Merge remote-tracking branch 'origin/ghini-1.0-dev' into ghini-1.0-dev

bauble/editor.py

@@ -2111,13 +2111,16 @@ def on_activate_browse_button(self, widget, data=None):
             fileChooserDialog.run()
             filename = fileChooserDialog.get_filename()
             if filename:
-                ## rememberl chosen location for next time
-                ## copy file to picture_root_dir (if not yet there).
+                ## remember chosen location for next time
                 PictureBox.last_folder, basename = os.path.split(unicode(filename))
                 logger.debug('new current folder is: %s' % self.last_folder)
-                utils.copy_picture_with_thumbnail(self.last_folder, basename)
+                ## copy file to picture_root_dir (if not yet there),
+                ## also receiving thumbnail base64
+                thumb = utils.copy_picture_with_thumbnail(self.last_folder, basename)
                 ## make sure the category is <picture>
                 self.set_model_attr('category', u'<picture>')
+                ## append thumbnail base64 to content string
+                basename = basename + "|data:image/jpeg;base64," + thumb
                 ## store basename in note field and fire callbacks.
                 self.set_model_attr('note', basename)
                 self.set_content(basename)

bauble/plugins/plants/default/genus.txt

@@ -19055,7 +19055,6 @@
 19059,"Richardsiella","Elffers & Kenn.-O'Byrne",214
 19060,"Hesperostipa","(Elias) Barkworth",214
 19061,"Dichelachne","Endl.",214
-19062,"Saxipoa","",214
 19063,"Spathia","Ewart",214
 19064,"Rehia","Fijten",214
 19065,"Ophiochloa","Filg. et al.",214
@@ -23154,7 +23153,6 @@
 23163,"Pongati","Adans.",1286
 23164,"Rapinia","Lour.",1286
 23165,"Sphenoclea","Gaertn.",1286
-23166,"Spiroplasma","",1289
 23167,"Stachyurus","Siebold & Zucc.",443
 23168,"Ochranthe","Lindl.",446
 23169,"Jahnia","Pittier & S. F. Blake",446

bauble/ui.py

@@ -429,8 +429,8 @@ def create_main_menu(self):
         # create and addaction group for menu actions
         menu_actions = gtk.ActionGroup("MenuActions")
         menu_actions.add_actions([("file", None, _("_File")),
-                                  #("file_new", gtk.STOCK_NEW, _("_New"),
-                                  # None, None, self.on_file_menu_new),
+                                  ("file_new", gtk.STOCK_NEW, _("_New"),
+                                   None, None, self.on_file_menu_new),
                                   ("file_open", gtk.STOCK_OPEN, _("_Open"),
                                    '<ctrl>o', None, self.on_file_menu_open),
                                   ("file_quit", gtk.STOCK_QUIT, _("_Quit"),
@@ -465,6 +465,8 @@ def create_main_menu(self):
                                   ("help_about", gtk.STOCK_ABOUT, _("About"),
                                    None, None, self.on_help_menu_about),
                                   ])
+        menu_actions.get_action('file_new').set_sensitive(False)
+        menu_actions.get_action('file_open').set_sensitive(False)
         self.ui_manager.insert_action_group(menu_actions, 0)
 
         # TODO: The menubar was made available in gtk.Builder in Gtk+
@@ -682,10 +684,9 @@ def on_file_menu_open(self, widget, data=None):
         """
         Open the connection manager.
         """
-        from connmgr import ConnMgrPresenter
+        from connmgr import start_connection_manager
         default_conn = prefs[bauble.conn_default_pref]
-        cm = ConnMgrPresenter(default=default_conn)
-        name, uri = cm.start()
+        name, uri = start_connection_manager(default_conn)
         if name is None:
             return
 

bauble/utils/__init__.py

@@ -95,6 +95,7 @@ def get(self, key, getter, on_hit=lambda x: None):
 def copy_picture_with_thumbnail(path, basename=None):
     """copy file from path to picture_root, and make thumbnail, preserving name
 
+    return base64 representation of thumbnail
     """
     import os.path
     if basename is None:
@@ -110,16 +111,23 @@ def copy_picture_with_thumbnail(path, basename=None):
     from PIL import Image
     full_dest_path = os.path.join(prefs.prefs[prefs.picture_root_pref],
                                   'thumbs', basename)
+    result = ""
     try:
         im = Image.open(filename)
         im.thumbnail((400, 400))
         logger.debug('copying %s to %s' % (filename, full_dest_path))
         im.save(full_dest_path)
+        from io import BytesIO
+        output = BytesIO()
+        im.save(output, format='JPEG')
+        im_data = output.getvalue()
+        result = base64.b64encode(im_data)
     except IOError, e:
         logger.warning("can't make thumbnail")
     except Exception, e:
         logger.warning("unexpected exception making thumbnail: "
                        "(%s)%s" % (type(e), e))
+    return result
 
