From e3eba8c5fafc8649fc331203e91d08f8f263e562 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 27 Jan 2017 16:06:14 +0000
Subject: [PATCH 01/28] Use ?offset=200 parameter instead of page=2

---
 components/tools/OmeroWeb/omeroweb/api/views.py            | 4 ++--
 .../tools/OmeroWeb/test/integration/test_api_containers.py | 2 +-
 .../tools/OmeroWeb/test/integration/test_api_images.py     | 2 +-
 .../tools/OmeroWeb/test/integration/test_api_projects.py   | 7 +++----
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/views.py b/components/tools/OmeroWeb/omeroweb/api/views.py
index 8d434f4e8b6..359e0bf3e51 100644
--- a/components/tools/OmeroWeb/omeroweb/api/views.py
+++ b/components/tools/OmeroWeb/omeroweb/api/views.py
@@ -251,7 +251,7 @@ class ObjectsView(ApiView):
     def get_opts(self, request, **kwargs):
         """Return an options dict based on request parameters."""
         try:
-            page = getIntOrDefault(request, 'page', 1)
+            offset = getIntOrDefault(request, 'offset', 0)
             limit = getIntOrDefault(request, 'limit', settings.PAGE)
             owner = getIntOrDefault(request, 'owner', None)
             child_count = request.GET.get('childCount', False) == 'true'
@@ -260,7 +260,7 @@ def get_opts(self, request, **kwargs):
             raise BadRequestError(str(ex))
 
         # orphaned and child_count not used by every subclass
-        opts = {'offset': (page - 1) * limit,
+        opts = {'offset': offset,
                 'limit': limit,
                 'owner': owner,
                 'orphaned': orphaned,
diff --git a/components/tools/OmeroWeb/test/integration/test_api_containers.py b/components/tools/OmeroWeb/test/integration/test_api_containers.py
index eb4a19d73a9..57ca9e60c18 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_containers.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_containers.py
@@ -269,7 +269,7 @@ def test_datasets_plates(self, user1, dtype, project_datasets,
         payload = {ptype: parent.id.val, 'limit': limit}
         rsp = _get_response_json(django_client, request_url, payload)
         assert_objects(conn, rsp['data'], children[0:limit], dtype=dtype)
-        payload['page'] = 2
+        payload['offset'] = limit   # page 2
         rsp = _get_response_json(django_client, request_url, payload)
         assert_objects(conn, rsp['data'], children[limit:limit * 2],
                        dtype=dtype)
diff --git a/components/tools/OmeroWeb/test/integration/test_api_images.py b/components/tools/OmeroWeb/test/integration/test_api_images.py
index 7c1884eb814..1f322c318d7 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_images.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_images.py
@@ -171,7 +171,7 @@ def test_dataset_images(self, user1, dataset_images):
         rsp = _get_response_json(django_client, dataset_images_url, payload)
         assert_objects(conn, rsp['data'], images[0:limit], dtype='Image',
                        opts={'load_pixels': True})
-        payload['page'] = 2
+        payload['offset'] = limit   # page 2
         rsp = _get_response_json(django_client, images_url, payload)
         assert_objects(conn, rsp['data'], images[limit:limit * 2],
                        dtype='Image', opts={'load_pixels': True})
diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index 83a867dfc51..2448300e9cf 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -395,17 +395,16 @@ def test_marshal_projects_pagination(self, user1, user2,
         version = settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
-        # First page, just 2 projects. Page = 1 by default
+        # First page, just 2 projects. offset = 0 by default
         limit = 2
         rsp = _get_response_json(django_client, request_url, {'limit': limit})
         assert len(rsp['data']) == limit
         assert_objects(conn, rsp['data'], projects[0:limit])
 
         # Check that page 2 gives next 2 projects
-        page = 2
-        payload = {'limit': limit, 'page': page}
+        payload = {'limit': limit, 'offset': limit}
         rsp = _get_response_json(django_client, request_url, payload)
-        assert_objects(conn, rsp['data'], projects[limit:limit * page])
+        assert_objects(conn, rsp['data'], projects[limit:limit * 2])
 
     def test_marshal_projects_params(self, user1, user2,
                                      projects_user1_group1,

From 4778aa8b656c0c81c764ea6c79222933ed09006c Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 30 Jan 2017 14:57:31 +0000
Subject: [PATCH 02/28] Blitz conn.buildCountQuery() based on conn.buildQuery()

---
 .../OmeroPy/src/omero/gateway/__init__.py     | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/components/tools/OmeroPy/src/omero/gateway/__init__.py b/components/tools/OmeroPy/src/omero/gateway/__init__.py
index a6fe2213217..1d018d94fc5 100644
--- a/components/tools/OmeroPy/src/omero/gateway/__init__.py
+++ b/components/tools/OmeroPy/src/omero/gateway/__init__.py
@@ -3177,6 +3177,38 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None,
 
         return (query, baseParams, wrapper)
 
+    def buildCountQuery(self, obj_type, opts=None):
+        """
+        Prepares a 'projection' query to count objects.
+
+        Based on buildQuery(), we modify the query to only return a count.
+        Modified query does not 'fetch' any data or add any other
+        unnecessary objects to query.
+        We return just the query and omero.sys.ParametersI for the query.
+
+        :param obj_type:    Object type. E.g. "Project" see above
+        :param opts:        Dict of options for filtering by
+                            offset, limit and owner for all objects.
+                            Additional opts handled by _getQueryString()
+                            E.g. filter Dataset by 'project'
+        :return:            (query, params)
+        """
+        # We disable pagination & loading of child_counts
+        opts_copy = opts.copy()
+        if 'limit' in opts_copy:
+            del opts_copy['limit']
+        opts_copy['child_count'] = False
+
+        # Get query with other options
+        query, params, wrapper = self.buildQuery(obj_type, opts=opts_copy)
+
+        # Modify query to only select count()
+        query = query.replace("select obj ", "select count(obj) ")
+        query = query.replace("fetch", "")
+        query = query.split("order by")[0]
+        return query, params
+
+
     def listFileAnnotations(self, eid=None, toInclude=[], toExclude=[]):
         """
         Lists FileAnnotations created by users, filtering by namespaces if

From 6bbdfc6a088803e383111550f76282016f055e2b Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 30 Jan 2017 15:16:12 +0000
Subject: [PATCH 03/28] api_query.py uses conn.buildCountQuery() to add
 'totalCount' to 'meta':{}

---
 .../tools/OmeroWeb/omeroweb/api/api_query.py      | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index db15cc70147..fc0250fb303 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -69,4 +69,17 @@ def query_objects(conn, object_type,
         for obj in result:
             objects.append(obj)
 
-    return marshal_objects(objects, extras=extras, normalize=normalize)
+    # Query the count() of objects & add to 'meta' dict
+    count_query, params = conn.buildCountQuery(object_type, opts=opts)
+    result = qs.projection(count_query, params, ctx)
+
+    meta = {}
+    if 'offset' in opts:
+        meta['offset'] = opts['offset']
+    if 'limit' in opts:
+        meta['limit'] = opts['limit']
+    meta['totalCount'] = result[0][0].val
+
+    marshalled = marshal_objects(objects, extras=extras, normalize=normalize)
+    marshalled['meta'] = meta
+    return marshalled

From 0e862fffee611872d92747dbac9857637750658e Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 31 Jan 2017 15:54:44 +0000
Subject: [PATCH 04/28] Test 'meta' dict for listing Datasets & Plates

---
 .../OmeroWeb/test/integration/test_api_containers.py     | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_containers.py b/components/tools/OmeroWeb/test/integration/test_api_containers.py
index 57ca9e60c18..c43dcac5d75 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_containers.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_containers.py
@@ -263,16 +263,25 @@ def test_datasets_plates(self, user1, dtype, project_datasets,
         assert len(rsp['data']) == 5
         assert_objects(conn, rsp['data'], children, dtype=dtype,
                        extra=child_counts)
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Pagination
         limit = 3
         payload = {ptype: parent.id.val, 'limit': limit}
         rsp = _get_response_json(django_client, request_url, payload)
         assert_objects(conn, rsp['data'], children[0:limit], dtype=dtype)
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': limit,
+                               'offset': 0}
         payload['offset'] = limit   # page 2
         rsp = _get_response_json(django_client, request_url, payload)
         assert_objects(conn, rsp['data'], children[limit:limit * 2],
                        dtype=dtype)
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': limit,
+                               'offset': limit}
 
     def test_screens(self, user1, user_screens):
         """Test listing of Screens."""

