Api wells

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

@@ -141,6 +141,23 @@ def fileread_gen(fin, fsize, bufsize):
     fin.close()
 
 
+def getPixelsQuery(imageName):
+    """Helper for building Query for Images or Wells & Images"""
+    return (' left outer join fetch %s.pixels as pixels'
+            ' left outer join fetch pixels.pixelsType' % imageName)
+
+
+def getChannelsQuery():
+    """Helper for building Query for Images or Wells & Images"""
+    return (' join fetch pixels.channels as channels'
+            ' join fetch channels.logicalChannel as logicalChannel'
+            ' left outer join fetch '
+            ' logicalChannel.photometricInterpretation'
+            ' left outer join fetch logicalChannel.illumination'
+            ' left outer join fetch logicalChannel.mode'
+            ' left outer join fetch logicalChannel.contrastMethod')
+
+
 class OmeroRestrictionWrapper (object):
 
     def canDownload(self):
@@ -3096,6 +3113,7 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None,
         :param opts:        Dict of additional options for filtering or
                             defining extra data to load.
                             offset, limit and owner for all objects.
+                            Also 'order_by': 'obj.name' to order results.
                             Additional opts handled by _getQueryString()
                             E.g. 'childCount', or filter Dataset by 'project'
         :return:            (query, params, wrapper)
@@ -3171,9 +3189,9 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None,
         if clauses:
             query += " where " + (" and ".join(clauses))
 
-        # Order by...
+        # Order by... e.g. 'lower(obj.name)' or 'obj.column, obj.row' for wells
         if order_by is not None:
-            query += " order by lower(obj.%s), obj.id" % order_by
+            query += " order by %s, obj.id" % order_by
 
         return (query, baseParams, wrapper)
 
@@ -6053,6 +6071,42 @@ def __reset__(self):
         """
         self._childcache = None
 
+    @classmethod
+    def _getQueryString(cls, opts=None):
+        """
+        Extend base query to handle filtering of Wells by Plate.
+        Returns a tuple of (query, clauses, params).
+        Supported opts: 'plate': <plate_id> to filter by Plate
+                        'load_images': <bool> to load wellSamples and images
+
+        :param opts:        Dictionary of optional parameters.
+        :return:            Tuple of string, list, ParametersI
+        """
+        query, clauses, params = super(
+            _WellWrapper, cls)._getQueryString(opts)
+        if opts is not None and 'plate' in opts:
+            clauses.append('obj.plate.id = :pid')
+            params.add('pid', rlong(opts['plate']))
+        load_images = False
+        load_pixels = False
+        load_channels = False
+        if opts is not None:
+            load_images = opts.get('load_images')
+            load_pixels = opts.get('load_pixels')
+            load_channels = opts.get('load_channels')
+        if load_images or load_pixels or load_channels:
+            # NB: Using left outer join, we may get Wells with no Images
+            query += " left outer join fetch obj.wellSamples as wellSamples"\
+                     " left outer join fetch wellSamples.image as image"\
+                     " left outer join fetch wellSamples.plateAcquisition"\
+                     " as plateAcquisition"
+        if load_pixels or load_channels:
+            query += getPixelsQuery("image")
+        if load_channels:
+            query += getChannelsQuery()
+
+        return (query, clauses, params)
+
     def __loadedHotSwap__(self):
         query = ("select well from Well as well "
                  "join fetch well.details.creationEvent "
@@ -7140,15 +7194,9 @@ def _getQueryString(cls, opts=None):
             orphaned = opts.get('orphaned')
         if load_pixels or load_channels:
             # We use 'left outer join', since we still want images if no pixels
-            query += ' left outer join fetch obj.pixels pixels' \
-                     ' left outer join fetch pixels.pixelsType'
+            query += getPixelsQuery("obj")
         if load_channels:
-            query += ' join fetch pixels.channels as channels' \
-                     ' join fetch channels.logicalChannel as logicalChannel' \
-                     ' left outer join fetch logicalChannel.photometricInterpretation' \
-                     ' left outer join fetch logicalChannel.illumination' \
-                     ' left outer join fetch logicalChannel.mode' \
-                     ' left outer join fetch logicalChannel.contrastMethod'
+            query += getChannelsQuery()
         if orphaned:
             clauses.append(
                 """

components/tools/OmeroWeb/omeroweb/api/urls.py

@@ -169,6 +169,30 @@
 Plate url to GET or DELETE a single Plate
 """
 
