Merge branch 'ghini-1.0-dev' into ghini-1.0, as 1.0.85

.gitignore

@@ -14,14 +14,13 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
-lib64/
 parts/
 sdist/
 var/
 *.egg-info/
 .installed.cfg
 *.egg
+*.deb
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

README.rst

@@ -2,7 +2,7 @@ Ghini
 ======
 
 .. |travis| image:: https://travis-ci.org/Ghini/ghini.desktop.svg?branch=ghini-1.0-dev
-.. |pypi| image:: https://img.shields.io/pypi/v/bauble.svg
+.. |pypi| image:: https://img.shields.io/pypi/v/ghini.desktop.svg
 .. |coveralls| image:: https://coveralls.io/repos/Ghini/ghini.desktop/badge.svg?branch=ghini-1.0-dev&service=github
 
 ======== ======== ============

bauble/__init__.py

@@ -275,6 +275,7 @@ def main(uri=None):
             sentry_client = Client('https://59105d22a4ad49158796088c26bf8e4c:'
                                    '00268114ed47460b94ce2b1b0b2a4a20@'
                                    'app.getsentry.com/45704')
+            sentry_client.name = hex(hash(sentry_client.name) + 2**64)[2:-1]
             handler = SentryHandler(sentry_client)
             logging.getLogger().addHandler(handler)
             handler.setLevel(logging.WARNING)

bauble/plugins/garden/institution.py

@@ -156,6 +156,7 @@ def get_sentry_handler(self):
             sentry_client = Client('https://59105d22a4ad49158796088c26bf8e4c:'
                                    '00268114ed47460b94ce2b1b0b2a4a20@'
                                    'app.getsentry.com/45704')
+            sentry_client.name = hex(hash(sentry_client.name) + 2**64)[2:-1]
             return SentryHandler(sentry_client)
 
     def on_inst_register_clicked(self, *args, **kwargs):

bauble/plugins/garden/picture_importer.py

@@ -262,7 +262,7 @@ def do_import(self):  # step 2
             epgn, epsp = unicode(row[binomial_col] + ' sp').split(' ')[:2]
             filename = unicode(row[filename_col])
             complete_plant_code = unicode(row[accno_col])
-            accession_code, plant_code = complete_plant_code.rsplit(Plant.get_delimiter(), 2)
+            accession_code, plant_code = complete_plant_code.rsplit(Plant.get_delimiter(), 1)
 
             # create or retrieve genus and species
             genus = session.query(Genus).filter_by(epithet=epgn).one()

bauble/plugins/imex/csv_.py

@@ -514,7 +514,7 @@ def do_insert():
             transaction.rollback()
             raise
         except Exception, e:
-            logger.error(e)
+            logger.error("%s(%s)" % (type(e).__name__, e))
             logger.error(traceback.format_exc())
             transaction.rollback()
             self.__error = True
@@ -591,8 +591,6 @@ def start(self, path=None):
             raise ValueError(_("CSVExporter: path does not exist.\n%s") % path)
 
         try:
-            # TODO: should we support exporting other metadata
-            # besides db.metadata
             bauble.task.queue(self.__export_task(path))
         except Exception, e:
             logger.debug(e)
@@ -609,7 +607,7 @@ def __export_task(self, path):
                         '<b>%(table)s</b> table already exists.\n\n<i>Would '
                         'you like to continue?</i>')\
                     % {'filename': filename, 'table': table.name}
-                if utils.yes_no_dialog(msg):
+                if not utils.yes_no_dialog(msg):  # if NO: return
                     return
 
         def replace(s):
@@ -625,13 +623,16 @@ def write_csv(filename, rows):
             f.close()
 
         update_every = 30
+        spinner = u'⣄⡆⠇⠋⠙⠸⢰⣠'
         for table in db.metadata.sorted_tables:
             filename = filename_template % table.name
             steps_so_far += 1
+            spinner_index = 0
             fraction = float(steps_so_far)/float(ntables)
             pb_set_fraction(fraction)
             msg = _('exporting %(table)s table to %(filename)s')\
                 % {'table': table.name, 'filename': filename}
+            msg = msg + '  ' + spinner[spinner_index]
             bauble.task.set_message(msg)
             logger.info("exporting %s" % table.name)
 