From bed8a339c7f75f083c36903fd498fe524e5b916f Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 31 Jan 2017 16:01:40 +0000
Subject: [PATCH 05/28] Test 'meta' dict for listing Images, orphans

---
 .../test/integration/test_api_containers.py       |  6 ++++++
 .../OmeroWeb/test/integration/test_api_images.py  | 15 +++++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_containers.py b/components/tools/OmeroWeb/test/integration/test_api_containers.py
index c43dcac5d75..efba6b8614a 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_containers.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_containers.py
@@ -249,11 +249,17 @@ def test_datasets_plates(self, user1, dtype, project_datasets,
         # List ALL Datasets or Plates
         rsp = _get_response_json(django_client, request_url, {})
         assert len(rsp['data']) == 6
+        assert rsp['meta'] == {'totalCount': 6,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Filter Datasets or Plates by Orphaned
         payload = {'orphaned': 'true'}
         rsp = _get_response_json(django_client, request_url, payload)
         assert_objects(conn, rsp['data'], [orphaned], dtype=dtype)
+        assert rsp['meta'] == {'totalCount': 1,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Filter Datasets by Project or Plates by Screen
         children.sort(cmp_name_insensitive)
diff --git a/components/tools/OmeroWeb/test/integration/test_api_images.py b/components/tools/OmeroWeb/test/integration/test_api_images.py
index 1f322c318d7..3bfaf651721 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_images.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_images.py
@@ -147,12 +147,18 @@ def test_dataset_images(self, user1, dataset_images):
         # List ALL Images
         rsp = _get_response_json(django_client, images_url, {})
         assert len(rsp['data']) == 6
+        assert rsp['meta'] == {'totalCount': 6,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Filter Images by Orphaned
         payload = {'orphaned': 'true'}
         rsp = _get_response_json(django_client, images_url, payload)
         assert_objects(conn, rsp['data'], [orphaned], dtype='Image',
                        opts={'load_pixels': True})
+        assert rsp['meta'] == {'totalCount': 1,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Filter Images by Dataset
         images.sort(cmp_name_insensitive)
@@ -163,6 +169,9 @@ def test_dataset_images(self, user1, dataset_images):
         assert 'Channels' not in rsp['data'][0]['Pixels']
         assert_objects(conn, rsp['data'], images, dtype='Image',
                        opts={'load_pixels': True})
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': settings.PAGE,
+                               'offset': 0}
 
         # Pagination, listing images via /datasets/:id/images/
         limit = 3
@@ -171,10 +180,16 @@ def test_dataset_images(self, user1, dataset_images):
         rsp = _get_response_json(django_client, dataset_images_url, payload)
         assert_objects(conn, rsp['data'], images[0:limit], dtype='Image',
                        opts={'load_pixels': True})
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': limit,
+                               'offset': 0}
         payload['offset'] = limit   # page 2
         rsp = _get_response_json(django_client, images_url, payload)
         assert_objects(conn, rsp['data'], images[limit:limit * 2],
                        dtype='Image', opts={'load_pixels': True})
+        assert rsp['meta'] == {'totalCount': 5,
+                               'limit': limit,
+                               'offset': limit}
 
         # Show ONLY the orphaned image (channels are loaded by default)
         img_url = images_url + '%s/' % orphaned.id.val

From f99f34a7d77a9756354024a61d7a8fd31ef409cc Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 7 Feb 2017 12:11:49 +0000
Subject: [PATCH 06/28] Added omero.web.max_page_size 500 to settings.py

---
 components/tools/OmeroWeb/omeroweb/settings.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/settings.py b/components/tools/OmeroWeb/omeroweb/settings.py
index 497a838a693..2f9be19c9ed 100644
--- a/components/tools/OmeroWeb/omeroweb/settings.py
+++ b/components/tools/OmeroWeb/omeroweb/settings.py
@@ -639,7 +639,12 @@ def leave_none_unset_int(s):
          200,
          int,
          ("Number of images displayed within a dataset or 'orphaned'"
-          " container to prevent from loading them all at once.")],
+          " container or default number of items returned from json api.")],
+    "omero.web.max_page_size":
+        ["MAX_PAGE",
+         500,
+         int,
+         ("Maximum number of items returned from json api.")],
     "omero.web.ui.top_links":
         ["TOP_LINKS",
          ('['

From c558aeddfc0661dc5892527083882ba9ef006e2a Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 7 Feb 2017 12:12:29 +0000
Subject: [PATCH 07/28] Limit page size to MAX_PAGE

---
 components/tools/OmeroWeb/omeroweb/api/api_query.py | 2 ++
 components/tools/OmeroWeb/omeroweb/api/views.py     | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index fc0250fb303..b69ef4a50b0 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -24,6 +24,7 @@
 
 from api_marshal import marshal_objects
 from copy import deepcopy
+from django.conf import settings
 
 
 def query_objects(conn, object_type,
@@ -78,6 +79,7 @@ def query_objects(conn, object_type,
         meta['offset'] = opts['offset']
     if 'limit' in opts:
         meta['limit'] = opts['limit']
+    meta['maxLimit'] = settings.MAX_PAGE
     meta['totalCount'] = result[0][0].val
 
     marshalled = marshal_objects(objects, extras=extras, normalize=normalize)
diff --git a/components/tools/OmeroWeb/omeroweb/api/views.py b/components/tools/OmeroWeb/omeroweb/api/views.py
index 359e0bf3e51..bd0d4a8b787 100644
--- a/components/tools/OmeroWeb/omeroweb/api/views.py
+++ b/components/tools/OmeroWeb/omeroweb/api/views.py
@@ -261,7 +261,7 @@ def get_opts(self, request, **kwargs):
 
         # orphaned and child_count not used by every subclass
         opts = {'offset': offset,
-                'limit': limit,
+                'limit': min(limit, settings.MAX_PAGE),
                 'owner': owner,
                 'orphaned': orphaned,
                 'child_count': child_count,

From 3e9b8eea54f894dcc2c891d39ad46b20d9310041 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 7 Feb 2017 15:02:47 +0000
Subject: [PATCH 08/28] flake8 fix

---
 components/tools/OmeroPy/src/omero/gateway/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/components/tools/OmeroPy/src/omero/gateway/__init__.py b/components/tools/OmeroPy/src/omero/gateway/__init__.py
index 1d018d94fc5..38f0d7c3f77 100644
--- a/components/tools/OmeroPy/src/omero/gateway/__init__.py
+++ b/components/tools/OmeroPy/src/omero/gateway/__init__.py
@@ -3208,7 +3208,6 @@ def buildCountQuery(self, obj_type, opts=None):
         query = query.split("order by")[0]
         return query, params
 
-
     def listFileAnnotations(self, eid=None, toInclude=[], toExclude=[]):
         """
         Lists FileAnnotations created by users, filtering by namespaces if

From cfa25305feaab0f679bada3d9e359b5a3e34db7a Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 8 Feb 2017 15:27:02 +0000
Subject: [PATCH 09/28] Moving api settings to api_settings.py

---
 .../tools/OmeroWeb/omeroweb/api/api_query.py  |  4 +-
 .../OmeroWeb/omeroweb/api/api_settings.py     | 57 +++++++++++++++++++
 .../tools/OmeroWeb/omeroweb/api/urls.py       |  4 +-
 .../tools/OmeroWeb/omeroweb/api/views.py      | 12 ++--
 .../tools/OmeroWeb/omeroweb/settings.py       | 23 +-------
 5 files changed, 69 insertions(+), 31 deletions(-)
 create mode 100644 components/tools/OmeroWeb/omeroweb/api/api_settings.py

