Merge pull request #34 from sbesson/set_helpers

render set: helper refactoring

src/omero_cli_render.py

@@ -584,21 +584,28 @@ def _read_default_planes(self, img, data, ignore_errors=False):
                 def_t = None
         return (def_z, def_t)
 
-    @gateway_required
-    def set(self, args):
-        """ Implements the 'set' command """
-        newchannels = {}
-        data = pydict_text_io.load(
-            args.channels, session=self.client.getSession())
+    def _load_rendering_settings(self, source, session=None):
+        """Load a rendering dictionary from a source (file or object)"""
+        try:
+            data = pydict_text_io.load(source, session=session)
+        except Exception as e:
+            self.ctx.dbg(e)
+            self.ctx.die(103, "Could not read %s" % source)
+
         if 'channels' not in data:
-            self.ctx.die(104, "ERROR: No channels found in %s" % args.channels)
+            self.ctx.die(104, "ERROR: No channels found in %s" % source)
 
         version = _getversion(data)
         if version == 0:
             self.ctx.die(124, "ERROR: Cannot determine version. Specify"
                               " version or use either start/end or min/max"
                               " (not both).")
+        return data
 
+    def _read_channels(self, data):
+        """Read new channels from settings dictionary"""
+        newchannels = {}
+        version = _getversion(data)
         # Read channel setttings from rendering dictionary
         for chindex, chdict in data['channels'].items():
             try:
@@ -611,18 +618,12 @@ def set(self, args):
             try:
                 cobj = ChannelObject(chdict, version)
                 newchannels[cindex] = cobj
-                print('%d:%s' % (cindex, cobj))
+                self.ctx.dbg('%d:%s' % (cindex, cobj))
             except Exception as e:
                 self.ctx.err('ERROR: %s' % e)
                 self.ctx.die(
                     105, "Invalid channel description: %s" % chdict)
 
-        try:
-            greyscale = data['greyscale']
-            print('greyscale=%s' % data['greyscale'])
-        except KeyError:
-            greyscale = None
-
         namedict = {}
         cindices = []
         rangelist = []
@@ -636,6 +637,18 @@ def set(self, args):
                 cindices.append(i)
             rangelist.append([c.start, c.end])
             colourlist.append(c.color)
+        return (namedict, cindices, rangelist, colourlist)
+
+    @gateway_required
+    def set(self, args):
+        """ Implements the 'set' command """
+        data = self._load_rendering_settings(
+            args.channels, session=self.client.getSession())
+        (namedict, cindices, rangelist, colourlist) = self._read_channels(
+            data)
+        greyscale = data.get('greyscale', None)
+        if greyscale is not None:
+            self.ctx.dbg('greyscale=%s' % greyscale)
 
         iids = []
         for img in self.render_images(self.gateway, args.object, batch=1):
@@ -657,6 +670,7 @@ def set(self, args):
 
             img.set_active_channels(
                 cindices, windows=rangelist, colors=colourlist)
+
             if greyscale is not None:
                 if greyscale:
                     img.setGreyscaleRenderingModel()

test/unit/test_set.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#
+# Copyright (C) 2015-2018 University of Dundee & Open Microscopy Environment.
+# All rights reserved.
+#
+# This program 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 program 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, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+
+from omero.cli import CLI, NonZeroReturnCode
+from omero_cli_render import RenderControl
+
+import pytest
+import uuid
+import yaml
+
+
+def write_yaml(d, tmpdir):
+    f = tmpdir.join(str(uuid.uuid4()) + ".yml")
+    f.write(yaml.dump(d, explicit_start=True, width=80, indent=4,
+                      default_flow_style=False))
+    return str(f)
+
+
+class TestLoadRenderingSettings:
+    def setup_method(self):
+        self.cli = CLI()
+        self.cli.register("render", RenderControl, "TEST")
+        self.render = self.cli.controls['render']
+
+    def test_none(self):
+        with pytest.raises(NonZeroReturnCode):
+            self.render._load_rendering_settings(None)
+
+    def test_non_existing_file(self):
+        with pytest.raises(NonZeroReturnCode) as e:
+            self.render._load_rendering_settings(str(uuid.uuid4()) + '.yml')
+        assert e.value.rv == 103
+
+    def test_no_channels(self, tmpdir):
+        d = {'version': 1}
+        f = write_yaml(d, tmpdir)
+        with pytest.raises(NonZeroReturnCode) as e:
+            self.render._load_rendering_settings(f)
+        assert e.value.rv == 104
+
+    def test_bad_version(self, tmpdir):
+        d = {'channels': {1: {'label': 'foo'}}}
+        f = write_yaml(d, tmpdir)
+        with pytest.raises(NonZeroReturnCode) as e:
+            self.render._load_rendering_settings(f)
+        assert e.value.rv == 124
+
+
+class TestReadChannels:
+    def setup_method(self):
+        self.cli = CLI()
+        self.cli.register("render", RenderControl, "TEST")
+        self.render = self.cli.controls['render']
+
+    def test_non_integer_channel(self):
+        d = {'channels': {'GFP': {'label': 'foo'}}}
+        with pytest.raises(NonZeroReturnCode) as e:
+            self.render._read_channels(d)
+        assert e.value.rv == 105
+
+    @pytest.mark.parametrize('key', ['min', 'max', 'start', 'end'])
+    def test_float_keys(self, key):
+        d = {'channels': {1: {key: 'foo'}}}
+        with pytest.raises(NonZeroReturnCode) as e:
+            self.render._read_channels(d)
+        assert e.value.rv == 105