Merge pull request #3776 from chris-allan/plate-metadata-perf-develop

Optimize plate grid metadata

components/tools/OmeroPy/src/omero/gateway/__init__.py

@@ -5603,10 +5603,14 @@ def getGridSize(self):
         :rtype:     dict of {'rows': rSize, 'columns':cSize}
         """
         if self._gridSize is None:
-            r, c = 0, 0
-            for child in self._listChildren():
-                r, c = max(child.row.val, r), max(child.column.val, c)
-            self._gridSize = {'rows': r+1, 'columns': c+1}
+            q = self._conn.getQueryService()
+            params = omero.sys.ParametersI()
+            params.addId(self.getId())
+            query = "select max(row), max(column) from Well "\
+                    "where plate.id = :id"
+            res = q.projection(query, params, self._conn.SERVICE_OPTS)
+            (row, col) = res[0]
+            self._gridSize = {'rows': row.val+1, 'columns': col.val+1}
         return self._gridSize
 
     def getWellGrid(self, index=0):

components/tools/OmeroPy/test/integration/gatewaytest/test_image_wrapper.py

@@ -0,0 +1,71 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2015 Glencoe Software, Inc.
+# All rights reserved.
+#
+# Use is subject to license terms supplied in LICENSE.txt
+
+"""
+   gateway tests - Testing the gateway image wrapper
+
+   pytest fixtures used as defined in conftest.py:
+   - gatewaywrapper
+
+"""
+
+import pytest
+
+from omero.model import ImageI
+from omero.rtypes import rstring, rtime
+from datetime import datetime
+
+
+@pytest.fixture()
+def image(request, gatewaywrapper):
+    """Creates an Image."""
+    gatewaywrapper.loginAsAuthor()
+    gw = gatewaywrapper.gateway
+    update_service = gw.getUpdateService()
+    image = ImageI()
+    image.name = rstring('an image')
+    # 2015-04-21 01:15:00
+    image.acquisitionDate = rtime(1429578900000L)
+    image_id, = update_service.saveAndReturnIds([image])
+    return gw.getObject('Image', image_id)
+
+
+@pytest.fixture()
+def image_no_acquisition_date(request, gatewaywrapper):
+    """Creates an Image."""
+    gatewaywrapper.loginAsAuthor()
+    gw = gatewaywrapper.gateway
+    update_service = gw.getUpdateService()
+    image = ImageI()
+    image.name = rstring('an image')
+    image.acquisitionDate = rtime(0L)
+    image_id, = update_service.saveAndReturnIds([image])
+    return gw.getObject('Image', image_id)
+
+
+class TestImageWrapper(object):
+
+    def testGetDate(self, gatewaywrapper, image):
+        date = image.getDate()
+        assert date == datetime.fromtimestamp(1429578900L)
+
+    def testGetDateNoAcquisitionDate(
+            self, gatewaywrapper, image_no_acquisition_date):
+        date = image_no_acquisition_date.getDate()
+        creation_event_date = image_no_acquisition_date.creationEventDate()
+        assert date == creation_event_date
+
+    def testSimpleMarshal(self, gatewaywrapper, image):
+        marshalled = image.simpleMarshal()
+        assert marshalled == {
+            'description': '',
+            'author': 'Author ',
+            'date': 1429578900.0,
+            'type': 'Image',
+            'id': image.getId(),
+            'name': 'an image'
+        }

components/tools/OmeroPy/test/integration/gatewaytest/test_plate_wrapper.py

@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2015 Glencoe Software, Inc.
+# All rights reserved.
+#
+# Use is subject to license terms supplied in LICENSE.txt
+
+"""
+   gateway tests - Testing the gateway plate wrapper
+
+   pytest fixtures used as defined in conftest.py:
+   - gatewaywrapper
+
+"""
+
+import pytest
+
+from omero.model import PlateI, WellI, WellSampleI, ImageI
+from omero.rtypes import rstring, rint, rtime
+from uuid import uuid4
+
+
+def uuid():
+    return str(uuid4())
+
+
+@pytest.fixture()
+def plate(request, gatewaywrapper):
+    """Creates a Plate."""
+    gatewaywrapper.loginAsAuthor()
+    gw = gatewaywrapper.gateway
+    update_service = gw.getUpdateService()
+    plate = PlateI()
+    plate.name = rstring(uuid())
+    for well_index in range(3):
+        well = WellI()
+        well.row = rint(well_index**2)
+        well.column = rint(well_index**3)
+        for well_sample_index in range(2):
+            well_sample = WellSampleI()
+            image = ImageI()
+            image.name = rstring('%s_%d' % (uuid(), well_sample_index))
+            image.acquisitionDate = rtime(0)
+            well_sample.image = image
+            well.addWellSample(well_sample)
+        plate.addWell(well)
+    plate_id, = update_service.saveAndReturnIds([plate])
+    return gw.getObject('Plate', plate_id)
+
+
+class TestPlateWrapper(object):
+
+    def testGetGridSize(self, gatewaywrapper, plate):
+        assert plate.getGridSize() == {'rows': 5L, 'columns': 9L}

