added methods for handling notes to sfftkrw.SFFSegmentation

sfftkrw/conf.py

@@ -1,2 +1,2 @@
-SFFTKRW_VERSION = 'v0.6.1.dev0'
+SFFTKRW_VERSION = 'v0.6.2.dev0'
 SFFTKRW_ENTRY_POINT = 'sff'

sfftkrw/schema/adapter_v0_8_0_dev1.py

@@ -2523,3 +2523,50 @@ def from_file(cls, fn, args=None):
     def to_file(self, *args, **kwargs):
         """Alias for :py:meth:`.export` method. Passes all args and kwargs onto :py:meth:`.export`"""
         return super(SFFSegmentation, self).export(*args, **kwargs)
+
+    def merge_annotation(self, other_seg):
+        """Merge the annotation from another sff_seg to this one
+
+        :param other_seg: segmentation to get annotations from
+        :type other_seg: :py:class:`sfftkrw.SFFSegmentation`
+        """
+        _assert_or_raise(other_seg, SFFSegmentation)
+        # global data
+        # self.name = other_seg.name
+        # self.software_list = other_seg.software_list
+        self.global_external_references = other_seg.global_external_references
+        # self.details = other_seg.details
+        # loop through segments
+        for segment in self.segments:
+            other_segment = other_seg.segments.get_by_id(segment.id)
+            segment.biological_annotation = other_segment.biological_annotation
+
+    def copy_annotation(self, from_id, to_id):
+        """Copy annotation across segments
+
+        :param int/list from_id: segment ID to get notes from; use -1 for for global notes
+        :param int/list to_id: segment ID to copy notes to; use -1 for global notes
+        """
+        if from_id == -1:
+            _from = self.global_external_references
+        else:
+            _from = self.segments.get_by_id(from_id).biological_annotation.external_references
+        if to_id == -1:
+            to = self.global_external_references
+        else:
+            to = self.segments.get_by_id(to_id).biological_annotation.external_references
+        # the id for global notes
+        for extref in _from:
+            to.append(extref)
+
+    def clear_annotation(self, from_id):
+        """Clear all annotations from the segment with ID specified
+
+        :param from_id: segment ID
+        :return:
+        """
+        if from_id == -1:
+            self.global_external_references.clear() # = SFFGlobalExternalReferenceList()
+        else:
+            segment = self.segments.get_by_id(from_id)
+            segment.biological_annotation.external_references.clear() # = SFFExternalReferenceList()

sfftkrw/unittests/test_adapter_v0_8_0_dev1.py

@@ -5238,3 +5238,66 @@ def test_export_json(self):
         with open(temp_file.name) as f:
             J = json.load(f)
             self.assertEqual(J[u'primary_descriptor'], u"three_d_volume")
+
+    def test_merge_annotation(self):
+        """Test that we can merge annotation from one to another"""
+        seg1_fn = os.path.join(TEST_DATA_PATH, u'sff', u'v0.8', u'annotated_emd_1014.json')
+        seg2_fn = os.path.join(TEST_DATA_PATH, u'sff', u'v0.8', u'emd_1014.json')
+        seg1 = adapter.SFFSegmentation.from_file(seg1_fn)
+        seg2 = adapter.SFFSegmentation.from_file(seg2_fn)
+        # perform the notes merge
+        seg1.merge_annotation(seg2)
+        self.assertEqual(seg1.global_external_references, seg2.global_external_references)
+        for segment in seg1.segment_list:
+            other_segment = seg2.segment_list.get_by_id(segment.id)
+            self.assertEqual(segment.biological_annotation.external_references, other_segment.biological_annotation.external_references)
+
+    def test_copy_annotation(self):
+        """Test that we can copy annotations: global and local"""
+        seg_fn = os.path.join(TEST_DATA_PATH, u'sff', u'v0.8', u'emd_1014.json')
+        seg = adapter.SFFSegmentation.from_file(seg_fn)
+        segment_ids = list(seg.segment_list.get_ids())
+        from_segment_id = random.choice(segment_ids)
+        from_segment = seg.segment_list.get_by_id(from_segment_id)
+        segment_ids.remove(from_segment_id)
+        try:
+            to_segment_ids = random.choices(segment_ids, k=len(segment_ids)//2)
+        except AttributeError:
+            to_segment_ids = list(set([random.choice(segment_ids) for _ in _xrange(len(segment_ids)//2)]))
+        # clear annotations; check no annotations left
+        for segment_id in to_segment_ids:
+            segment = seg.segment_list.get_by_id(segment_id)
+            segment.biological_annotation.external_references.clear()
+            self.assertEqual(len(segment.biological_annotation.external_references), 0)
+        # copy annotations
+        # noinspection PyStatementEffect
+        (seg.copy_annotation(from_segment_id, to_id) for to_id in to_segment_ids)
+        # now ensure they are similar to the one copied from
+        for segment_id in to_segment_ids:
+            segment = seg.segment_list.get_by_id(segment_id)
+            self.assertEqual(segment.biological_annotation.external_references, from_segment.biological_annotation.external_references)
+        # for global
+        seg.global_external_references.clear()
+        self.assertEqual(len(seg.global_external_references), 0)
+        seg.copy_annotation(from_segment_id, -1) # -1 for global
+        self.assertEqual(len(from_segment.biological_annotation.external_references), len(seg.global_external_references))
+        for i, er in enumerate(from_segment.biological_annotation.external_references):
+            self.assertEqual(er, seg.global_external_references[i])
+
+    def test_clear_annotation(self):
+        """Test that we can clear annotations"""
+        seg_fn = os.path.join(TEST_DATA_PATH, u'sff', u'v0.8', u'emd_1014.json')
+        seg = adapter.SFFSegmentation.from_file(seg_fn)
+        # global
+        self.assertTrue(len(seg.global_external_references) > 0)
+        seg.clear_annotation(-1)
+        self.assertEqual(len(seg.global_external_references), 0)
+        # local
+        segment_ids = list(seg.segment_list.get_ids())
+        from_segment_id = random.choice(segment_ids)
+        from_segment = seg.segment_list.get_by_id(from_segment_id)
+        self.assertTrue(len(from_segment.biological_annotation.external_references) > 0)
+        seg.clear_annotation(from_segment_id)
+        self.assertEqual(len(from_segment.biological_annotation.external_references), 0)
+
+