 
 class ImageLoader(threading.Thread):
@@ -129,7 +137,11 @@ def __init__(self, box, url, *args, **kwargs):
         super(ImageLoader, self).__init__(*args, **kwargs)
         self.box = box  # will hold image or label
         self.loader = gtk.gdk.PixbufLoader()
-        if (url.startswith('http://') or url.startswith('https://')):
+        self.inline_picture_marker = "|data:image/jpeg;base64,"
+        if url.find(self.inline_picture_marker) != -1:
+            self.reader_function = self.read_base64
+            self.url = url
+        elif (url.startswith('http://') or url.startswith('https://')):
             self.reader_function = self.read_global_url
             self.url = url
         else:
@@ -178,6 +190,13 @@ def run(self):
             self.url, self.reader_function, on_hit=self.loader.write)
         self.loader.close()
 
+    def read_base64(self):
+        self.loader.connect("area-prepared", self.loader_notified)
+        thumb64pos = self.url.find(self.inline_picture_marker)
+        offset = thumb64pos + len(self.inline_picture_marker)
+        import base64
+        return base64.b64decode(self.url[offset:])
+
     def read_global_url(self):
         self.loader.connect("area-prepared", self.loader_notified)
         import urllib

doc/_static/custom.css

@@ -1,3 +1,8 @@
+h1, h2, h3, h4 {
+    background-color: #f2f2f2;
+    border-bottom: 1px solid #ccc;
+}
+
 .toggle .admonition-title {
     display: block;
     clear: both;
@@ -15,3 +20,12 @@
 .toggle .admonition-title.open:after {
     content: " ▲";
 }
+
+.tight-table td {
+    white-space: normal !important;
+}
+
+p {
+    margin-bottom: 12px;
+}
+

doc/building.rst

@@ -579,7 +579,7 @@ export dialog box. The following command will give you a list of
 ``GenericEditorView`` instantiations::
 
   grep -nHr -e GenericEditorView\( bauble
-
+   
 Extending Ghini with Plugins
 -----------------------------
 

