Api wells2

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

@@ -158,6 +158,13 @@ def getChannelsQuery():
             ' left outer join fetch logicalChannel.contrastMethod')
 
 
+def add_plate_filter(clauses, params, opts):
+    """Helper for adding 'plate' to filtering clauses and parameters."""
+    if opts is not None and 'plate' in opts:
+        clauses.append('obj.plate.id = :pid')
+        params.add('pid', rlong(opts['plate']))
+
+
 class OmeroRestrictionWrapper (object):
 
     def canDownload(self):
@@ -6038,6 +6045,21 @@ class _PlateAcquisitionWrapper (BlitzObjectWrapper):
 
     OMERO_CLASS = 'PlateAcquisition'
 
+    @classmethod
+    def _getQueryString(cls, opts=None):
+        """
+        Extend base query to handle filtering of PlateAcquisitions by Plate.
+        Returns a tuple of (query, clauses, params).
+        Supported opts: 'plate': <plate_id> to filter by Plate
+
+        :param opts:        Dictionary of optional parameters.
+        :return:            Tuple of string, list, ParametersI
+        """
+        query, clauses, params = super(
+            _PlateAcquisitionWrapper, cls)._getQueryString(opts)
+        add_plate_filter(clauses, params, opts)
+        return (query, clauses, params)
+
     def getName(self):
         name = super(_PlateAcquisitionWrapper, self).getName()
         if name is None:
@@ -6099,16 +6121,19 @@ def _getQueryString(cls, opts=None):
         """
         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 opts is None:
+            opts = {}
+        add_plate_filter(clauses, params, opts)
+        load_images = opts.get('load_images')
+        load_pixels = opts.get('load_pixels')
+        load_channels = opts.get('load_channels')
+        if 'plateacquisition' in opts:
+            clauses.append('plateAcquisition.id = :plateAcq')
+            params.add('plateAcq', rlong(opts['plateacquisition']))
+            load_images = True
+        if 'wellsample_index' in opts:
+            clauses.append('index(wellSamples) = :wellsample_index')
+            params.add('wellsample_index', rint(opts['wellsample_index']))
         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"\

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

@@ -32,6 +32,31 @@
 DEFAULT_LIMIT = max(1, api_settings.API_LIMIT)
 
 
+def get_wellsample_indices(conn, plate_id=None, plateacquisition_id=None):
+    """
+    Return min and max WellSample index for a Plate OR PlateAcquisition
+
+    @param conn:        BlitzGateway
+    @param plate_id:    Plate ID
+    @param plateacquisition_id:    PlateAcquisition ID
+    @return             A dict of parent_id: child_count
+    """
+    ctx = deepcopy(conn.SERVICE_OPTS)
+    ctx.setOmeroGroup(-1)
+    params = ParametersI()
+    query = "select minIndex(ws), maxIndex(ws) from Well well " \
+            "join well.wellSamples ws"
+    if plate_id is not None:
+        query += " where well.plate.id=:plate_id "
+        params.add('plate_id', wrap(plate_id))
+    elif plateacquisition_id is not None:
+        query += " where ws.plateAcquisition.id=:plateacquisition_id"
+        params.add('plateacquisition_id', wrap(plateacquisition_id))
+    result = conn.getQueryService().projection(query, params, ctx)
+    result = [r for r in unwrap(result)[0] if r is not None]
+    return result
+
+
 def get_child_counts(conn, link_class, parent_ids):
     """
     Count child links for the specified parent_ids.

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

@@ -176,6 +176,44 @@
 GET all wells, using omero-marshal to generate json
 """
 
+api_plate_plateacquisitions = url(
+    r'^v(?P<api_version>%s)/m/plates/'
+    '(?P<plate_id>[0-9]+)/plateacquisitions/$' % versions,
+    views.PlateAcquisitionsView.as_view(),
+    name='api_plate_plateacquisitions')
+"""
+GET PlateAcquisitions in Plate, using omero-marshal to generate json
+"""
+
+api_plateacquisition = url(
+    r'^v(?P<api_version>%s)/m/plateacquisitions/'
+    '(?P<object_id>[0-9]+)/$' % versions,
+    views.PlateAcquisitionView.as_view(),
+    name='api_plateacquisition')
+"""
+Well url to GET or DELETE a single Well
+"""
+
+api_plateacquisition_wellsampleindex_wells = url(
+    r'^v(?P<api_version>%s)/m/plateacquisitions/'
+    '(?P<plateacquisition_id>[0-9]+)/wellsampleindex/'
+    '(?P<index>[0-9]+)/wells/$' % versions,
+    views.WellsView.as_view(),
+    name='api_plateacquisition_wellsampleindex_wells')
+"""
+GET Wells from a single Index in PlateAcquisition
+"""
+
+api_plate_wellsampleindex_wells = url(
+    r'^v(?P<api_version>%s)/m/plates/'
+    '(?P<plate_id>[0-9]+)/wellsampleindex/'
+    '(?P<index>[0-9]+)/wells/$' % versions,
+    views.WellsView.as_view(),
+    name='api_plate_wellsampleindex_wells')
+"""
+GET Wells from a single Index in Plate
+"""
+
 api_plate_wells = url(
     r'^v(?P<api_version>%s)/m/plates/'
     '(?P<plate_id>[0-9]+)/wells/$' % versions,
@@ -185,6 +223,15 @@
 GET Wells in Plate, using omero-marshal to generate json
 """
 