@@ -648,9 +649,15 @@ def write_csv(filename, rows):
             rows.append(table.c.keys())  # append col names
             ctr = 0
             for row in results:
-                values = map(replace, row.values())
-                rows.append(values)
+                try:
+                    rows.append(map(replace, row.values()))
+                except:
+                    import traceback
+                    logger.error(traceback.format_exc())
                 if ctr == update_every:
+                    spinner_index = (spinner_index + 1) % len(spinner)
+                    msg = msg[:-1] + spinner[spinner_index]
+                    bauble.task.set_message(msg)
                     yield
                     ctr = 0
                 ctr += 1
@@ -705,6 +712,3 @@ class CSVExportTool(pluginmgr.Tool):
     def start(cls):
         c = CSVExporter()
         c.start()
-
-
-# TODO: add support to import from the command line

bauble/plugins/plants/taxonomy_check.py

@@ -134,7 +134,7 @@ def __init__(self, *args, **kwargs):
         super(BatchTaxonomicCheckPresenter, self).__init__(*args, **kwargs)
         self.refresh_visible_frame()
         self.tick_off_list = self.view.widgets.liststore2
-        self.binomials = [item.str(item, remove_zws=True)
+        self.binomials = [item.str(remove_zws=True)
                           for item in self.model.selection
                           if isinstance(item, Species) and item.sp != '']
 

bauble/plugins/report/mako/__init__.py

@@ -372,6 +372,14 @@ def install(cls, import_defaults=True):
         cls.plugin_dir = os.path.join(paths.appdata_dir(), "templates", "mako")
         if not os.path.exists(cls.plugin_dir):
             os.mkdir(cls.plugin_dir)
+        cls.templates = []
+        src_dir = os.path.join(paths.lib_dir(), "plugins", "report", 'mako', 'templates')
+        for template in list(os.walk(src_dir))[0][2]:
+            if template.endswith('~'):
+                continue
+            if template.startswith('__'):
+                continue
+            cls.templates.append(template)
 
     @classmethod
     def init(cls):
@@ -384,9 +392,7 @@ def init(cls):
         cls.install()  # plugins still not versioned...
 
         src_dir = os.path.join(paths.lib_dir(), "plugins", "report", 'mako', 'templates')
-        for template in os.listdir(src_dir):
-            if template.endswith('~'):
-                continue
+        for template in cls.templates:
             src = os.path.join(src_dir, template)
             dst = os.path.join(cls.plugin_dir, template)
             if not os.path.exists(dst) and os.path.exists(src):

bauble/plugins/report/mako/test.py

@@ -89,11 +89,7 @@ def test_format_all_templates(self):
         """
         plants = self.session.query(Plant).all()
         td = os.path.join(os.path.dirname(__file__), 'templates')
-        for tn in os.listdir(td):
-            if tn.endswith('~'):
-                continue
-            if tn.startswith('__init__.'):
-                continue
+        for tn in MakoFormatterPlugin.templates:
             filename = os.path.join(td, tn)
             report = MakoFormatterPlugin.format(plants, template=filename)
             self.assertTrue(isinstance(report, basestring))

