()
-db.create(import_defaults=False)
+# the one thing this script doesn't do that bauble does is called
+# pluginmgr.init()
+#pluginmgr.init(force=True)
+#db.create(import_defaults=True)
 
 from bauble.plugins.plants import Family, Genus, Species
 from bauble.plugins.garden import Accession, Plant, Location
 
 session = bauble.Session()
 
-f = Family(family=u'family')
-g = Genus(family=f, genus=u'genus')
-s = Species(genus=g, sp=u's')
-a = Accession(species=s, code=u'1')
-l = Location(site=u'site')
-p = Plant(accession=a, location=l, code=u'1')
+# f = Family(family=u'family')
+# g = Genus(family=f, genus=u'genus')
+# s = Species(genus=g, sp=u's')
+# a = Accession(species=s, code=u'1')
+# l = Location(site=u'site')
+# p = Plant(accession=a, location=l, code=u'1')
+
+# session.add_all([f, g, s, a, p])
+# session.commit()
+
+# print 'drop'
+# pluginmgr.PluginRegistry.__table__.drop()
+# print 'create'
+# pluginmgr.PluginRegistry.__table__.create()
+# print 'done.'
 
-session.add_all([f, g, s, a, p])
-session.commit()