+api_plateacquisition_wells = url(
+    r'^v(?P<api_version>%s)/m/plateacquisitions/'
+    '(?P<plateacquisition_id>[0-9]+)/wells/$' % versions,
+    views.WellsView.as_view(),
+    name='api_plateacquisition_wells')
+"""
+GET Wells in Plate, using omero-marshal to generate json
+"""
+
 api_well = url(
     r'^v(?P<api_version>%s)/m/wells/(?P<object_id>[0-9]+)/$' % versions,
     views.WellView.as_view(),
@@ -215,6 +262,11 @@
     api_screen_plates,
     api_plate,
     api_wells,
+    api_plate_plateacquisitions,
+    api_plateacquisition,
+    api_plateacquisition_wellsampleindex_wells,
+    api_plate_wellsampleindex_wells,
     api_plate_wells,
+    api_plateacquisition_wells,
     api_well,
 )

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

@@ -28,7 +28,7 @@
 import traceback
 import json
 
-from api_query import query_objects, get_child_counts
+from api_query import query_objects, get_child_counts, get_wellsample_indices
 from omero_marshal import get_encoder, get_decoder, OME_SCHEMA_URL
 from omero import ValidationException
 from omeroweb.connector import Server
@@ -125,7 +125,7 @@ def dispatch(self, *args, **kwargs):
         """Wrap other methods to add decorators."""
         return super(ApiView, self).dispatch(*args, **kwargs)
 
-    def add_data(self, marshalled, request, urls=None, **kwargs):
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
         """
         Post-process marshalled object to add any extra data.
 
@@ -179,7 +179,7 @@ def get(self, request, object_id, conn=None, **kwargs):
             ch_count = counts[object_id] if object_id in counts else 0
             marshalled['omero:childCount'] = ch_count
 
-        self.add_data(marshalled, request, self.urls, **kwargs)
+        self.add_data(marshalled, request, conn, self.urls, **kwargs)
         return {'data': marshalled}
 
     def delete(self, request, object_id, conn=None, **kwargs):
@@ -264,9 +264,59 @@ class PlateView(ObjectView):
     # Urls to add to marshalled object. See ProjectsView for more details
     urls = {
         'url:wells': {'name': 'api_plate_wells',
-                      'kwargs': {'plate_id': 'OBJECT_ID'}}
+                      'kwargs': {'plate_id': 'OBJECT_ID'}},
+        'url:plateacquisitions': {'name': 'api_plate_plateacquisitions',
+                                  'kwargs': {'plate_id': 'OBJECT_ID'}},
     }
 
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
+        """Add min/max WellSampleIndex."""
+        marshalled = super(PlateView, self).add_data(marshalled, request, conn,
+                                                     urls=urls, **kwargs)
+        idx = get_wellsample_indices(conn, marshalled['@id'])
+        marshalled['omero:wellsampleIndex'] = idx
+
+        # Add link to Wells for each WellSample index in this Plate
+        ws_urls = []
+        if len(idx) == 2:
+            for ws_index in range(idx[0], idx[1]+1):
+                version = kwargs['api_version']
+                extra = {'plate_id': marshalled['@id'],
+                         'index': ws_index}
+                url = build_url(request, 'api_plate_wellsampleindex_wells',
+                                version, **extra)
+                ws_urls.append(url)
+        marshalled['url:wellsampleindex_wells'] = ws_urls
+
+        return marshalled
+
+
+class PlateAcquisitionView(ObjectView):
+    """Handles GET for /plates/:plate_id/plateacquisitions."""
+
+    OMERO_TYPE = 'PlateAcquisition'
+
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
+        """Add min/max WellSampleIndex."""
+        marshalled = super(PlateAcquisitionView, self).add_data(
+            marshalled, request, conn, urls=urls, **kwargs)
+        idx = get_wellsample_indices(conn,
+                                     plateacquisition_id=marshalled['@id'])
+        marshalled['omero:wellsampleIndex'] = idx
+
+        # Add link to Wells for each WellSample index in this PlateAcquisition
+        ws_urls = []
+        for ws_index in range(idx[0], idx[1]+1):
+            version = kwargs['api_version']
+            extra = {'plateacquisition_id': marshalled['@id'],
+                     'index': ws_index}
+            url = build_url(request,
+                            'api_plateacquisition_wellsampleindex_wells',
+                            version, **extra)
+            ws_urls.append(url)
+        marshalled['url:wellsampleindex_wells'] = ws_urls
+        return marshalled
+
 
 class WellView(ObjectView):
     """Handle access to an individual Well to GET or DELETE it."""
@@ -282,9 +332,9 @@ def get_opts(self, request):
         opts['load_pixels'] = True
         return opts
 