bauble/plugins/tag/__init__.py

@@ -122,14 +122,39 @@ def build_menu(self):
         has_tags = query.first()
         if has_tags:
             tags_menu.append(gtk.SeparatorMenuItem())
+        submenu = {'': [None, tags_menu]}  # menuitem and submenu
+                                           # corresponding to full item
+                                           # path; it is a list because it
+                                           # needs to be mutable
+        def confirm_attach_path(parts):
+            full_path = ''
+            parent = tags_menu
+            while parts:
+                name = parts.pop()
+                full_path += name
+                if full_path not in submenu:
+                    item = gtk.ImageMenuItem(name)
+                    parent.append(item)
+                    submenu[full_path] = [item, None]
+                if submenu[full_path][1] is None:
+                    take_this = gtk.Menu()
+                    submenu[full_path] = [item, take_this]
+                    item.set_submenu(take_this)
+                parent = submenu[full_path]
+                full_path += '/'
         try:
             for tag in query:
-                item = gtk.ImageMenuItem(tag.tag)
+                path = tag.tag.split('/')
+                tail = path.pop()
+                head = '/'.join(path)
+                item = gtk.ImageMenuItem(tail)
+                submenu[tag.tag] = [item, None]
                 item.set_image(None)
                 item.set_always_show_image(True)
                 self.item_list[tag.tag] = item
                 item.connect("activate", self.item_activated, tag.tag)
-                tags_menu.append(item)
+                confirm_attach_path(path)
+                submenu[head][1].append(item)
         except Exception:
             logger.debug(traceback.format_exc())
             msg = _('Could not create the tags menus')

bauble/test/test_editor.py

@@ -95,3 +95,53 @@ def test_set_visible_get_visible(self):
         view.widget_set_visible('noconnectionlabel', False)
         self.assertFalse(view.widget_get_visible('noconnectionlabel'))
         self.assertFalse(view.widgets.noconnectionlabel.get_visible())
+
+
+from dateutil.parser import parse as parse_date
+import datetime
+import unittest
+class TimeStampParserTests(unittest.TestCase):
+
+    def test_date_parser_generic(self):
+        import dateutil
+        print(help(dateutil.tz))
+        target = parse_date('2019-01-18 18:20 +0500')
+        result = parse_date('18 January 2019 18:20 +0500')
+        self.assertEquals(result, target)
+        result = parse_date('18:20, 18 January 2019 +0500')
+        self.assertEquals(result, target)
+        result = parse_date('18:20+0500, 18 January 2019')
+        self.assertEquals(result, target)
+        result = parse_date('18:20+0500, 18 Jan 2019')
+        self.assertEquals(result, target)
+        result = parse_date('18:20+0500, 2019-01-18')
+        self.assertEquals(result, target)
+        result = parse_date('18:20+0500, 1/18 2019')
+        self.assertEquals(result, target)
+        result = parse_date('18:20+0500, 18/1 2019')
+        self.assertEquals(result, target)
+
+    def test_date_parser_ambiguous(self):
+        ## defaults to European: day, month, year - FAILS
+        #result = parse_date('5 1 4')
+        #self.assertEquals(result, datetime.datetime(2004, 1, 5, 0, 0))
+        # explicit, American: month, day, year
+        result = parse_date('5 1 4', dayfirst=False, yearfirst=False)
+        self.assertEquals(result, datetime.datetime(2004, 5, 1, 0, 0))
+        # explicit, European: day, month, year
+        result = parse_date('5 1 4', dayfirst=True, yearfirst=False)
+        self.assertEquals(result, datetime.datetime(2004, 1, 5, 0, 0))
+        # explicit, Japanese: year, month, day (month, day, year)
+        result = parse_date('5 1 4', dayfirst=False, yearfirst=True)
+        self.assertEquals(result, datetime.datetime(2005, 1, 4, 0, 0))
+        ## explicit, illogical: year, day, month - FAILS
+        #result = parse_date('5 1 4', dayfirst=True, yearfirst=True)
+        #self.assertEquals(result, datetime.datetime(2005, 4, 1, 0, 0))
+
+    def test_date_parser_365(self):
+        target = datetime.datetime(2014, 1, 1, 20)
+        result = parse_date('2014-01-01 20')
+        self.assertEquals(result, target)
+        target = parse_date('2014-01-01 20:00 +0000')
+        result = parse_date('2014-01-01 20+0')
+        self.assertEquals(result, target)

bauble/ui.py

@@ -771,8 +771,8 @@ def on_help_menu_about(self, widget, data=None):
         about.set_copyright(_(u'Copyright © by its contributors.'))
 