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index b69ef4a50b0..322570fd920 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -24,7 +24,7 @@
 
 from api_marshal import marshal_objects
 from copy import deepcopy
-from django.conf import settings
+from . import api_settings
 
 
 def query_objects(conn, object_type,
@@ -79,7 +79,7 @@ def query_objects(conn, object_type,
         meta['offset'] = opts['offset']
     if 'limit' in opts:
         meta['limit'] = opts['limit']
-    meta['maxLimit'] = settings.MAX_PAGE
+    meta['maxLimit'] = api_settings.API_MAX_LIMIT
     meta['totalCount'] = result[0][0].val
 
     marshalled = marshal_objects(objects, extras=extras, normalize=normalize)
diff --git a/components/tools/OmeroWeb/omeroweb/api/api_settings.py b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
new file mode 100644
index 00000000000..b15e381105d
--- /dev/null
+++ b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2017 University of Dundee & Open Microscopy Environment.
+# All rights reserved.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Settings for the OMERO JSON api app."""
+
+import sys
+from omeroweb.settings import process_custom_settings, report_settings, \
+    str_slash
+
+# load settings
+API_SETTINGS_MAPPING = {
+
+    "omero.web.api.limit":
+        ["API_LIMIT",
+         200,
+         int,
+         "Default number of items returned from json api."],
+    "omero.web.api.max_limit":
+        ["API_MAX_LIMIT",
+         500,
+         int,
+         "Maximum number of items returned from json api."],
+    "omero.web.api.absolute_url":
+        ["API_ABSOLUTE_URL",
+         None,
+         str_slash,
+         ("URL to use for generating urls within API json responses. "
+          "By default this is None, and we use Django's "
+          "request.build_absolute_uri() to generate absolute urls "
+          "based on each request. If set to a string or empty string, "
+          "this will be used as prefix to relative urls.")],
+}
+
+process_custom_settings(sys.modules[__name__], 'API_SETTINGS_MAPPING')
+report_settings(sys.modules[__name__])
+
+# For any given release of api, we may support
+# one or more versions of the api.
+# E.g. /api/v1.0/
+# TODO - need to decide how this is configured, strategy for extending etc.
+API_VERSIONS = ('0.1',)
diff --git a/components/tools/OmeroWeb/omeroweb/api/urls.py b/components/tools/OmeroWeb/omeroweb/api/urls.py
index f2a77063fd3..311d2058029 100644
--- a/components/tools/OmeroWeb/omeroweb/api/urls.py
+++ b/components/tools/OmeroWeb/omeroweb/api/urls.py
@@ -22,11 +22,11 @@
 from django.conf.urls import url, patterns
 from omeroweb.api import views
 from omeroweb.webgateway.views import LoginView
-from django.conf import settings
+from . import api_settings
 import re
 
 versions = '|'.join([re.escape(v)
-                    for v in settings.API_VERSIONS])
+                    for v in api_settings.API_VERSIONS])
 
 api_versions = url(r'^$', views.api_versions, name='api_versions')
 
diff --git a/components/tools/OmeroWeb/omeroweb/api/views.py b/components/tools/OmeroWeb/omeroweb/api/views.py
index bd0d4a8b787..e6c6a24ae74 100644
--- a/components/tools/OmeroWeb/omeroweb/api/views.py
+++ b/components/tools/OmeroWeb/omeroweb/api/views.py
@@ -23,7 +23,7 @@
 from django.middleware import csrf
 from django.utils.decorators import method_decorator
 from django.core.urlresolvers import reverse
-from django.conf import settings
+from . import api_settings
 
 import traceback
 import json
@@ -52,11 +52,11 @@ def build_url(request, name, api_version, **kwargs):
     """
     kwargs['api_version'] = api_version
     url = reverse(name, kwargs=kwargs)
-    if settings.API_ABSOLUTE_URL is None:
+    if api_settings.API_ABSOLUTE_URL is None:
         return request.build_absolute_uri(url)
     else:
         # remove trailing slash
-        prefix = settings.API_ABSOLUTE_URL.rstrip('/')
+        prefix = api_settings.API_ABSOLUTE_URL.rstrip('/')
         return "%s%s" % (prefix, url)
 
 
@@ -64,7 +64,7 @@ def build_url(request, name, api_version, **kwargs):
 def api_versions(request, **kwargs):
     """Base url of the webgateway json api."""
     versions = []
-    for v in settings.API_VERSIONS:
+    for v in api_settings.API_VERSIONS:
         versions.append({
             'version': v,
             'url:base': build_url(request, 'api_base', v)
@@ -252,7 +252,7 @@ def get_opts(self, request, **kwargs):
         """Return an options dict based on request parameters."""
         try:
             offset = getIntOrDefault(request, 'offset', 0)
-            limit = getIntOrDefault(request, 'limit', settings.PAGE)
+            limit = getIntOrDefault(request, 'limit', api_settings.API_LIMIT)
             owner = getIntOrDefault(request, 'owner', None)
             child_count = request.GET.get('childCount', False) == 'true'
             orphaned = request.GET.get('orphaned', False) == 'true'
@@ -261,7 +261,7 @@ def get_opts(self, request, **kwargs):
 
         # orphaned and child_count not used by every subclass
         opts = {'offset': offset,
-                'limit': min(limit, settings.MAX_PAGE),
+                'limit': min(limit, api_settings.API_MAX_LIMIT),
                 'owner': owner,
                 'orphaned': orphaned,
                 'child_count': child_count,
diff --git a/components/tools/OmeroWeb/omeroweb/settings.py b/components/tools/OmeroWeb/omeroweb/settings.py
index 2f9be19c9ed..50ad5e035f1 100644
--- a/components/tools/OmeroWeb/omeroweb/settings.py
+++ b/components/tools/OmeroWeb/omeroweb/settings.py
@@ -472,15 +472,6 @@ def leave_none_unset_int(s):
          ("Workers silent for more than this many seconds are killed "
           "and restarted. Check Gunicorn Documentation "
           "http://docs.gunicorn.org/en/stable/settings.html#timeout")],
-    "omero.web.api.absolute_url":
-        ["API_ABSOLUTE_URL",
-         None,
-         str_slash,
-         ("URL to use for generating urls within API json responses. "
-          "By default this is None, and we use Django's "
-          "request.build_absolute_uri() to generate absolute urls "
-          "based on each request. If set to a string or empty string, "
-          "this will be used as prefix to relative urls.")],
 
     # Public user
     "omero.web.public.enabled":
@@ -639,12 +630,7 @@ def leave_none_unset_int(s):
          200,
          int,
          ("Number of images displayed within a dataset or 'orphaned'"
-          " container or default number of items returned from json api.")],
-    "omero.web.max_page_size":
-        ["MAX_PAGE",
-         500,
-         int,
-         ("Maximum number of items returned from json api.")],
+          " container to prevent from loading them all at once.")],
     "omero.web.ui.top_links":
         ["TOP_LINKS",
          ('['
@@ -1100,6 +1086,7 @@ def report_settings(module):
     'omeroweb.webclient',
     'omeroweb.webgateway',
     'omeroweb.webredirect',
+    'omeroweb.api',
     'pipeline',
 )
 
@@ -1180,12 +1167,6 @@ def report_settings(module):
 # FEEDBACK_APP: 6 = OMERO.web
 FEEDBACK_APP = 6
 
-# For any given release of api, we may support
-# one or more versions of the api.
-# E.g. /api/v1.0/
-# TODO - need to decide how this is configured, strategy for extending etc.
-API_VERSIONS = ('0.1',)
-
 # IGNORABLE_404_STARTS:
 # Default: ('/cgi-bin/', '/_vti_bin', '/_vti_inf')
 # IGNORABLE_404_ENDS:

From 7fbb04d2dd5b7b7e4f810fffd2d683d473b4a9a3 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 17 Feb 2017 12:48:18 +0000
Subject: [PATCH 10/28] Fix merge conflict

---
 components/tools/OmeroWeb/test/integration/test_api_images.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_images.py b/components/tools/OmeroWeb/test/integration/test_api_images.py
index d1db0484861..9389be5d105 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_images.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_images.py
@@ -24,7 +24,6 @@
 from django.core.urlresolvers import reverse
 from django.conf import settings
 import pytest
-from omero_marshal import get_encoder
 from test_api_projects import cmp_name_insensitive, get_update_service, \
     get_connection, marshal_objects
 from omero.model import DatasetI, ImageI

From 5eb47b9a147ff0111b2d5799ecfd2fb3e520673a Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 17 Feb 2017 12:56:23 +0000
Subject: [PATCH 11/28] Don't need to remove opts['child_count'] in
 buildCountQuery()

---
 components/tools/OmeroPy/src/omero/gateway/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/components/tools/OmeroPy/src/omero/gateway/__init__.py b/components/tools/OmeroPy/src/omero/gateway/__init__.py
index 6192966599d..fa10f9f12d5 100644
--- a/components/tools/OmeroPy/src/omero/gateway/__init__.py
+++ b/components/tools/OmeroPy/src/omero/gateway/__init__.py
@@ -3197,11 +3197,10 @@ def buildCountQuery(self, obj_type, opts=None):
                             E.g. filter Dataset by 'project'
         :return:            (query, params)
         """
-        # We disable pagination & loading of child_counts
+        # We disable pagination since we want to count ALL results
         opts_copy = opts.copy()
         if 'limit' in opts_copy:
             del opts_copy['limit']
-        opts_copy['child_count'] = False
 
         # Get query with other options
         query, params, wrapper = self.buildQuery(obj_type, opts=opts_copy)

From 1057dceb7efa6329bcbe181cc39cdbbc6aa4d409 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Fri, 17 Feb 2017 13:04:56 +0000
Subject: [PATCH 12/28] Fix test_api_images.py to use api_settings and
 MAX_LIMIT

---
 .../test/integration/test_api_images.py        | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_images.py b/components/tools/OmeroWeb/test/integration/test_api_images.py
index 9389be5d105..1d088ff4bb1 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_images.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_images.py
@@ -22,13 +22,14 @@
 from omeroweb.testlib import IWebTest, _get_response_json, \
     _csrf_post_json, _csrf_put_json, _csrf_delete_response_json
 from django.core.urlresolvers import reverse
-from django.conf import settings
+from omeroweb.api import api_settings
 import pytest
 from test_api_projects import cmp_name_insensitive, get_update_service, \
     get_connection, marshal_objects
 from omero.model import DatasetI, ImageI
 from omero.rtypes import rstring
 import json
+from omero_marshal import OME_SCHEMA_URL
 
 
 def get_query_service(user):
@@ -106,7 +107,7 @@ def test_dataset_images(self, user1, dataset_images):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
 
         dataset = dataset_images[0]
         images = dataset.linkedImageList()
@@ -119,7 +120,8 @@ def test_dataset_images(self, user1, dataset_images):
         rsp = _get_response_json(django_client, images_url, {})
         assert len(rsp['data']) == 6
         assert rsp['meta'] == {'totalCount': 6,
-                               'limit': settings.PAGE,
+                               'limit': api_settings.API_LIMIT,
+                               'maxLimit': api_settings.API_MAX_LIMIT,
                                'offset': 0}
 
         # Filter Images by Orphaned
@@ -128,7 +130,8 @@ def test_dataset_images(self, user1, dataset_images):
         assert_objects(conn, rsp['data'], [orphaned], dtype='Image',
                        opts={'load_pixels': True})
         assert rsp['meta'] == {'totalCount': 1,
-                               'limit': settings.PAGE,
+                               'limit': api_settings.API_LIMIT,
+                               'maxLimit': api_settings.API_MAX_LIMIT,
                                'offset': 0}
 
         # Filter Images by Dataset
@@ -141,7 +144,8 @@ def test_dataset_images(self, user1, dataset_images):
         assert_objects(conn, rsp['data'], images, dtype='Image',
                        opts={'load_pixels': True})
         assert rsp['meta'] == {'totalCount': 5,
-                               'limit': settings.PAGE,
+                               'limit': api_settings.API_LIMIT,
+                               'maxLimit': api_settings.API_MAX_LIMIT,
                                'offset': 0}
 
         # Pagination, listing images via /datasets/:id/images/
@@ -153,6 +157,7 @@ def test_dataset_images(self, user1, dataset_images):
                        opts={'load_pixels': True})
         assert rsp['meta'] == {'totalCount': 5,
                                'limit': limit,
+                               'maxLimit': api_settings.API_MAX_LIMIT,
                                'offset': 0}
         payload['offset'] = limit   # page 2
         rsp = _get_response_json(django_client, images_url, payload)
@@ -160,6 +165,7 @@ def test_dataset_images(self, user1, dataset_images):
                        dtype='Image', opts={'load_pixels': True})
         assert rsp['meta'] == {'totalCount': 5,
                                'limit': limit,
+                               'maxLimit': api_settings.API_MAX_LIMIT,
                                'offset': limit}
 
         # Show ONLY the orphaned image (channels are loaded by default)
@@ -176,7 +182,7 @@ def test_image_create_update_delete(self, user1):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         payload = {'Name': 'Image test',
                    '@type': OME_SCHEMA_URL + '#Image'}

From 88ee449729f54b34373992754843476dc02c1ce2 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Sun, 19 Feb 2017 22:52:27 +0000
Subject: [PATCH 13/28] Fix API_VERSIONS to '0' from merge conflict

---
 components/tools/OmeroWeb/omeroweb/api/api_settings.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_settings.py b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
index b15e381105d..0515a0ebcbf 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_settings.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
@@ -54,4 +54,4 @@
 # one or more versions of the api.
 # E.g. /api/v1.0/
 # TODO - need to decide how this is configured, strategy for extending etc.
-API_VERSIONS = ('0.1',)
+API_VERSIONS = ('0',)

From 418eb3b9effb0a6c080a72e41afb6fa9c94a0fe2 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 20 Feb 2017 23:13:37 +0000
Subject: [PATCH 14/28] flake8 fixes from merge conflict

---
 .../tools/OmeroWeb/test/integration/test_api_containers.py    | 4 ++--
 components/tools/OmeroWeb/test/integration/test_api_images.py | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_containers.py b/components/tools/OmeroWeb/test/integration/test_api_containers.py
index 3fbf98c2c82..4b5c6fef5d1 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_containers.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_containers.py
@@ -188,7 +188,7 @@ def test_create_update_unsupported(self, user1, dtype, method):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         payload = {'Name': 'test',
                    '@type': OME_SCHEMA_URL + '#%s' % dtype}
@@ -203,7 +203,7 @@ def test_delete_unsupported(self, user1, dtype):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         # Delete (fake url - image doesn't need to exist for test)
         url_name = 'api_%s' % dtype.lower()
         delete_url = reverse(url_name, kwargs={'api_version': version,
diff --git a/components/tools/OmeroWeb/test/integration/test_api_images.py b/components/tools/OmeroWeb/test/integration/test_api_images.py
index f1291a35d6e..52886269157 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_images.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_images.py
@@ -28,7 +28,6 @@
 from omero.model import DatasetI, ImageI
 from omero.rtypes import rstring
 import json
-from omero_marshal import OME_SCHEMA_URL
 
 
 def get_query_service(user):

From faddc5d730dbd28d80cdc9e81ca99c20e3734ae4 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Mon, 20 Feb 2017 23:20:24 +0000
Subject: [PATCH 15/28] Tiny fix to avoid merge conflict

---
 components/tools/OmeroWeb/omeroweb/api/api_query.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index 90c43af6a3a..f681b5b0165 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -22,10 +22,10 @@
 
 from omero.rtypes import unwrap, wrap
 from omero.sys import ParametersI
+from . import api_settings
 
 from api_marshal import marshal_objects
 from copy import deepcopy
-from . import api_settings
 
 
 def get_child_counts(conn, link_class, parent_ids):

From 400ae402ffeb6f904d34fbe8843a4e7e893e43db Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 11:41:59 +0000
Subject: [PATCH 16/28] Fix 'settings' -> 'api_settings' in tests

---
 .../test/integration/test_api_errors.py       | 14 +++++-----
 .../test/integration/test_api_login.py        | 16 +++++------
 .../test/integration/test_api_projects.py     | 28 +++++++++----------
 .../test/integration/test_api_wells.py        |  6 ++--
 4 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_errors.py b/components/tools/OmeroWeb/test/integration/test_api_errors.py
index d48d1680c5a..3bab8ed0267 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_errors.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_errors.py
@@ -21,7 +21,7 @@
 
 from omeroweb.testlib import IWebTest, _csrf_post_json, _csrf_put_json
 from django.core.urlresolvers import reverse
-from django.conf import settings
+from omeroweb.api import api_settings
 import pytest
 from test_api_projects import get_connection
 from omero.model import ProjectI, TagAnnotationI
@@ -56,7 +56,7 @@ def user_A(self, group_A, group_B):
     def test_save_post_no_id(self):
         """If POST to /save/ data shouldn't contain @id."""
         django_client = self.django_root_client
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         payload = {'Name': 'test_save_post_no_id',
                    '@type': '%s#Project' % OME_SCHEMA_URL,
@@ -69,7 +69,7 @@ def test_save_post_no_id(self):
     def test_save_put_id(self):
         """If PUT to /save/ to update, data must contain @id."""
         django_client = self.django_root_client
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         payload = {'Name': 'test_save_put_id',
                    '@type': '%s#Project' % OME_SCHEMA_URL}
@@ -81,7 +81,7 @@ def test_save_put_id(self):
     def test_marshal_type(self):
         """If no decoder found for @type, get suitable message."""
         django_client = self.django_root_client
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         objType = 'SomeInvalidSchema#Project'
         payload = {'Name': 'test_marshal_type',
@@ -94,7 +94,7 @@ def test_marshal_type(self):
     def test_marshal_validation(self):
         """Test that we get expected error with invalid @type in json."""
         django_client = self.django_root_client
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         payload = {'Name': 'test_marshal_validation',
                    '@type': OME_SCHEMA_URL + '#Project',
@@ -112,7 +112,7 @@ def test_security_violation(self, group_B, user_A):
         group_A_id = conn.getEventContext().groupId
         userName = conn.getUser().getName()
         django_client = self.new_django_client(userName, userName)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         group_B_id = group_B.id.val
         save_url = reverse('api_save', kwargs={'api_version': version})
         # Create project in group_A (default group)
@@ -139,7 +139,7 @@ def test_validation_exception(self, user_A):
         group = conn.getEventContext().groupId
         userName = conn.getUser().getName()
         django_client = self.new_django_client(userName, userName)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         save_url = reverse('api_save', kwargs={'api_version': version})
         save_url += '?group=' + str(group)
 
diff --git a/components/tools/OmeroWeb/test/integration/test_api_login.py b/components/tools/OmeroWeb/test/integration/test_api_login.py
index 2c316c9e4cd..b161e8cad58 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_login.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_login.py
@@ -25,7 +25,7 @@
 from omeroweb.testlib import IWebTest, _get_response_json, \
     _post_response_json, _csrf_post_response_json
 from django.core.urlresolvers import reverse, NoReverseMatch
-from django.conf import settings
+from omeroweb.api import api_settings
 from django.test import Client
 from omero_marshal import OME_SCHEMA_URL
 import json
@@ -44,9 +44,9 @@ def test_versions(self):
         request_url = reverse('api_versions')
         rsp = _get_response_json(django_client, request_url, {})
         versions = rsp['data']
-        assert len(versions) == len(settings.API_VERSIONS)
+        assert len(versions) == len(api_settings.API_VERSIONS)
         for v in versions:
-            assert v['version'] in settings.API_VERSIONS
+            assert v['version'] in api_settings.API_VERSIONS
 
     def test_base_url(self):
         """
@@ -54,7 +54,7 @@ def test_base_url(self):
         """
         django_client = self.django_root_client
         # test the most recent version
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_base', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
         assert 'url:servers' in rsp
@@ -71,7 +71,7 @@ def test_base_url_versions_404(self):
         """
         Tests that the base url gives 404 for invalid versions
         """
-        version = settings.API_VERSIONS[-1] + "1"
+        version = api_settings.API_VERSIONS[-1] + "1"
         with pytest.raises(NoReverseMatch):
             reverse('api_base', kwargs={'api_version': version})
 
@@ -80,7 +80,7 @@ def test_login_get(self):
         Tests that we get a suitable message if we try to GET login_url
         """
         django_client = self.django_root_client
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_login', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {},
                                  status_code=405)
@@ -93,7 +93,7 @@ def test_login_csrf(self):
         """
         django_client = self.django_root_client
         # test the most recent version
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_login', kwargs={'api_version': version})
         rsp = _post_response_json(django_client, request_url, {},
                                   status_code=403)
@@ -123,7 +123,7 @@ def test_login_errors(self, credentials):
         """
         django_client = self.django_root_client
         # test the most recent version
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_login', kwargs={'api_version': version})
         data = credentials[0]
         message = credentials[1]
diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index f3a02d266c7..9c100d87a6d 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -24,7 +24,7 @@
 from omeroweb.testlib import IWebTest, _get_response_json, \
     _csrf_post_json, _csrf_put_json, _csrf_delete_response_json
 from django.core.urlresolvers import reverse
-from django.conf import settings
+from omeroweb.api import api_settings
 from django.test import Client
 import pytest
 from omero.gateway import BlitzGateway
@@ -265,7 +265,7 @@ def test_marshal_projects_not_logged_in(self):
         Test marshalling projects without log-in
         """
         django_client = Client()
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {},
                                  status_code=403)
@@ -278,7 +278,7 @@ def test_marshal_projects_no_results(self, user1):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
         assert rsp['data'] == []
@@ -290,7 +290,7 @@ def test_marshal_projects_user(self, user1, projects_user1_group1):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
         # Reload projects with group '-1' to get same 'canLink' perms
@@ -306,7 +306,7 @@ def test_marshal_projects_another_user(self, user1, user2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
         # user1 reloads user2's projects
@@ -320,7 +320,7 @@ def test_marshal_projects_another_group(self, user1, group2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
 
@@ -339,7 +339,7 @@ def test_marshal_projects_all_groups(self, user1, group1, group2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
         # All groups
@@ -366,7 +366,7 @@ def test_marshal_projects_all_users(self, user1, user2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
         # Both users
@@ -392,7 +392,7 @@ def test_marshal_projects_pagination(self, user1, user2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
         # First page, just 2 projects. offset = 0 by default
@@ -417,7 +417,7 @@ def test_marshal_projects_params(self, user1, user2,
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
         # Test 'childCount' parameter
@@ -462,7 +462,7 @@ def test_project_create_read(self):
         """
         django_client = self.django_root_client
         group = self.ctx.groupId
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         # Need to get the Schema url to create @type
         base_url = reverse('api_base', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, base_url, {})
@@ -495,7 +495,7 @@ def test_project_create_other_group(self, user1, projects_user1_group2):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         # We're only using projects_user1_group2 to get group2 id
         group2_id = projects_user1_group2[0].getDetails().group.id.val
         # This seems to be the minimum details needed to pass group ID
@@ -539,7 +539,7 @@ def test_project_update(self, user1):
         project = get_update_service(user1).saveAndReturnObject(project)
 
         # Update Project in 2 ways...
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         project_url = reverse('api_project',
                               kwargs={'api_version': version,
                                       'object_id': project.id.val})
@@ -590,7 +590,7 @@ def test_project_delete(self, user1):
         project.name = rstring('test_project_delete')
         project.description = rstring('Test update')
         project = get_update_service(user1).saveAndReturnObject(project)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
         project_url = reverse('api_project',
                               kwargs={'api_version': version,
                                       'object_id': project.id.val})
diff --git a/components/tools/OmeroWeb/test/integration/test_api_wells.py b/components/tools/OmeroWeb/test/integration/test_api_wells.py
index d746b2b0cc5..c18e1fc6ad2 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_wells.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_wells.py
@@ -21,7 +21,7 @@
 
 from omeroweb.testlib import IWebTest, _get_response_json
 from django.core.urlresolvers import reverse
-from django.conf import settings
+from omeroweb.api import api_settings
 import pytest
 from test_api_projects import get_update_service, \
     get_connection, marshal_objects
@@ -173,7 +173,7 @@ def test_plate_wells(self, user1, small_plate, bigger_plate):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
 
         wells_url = reverse('api_wells', kwargs={'api_version': version})
 
@@ -206,7 +206,7 @@ def test_well(self, user1, small_plate):
         conn = get_connection(user1)
         user_name = conn.getUser().getName()
         django_client = self.new_django_client(user_name, user_name)
-        version = settings.API_VERSIONS[-1]
+        version = api_settings.API_VERSIONS[-1]
 
         small_plate = conn.getObject('Plate', small_plate.id.val)
         wells = [w._obj for w in small_plate.listChildren()]

From 4b1476049afd4cbcab33b84d7ebcfafbec450b3b Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 11:44:35 +0000
Subject: [PATCH 17/28] Blitz E.g. -> e.g. fixes

---
 .../tools/OmeroPy/src/omero/gateway/__init__.py      | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/components/tools/OmeroPy/src/omero/gateway/__init__.py b/components/tools/OmeroPy/src/omero/gateway/__init__.py
index fa10f9f12d5..96f8ffdc2fd 100644
--- a/components/tools/OmeroPy/src/omero/gateway/__init__.py
+++ b/components/tools/OmeroPy/src/omero/gateway/__init__.py
@@ -3020,7 +3020,7 @@ def getObject(self, obj_type, oid=None, params=None, attributes=None,
         If more than one object found, raises ome.conditions.ApiUsageException
         See :meth:`getObjects` for more info.
 
-        :param obj_type:    Object type. E.g. "Project" see above
+        :param obj_type:    Object type, e.g. "Project" see above
         :type obj_type:     String
         :param ids:         object IDs
         :type ids:          List of Long
@@ -3048,7 +3048,7 @@ def getObjects(self, obj_type, ids=None, params=None, attributes=None,
         be returned. i.e. listObjects() Filter objects by attributes. E.g.
         attributes={'name':name}
 
-        :param obj_type:    Object type. E.g. "Project" see above
+        :param obj_type:    Object type, e.g. "Project" see above
         :type obj_type:     String
         :param ids:         object IDs
         :type ids:          List of Long
@@ -3087,7 +3087,7 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None,
         can be used with the appropriate query method. Used by
         :meth:`getObjects` and :meth:`getObject` above.
 
-        :param obj_type:    Object type. E.g. "Project" see above
+        :param obj_type:    Object type, e.g. "Project" see above
         :type obj_type:     String
         :param ids:         object IDs
         :type ids:          List of Long
@@ -3190,11 +3190,11 @@ def buildCountQuery(self, obj_type, opts=None):
         unnecessary objects to query.
         We return just the query and omero.sys.ParametersI for the query.
 
-        :param obj_type:    Object type. E.g. "Project" see above
+        :param obj_type:    Object type, e.g. "Project" see above
         :param opts:        Dict of options for filtering by
                             offset, limit and owner for all objects.
                             Additional opts handled by _getQueryString()
-                            E.g. filter Dataset by 'project'
+                            e.g. filter Dataset by 'project'
         :return:            (query, params)
         """
         # We disable pagination since we want to count ALL results
@@ -3252,7 +3252,7 @@ def getAnnotationLinks(self, parent_type, parent_ids=None, ann_ids=None,
         If parent_ids is None, all available objects will be returned.
         i.e. listObjects()
 
-        :param obj_type:    Object type. E.g. "Project" see above
+        :param obj_type:    Object type, e.g. "Project" see above
         :type obj_type:     String
         :param ids:         object IDs
         :type ids:          List of Long

From c2464537063b583b47bcd7b395de04b2abc800d8 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 12:03:38 +0000
Subject: [PATCH 18/28] More fixes for PR #5067

---
 .../OmeroWeb/omeroweb/api/api_settings.py     |  2 +-
 .../test/integration/test_api_projects.py     | 21 ++++++++++---------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_settings.py b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
index 0515a0ebcbf..3c8ec797b1f 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_settings.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_settings.py
@@ -52,6 +52,6 @@
 
 # For any given release of api, we may support
 # one or more versions of the api.
-# E.g. /api/v1.0/
+# E.g. /api/v0/
 # TODO - need to decide how this is configured, strategy for extending etc.
 API_VERSIONS = ('0',)
diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index 9c100d87a6d..179ceec7691 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -395,16 +395,17 @@ def test_marshal_projects_pagination(self, user1, user2,
         version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
-        # First page, just 2 projects. offset = 0 by default
-        limit = 2
-        rsp = _get_response_json(django_client, request_url, {'limit': limit})
-        assert len(rsp['data']) == limit
-        assert_objects(conn, rsp['data'], projects[0:limit])
-
-        # Check that page 2 gives next 2 projects
-        payload = {'limit': limit, 'offset': limit}
-        rsp = _get_response_json(django_client, request_url, payload)
-        assert_objects(conn, rsp['data'], projects[limit:limit * 2])
+        # Test a range of limits. offset = 0 by default
+        for limit in range(1, 4):
+            rsp = _get_response_json(django_client, request_url,
+                                     {'limit': limit})
+            assert len(rsp['data']) == limit
+            assert_objects(conn, rsp['data'], projects[0:limit])
+
+            # Check that page 2 gives next n projects
+            payload = {'limit': limit, 'offset': limit}
+            rsp = _get_response_json(django_client, request_url, payload)
+            assert_objects(conn, rsp['data'], projects[limit:limit * 2])
 
     def test_marshal_projects_params(self, user1, user2,
                                      projects_user1_group1,

From 9b480c5ed6570bcdbfcdbd8614facfbc618efcbf Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 13:08:28 +0000
Subject: [PATCH 19/28] Test 'meta' 'totalCount' respects filtering by 'owner'

---
 .../tools/OmeroWeb/test/integration/test_api_projects.py       | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index 179ceec7691..c40d7971eda 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -372,14 +372,17 @@ def test_marshal_projects_all_users(self, user1, user2,
         # Both users
         rsp = _get_response_json(django_client, request_url, {})
         assert_objects(conn, rsp['data'], projects)
+        assert rsp['meta']['totalCount'] == len(projects)
 
         eid = user1[1].id.val
         rsp = _get_response_json(django_client, request_url, {'owner': eid})
         assert_objects(conn, rsp['data'], projects_user1_group1)
+        assert rsp['meta']['totalCount'] == len(projects_user1_group1)
 
         eid = user2[1].id.val
         rsp = _get_response_json(django_client, request_url, {'owner': eid})
         assert_objects(conn, rsp['data'], projects_user2_group1)
+        assert rsp['meta']['totalCount'] == len(projects_user2_group1)
 
     def test_marshal_projects_pagination(self, user1, user2,
                                          projects_user1_group1,

From 33b817291ad16666e10d12ce24f42a947d86998d Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 13:13:26 +0000
Subject: [PATCH 20/28] Test 'meta' 'totalCount' respects filtering by 'group'

---
 .../tools/OmeroWeb/test/integration/test_api_projects.py       | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index c40d7971eda..ffd65d533f5 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -345,14 +345,17 @@ def test_marshal_projects_all_groups(self, user1, group1, group2,
         # All groups
         rsp = _get_response_json(django_client, request_url, {})
         assert_objects(conn, rsp['data'], projects_user1)
+        assert rsp['meta']['totalCount'] == len(projects_user1)
         # Filter by group A...
         gid = group1.id.val
         rsp = _get_response_json(django_client, request_url, {'group': gid})
         assert_objects(conn, rsp['data'], projects_user1, group=gid)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
         # ...and group B
         gid = group2.id.val
         rsp = _get_response_json(django_client, request_url, {'group': gid})
         assert_objects(conn, rsp['data'], projects_user1, group=gid)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
 
     def test_marshal_projects_all_users(self, user1, user2,
                                         projects_user1_group1,

From 39aeee1518a961e44175bc947a36a994b2e2b7bb Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 13:28:51 +0000
Subject: [PATCH 21/28] Handle negative ?limit=-1 and ?offset=-1 use defaults
 instead

---
 components/tools/OmeroWeb/omeroweb/api/views.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/components/tools/OmeroWeb/omeroweb/api/views.py b/components/tools/OmeroWeb/omeroweb/api/views.py
index e94d585468c..5564bbed20c 100644
--- a/components/tools/OmeroWeb/omeroweb/api/views.py
+++ b/components/tools/OmeroWeb/omeroweb/api/views.py
@@ -311,6 +311,10 @@ def get_opts(self, request, **kwargs):
             orphaned = request.GET.get('orphaned', False) == 'true'
         except ValueError as ex:
             raise BadRequestError(str(ex))
+        if limit < 0:
+            limit = api_settings.API_LIMIT
+        if offset < 0:
+            offset = 0
 
         # orphaned and child_count not used by every subclass
         opts = {'offset': offset,

From ca8807d2c48879f27869157da34d632581ddf511 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 16:11:51 +0000
Subject: [PATCH 22/28] Use 'select count(distinct obj) to avoid duplicates

for example, duplicate Wells were being counted, 1 per WellSample.
---
 components/tools/OmeroPy/src/omero/gateway/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/tools/OmeroPy/src/omero/gateway/__init__.py b/components/tools/OmeroPy/src/omero/gateway/__init__.py
index 96f8ffdc2fd..beaa744421d 100644
--- a/components/tools/OmeroPy/src/omero/gateway/__init__.py
+++ b/components/tools/OmeroPy/src/omero/gateway/__init__.py
@@ -3206,7 +3206,7 @@ def buildCountQuery(self, obj_type, opts=None):
         query, params, wrapper = self.buildQuery(obj_type, opts=opts_copy)
 
         # Modify query to only select count()
-        query = query.replace("select obj ", "select count(obj) ")
+        query = query.replace("select obj ", "select count(distinct obj) ")
         query = query.replace("fetch", "")
         query = query.split("order by")[0]
         return query, params

From d094f4919c1d8342b9363b1a37d121ad20faccd4 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 21 Feb 2017 21:34:12 +0000
Subject: [PATCH 23/28] Check ['meta']['totalCount'] for api_project and
 api_wells tests

---
 .../tools/OmeroWeb/test/integration/test_api_projects.py  | 8 ++++++--
 .../tools/OmeroWeb/test/integration/test_api_wells.py     | 1 +
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index ffd65d533f5..dea52bc1897 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -293,9 +293,8 @@ def test_marshal_projects_user(self, user1, projects_user1_group1):
         version = api_settings.API_VERSIONS[-1]
         request_url = reverse('api_projects', kwargs={'api_version': version})
         rsp = _get_response_json(django_client, request_url, {})
-        # Reload projects with group '-1' to get same 'canLink' perms
-        # on owner and group permissions
         assert_objects(conn, rsp['data'], projects_user1_group1)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
 
     def test_marshal_projects_another_user(self, user1, user2,
                                            projects_user2_group1):
@@ -311,6 +310,7 @@ def test_marshal_projects_another_user(self, user1, user2,
         rsp = _get_response_json(django_client, request_url, {})
         # user1 reloads user2's projects
         assert_objects(conn, rsp['data'], projects_user2_group1)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
 
     def test_marshal_projects_another_group(self, user1, group2,
                                             projects_user1_group2):
@@ -329,6 +329,7 @@ def test_marshal_projects_another_group(self, user1, group2,
         # are same as owner's default group Group 1 (rwra--) instead of
         # group that the data is in Group 2 (rwr--)
         assert_objects(conn, rsp['data'], projects_user1_group2)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
 
     def test_marshal_projects_all_groups(self, user1, group1, group2,
                                          projects_user1):
@@ -407,11 +408,13 @@ def test_marshal_projects_pagination(self, user1, user2,
                                      {'limit': limit})
             assert len(rsp['data']) == limit
             assert_objects(conn, rsp['data'], projects[0:limit])
+            assert rsp['meta']['totalCount'] == len(projects)
 
             # Check that page 2 gives next n projects
             payload = {'limit': limit, 'offset': limit}
             rsp = _get_response_json(django_client, request_url, payload)
             assert_objects(conn, rsp['data'], projects[limit:limit * 2])
+            assert rsp['meta']['totalCount'] == len(projects)
 
     def test_marshal_projects_params(self, user1, user2,
                                      projects_user1_group1,
@@ -446,6 +449,7 @@ def test_marshal_projects_params(self, user1, user2,
         # Test 'normalize' parameter.
         payload = {'normalize': 'true'}
         rsp = _get_response_json(django_client, request_url, payload)
+        assert rsp['meta']['totalCount'] == len(rsp['data'])
         for p in rsp['data']:
             details = p['omero:details']
             owner = details['owner']
diff --git a/components/tools/OmeroWeb/test/integration/test_api_wells.py b/components/tools/OmeroWeb/test/integration/test_api_wells.py
index c18e1fc6ad2..643a399a0f7 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_wells.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_wells.py
@@ -193,6 +193,7 @@ def test_plate_wells(self, user1, small_plate, bigger_plate):
             rsp = _get_response_json(django_client, wells_url, payload)
             # Manual check that Images are loaded but Pixels are not
             assert len(rsp['data']) == well_count
+            assert rsp['meta']['totalCount'] == well_count
             well_sample = rsp['data'][0]['WellSamples'][0]
             assert 'Image' in well_sample
             assert ('PlateAcquisition' in well_sample) == with_acq

From 832b433b5a4bb8b14ecdc82e5da421db3f2b804d Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 22 Feb 2017 14:17:32 +0000
Subject: [PATCH 24/28] Move 'offset' and 'limit' validation to validate_opts()

---
 .../tools/OmeroWeb/omeroweb/api/api_query.py  | 25 +++++++++++++++----
 .../tools/OmeroWeb/omeroweb/api/views.py      |  8 ++----
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index f681b5b0165..2ff244aef03 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -28,6 +28,10 @@
 from copy import deepcopy
 
 
+MAX_LIMIT = max(1, api_settings.API_MAX_LIMIT)
+DEFAULT_LIMIT = max(1, api_settings.API_LIMIT)
+
+
 def get_child_counts(conn, link_class, parent_ids):
     """
     Count child links for the specified parent_ids.
@@ -51,6 +55,18 @@ def get_child_counts(conn, link_class, parent_ids):
     return counts
 
