Spw grid view by will-moore · Pull Request #4863 · ome/openmicroscopy

will-moore · 2016-09-23T14:59:40Z

What this PR does

First PR towards support for new SPW 'grid' layout.
This introduces a few changes, but not "full support" of ome/design#52

When a Well is selected, right panel shows Well details & annotations (instead of Image)
Image thumbnails are shown for selected well(s) below plate.
Click to select an Image - this image will be shown in right panel.
Plate and Well Images can both be zoomed with sliders

This PR does not support a number of 'grid view' features (to come in future PRs)

Spacial layout of fields within well
Set number of columns in grid-view

Testing this PR

Test Well annotations (Wells have not previously been annotatable)
- Add, remove etc all types of annotations on Well.
- Batch select Wells and add/remove annotations.
- Metadata and Preview panels should be disabled for Wells
Test loading of thumbnails for selected wells:
- Select wells by Click or multi-select by drag or shift-click
- For each selected well, a row of images will be loaded in bottom pane
- Bottom pane can be resized by drag handle
- Plate and well Images can be zoomed with sliders in bottom-right of each panel
Clicking a single Image in bottom panel will load that image in Right panel.
Can select Images / Wells in turn.

TODO for this PR:

Multi-select Images
Indicate selected images with border etc.
Preserve zoom sizes when switching between Plates
Refresh Well grid thumbnails ( 'Save To All' or just 'Save')
Handle browsing Tag tree -> Well. What do we show in tree/centre/right panels?
Tests for marshal_tagged in tree.py to test wells

gusferguson · 2016-09-27T09:16:41Z

Tested using http://web-dev-merge.openmicroscopy.org/webclient/usertags/?show=tag-14953 user-3 Safari

Works as expected:

annotation of individual wells
batch annotation of wells
selection of wells by dragging or shift-click
zooming of top and bottom panes - plate and well Images
right pane displaying correct information

Not working as expected:

tagged wells are not showing up in the Tags tab tree

dominikl · 2016-09-27T09:32:30Z

I still struggle with this whole data model... in the clients we have runs and fields, in the data model there are plateacquisitions, wellsamples, etc. is that the same, how does that fit together?

mtbc · 2016-09-27T09:35:15Z

Yes, plate acquisitions are runs, well samples are fields. You'll tend to find the former terms more in the guts of the system and the latter more as we face users.

will-moore · 2016-09-27T09:46:13Z

As expected, lots of robot failures: https://ci.openmicroscopy.org/view/Failing/job/OMERO-DEV-merge-robotframework/400/robot/

will-moore · 2016-09-27T10:27:21Z

To test last commit: resize thumbnails in both panels and also resize lower panel.
Then load a different Plate - thumb sizes and panel height should be maintained.

pwalczysko · 2016-09-27T10:36:50Z

Ditto to all points raised by @gusferguson in #4863 (comment), including the Bug with Tags not containing wells in Tags tab.

I have one more issue: When the numerals are added (going from 9 to 10, i.e. from 1 to 2 numerals) there is a sudden formatting shift in lower pane (images). I do not see this as desirable.

snoopycrimecop · 2016-09-29T02:34:21Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#458. See the console output for more details.
Possible conflicts:

PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Codomain web #4839 will-moore 'Codomain web'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Tag removal performance #4842 will-moore 'Tag removal performance'
- components/tools/OmeroWeb/omeroweb/webclient/views.py

jburel · 2016-10-20T14:36:36Z

                            }

-                            // Add plates to the jstree data structure
+                            // Add acquistions (runs) to the jstree data structure


jburel · 2016-10-20T14:41:53Z

    get_connection(userB).getUpdateService().saveObject(image_link)

-    # links is: project, dataset, image, screen, plate, acquisition
+    # links is: project, dataset, image, screen, plate, acquisition, well, well


That's what's returned in the array (2 wells).

why is that?

Because we want to test the retrieval of 2 wells

could you add a check for naming of columns/rows i.e. number vs letter

That's what we're testing here: See def expected_wells(user, wells): which generates the dictionary that we compare to what's returned by the tagged json, and includes 'name'.

thanks I missed it

will-moore · 2016-10-21T14:29:08Z

@pwalczysko Last commits fix the slider display as reported in #4863 (comment)

pwalczysko · 2016-10-25T09:33:47Z

The slider display and the reformatting of the borders is great.
Happy to merge, but probably one more look of @gusferguson and or @bramalingam would be good.

gusferguson · 2016-10-25T09:43:29Z

Agree with @pwalczysko - layout and sliders look good.
Good to merge from my POV.

will-moore · 2016-10-25T14:46:00Z

Great, if we can get this merged now, I can fix conflicts with #4708 and re-open it. Thanks.

jburel · 2016-10-26T14:28:13Z

One item that has not been addressed in this PR is the unticked item in the description
i.e. what to display when a well is tagged and display.

We can certainly do that in another PR

Currently we have for example B4, and we have no way to find where that well is
e.g. user-1 test tag
when an image is tagged at least we know where it is located

jburel · 2016-10-27T14:07:03Z

https://trello.com/c/GxqDnD0P/211-spw-follow-up for next actions

snoopycrimecop · 2016-10-31T03:33:07Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#489. See the console output for more details.
Possible conflicts:

PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

snoopycrimecop · 2016-10-31T21:58:54Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#490. See the console output for more details.
Possible conflicts:

PR histograms #4703 will-moore 'histograms'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

snoopycrimecop · 2016-11-01T03:32:50Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#491. See the console output for more details.
Possible conflicts:

PR histograms #4703 will-moore 'histograms'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

snoopycrimecop · 2016-11-01T06:37:30Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#492. See the console output for more details.
Possible conflicts:

PR histograms #4703 will-moore 'histograms'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

snoopycrimecop · 2016-11-01T11:19:49Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#493. See the console output for more details.
Possible conflicts:

PR histograms #4703 will-moore 'histograms'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

snoopycrimecop · 2016-11-02T03:34:30Z

Conflicting PR. Removed from build OMERO-DEV-merge-push#494. See the console output for more details.
Possible conflicts:

PR histograms #4703 will-moore 'histograms'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
PR Webgateway api2 #4708 will-moore 'Webgateway api2'
- components/tools/OmeroWeb/omeroweb/webclient/views.py
Upstream changes
- components/tools/OmeroWeb/omeroweb/webclient/views.py

jburel · 2016-11-03T22:14:11Z

Merging so we can move forward

will-moore added 15 commits August 29, 2016 14:39

webclient annotate_tags() handles wells, not well->image

c4d1b2d

Handle special case 'well' handling from other annotation types

c84751e

metadata_general.html shows Well, not image in well

b64927f

Fix batch_annotate and remove Well index everywhere

f3b32f2

Starting work on loading of Well Images

658aebd

Basic #wellImages panel show thumbs below plate

bc47d06

Drag handle to resize well-images panel

fc02a6c

Add slider for plate thumbnail zooming

a20cc32

Fix positioning of thumbslider, range down to 10px

8c0b9c2

Second slider for wellImages

d1a19e9

Offset well labels when wells are small

46e7b48

Disable 'well' support for metadata and preview right tabs

8c525de

Handle single wellImage click to select

5317cb8

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

683e370

Add well.getWellPos() to Blitz WellWrapper

42a78b2

jburel added the develop label Sep 26, 2016

will-moore added 4 commits September 26, 2016 14:10

Indent {% if %} {% else %} in metadata_general.html

a1a51d8

Show Well label getWellPos() in right panel

652e049

Use handleClickSelected to handle clicks & multiselect of well Images

bb1d68a

Drag selection working on Well Images

afb6cfa

Save thumb sizes and panel height on resize

29af8a1

dominikl mentioned this pull request Sep 30, 2016

Spw grid view (Insight) #4874

Merged

Fix width of Well Labels

76d3b0b

Add toolbars to bottom of spw grid_view panels

c5d761d

jburel reviewed Oct 20, 2016

View reviewed changes

will-moore added 2 commits October 20, 2016 16:54

Extra toolbar placeholder above lower wellImages panel

a29825c

Increase initial height of bottom panel

122d277

will-moore closed this Oct 21, 2016

will-moore reopened this Oct 21, 2016

will-moore closed this Oct 21, 2016

will-moore reopened this Oct 21, 2016

will-moore closed this Oct 24, 2016

will-moore reopened this Oct 24, 2016

acquisitions typo fix

6fc24bf

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

1ee09e0

will-moore mentioned this pull request Nov 3, 2016

Spw grid view2 #4924

Merged

1 task

jburel merged commit 7aa898d into ome:develop Nov 3, 2016

will-moore mentioned this pull request Nov 7, 2016

tables data on images #4929

Merged

jburel added this to the 5.3.0 milestone Mar 29, 2017

will-moore deleted the spw_grid_view branch February 18, 2019 04:12

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will-moore commented Sep 23, 2016 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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What this PR does

Testing this PR

TODO for this PR:

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gusferguson commented Sep 27, 2016

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will-moore commented Sep 23, 2016 •

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