+api_wells = url(r'^v(?P<api_version>%s)/m/wells/$' % versions,
+                views.WellsView.as_view(),
+                name='api_wells')
+"""
+GET all wells, using omero-marshal to generate json
+"""
+
+api_plate_wells = url(
+    r'^v(?P<api_version>%s)/m/plates/'
+    '(?P<plate_id>[0-9]+)/wells/$' % versions,
+    views.WellsView.as_view(),
+    name='api_plate_wells')
+"""
+GET Wells in Plate, using omero-marshal to generate json
+"""
+
+api_well = url(
+    r'^v(?P<api_version>%s)/m/wells/(?P<object_id>[0-9]+)/$' % versions,
+    views.WellView.as_view(),
+    name='api_well')
+"""
+Well url to GET or DELETE a single Well
+"""
+
 urlpatterns = patterns(
     '',
     api_versions,
@@ -190,4 +214,7 @@
     api_plates,
     api_screen_plates,
     api_plate,
+    api_wells,
+    api_plate_wells,
+    api_well,
 )

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

@@ -123,7 +123,7 @@ def dispatch(self, *args, **kwargs):
         """Wrap other methods to add decorators."""
         return super(ApiView, self).dispatch(*args, **kwargs)
 
-    def add_data(self, marshalled, request, **kwargs):
+    def add_data(self, marshalled, request, urls=None, **kwargs):
         """
         Post-process marshalled object to add any extra data.
 
@@ -133,15 +133,16 @@ def add_data(self, marshalled, request, **kwargs):
         """
         object_id = marshalled['@id']
         version = kwargs['api_version']
-        for key, args in self.urls.items():
-            name = args['name']
-            kwargs = args['kwargs'].copy()
-            # If kwargs has 'OBJECT_ID' placeholder, we replace with id
-            for k, v in kwargs.items():
-                if v == 'OBJECT_ID':
-                    kwargs[k] = object_id
-            url = build_url(request, name, version, **kwargs)
-            marshalled[key] = url
+        if urls is not None:
+            for key, args in urls.items():
+                name = args['name']
+                kwargs = args['kwargs'].copy()
+                # If kwargs has 'OBJECT_ID' placeholder, we replace with id
+                for k, v in kwargs.items():
+                    if v == 'OBJECT_ID':
+                        kwargs[k] = object_id
+                url = build_url(request, name, version, **kwargs)
+                marshalled[key] = url
         return marshalled
 
 
@@ -161,7 +162,7 @@ def get(self, request, object_id, conn=None, **kwargs):
                                                      object_id))
         encoder = get_encoder(obj._obj.__class__)
         marshalled = encoder.encode(obj._obj)
-        self.add_data(marshalled, request, **kwargs)
+        self.add_data(marshalled, request, self.urls, **kwargs)
         return marshalled
 
     def delete(self, request, object_id, conn=None, **kwargs):
@@ -214,7 +215,6 @@ class ImageView(ObjectView):
     def get_opts(self, request):
         """Add support for load_pixels and load_channels."""
         opts = super(ImageView, self).get_opts(request)
-        opts['orphaned'] = request.GET.get('orphaned', False) == 'true'
         # for single image, we always load channels
         opts['load_channels'] = True
         return opts
@@ -237,6 +237,40 @@ class PlateView(ObjectView):
 
     OMERO_TYPE = 'Plate'
 
+    # Urls to add to marshalled object. See ProjectsView for more details
+    urls = {
+        'url:wells': {'name': 'api_plate_wells',
+                      'kwargs': {'plate_id': 'OBJECT_ID'}}
+    }
+
+
+class WellView(ObjectView):
+    """Handle access to an individual Well to GET or DELETE it."""
+
+    OMERO_TYPE = 'Well'
+
+    def get_opts(self, request):
+        """Add support for load_images."""
+        opts = super(WellView, self).get_opts(request)
+        # for single well, we load images with pixels
+        opts['load_pixels'] = True
+        return opts
+
+    def add_data(self, marshalled, request, urls=None, **kwargs):
+        """Add 'url:image' to any 'Image' in 'WellSamples'."""
+        marshalled = super(WellView, self).add_data(marshalled, request,
+                                                    urls=urls, **kwargs)
+        image_urls = {
+            'url:image': {'name': 'api_image',
+                          'kwargs': {'object_id': 'OBJECT_ID'}},
+        }
+        if 'WellSamples' in marshalled:
+            # For each WellSample, add image urls to Image
+            for ws in marshalled['WellSamples']:
+                if 'Image' in ws:
+                    self.add_data(ws['Image'], request, image_urls, **kwargs)
+        return marshalled
+
 
 class ObjectsView(ApiView):
     """Base class for listing objects."""
@@ -258,7 +292,6 @@ def get_opts(self, request, **kwargs):
                 'owner': owner,
                 'orphaned': orphaned,
                 'child_count': child_count,
-                'order_by': 'name',     # NB: will break if object has no name
                 }
         return opts
 
