Api filter by children by will-moore · Pull Request #5088 · ome/openmicroscopy

will-moore · 2017-02-07T15:44:57Z

What this PR does

Supports filtering of Projects by Datasets and filtering of Datasets by Image.
This allows users to find the parents of a given Image or Dataset and
so browse Image -> Dataset -> Project.
Also, we now add the version number in the header of every request:

X-OMERO-ApiVersion: 0.0

Also I've updated the example at examples/Training/python/Json_Api/Login.py to work with recent changes to the API.

Testing this PR

Filter Projects by Dataset /projects/?dataset=:id or via /datasets/:id/projects/
Filter Datasets by Image /datasets/?image=:id or via /images/:id/datasets/
Datasets listed at /datasets/ or single object at /datasets/:id/ have 'url: projects to browse to parents.
Images listed at /images/ or single object at /images/:id/ have 'url: datasets to browse to parents.
Browse from /wells/ -> url:plates -> Plate -> url:Screens -> Screen.
Check header in browser dev tools for X-OMERO-ApiVersion: 0.0
I've added examples/Training/python/Json_Api/Login.py to the Training test suite, so it should be tested by ci job now.

TODO:

Write Tests
When Wells PR is merged, support /wells/:id/plates/ etc.

Related reading

snoopycrimecop · 2017-02-08T03:33:14Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#584. See the console output for more details.
Possible conflicts:

PR Api wells #5047 will-moore 'Api wells'
- components/tools/OmeroWeb/omeroweb/api/views.py
- components/tools/OmeroWeb/omeroweb/api/urls.py
PR Api child count #5058 will-moore 'Api child count'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api pagination #5067 will-moore 'Api pagination'
- components/tools/OmeroWeb/omeroweb/api/views.py

snoopycrimecop · 2017-02-09T03:33:24Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#585. See the console output for more details.
Possible conflicts:

PR Api wells #5047 will-moore 'Api wells'
- components/tools/OmeroWeb/omeroweb/api/views.py
- components/tools/OmeroWeb/omeroweb/api/urls.py
PR Api child count #5058 will-moore 'Api child count'
- components/tools/OmeroWeb/omeroweb/api/views.py
PR Api pagination #5067 will-moore 'Api pagination'
- components/tools/OmeroWeb/omeroweb/api/views.py
- components/tools/OmeroWeb/omeroweb/api/urls.py

…dren

jburel · 2017-02-28T12:05:12Z

./components/tools/OmeroWeb/test/integration/test_api_containers.py:562:19: F821 undefined name 'settings'

jburel · 2017-02-28T13:07:14Z

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

+    views.ProjectsView.as_view(),
+    name='api_dataset_projects')
+"""
+GET Projects in Dataset, using omero-marshal to generate json


Projects Parents of Dataset

jburel · 2017-02-28T13:10:15Z

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

+    views.ScreensView.as_view(),
+    name='api_plate_screens')
+"""
+GET Screens for child Plate, using omero-marshal to generate json


Unify comment i.e. Screens that contain a Plate

will-moore · 2017-03-01T23:44:07Z

Adding the Json_Api/Login.py script to the Training test suite has broken the Training test because it requires import requests
https://ci.openmicroscopy.org/view/Failing/job/OMERO-DEV-merge-training/534/console

File "/opt/hudson/workspace/OMERO-DEV-merge-training/src/examples/Training/python/Json_Api/Login.py", line 10, in <module>
    import requests
ImportError: No module named requests

Do we want to add this to a requirements.txt somewhere, or should I remove Login.py from the Training test suite? cc @aleksandra-tarkowska @sbesson

joshmoore · 2017-03-02T08:34:57Z

From my POV, requests is a generally useful library

jburel · 2017-03-03T20:19:13Z

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

+        if opts is None:
+            opts = {}
+        if 'project' in opts:
            query += ' join obj.projectLinks plink'


minor: to align with the rest of the query, you could use projectlinks instead of plink

jburel · 2017-03-06T06:46:41Z

Restarted travis
minor: method comment to fix

jburel · 2017-03-07T13:30:31Z

looks good

jburel added the develop label Feb 8, 2017

will-moore closed this Feb 9, 2017

will-moore added 12 commits February 24, 2017 11:22

Blitz Dataset getQueryString() handles filter by 'image'

7a54d92

api DatasetsView handles ?image=1

0bf88d2

Blitz Project getQueryString() support filter by 'dataset'

ec492b8

api ProjectsView supports filter by ?dataset=1

cd2ea10

url:datasets and url:projects for browsing I->D->P

415c095

Blitz Screen getQueryString() supports filtering by 'plate'

dac376d

api support filtering /screens/?plate=id and plate/:id/screens

0620179

Add 'url:screens' to plate json

b5972a6

New test 'test_pdi_parent_urls' in teat_api_containers.py

861d645

Tiny fix to avoid merge conflict

52359aa

Add 'X-OMERO-ApiVersion' = '0.0' to response Headers

304b8e8

Update Training/python/Json_Api/Login.py with new urls etc

9f620a5

will-moore reopened this Feb 28, 2017

will-moore force-pushed the api_filter_by_children branch from bbe983c to 9f620a5 Compare February 28, 2017 09:50

Merge remote-tracking branch 'origin/develop' into api_filter_by_chil…

1d3a952

…dren

will-moore added 2 commits February 28, 2017 12:27

flake8 fix

68ba82d

Fix test_pdi_parent_urls

81b3ce8

jburel reviewed Feb 28, 2017

View reviewed changes

will-moore added 7 commits February 28, 2017 15:16

Blitz Plate.getQueryString() supports filter by 'well'

f461940

Add support for /wells/:id/plates/

8c27b92

Blitz docstring update

9cc3938

Add test 'test_spw_parent_urls'

8f81f9f

Remove print from Training Login.py

149669e

Add Json_Api/Login.py to Training test suite

73372cd

flake8 fix

65777ad

will-moore closed this Mar 1, 2017

will-moore reopened this Mar 1, 2017

jburel reviewed Mar 3, 2017

View reviewed changes

Blitz rename plink -> projectLinks in Dataset.getQueryString()

4d036ed

Update comment in urls.py

c42a896

jburel merged commit 355f565 into ome:develop Mar 7, 2017

jburel added this to the 5.3.0 milestone Mar 29, 2017

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

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Api filter by children#5088

Api filter by children#5088
jburel merged 24 commits intoome:developfrom
will-moore:api_filter_by_children

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What this PR does

Testing this PR

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