 
+def validate_opts(opts):
+    """Check that opts dict has valid 'limit' and 'offset'."""
+    if opts is None:
+        opts = {}
+    if opts.get('limit') is None or opts.get('limit') < 0:
+        opts['limit'] = DEFAULT_LIMIT
+    opts['limit'] = min(opts['limit'], MAX_LIMIT)
+    if opts.get('offset') is None or opts.get('offset') < 0:
+        opts['offset'] = 0
+    return opts
+
+
 def query_objects(conn, object_type,
                   group=None,
                   opts=None,
@@ -67,6 +83,7 @@ def query_objects(conn, object_type,
     @param opts:        Options dict for conn.buildQuery()
     @param normalize:   If true, marshal groups and experimenters separately
     """
+    opts = validate_opts(opts)
     # buildQuery is used by conn.getObjects()
     query, params, wrapper = conn.buildQuery(object_type, opts=opts)
     # Set the desired group context
@@ -97,11 +114,9 @@ def query_objects(conn, object_type,
     result = qs.projection(count_query, params, ctx)
 
     meta = {}
-    if 'offset' in opts:
-        meta['offset'] = opts['offset']
-    if 'limit' in opts:
-        meta['limit'] = opts['limit']
-    meta['maxLimit'] = api_settings.API_MAX_LIMIT
+    meta['offset'] = opts['offset']
+    meta['limit'] = opts['limit']
+    meta['maxLimit'] = MAX_LIMIT
     meta['totalCount'] = result[0][0].val
 
     marshalled = marshal_objects(objects, extras=extras, normalize=normalize)
diff --git a/components/tools/OmeroWeb/omeroweb/api/views.py b/components/tools/OmeroWeb/omeroweb/api/views.py
index 5564bbed20c..4c7add6389e 100644
--- a/components/tools/OmeroWeb/omeroweb/api/views.py
+++ b/components/tools/OmeroWeb/omeroweb/api/views.py
@@ -305,20 +305,16 @@ def get_opts(self, request, **kwargs):
         """Return an options dict based on request parameters."""
         try:
             offset = getIntOrDefault(request, 'offset', 0)
-            limit = getIntOrDefault(request, 'limit', api_settings.API_LIMIT)
+            limit = getIntOrDefault(request, 'limit', None)
             owner = getIntOrDefault(request, 'owner', None)
             child_count = request.GET.get('childCount', False) == 'true'
             orphaned = request.GET.get('orphaned', False) == 'true'
         except ValueError as ex:
             raise BadRequestError(str(ex))
-        if limit < 0:
-            limit = api_settings.API_LIMIT
-        if offset < 0:
-            offset = 0
 
         # orphaned and child_count not used by every subclass
         opts = {'offset': offset,
-                'limit': min(limit, api_settings.API_MAX_LIMIT),
+                'limit': limit,
                 'owner': owner,
                 'orphaned': orphaned,
                 'child_count': child_count,

From 57d9199400f844049d5b511c1c360169c138894f Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 22 Feb 2017 14:21:15 +0000
Subject: [PATCH 25/28] Remove try/except from gateway.util.getIntOrDefault()

Having this fail silently and return 0 is not helpful. Users need to know
that something has gone wrong.
Now uses same logic as webcient views.get_long_or_default()
---
 components/tools/OmeroWeb/omeroweb/webgateway/util.py | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/components/tools/OmeroWeb/omeroweb/webgateway/util.py b/components/tools/OmeroWeb/omeroweb/webgateway/util.py
index ec006cd9486..953e42dd84b 100644
--- a/components/tools/OmeroWeb/omeroweb/webgateway/util.py
+++ b/components/tools/OmeroWeb/omeroweb/webgateway/util.py
@@ -28,12 +28,9 @@
 
 # helper method
 def getIntOrDefault(request, name, default):
-    try:
-        index = request.GET.get(name, request.POST.get(name, default))
-        if index is not None:
-            index = int(index)
-    except ValueError:
-        index = 0
+    index = request.GET.get(name, request.POST.get(name, default))
+    if index is not None:
+        index = int(index)
     return index
 
 

From fb4b621e65669237f59677a865e76a573e9bb7f0 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 22 Feb 2017 23:02:19 +0000
Subject: [PATCH 26/28] Add test_invalid_parameter() to test_api_errors.py

---
 .../OmeroWeb/test/integration/test_api_errors.py   | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_errors.py b/components/tools/OmeroWeb/test/integration/test_api_errors.py
index 3bab8ed0267..3279bcb2bac 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_errors.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_errors.py
@@ -19,7 +19,8 @@
 
 """Tests querying & editing Projects with webgateway json api."""
 
-from omeroweb.testlib import IWebTest, _csrf_post_json, _csrf_put_json
+from omeroweb.testlib import IWebTest, _csrf_post_json, _csrf_put_json, \
+    _get_response_json
 from django.core.urlresolvers import reverse
 from omeroweb.api import api_settings
 import pytest
@@ -91,6 +92,17 @@ def test_marshal_type(self):
         assert (rsp['message'] ==
                 'No decoder found for type: %s' % objType)
 
+    def test_invalid_parameter(self):
+        """Test that invalid query parameter gives suitable message."""
+        django_client = self.django_root_client
+        version = api_settings.API_VERSIONS[-1]
+        projects_url = reverse('api_projects', kwargs={'api_version': version})
+        payload = {'limit': 'foo'}
+        rsp = _get_response_json(django_client, projects_url, payload,
+                                 status_code=400)
+        assert (rsp['message'] ==
+                "invalid literal for int() with base 10: 'foo'")
+
     def test_marshal_validation(self):
         """Test that we get expected error with invalid @type in json."""
         django_client = self.django_root_client

From 2d9cbfbeea4ec5ecc035ca48496bc3760dffde5d Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 22 Feb 2017 23:11:33 +0000
Subject: [PATCH 27/28] tests include limit=-1 and limit=0

---
 .../OmeroWeb/test/integration/test_api_projects.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/components/tools/OmeroWeb/test/integration/test_api_projects.py b/components/tools/OmeroWeb/test/integration/test_api_projects.py
index dea52bc1897..60bdd40ef41 100644
--- a/components/tools/OmeroWeb/test/integration/test_api_projects.py
+++ b/components/tools/OmeroWeb/test/integration/test_api_projects.py
@@ -168,6 +168,9 @@ def assert_objects(conn, json_objects, omero_ids_objects, dtype="Project",
             pids.append(long(p))
         except TypeError:
             pids.append(p.id.val)
+    if len(pids) == 0:
+        assert len(json_objects) == 0
+        return
     conn.SERVICE_OPTS.setOmeroGroup(group)
     projects = conn.getObjects(dtype, pids, respect_order=True)
     projects = [p._obj for p in projects]
@@ -403,12 +406,17 @@ def test_marshal_projects_pagination(self, user1, user2,
         request_url = reverse('api_projects', kwargs={'api_version': version})
 
         # Test a range of limits. offset = 0 by default
-        for limit in range(1, 4):
+        for limit in range(-1, 4):
             rsp = _get_response_json(django_client, request_url,
                                      {'limit': limit})
-            assert len(rsp['data']) == limit
-            assert_objects(conn, rsp['data'], projects[0:limit])
             assert rsp['meta']['totalCount'] == len(projects)
+            if limit == -1:
+                # if we passed a negative number, expect the default to be used
+                limit = api_settings.API_LIMIT
+            else:
+                assert len(rsp['data']) == limit
+            assert rsp['meta']['limit'] == limit
+            assert_objects(conn, rsp['data'], projects[0:limit])
 
             # Check that page 2 gives next n projects
             payload = {'limit': limit, 'offset': limit}

From f08de8da82ed0a6c8367da0e0b9eafcd6f138919 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Thu, 23 Feb 2017 23:17:34 +0000
Subject: [PATCH 28/28] If ?limit=0 result = []

---
 components/tools/OmeroWeb/omeroweb/api/api_query.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/components/tools/OmeroWeb/omeroweb/api/api_query.py b/components/tools/OmeroWeb/omeroweb/api/api_query.py
index 2ff244aef03..dd08b8fe47a 100644
--- a/components/tools/OmeroWeb/omeroweb/api/api_query.py
+++ b/components/tools/OmeroWeb/omeroweb/api/api_query.py
@@ -97,7 +97,10 @@ def query_objects(conn, object_type,
     objects = []
     extras = {}
 
-    result = qs.findAllByQuery(query, params, ctx)
+    if opts['limit'] == 0:
+        result = []
+    else:
+        result = qs.findAllByQuery(query, params, ctx)
     for obj in result:
         objects.append(obj)