components/tools/OmeroWeb/omeroweb/webgateway/plategrid.py

@@ -0,0 +1,86 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2015 Glencoe Software, Inc.
+# All rights reserved.
+#
+# Use is subject to license terms supplied in LICENSE.txt
+
+"""
+   Module to encapsulate operations concerned with displaying the contents of a
+   plate as a grid.
+"""
+
+import logging
+
+import omero.sys
+from omero.rtypes import rint
+
+logger = logging.getLogger(__name__)
+
+
+class PlateGrid(object):
+    """
+    A PlateGrid object encapsulates a PlateI reference and provides a number of
+    methods useful for displaying the contents of the plate as a grid.
+    """
+
+    def __init__(self, conn, pid, fid, thumbprefix=''):
+        self.plate = conn.getObject('plate', long(pid))
+        self._conn = conn
+        self.field = fid
+        self._thumbprefix = thumbprefix
+        self._metadata = None
+
+    @property
+    def metadata(self):
+        if self._metadata is None:
+            self.plate.setGridSizeConstraints(8, 12)
+            size = self.plate.getGridSize()
+            grid = [[None] * size['columns'] for _ in range(size['rows'])]
+
+            q = self._conn.getQueryService()
+            params = omero.sys.ParametersI()
+            params.addId(self.plate.id)
+            params.add('wsidx', rint(self.field))
+            query = "select well.row, well.column, img.id, img.name, "\
+                    "author.firstName||' '||author.lastName, "\
+                    "well.id, img.acquisitionDate, "\
+                    "img.details.creationEvent.time, "\
+                    "img.description "\
+                    "from Well well "\
+                    "join well.wellSamples ws "\
+                    "join ws.image img "\
+                    "join img.details.owner author "\
+                    "where well.plate.id = :id "\
+                    "and index(ws) = :wsidx"
+
+            for res in q.projection(query, params, self._conn.SERVICE_OPTS):
+                row, col, img_id, img_name, author, well_id, acq_date, \
+                    create_date, description = res
+
+                if acq_date is not None and acq_date.val > 0:
+                    date = acq_date.val / 1000
+                else:
+                    date = create_date.val / 1000
+                description = (description and description.val) or ''
+
+                wellmeta = {'type': 'Image',
+                            'id': img_id.val,
+                            'name': img_name.val,
+                            'description': description,
+                            'author': author.val,
+                            'date': date,
+                            'wellId': well_id.val,
+                            'field': self.field}
+
+                if callable(self._thumbprefix):
+                    wellmeta['thumb_url'] = self._thumbprefix(str(img_id.val))
+                else:
+                    wellmeta['thumb_url'] = self._thumbprefix + str(img_id.val)
+
+                grid[row.val][col.val] = wellmeta
+
+            self._metadata = {'grid': grid,
+                              'collabels': self.plate.getColumnLabels(),
+                              'rowlabels': self.plate.getRowLabels()}
+        return self._metadata

components/tools/OmeroWeb/omeroweb/webgateway/views.py

@@ -28,6 +28,7 @@
 from django.core.servers.basehttp import FileWrapper
 from omero.rtypes import rlong, unwrap
 from omero.constants.namespaces import NSBULKANNOTATIONS
+from plategrid import PlateGrid
 from omero_version import build_year
 from marshal import imageMarshal, shapeMarshal
 
@@ -1328,43 +1329,27 @@ def urlprefix(iid):
 def plateGrid_json(request, pid, field=0, conn=None, **kwargs):
     """
     """
-    plate = conn.getObject('plate', long(pid))
     try:
         field = long(field or 0)
     except ValueError:
         field = 0
-    if plate is None:
-        return HttpJavascriptResponseServerError('""')
-    grid = []
     prefix = kwargs.get('thumbprefix', 'webgateway.views.render_thumbnail')
     thumbsize = int(request.REQUEST.get('size', 64))
     logger.debug(thumbsize)
+    server_id = kwargs['server_id']
 
     def urlprefix(iid):
         return reverse(prefix, args=(iid, thumbsize))
-    xtra = {'thumbUrlPrefix': kwargs.get('urlprefix', urlprefix)}
-    server_id = kwargs['server_id']
+    plateGrid = PlateGrid(conn, pid, field,
+                          kwargs.get('urlprefix', urlprefix))
+    plate = plateGrid.plate
+    if plate is None:
+        return Http404
 
     rv = webgateway_cache.getJson(request, server_id, plate,
                                   'plategrid-%d-%d' % (field, thumbsize))
     if rv is None:
-        plate.setGridSizeConstraints(8, 12)
-        for row in plate.getWellGrid(field):
-            tr = []
-            for e in row:
-                if e:
-                    i = e.getImage()
-                    if i:
-                        t = i.simpleMarshal(xtra=xtra)
-                        t['wellId'] = e.getId()
-                        t['field'] = field
-                        tr.append(t)
-                        continue
-                tr.append(None)
-            grid.append(tr)
-        rv = {'grid': grid,
-              'collabels': plate.getColumnLabels(),
-              'rowlabels': plate.getRowLabels()}
+        rv = plateGrid.metadata
         webgateway_cache.setJson(request, server_id, plate, json.dumps(rv),
                                  'plategrid-%d-%d' % (field, thumbsize))
     else: