Obj id bitmask endpoint #308

kkoz · 2021-08-05T12:37:05Z

This PR adds an endpoint to make label image data retrieval more efficient from omero tables. Rather than returning the entire result of a query which could be a very large number of objects, the endpoint returns a bitmask representing the object IDs, where the bit is set to 1 if that ID matched the query and 0 otherwise. You can hit the endpoint using a URL like http://localhost/webgateway/table/123/obj_id_bitmask/?query=value<14. A col_name parameter can also be passed if your object ID column name is not named object

snoopycrimecop · 2021-08-06T00:41:27Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#779. See the console output for more details.
Possible conflicts:

PR constrain plate grid #270 will-moore 'constrain plate grid'
- omeroweb/webgateway/views.py
PR Improve OMERO.table download usability #300 will-moore 'Improve OMERO.table download usability'
- omeroweb/webgateway/views.py
PR Only return the column names that were requested #305 kkoz 'Only return the column names that were requested'
- omeroweb/webgateway/views.py

--conflicts

will-moore · 2021-08-09T21:17:43Z

omeroweb/webgateway/views.py

+    data = bytearray()
+    for obj in rsp_data["data"]["rows"]:
+        obj_id = obj[0]
+        while index < obj_id:


In my case, the first column in this row is a 'StringColumn', so that obj_id is a string (and this comparison line fails).

snoopycrimecop · 2021-08-10T00:40:53Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#783. See the console output for more details.
Possible conflicts:

PR constrain plate grid #270 will-moore 'constrain plate grid'
- omeroweb/webgateway/views.py
PR Improve OMERO.table download usability #300 will-moore 'Improve OMERO.table download usability'
- omeroweb/webgateway/views.py
PR Only return the column names that were requested #305 kkoz 'Only return the column names that were requested'
- omeroweb/webgateway/views.py

--conflicts

for more information, see https://pre-commit.ci

snoopycrimecop · 2021-08-13T00:40:30Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#786. See the console output for more details.
Possible conflicts:

PR constrain plate grid #270 will-moore 'constrain plate grid'
- omeroweb/webgateway/views.py
PR Improve OMERO.table download usability #300 will-moore 'Improve OMERO.table download usability'
- omeroweb/webgateway/views.py

--conflicts

snoopycrimecop · 2021-08-14T00:39:24Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#787. See the console output for more details.
Possible conflicts:

PR constrain plate grid #270 will-moore 'constrain plate grid'
- omeroweb/webgateway/views.py
PR Improve OMERO.table download usability #300 will-moore 'Improve OMERO.table download usability'
- omeroweb/webgateway/views.py

--conflicts

kkoz · 2021-08-17T14:11:54Z

@will-moore Is there something I can or should do on this PR to resolve SCC's conflict comments?

will-moore · 2021-08-17T15:13:54Z

Apologies: I meant to ping @chris-allan and @erindiel for final feedback on those (#270 and #300) but I think they should be close to getting merged.
In the meantime, I can test this PR again locally...

will-moore · 2021-08-17T15:34:42Z

Testing locally with a table where this URL /webgateway/table/68129/query/?query=Count<400 gives me...

this JSON

{
"data": {
    "column_types": [
        "StringColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "DoubleColumn",
        "StringColumn",
        "DoubleColumn",
        "DoubleColumn",
        "ImageColumn"
    ],
    "columns": [
        "Slice",
        "Count",
        "Total_Area",
        "Average_Size",
        "%Area",
        "Mean",
        "Mode",
        "Perim.",
        "Feret",
        "FeretX",
        "FeretY",
        "FeretAngle",
        "MinFeret",
        "Dataset",
        "Bounding_Box",
        "Channel_Index",
        "Image"
    ],
    "rows": [
        [
            "c:1/2 - PCNT_gtub_I_044_SIR_PRJ.dv",
            200,
            74.26790595054626,
            37.13395297527313,
            72.6318359375,
            0,
            0,
            341.06953144073486,
            92.94512271881104,
            12900,
            11050,
            8191.774749755859,
            62.0566189289093,
            "PCNT-N1",
            177.86849737167358,
            100,
            1101
        ],
        [
            "c:2/2 - N20_PCNTab_ctrl_20110618_Sat-1400_0_SIR_PRJ.dv",
            200,
            46.88798189163208,
            23.44399094581604,
            45.623779296875,
            0,
            0,
            197.2864270210266,
            63.870203495025635,
            10800,
            10750,
            13633.149719238281,
            55.110132694244385,
            "PCNT-N1",
            42.66819953918457,
            200,
            1091
        ],
        [
            "c:1/2 - PCNT_gtub_I_010_SIR_PRJ.dv",
            300,
            55.70092797279358,
            18.566976487636566,
            54.473876953125,
            0,
            0,
            145.4495906829834,
            52.599912881851196,
            13933.332824707031,
            12633.333587646484,
            4308.696746826172,
            32.88620710372925,
            "PCNT-N1",
            85.24099588394165,
            100,
            1106
        ],
        ...

When I use: /webgateway/table/68129/obj_id_bitmask/?query=Count<400&col_name=Image I get:

{
"message": "byte must be in range(0, 256)",
"stacktrace": "Traceback (most recent call last):\n  File \"/Users/wmoore/Desktop/WEB/omero-web/omeroweb/webgateway/views.py\", line 1431, in wrap\n    rv = f(request, *args, **kwargs)\n  File \"/Users/wmoore/Desktop/WEB/omero-web/omeroweb/webgateway/views.py\", line 3125, in obj_id_bitmask\n    data.append(value)\nValueError: byte must be in range(0, 256)\n"
}

So either I'm not understanding the usage or my data is not as expected?

snoopycrimecop · 2021-08-18T00:38:47Z

Conflicting PR. Removed from build OMERO-python-superbuild-push#790. See the console output for more details.
Possible conflicts:

PR constrain plate grid #270 will-moore 'constrain plate grid'
- omeroweb/webgateway/views.py
PR Improve OMERO.table download usability #300 will-moore 'Improve OMERO.table download usability'
- omeroweb/webgateway/views.py

~~--conflicts~~ Conflict resolved in build OMERO-python-superbuild-push#792. See the console output for more details.

… there are duplicates

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will-moore · 2021-08-19T14:43:37Z

So, the URL I was testing above /webgateway/table/68129/obj_id_bitmask/?query=Count<400&col_name=Image is now downloading something.
Do you have any sample code to help me validate whether this is correct? thx.

kkoz · 2021-08-23T15:30:39Z

@will-moore I've put a test script I wrote here: https://gist.github.com/kkoz/791555afe60bc8dc6a4cd6c3c57988ed
Run this script against a table with an 'object' column and you should get back a bitmask where the bit is set to 1 if the object ID is returned by your query or 0 otherwise. E.g. if you had object IDs 0, 1, 3, 9, 22, and 23 and used the query object < 10 you should get back 1101000001000000 (there will probably be some extra 0s at the end). Let me know if that works for you

will-moore · 2021-08-23T21:37:38Z

I'm not sure if I understand your example:

>>> ids = [0, 1, 3, 9, 22, 23]
>>> ''.join(["1" if id < 10 else "0" for id in ids])
'111100'

not 1101000001000000 (even with some padding)?

I'm adding a test which should help us run the same tests.
I didn't manage to get your gist working (kept getting the login page returned - maybe using wrong sessionid) but the code sample was useful for writing a test.

Test added at ome/openmicroscopy#6289

kkoz · 2021-08-24T12:09:22Z

@will-moore The sessionid is supposed to be a omero web session ID, the one stored as the 'sessionid' cookie in the browser. Sorry I should have specified that.

chris-allan

As this is going into the public API at a minimum we need an extensive docstring in urls.py describing what the intent is here and what the caller can be expected to receive. Things like endianness, padding, and the layout of the bytes need to be explicitly defined.

Furthermore, some unit tests at least enforcing the byte layout need to be added. This probably necessitates refactoring the logic for producing the resulting bytes out of the view method.

omeroweb/webgateway/views.py

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will-moore · 2021-09-06T13:59:11Z

Updated the test at will-moore/openmicroscopy@8b0991d to correspond with the usage of numpy.packbits() above.

chris-allan · 2021-10-27T12:37:57Z

@will-moore: Anything else from your side that you think we need to do before getting this merged?

/cc @sbesson, @jburel

will-moore · 2021-10-27T13:15:01Z

Tests for this (ome/openmicroscopy#6289) are passing: https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-test-integration/931/testReport/OmeroWeb.test.integration.test_table/TestOmeroTables/
So, LGTM 👍

sbesson · 2021-11-04T13:15:16Z

@chris-allan could you also update your previous review #308 (review).

No objections to getting this merged from my side. I have two follow-up questions regarding the versioning and distribution:

I assume the development version number could be immediately incremented to 5.12.0.dev0 to communicate that a new backwards compatible API and endpoint have been introduced in the main development line
should this feature be released immediately or can we define a roadmap towards OMERO.web 5.12.0?

chris-allan · 2021-11-04T13:47:45Z

I assume the development version number could be immediately incremented to 5.12.0.dev0 to communicate that a new backwards compatible API and endpoint have been introduced in the main development line

Certainly.

should this feature be released immediately or can we define a roadmap towards OMERO.web 5.12.0?

Unless there's a really compelling reason not to, from our side it would be really nice to have this released.

will-moore reviewed Aug 9, 2021

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kkoz and others added 5 commits August 12, 2021 05:47

Add endpoint to return bit mask for table with object id column

43c6cda

Remove logging

ab9cd8d

Return errors as JSON; remove unused variables

f178cad

Fix rebase issues

ec1921d

Cast object to int for object id bitmask query

65d4534

kkoz force-pushed the obj-id-bitmask-endpoint branch from aa308bf to 65d4534 Compare August 12, 2021 13:06

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kkoz and others added 5 commits August 18, 2021 12:58

Fix bitmask endpoint to work if ids are not in ascending order and if…

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… there are duplicates

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Merge from master

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Disable table download row check for bitmask endpoint

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will-moore mentioned this pull request Aug 23, 2021

Add test_table_bitmask ome/openmicroscopy#6289

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Have object id bitmask endpoint handle errors the same as queries

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kkoz and others added 5 commits August 30, 2021 07:57

Add documentation for obj_id_bitmask endpoint

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Factor out byte array logic and add unit test

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kkoz and others added 5 commits August 31, 2021 08:05

Remove duplicate import numpy

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will-moore approved these changes Oct 27, 2021

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will-moore added this to the 5.12.0 release milestone Nov 5, 2021

will-moore merged commit c015afb into ome:master Nov 9, 2021

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Obj id bitmask endpoint #308

Obj id bitmask endpoint #308

kkoz commented Aug 5, 2021

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Obj id bitmask endpoint #308

Obj id bitmask endpoint #308

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