@@ -271,7 +304,7 @@ def get(self, request, conn=None, **kwargs):
         marshalled = query_objects(conn, self.OMERO_TYPE, group,
                                    opts, normalize)
         for m in marshalled['data']:
-            self.add_data(m, request, **kwargs)
+            self.add_data(m, request, self.urls, **kwargs)
         return marshalled
 
 
@@ -280,6 +313,12 @@ class ProjectsView(ObjectsView):
 
     OMERO_TYPE = 'Project'
 
+    def get_opts(self, request, **kwargs):
+        """Add extra parameters to the opts dict."""
+        opts = super(ProjectsView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
+        return opts
+
     # To add a url to marshalled object add to this dict
     # 'name' is url name, kwargs are passed to reverse()
     # If any kwargs values are 'OBJECT_ID' then this placeholder will be
@@ -298,8 +337,9 @@ class DatasetsView(ObjectsView):
     OMERO_TYPE = 'Dataset'
 
     def get_opts(self, request, **kwargs):
-        """Add filtering by 'project' to the opts dict."""
+        """Add extra parameters to the opts dict."""
         opts = super(DatasetsView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
         # at /projects/:project_id/datasets/ we have 'project_id' in kwargs
         if 'project_id' in kwargs:
             opts['project'] = long(kwargs['project_id'])
@@ -324,6 +364,12 @@ class ScreensView(ObjectsView):
 
     OMERO_TYPE = 'Screen'
 
+    def get_opts(self, request, **kwargs):
+        """Add extra parameters to the opts dict."""
+        opts = super(ScreensView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
+        return opts
+
     # Urls to add to marshalled object. See ProjectsView for more details
     urls = {
         'url:plates': {'name': 'api_screen_plates',
@@ -339,8 +385,9 @@ class PlatesView(ObjectsView):
     OMERO_TYPE = 'Plate'
 
     def get_opts(self, request, **kwargs):
-        """Add filtering by 'screen' to the opts dict."""
+        """Add extra parameters to the opts dict."""
         opts = super(PlatesView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
         # at /screens/:screen_id/plates/ we have 'screen_id' in kwargs
         if 'screen_id' in kwargs:
             opts['screen'] = long(kwargs['screen_id'])
@@ -353,6 +400,8 @@ def get_opts(self, request, **kwargs):
 
     # Urls to add to marshalled object. See ProjectsView for more details
     urls = {
+        'url:wells': {'name': 'api_plate_wells',
+                      'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:plate': {'name': 'api_plate',
                       'kwargs': {'object_id': 'OBJECT_ID'}}
     }
@@ -370,8 +419,9 @@ class ImagesView(ObjectsView):
     }
 
     def get_opts(self, request, **kwargs):
-        """Add filtering by 'dataset' and other params to the opts dict."""
+        """Add extra parameters to the opts dict."""
         opts = super(ImagesView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
         # at /datasets/:dataset_id/images/ we have 'dataset_id' in kwargs
         if 'dataset_id' in kwargs:
             opts['dataset'] = long(kwargs['dataset_id'])
@@ -385,6 +435,49 @@ def get_opts(self, request, **kwargs):
         return opts
 
 
+class WellsView(ObjectsView):
+    """Handles GET for /wells/ to list available Images."""
+
+    OMERO_TYPE = 'Well'
+
+    # Urls to add to marshalled object. See ProjectsView for more details
+    urls = {
+        'url:well': {'name': 'api_well',
+                     'kwargs': {'object_id': 'OBJECT_ID'}},
+    }
+
+    def get_opts(self, request, **kwargs):
+        """Add extra parameters to the opts dict."""
+        opts = super(WellsView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'obj.column, obj.row'
+        # at /plates/:plate_id/wells/ we have 'plate_id' in kwargs
+        if 'plate_id' in kwargs:
+            opts['plate'] = long(kwargs['plate_id'])
+        else:
+            # filter by query /wells/?plate=:id
+            plate = getIntOrDefault(request, 'plate', None)
+            if plate is not None:
+                opts['plate'] = plate
+        # Listing Wells, load Images
+        opts['load_images'] = True
+        return opts
+
+    def add_data(self, marshalled, request, urls=None, **kwargs):
+        """Add 'url:image' to any 'Image' in 'WellSamples'."""
+        marshalled = super(WellsView, self).add_data(marshalled, request,
+                                                     urls=urls, **kwargs)
+        image_urls = {
+            'url:image': {'name': 'api_image',
+                          'kwargs': {'object_id': 'OBJECT_ID'}},
+        }
+        if 'WellSamples' in marshalled:
+            # For each WellSample, add image urls to Image
+            for ws in marshalled['WellSamples']:
+                if 'Image' in ws:
+                    self.add_data(ws['Image'], request, image_urls, **kwargs)
+        return marshalled
+
+
 class SaveView(View):
     """
     This view provides 'Save' functionality for all types of objects.