Api wells2 by will-moore · Pull Request #5069 · ome/openmicroscopy

will-moore · 2017-02-01T10:36:18Z

What this PR does

Follow-up PR on listing Wells in Plate, filtering by PlateAcquisition and WellSample Index.
Allows api user to "browse" Plate -> (PlateAcquisition) -> Wells (for single index) as in the client UIs.

To discuss: Implementing 'childCount' for Plates should count PlateAcquisitions (as in webclient tree) OR Well_Sample indices, which might be more useful since many Plates have a single PlateAcquisition.

Testing this PR

User starts at /plates/. When listing plates we don't include Index counts.
Choose a single plate /plates/:id/ which gives min/max WellSample index.
Also lists urls for filtering wells by index:

   "url:wellsampleindex_wells": [
         "/plates/:id/wellsampleindex/0/wells/",
         "/plates/:id/wellsampleindex/1/wells/",
         "/plates/:id/wellsampleindex/2/wells/"
       ]

To get PlateAcquisitions in the plate, follow link to /plates/:id/plateacquisitions/
To get Wells in a particular Index follow link to /plateacquisitions/:id/wellsampleindex/:idx/wells/

When filtering Wells by Index, each WellSample list should have a single item.

snoopycrimecop · 2017-02-02T03:33:50Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#580. See the console output for more details.
Possible conflicts:

PR Api wells #5047 will-moore 'Api wells'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api child count #5058 will-moore 'Api child count'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api save whitelist #5059 will-moore 'Api save whitelist'
- components/tools/OmeroWeb/omeroweb/api/views.py

snoopycrimecop · 2017-02-03T03:34:15Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#581. See the console output for more details.
Possible conflicts:

PR Api wells #5047 will-moore 'Api wells'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api child count #5058 will-moore 'Api child count'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api save whitelist #5059 will-moore 'Api save whitelist'
- components/tools/OmeroWeb/omeroweb/api/views.py

jburel · 2017-02-21T20:02:47Z

./components/tools/OmeroWeb/test/integration/test_api_containers.py:346:30: E225 missing whitespace around operator

jburel · 2017-02-21T20:04:54Z

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

+        """
+        query, clauses, params = super(
+            _PlateAcquisitionWrapper, cls)._getQueryString(opts)
+        if opts is not None and 'plate' in opts:


maybe good to have one method to prepare the query for plate filtering
Same check in this method and getName

Sorry - I'm not sure what you mean here.

code like
if 'plate' in opts: clauses.append('obj.plate.id = :pid') params.add('pid', rlong(opts['plate']))

jburel · 2017-02-21T20:10:31Z

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

        # at /plates/:plate_id/wells/ we have 'plate_id' in kwargs
        if 'plate_id' in kwargs:
            opts['plate'] = long(kwargs['plate_id'])
+        elif 'plateacquisition_id' in kwargs:


Do we want to allow to filter by plate id and plateacquisition id?

I don't think there's a case for that, since plateacquisition ID would also define plate ID.

jburel · 2017-02-21T20:11:45Z

components/tools/OmeroWeb/test/integration/test_api_wells.py

 import pytest
 from test_api_projects import get_update_service, \
-    get_connection, marshal_objects
+    get_connection, marshal_objects, cmp_name_insensitive


order.Maybe also one per line

jburel · 2017-02-21T20:14:11Z

components/tools/OmeroWeb/test/integration/test_api_wells.py

+
+    def test_plate_index_wells(self, user1, multi_acquisition_plate):
+        """
+        Test filtering of Wells by Plate/Acquisition AND index.


Plate/PlateAcquisition to match the rest

jburel · 2017-02-22T13:39:47Z

/plates/:id/plateacquisitions/:id/index/:idx/wells/ this is probably an error in the description since it combines plate id and plate acquisition i.e. ````/plates/:id/plateacquisitions/:id`` gives a 404

http://web-dev-merge.openmicroscopy.org/api/v0/m/plateacquisitions/2053/index/2/wells/ this works

http://web-dev-merge.openmicroscopy.org/api/v0/m/wells/338626/ works
We might have a case for limit/MaxLimit and count and offset to handle the case of wells with very large number of fields
e.g. 700 fields from Damir

will-moore · 2017-02-22T13:47:11Z

@jburel Yes, description was wrong. Fixed now.

will-moore · 2017-02-23T06:47:40Z

NB: this is now conflicting with #5067.

snoopycrimecop · 2017-02-24T03:33:04Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#597. See the console output for more details.
Possible conflicts:

PR Api pagination #5067 will-moore 'Api pagination'
- components/tools/OmeroWeb/omeroweb/api/api_query.py

jburel · 2017-02-26T06:47:05Z

https://ci.openmicroscopy.org/job/OMERO-DEV-merge-integration-Python27/lastCompletedBuild/testReport/OmeroWeb.test.integration.test_api_containers/TestContainers/test_spw_urls/

will-moore · 2017-02-27T15:03:00Z

@jburel I'm thinking maybe I should use the full term wellsampleindex in these urls instead of index.
E.g. "/plates/:id/wellsampleindex/0/wells/"
Since this provides a clearer idea what the url is giving you.

jburel · 2017-02-27T15:07:57Z

@will-moore: I think making it more explicit will be better.

jburel · 2017-02-27T15:52:31Z

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

    api_wells,
+    api_plate_plateacquisitions,
+    api_plateacquisition,
+    api_plateacquisition_index_wells,


I will also replace here wellsample_index instead of just index

jburel · 2017-02-27T15:52:40Z

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

+    api_plate_plateacquisitions,
+    api_plateacquisition,
+    api_plateacquisition_index_wells,
+    api_plate_index_wells,


jburel · 2017-02-28T09:50:05Z

Tests are passing
wellsampleindex is now used e.g. http://web-dev-merge.openmicroscopy.org/api/v0/m/plateacquisitions/2053/wellsampleindex/1/wells/?limit=10&offset=0

jburel · 2017-02-28T09:52:00Z

Merging

will-moore added 5 commits January 31, 2017 21:31

PlateView.add_data() uses api_query.get_wellsample_indices()

7c302c1

Blitz PlateAcquisition getQueryString() to filter by plate

a69833a

Support /plates/:id/plateacquisitions/

a0e0063

Blitz Well.getQueryString() supports filter by 'plateacquisition'

6b2d29f

/plateacquisition/:id/wells/ filters Wells by plate_acquisition

7c70b45

jburel added the develop label Feb 1, 2017

will-moore closed this Feb 3, 2017

will-moore added 5 commits February 8, 2017 15:49

Add 'url:plateacquisitions' to plate json

048adc0

Support /plateacquistions/:id/ includes min/max wellsampleIndex

edbb992

Add url 'plateacquisitions/:id/index/:idx/wells' to plate_acq json

1bfe9b8

Blitz Well getQueryString() supports filter by 'wellsample_index'

9253577

api WellsView handles 'index' to filter by wellsample_index

8e3e5d6

will-moore reopened this Feb 20, 2017

will-moore added 7 commits February 20, 2017 11:42

Merge remote-tracking branch 'origin/develop' into api_wells2

83f675e

Add support for /plates/id/index/0/wells/

84d177c

Add 'urls:wellsampleindex_wells' to PlateAcquisition and Plate views

be36738

Add tests for listing 'index' urls in plate/plate_acquisition

58b6c30

Remove duplicate imports

fc3d278

Use 'url:' prefix for url:wellsampleindex_wells.

c03093a

Fix merge conflict

424ef1b

jburel reviewed Feb 21, 2017

View reviewed changes

will-moore added 2 commits February 21, 2017 21:54

Tidy imports in test_api_wells.py

f17506b

Tiny fix in docstring

3a71a64

Blitz helper add_plate_filter() used in getQueryString()

1f6229e

will-moore closed this Feb 23, 2017

will-moore reopened this Feb 23, 2017

will-moore added 2 commits February 24, 2017 11:21

Merge remote-tracking branch 'origin/develop' into api_wells2

7918868

flake8 fix

50efc29

will-moore closed this Feb 24, 2017

will-moore reopened this Feb 24, 2017

Fix test_spw_urls

1320d39

will-moore closed this Feb 26, 2017

will-moore reopened this Feb 26, 2017

Use 'wellsampleindex' in urls

2b2a9b9

jburel reviewed Feb 27, 2017

View reviewed changes

Update 'index' -> 'wellsampleindex' in url names

2d94baf

jburel merged commit c954eb1 into ome:develop Feb 28, 2017

jburel added this to the 5.3.0 milestone Mar 29, 2017

will-moore deleted the api_wells2 branch February 18, 2019 04:16

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