         import codecs
-        with codecs.open(os.path.join(paths.installation_dir(), 'share',
-                                      'LICENSE.ghini')) as f:
+        with codecs.open(os.path.join(paths.installation_dir(), 'share', 'ghini',
+                                      'LICENSE')) as f:
             license = f.read()
         about.set_license(license)  # not translated
         about.set_comments(_('This version installed on: %s\n'

bauble/version.py

@@ -21,4 +21,4 @@
 # The Ghini version.
 # major, minor, revision version tuple
 
-version = "1.0.82"  # :bump
+version = "1.0.85"  # :bump

data/ghini.desktop

@@ -1,7 +1,7 @@
 [Desktop Entry]
 Encoding=UTF-8
 Name=Ghini
-Version=1.0.82  # :bump
+Version=1.0.85  # :bump
 Comment=An application for managing botanical collections
 Terminal=False
 Icon=ghini

debian/changelog

@@ -0,0 +1,47 @@
+ghini.desktop (1.0.85-1) unstable; urgency=medium
+
+  * merging with upstream.
+
+ -- Mario Frasca <[email protected]>  Thu, 31 May 2018 11:20:00 -0500
+
+ghini.desktop (1.0.84-1) unstable; urgency=medium
+
+  * merging with upstream.
+
+ -- Mario Frasca <[email protected]>  Fri, 25 May 2018 10:30:00 -0500
+
+ghini.desktop (1.0.83-2) unstable; urgency=medium
+
+  * updating to upstream, which is now mostly compatible with Python3
+
+ -- Mario Frasca <[email protected]>  Fri, 25 May 2018 10:28:27 -0500
+
+ghini.desktop (1.0.83-1) unstable; urgency=medium
+
+  * Initial release
+
+ -- Mario Frasca <[email protected]>  Fri, 18 May 2018 10:28:27 -0500
+
+bauble (1.0.56-4) unstable; urgency=medium
+
+  * correcting timestamp and shortening comment
+
+ -- Mario Frasca <[email protected]>  Thu, 17 May 2018 18:32:24 -0500
+
+bauble (1.0.56-3) unstable; urgency=medium
+
+  * correcting bauble.desktop (removing redundant encoding and adding keywords); and control (priority: optional).
+
+ -- Mario Frasca <[email protected]>  Thu, 17 May 2018 17:08:58 -0500
+
+bauble (1.0.56-2) unstable; urgency=medium
+
+  * solving QA issues that became visible after uploading to mentors.
+
+ -- Mario Frasca <[email protected]>  Thu, 17 May 2018 17:08:58 -0500
+
+bauble (1.0.56-1) unstable; urgency=medium
+
+  * Initial release (Closes: #755185)
+
+ -- Mario Frasca <[email protected]>  Thu, 17 May 2018 13:18:11 -0500

debian/control

@@ -0,0 +1,18 @@
+Source: ghini.desktop
+Section: science
+Priority: optional
+Maintainer: Mario Frasca <[email protected]>
+Build-Depends: debhelper (>= 9), python:any
+Standards-Version: 3.9.8
+Homepage: https://ghini.github.io
+
+Package: ghini.desktop
+Architecture: all
+Depends: python-fibra, python-dateutil, python-pyqrcode, xdg-utils, python-egenix-mxdatetime, python-sqlalchemy (>= 0.6), python-lxml (>= 2.0), python-pyparsing, python-gtk2 (>= 2.12), librsvg2-common, python-glade2, python-gdata (>= 1.1.1), python-mako (>= 0.2.2), python-pysqlite2 (>= 2.3.2) | python-mysqldb | python-psycopg2, python:any (>= 2.7.5-5~)
+Recommends: python-mysqldb | python-psycopg2
+Description: biodiversity collection manager software application
+ Bauble is a software application to help you manage a collection of
+ botanical specimens. It is intended to be used by botanic gardens,
+ herbaria, arboreta, etc. to manage their collection information.
+ It is a open, free, cross-platform alternative to BG-Base and
+ similar software.

debian/copyright

@@ -0,0 +1,42 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ghini.desktop
+Source: <http://github.com/Ghini/ghini.desktop>
+
+Files: *
+Copyright: 2004-2011 Brett Adams
+           2014-2018 Mario Frasca
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: debian/*
+Copyright: 2018 Mario Frasca <[email protected]>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".