-    def add_data(self, marshalled, request, urls=None, **kwargs):
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
         """Add 'url:image' to any 'Image' in 'WellSamples'."""
-        marshalled = super(WellView, self).add_data(marshalled, request,
+        marshalled = super(WellView, self).add_data(marshalled, request, conn,
                                                     urls=urls, **kwargs)
         image_urls = {
             'url:image': {'name': 'api_image',
@@ -294,7 +344,8 @@ def add_data(self, marshalled, request, urls=None, **kwargs):
             # 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)
+                    self.add_data(ws['Image'], request, conn,
+                                  image_urls, **kwargs)
         return marshalled
 
 
@@ -330,7 +381,7 @@ 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, self.urls, **kwargs)
+            self.add_data(m, request, conn, self.urls, **kwargs)
         return marshalled
 
 
@@ -429,7 +480,9 @@ def get_opts(self, request, **kwargs):
         'url:wells': {'name': 'api_plate_wells',
                       'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:plate': {'name': 'api_plate',
-                      'kwargs': {'object_id': 'OBJECT_ID'}}
+                      'kwargs': {'object_id': 'OBJECT_ID'}},
+        'url:plateacquisitions': {'name': 'api_plate_plateacquisitions',
+                                  'kwargs': {'plate_id': 'OBJECT_ID'}},
     }
 
 
@@ -461,6 +514,49 @@ def get_opts(self, request, **kwargs):
         return opts
 
 
+class PlateAcquisitionsView(ObjectsView):
+    """Handles GET for /plates/:plate_id/plateacquisitions."""
+
+    OMERO_TYPE = 'PlateAcquisition'
+
+    # Urls to add to marshalled object. See ProjectsView for more details
+    urls = {
+        'url:plateacquisition': {'name': 'api_plateacquisition',
+                                 'kwargs': {'object_id': 'OBJECT_ID'}},
+    }
+
+    def get_opts(self, request, **kwargs):
+        """Add extra parameters to the opts dict."""
+        opts = super(PlateAcquisitionsView, self).get_opts(request, **kwargs)
+        opts['order_by'] = 'lower(obj.name)'
+        # at /plates/:plate_id/plateacquisitions/ we have 'plate_id' in kwargs
+        if 'plate_id' in kwargs:
+            opts['plate'] = long(kwargs['plate_id'])
+        return opts
+
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
+        """Add min/max WellSampleIndex."""
+        marshalled = super(PlateAcquisitionsView, self).add_data(
+            marshalled, request, conn, urls=urls, **kwargs)
+        idx = get_wellsample_indices(conn,
+                                     plateacquisition_id=marshalled['@id'])
+        marshalled['omero:wellsampleIndex'] = idx
+
+        # Add link to Wells for each WellSample index in this PlateAcquisition
+        ws_urls = []
+        for ws_index in range(idx[0], idx[1]+1):
+            version = kwargs['api_version']
+            extra = {'plateacquisition_id': marshalled['@id'],
+                     'index': ws_index}
+            url = build_url(request,
+                            'api_plateacquisition_wellsampleindex_wells',
+                            version, **extra)
+            ws_urls.append(url)
+        marshalled['url:wellsampleindex_wells'] = ws_urls
+
+        return marshalled
+
+
 class WellsView(ObjectsView):
     """Handles GET for /wells/ to list available Images."""
 
@@ -479,18 +575,23 @@ def get_opts(self, request, **kwargs):
         # at /plates/:plate_id/wells/ we have 'plate_id' in kwargs
         if 'plate_id' in kwargs:
             opts['plate'] = long(kwargs['plate_id'])
+        elif 'plateacquisition_id' in kwargs:
+            opts['plateacquisition'] = long(kwargs['plateacquisition_id'])
         else:
             # filter by query /wells/?plate=:id
             plate = getIntOrDefault(request, 'plate', None)
             if plate is not None:
                 opts['plate'] = plate
+        # When filtering by plate or plateacquisition, can filter by ws index
+        if 'index' in kwargs:
+            opts['wellsample_index'] = int(kwargs['index'])
         # Listing Wells, load Images
         opts['load_images'] = True
         return opts
 
-    def add_data(self, marshalled, request, urls=None, **kwargs):
+    def add_data(self, marshalled, request, conn, urls=None, **kwargs):
         """Add 'url:image' to any 'Image' in 'WellSamples'."""
-        marshalled = super(WellsView, self).add_data(marshalled, request,
+        marshalled = super(WellsView, self).add_data(marshalled, request, conn,
                                                      urls=urls, **kwargs)
         image_urls = {
             'url:image': {'name': 'api_image',
@@ -500,7 +601,8 @@ def add_data(self, marshalled, request, urls=None, **kwargs):
             # 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)
+                    self.add_data(ws['Image'], request, conn,
+                                  image_urls, **kwargs)
         return marshalled