doc/ghini-family.rst

@@ -0,0 +1,234 @@
+==================
+ the Ghini family
+==================
+
+Let's start by recalling the composition of the Ghini family, as shown in the diagram:
+
+.. image:: images/ghini-family-clean.png
+
+You have learned how to use ghini.desktop, here we introduce the other
+members of the family, and their interaction.
+
+.. _ghini.pocket:
+
+ghini.pocket
+============
+
+.. image:: images/ghini-pocket-installed.png
+   :align: left
+
+ghini.pocket is an Android app which you can install from the `play
+store
+<https://play.google.com/store/apps/details?id=me.ghini.pocket>`_.
+ghini.pocket is definitely the tool you will use most, next to
+ghini.desktop.
+
+With ghini.pocket you always have the latest snapshot of your
+database with you.
+
+Type an accession number, or scan its barcode or QR label, and you know:
+
+- the identification of the plant,
+- whether it already has pictures,
+- when it entered the garden and
+- from which source.
+
+Apart as a quick data viewer, you can use ghini.pocket for...
+
+  ..  admonition:: data correction
+      :class: toggle
+
+         If by your judgement, some of the information is incorrect, or if
+         the plant is flowering and you want to immediately take a picture
+         and store it in the database, you do not need take notes on paper,
+         nor follow convolute procedures: ghini.pocket lets you write your
+         corrections in a log file, take pictures associated to the plant,
+         and you will import this information straight into the database,
+         with further minimal user intervention.
+
+  ..  admonition:: inventory review
+      :class: toggle
+
+         The initial idea on which we based ghini.pocket is still one of its
+         functionalities: inventory review.
+
+         Using ghini.pocket, reviewing the inventory of a greenhouse, in
+         particular if you have QR codes on plant labels, goes as fast as
+         you can walk: simply enter the location code of your greenhouse,
+         reset the log, then one by one scan the plant codes of the plants
+         in the greenhouse.  No further data collection action is required.
+
+         When you're done, import the log in ghini.desktop.  The procedure
+         available in ghini.desktop includes adding unknown but labelled
+         plants in the database, marking as lost/dead all plants that the
+         database reports as alive and present in the inventoried location,
+         but were not found during the inventory.
+
+  ..  admonition:: taxonomic support
+      :class: toggle
+
+         As a bonus, ghini.pocket contains a phonetic genus search, and a
+         quite complete database of botanic taxa with rank between order and
+         genus, including tribes, and synonymies.
+
+check further :any:`interaction among components`.
+
+.. _ghini.web:
+
+ghini.web
+=========
+
+.. image:: images/ghini-web-installed.png
+   :align: left
+
+ghini.web is a web server, written in nodejs.
+
+Its most visible part runs at http://gardens.ghini.me and shows as a
+map of the world, where you browse gardens and search their published
+collection.
+
+It also serves configuration data to ghini.tour instances.
+
+check further :any:`interaction among components`.
+
+
+.. _ghini.tour:
+
+ghini.tour
+==========
+
+.. image:: images/ghini-tour-installed.png
+   :align: left
+
+ghini.tour is an Android app which you can install from the `play
+store
+<https://play.google.com/store/apps/details?id=me.ghini.tour>`_.
+
+People visiting your garden will install ghini.tour on their phone or
+tablet, enjoy having a map of the garden, knowing where they are, and
+will be able to listen to audio files that you have placed as virtual
+information panels in strategic spots in your garden.
+
+.. admonition:: world view
+   :class: toggle
+
+      at startup, you see the world and gardens.  select a garden, and enter.
+
+.. admonition:: garden view
+   :class: toggle
+
+      when viewing at garden level, you see panels.  select a panel, and listen.
+
+check further :any:`interaction among components`.
+
+
+.. _interaction among components:
+
+data streams between software components
+========================================
+
+.. note:: This section contains technical information for database managers and
+          software developers.
+
+.. image:: images/ghini-streams-installed.png
+   :align: left
+
+In the diagram showing the composition of the Ghini family, the alert
+reader noticed how different arrows representing different data
+flows, had different colours: some are deep green, some have a
+lighter tint.
+
+
+Deeper green streams are constant flows of data, representing the core
+activity of a component, eg: the interaction between ghini.desktop and its
+database server, or your internet browser and ghini.web.
+
+Lighter green streams are import/export actions, initiated by the user at the
+command panel of ghini.desktop, or in the ghini.tour settings page.
+
+This is the same graph, in which all import data streams have been given an
+identifier.
+
+.. image:: images/ghini-family-streams.png
+
+..  admonition:: d2p: copy a snapshot of the desktop database to ghini.pocket
+    :class: toggle
+
+       - export the desktop database to a pocket snapshot
+       - copy the snapshot to the handheld device
+
+       ghini.pocket integrates closely with ghini.desktop, and it's not a
+       tool for the casual nor the external user.  One task of your garden
+       database manager is to regularly copy an updated database snapshot to
+       your Android device.
+
+       We advise enabling USB debugging on the device.  In perspective, this will
+       allow ghini.desktop writing directily into the ghini.pocket device.
+
+       Export the file from ghini.desktop, call the file pocket.db, copy it to the phone::
+
+         adb -d push /tmp/pocket.db /sdcard/Android/data/me.ghini.pocket/files/
+
+       The above location is valid even if your phone does not have a memory card.
+
+       Other options include bluetooth, or whatever other way you normally use to
+       copy regular files into your Android device.
+
+
+
+..  admonition:: p2d: import from the ghini.pocket log file and pictures into the central database
+    :class: toggle
+
+       even if we're still calling it “inventory log”, ghini.pocket's log
+       contains more than just inventory corrections.
+
+       - produce a log on the handheld device
+       - import the log in the desktop database
+
+       first of all, copy the collected information from ghini.pocket into your computer::
+
+         export DIR=/some/directory/on/your/computer
+         adb -d pull /sdcard/Android/data/me.ghini.pocket/files/searches.txt $DIR
+         adb -d pull -a /sdcard/Android/data/me.ghini.pocket/files/Pictures $DIR
+
+       then use ghini.desktop to import this information into your database.
+
+
+..  admonition:: d2w: send a selection of your garden data to ghini.web
+    :class: toggle
+
+       Offer a selection of your garden data to a central ghini.web site, so
+       online virtual visitors can browse it.  This includes plant
+       identification and their geographic location.
+
+       content of this flow:
+
+       - garden: coords, name, zoom level (for initial view)
+       - plants: coords, identification, zoom level (for visibility)
+       - species: binomial, phonetic approximation
+
+
+
+..  admonition:: g2w: add geographic non-botanic data to ghini.web
+    :class: toggle
+
+     - Write geographic information about non-botanic data (ie: point of
+       interest within the garden, required by ghini.tour) in the central
+       ghini.web site.
+
+       content of this flow:
+
+       - virtual panels: coords, title, audio file
+       - photos: coords, title, picture
+
+       virtual panels don't necessarily have an associated photo, photos
+       don't necessarily have an associated audio file.
+
+
+..  admonition:: w2t: importing locations and POIs from ghini.web to tour
+    :class: toggle
+
+       content of this flow:
+
+       - Garden (coords, name, zoom level)
+       - Points of Interest (coords, title, audio file, photo)