Api filter by children

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

@@ -5732,18 +5732,25 @@ def _getQueryString(cls, opts=None):
         Extend base query to handle filtering of Datasets by Projects.
         Returns a tuple of (query, clauses, params).
         Supported opts: 'project': <project_id> to filter by Project
+                        'image': <image_id> to filter by child Image
                         'orphaned': <bool>. Filter by 'not in Project'
 
         :param opts:        Dictionary of optional parameters.
         :return:            Tuple of string, list, ParametersI
         """
         query, clauses, params = super(
             _DatasetWrapper, cls)._getQueryString(opts)
-        if opts is not None and 'project' in opts:
-            query += ' join obj.projectLinks plink'
-            clauses.append('plink.parent.id = :pid')
+        if opts is None:
+            opts = {}
+        if 'project' in opts:
+            query += ' join obj.projectLinks projectLinks'
+            clauses.append('projectLinks.parent.id = :pid')
             params.add('pid', rlong(opts['project']))
-        if opts is not None and opts.get('orphaned'):
+        if 'image' in opts:
+            query += ' join obj.imageLinks imagelinks'
+            clauses.append('imagelinks.child.id = :iid')
+            params.add('iid', rlong(opts['image']))
+        if opts.get('orphaned'):
             clauses.append(
                 """
                 not exists (
@@ -5781,6 +5788,26 @@ class _ProjectWrapper (BlitzObjectWrapper):
     CHILD_WRAPPER_CLASS = 'DatasetWrapper'
     PARENT_WRAPPER_CLASS = None
 
+    @classmethod
+    def _getQueryString(cls, opts=None):
+        """
+        Extend base query to handle filtering of Projects by Datasets.
+        Returns a tuple of (query, clauses, params).
+        Supported opts: 'dataset': <dataset_id> to filter by Dataset
+
+        :param opts:        Dictionary of optional parameters.
+        :return:            Tuple of string, list, ParametersI
+        """
+        query, clauses, params = super(
+            _ProjectWrapper, cls)._getQueryString(opts)
+        if opts is None:
+            opts = {}
+        if 'dataset' in opts:
+            query += ' join obj.datasetLinks datasetLinks'
+            clauses.append('datasetLinks.child.id = :dataset_id')
+            params.add('dataset_id', rlong(opts['dataset']))
+        return (query, clauses, params)
+
 ProjectWrapper = _ProjectWrapper
 
 
@@ -5794,6 +5821,26 @@ class _ScreenWrapper (BlitzObjectWrapper):
     CHILD_WRAPPER_CLASS = 'PlateWrapper'
     PARENT_WRAPPER_CLASS = None
 
+    @classmethod
+    def _getQueryString(cls, opts=None):
+        """
+        Extend base query to handle filtering of Screens 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(
+            _ScreenWrapper, cls)._getQueryString(opts)
+        if opts is None:
+            opts = {}
+        if 'plate' in opts:
+            query += ' join obj.plateLinks plateLinks'
+            clauses.append('plateLinks.child.id = :plate_id')
+            params.add('plate_id', rlong(opts['plate']))
+        return (query, clauses, params)
+
 ScreenWrapper = _ScreenWrapper
 
 
@@ -6011,6 +6058,7 @@ def _getQueryString(cls, opts=None):
         Also handles filtering of Plates by Screens.
         Returns a tuple of (query, clauses, params).
         Supported opts: 'screen': <screen_id> to filter by Screen
+                        'well': <well_id> to filter by Well
                         'orphaned': <bool>. Filter by 'not in Screen'
 
         :param opts:        Dictionary of optional parameters.
@@ -6024,10 +6072,16 @@ def _getQueryString(cls, opts=None):
         # NB: we don't use base _getQueryString.
         clauses = []
         params = omero.sys.ParametersI()
-        if opts is not None and 'screen' in opts:
+        if opts is None:
+            opts = {}
+        if 'screen' in opts:
             clauses.append('spl.parent.id = :sid')
             params.add('sid', rlong(opts['screen']))
-        if opts is not None and opts.get('orphaned'):
+        if 'well' in opts:
+            query += ' join obj.wells wells'
+            clauses.append('wells.id = :well_id')
+            params.add('well_id', rlong(opts['well']))
+        if opts.get('orphaned'):
             clauses.append(
                 """
                 not exists (

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

@@ -55,3 +55,5 @@
 # E.g. /api/v0/
 # TODO - need to decide how this is configured, strategy for extending etc.
 API_VERSIONS = ('0',)
+
+API_VERSION = '0.0'

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

@@ -27,6 +27,7 @@
 import traceback
 from django.http import JsonResponse
 from functools import update_wrapper
+from . import api_settings
 from api_exceptions import BadRequestError, \
     CreatedObject, \
     MethodNotSupportedError, \
@@ -58,14 +59,20 @@ def __init__(self):
         """Initialise the decorator."""
         pass
 
+    def create_response(self, response, status=200):
+        """Create the Json response and set global headers."""
+        response = JsonResponse(response, status=status)
+        response['X-OMERO-ApiVersion'] = api_settings.API_VERSION
+        return response
+
     def handle_success(self, rv):
         """
         Handle successful response from wrapped function.
 
         By default, we simply return a JsonResponse() but this can be
         overwritten by subclasses if needed.
         """
-        return JsonResponse(rv)
+        return self.create_response(rv)
 
     def handle_error(self, ex, trace):
         """
@@ -96,7 +103,7 @@ def handle_error(self, ex, trace):
         if isinstance(ex, CreatedObject):
             status = ex.status
             rsp_json = ex.response
-        return JsonResponse(rsp_json, status=status)
+        return self.create_response(rsp_json, status=status)
 
     def __call__(self, f):
         """

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

@@ -122,6 +122,15 @@
 GET Images in Dataset, using omero-marshal to generate json
 """
 
+api_dataset_projects = url(
+    r'^v(?P<api_version>%s)/m/datasets/'
+    '(?P<dataset_id>[0-9]+)/projects/$' % versions,
+    views.ProjectsView.as_view(),
+    name='api_dataset_projects')
+"""
+GET Projects that contain a Dataset, using omero-marshal to generate json
+"""
+
 api_image = url(
     r'^v(?P<api_version>%s)/m/images/(?P<object_id>[0-9]+)/$' % versions,
     views.ImageView.as_view(),
@@ -130,6 +139,15 @@
 Image url to GET or DELETE a single Image
 """
 
+api_image_datasets = url(
+    r'^v(?P<api_version>%s)/m/images/'
+    '(?P<image_id>[0-9]+)/datasets/$' % versions,
+    views.DatasetsView.as_view(),
+    name='api_image_datasets')
+"""
+GET Datasets that contain an Image, using omero-marshal to generate json
+"""
+
 api_screen = url(
     r'^v(?P<api_version>%s)/m/screens/(?P<object_id>[0-9]+)/$' % versions,
     views.ScreenView.as_view(),
@@ -161,6 +179,15 @@
 GET Plates in Screen, using omero-marshal to generate json
 """
 
+api_well_plates = url(
+    r'^v(?P<api_version>%s)/m/wells/'
+    '(?P<well_id>[0-9]+)/plates/$' % versions,
+    views.PlatesView.as_view(),
+    name='api_well_plates')
+"""
+GET Plates that contain a Well, using omero-marshal to generate json
+"""
+
 api_plate = url(
     r'^v(?P<api_version>%s)/m/plates/(?P<object_id>[0-9]+)/$' % versions,
     views.PlateView.as_view(),
@@ -240,6 +267,15 @@
 Well url to GET or DELETE a single Well
 """
 
+api_plate_screens = url(
+    r'^v(?P<api_version>%s)/m/plates/'
+    '(?P<plate_id>[0-9]+)/screens/$' % versions,
+    views.ScreensView.as_view(),
+    name='api_plate_screens')
+"""
+GET Screens that contain a Plate, using omero-marshal to generate json
+"""
+
 urlpatterns = patterns(
     '',
     api_versions,
@@ -255,11 +291,14 @@
     api_dataset,
     api_images,
     api_dataset_images,
+    api_dataset_projects,
     api_image,
+    api_image_datasets,
     api_screen,
     api_screens,
     api_plates,
     api_screen_plates,
+    api_well_plates,
     api_plate,
     api_wells,
     api_plate_plateacquisitions,
@@ -269,4 +308,5 @@
     api_plate_wells,
     api_plateacquisition_wells,
     api_well,
+    api_plate_screens,
 )

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

@@ -224,6 +224,8 @@ class DatasetView(ObjectView):
     urls = {
         'url:images': {'name': 'api_dataset_images',
                        'kwargs': {'dataset_id': 'OBJECT_ID'}},
+        'url:projects': {'name': 'api_dataset_projects',
+                         'kwargs': {'dataset_id': 'OBJECT_ID'}},
     }
 
 
@@ -234,6 +236,12 @@ class ImageView(ObjectView):
 
     CAN_DELETE = False
 
+    # Urls to add to marshalled object. See ProjectsView for more details
+    urls = {
+        'url:datasets': {'name': 'api_image_datasets',
+                         'kwargs': {'image_id': 'OBJECT_ID'}},
+    }
+
     def get_opts(self, request):
         """Add support for load_pixels and load_channels."""
         opts = super(ImageView, self).get_opts(request)
@@ -263,6 +271,8 @@ class PlateView(ObjectView):
 
     # Urls to add to marshalled object. See ProjectsView for more details
     urls = {
+        'url:screens': {'name': 'api_plate_screens',
+                        'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:wells': {'name': 'api_plate_wells',
                       'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:plateacquisitions': {'name': 'api_plate_plateacquisitions',
@@ -325,6 +335,12 @@ class WellView(ObjectView):
 
     CAN_DELETE = False
 
+    # Urls to add to marshalled object. See ProjectsView for more details
+    urls = {
+        'url:plates': {'name': 'api_well_plates',
+                       'kwargs': {'well_id': 'OBJECT_ID'}},
+    }
+
     def get_opts(self, request):
         """Add support for load_images."""
         opts = super(WellView, self).get_opts(request)
@@ -394,6 +410,14 @@ 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)'
+        # at /datasets/:dataset_id/projects/ we have 'dataset_id' in kwargs
+        if 'dataset_id' in kwargs:
+            opts['dataset'] = long(kwargs['dataset_id'])
+        else:
+            # Filter Projects by child 'dataset'
+            dataset = getIntOrDefault(request, 'dataset', None)
+            if dataset is not None:
+                opts['dataset'] = dataset
         return opts
 
     # To add a url to marshalled object add to this dict
@@ -425,6 +449,13 @@ def get_opts(self, request, **kwargs):
             project = getIntOrDefault(request, 'project', None)
             if project is not None:
                 opts['project'] = project
+        # Filter Datasets by child 'image'
+        if 'image_id' in kwargs:
+            opts['image'] = long(kwargs['image_id'])
+        else:
+            image = getIntOrDefault(request, 'image', None)
+            if image is not None:
+                opts['image'] = image
         return opts
 
     # Urls to add to marshalled object. See ProjectsView for more details
@@ -433,6 +464,8 @@ def get_opts(self, request, **kwargs):
                        'kwargs': {'dataset_id': 'OBJECT_ID'}},
         'url:dataset': {'name': 'api_dataset',
                         'kwargs': {'object_id': 'OBJECT_ID'}},
+        'url:projects': {'name': 'api_dataset_projects',
+                         'kwargs': {'dataset_id': 'OBJECT_ID'}},
     }
 
 
@@ -445,6 +478,14 @@ 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)'
+        # at /plate/:plate_id/screens/ we have 'plate_id' in kwargs
+        if 'plate_id' in kwargs:
+            opts['plate'] = long(kwargs['plate_id'])
+        else:
+            # filter by query /screens/?plate=:id
+            plate = getIntOrDefault(request, 'plate', None)
+            if plate is not None:
+                opts['plate'] = plate
         return opts
 
     # Urls to add to marshalled object. See ProjectsView for more details
@@ -473,10 +514,20 @@ def get_opts(self, request, **kwargs):
             screen = getIntOrDefault(request, 'screen', None)
             if screen is not None:
                 opts['screen'] = screen
+        # Filter Plates by Well
+        if 'well_id' in kwargs:
+            opts['well'] = long(kwargs['well_id'])
+        else:
+            # filter by query /plates/?well=:id
+            well = getIntOrDefault(request, 'well', None)
+            if well is not None:
+                opts['well'] = well
         return opts
 
     # Urls to add to marshalled object. See ProjectsView for more details
     urls = {
+        'url:screens': {'name': 'api_plate_screens',
+                        'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:wells': {'name': 'api_plate_wells',
                       'kwargs': {'plate_id': 'OBJECT_ID'}},
         'url:plate': {'name': 'api_plate',
@@ -495,6 +546,8 @@ class ImagesView(ObjectsView):
     urls = {
         'url:image': {'name': 'api_image',
                       'kwargs': {'object_id': 'OBJECT_ID'}},
+        'url:datasets': {'name': 'api_image_datasets',
+                         'kwargs': {'image_id': 'OBJECT_ID'}},
     }
 
     def get_opts(self, request, **kwargs):
@@ -566,6 +619,8 @@ class WellsView(ObjectsView):
     urls = {
         'url:well': {'name': 'api_well',
                      'kwargs': {'object_id': 'OBJECT_ID'}},
+        'url:plates': {'name': 'api_well_plates',
+                       'kwargs': {'well_id': 'OBJECT_ID'}},
     }
 
     def get_opts(self, request, **kwargs):