-
Notifications
You must be signed in to change notification settings - Fork 10
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Make 'info' output yamllint compatible #26
Conversation
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Using this branch, tested against a public IDR image
(render) sbesson@ls30630:render $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero login public@idr.openmicroscopy.org
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Password:
Created session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
(render) sbesson@ls30630:render $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero render info Image:4007801
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Using session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
rdefv1: model=color, z=494, t=265
tiles: False
ch0: active=True,color=00FF00,label=H2B-eGFP,min=0.0,start=0.0,end=1093.0,max=65535.0
ch1: active=True,color=FF0000,label=myr-tdTomato,min=0.0,start=0.0,end=439.0,max=65535.0
(render) sbesson@ls30630:render $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero render info Image:4007801 --style yaml
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Using session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
---
channels:
1:
active: true
color: 00FF00
end: 1093.0
label: H2B-eGFP
max: 65535.0
min: 0.0
start: 0.0
2:
active: true
color: FF0000
end: 439.0
label: myr-tdTomato
max: 65535.0
min: 0.0
start: 0.0
greyscale: false
t: 266
version: 2
z: 495
(render) sbesson@ls30630:render $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero render info Image:4007801 --style yaml > out.yml
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Using session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
(render) sbesson@ls30630:render $ bin/yamllint out.yml
(render) sbesson@ls30630:render $ cat out.yml
---
channels:
1:
active: true
color: 00FF00
end: 1093.0
label: H2B-eGFP
max: 65535.0
min: 0.0
start: 0.0
2:
active: true
color: FF0000
end: 439.0
label: myr-tdTomato
max: 65535.0
min: 0.0
start: 0.0
greyscale: false
t: 266
version: 2
z: 495
(render) sbesson@ls30630:render $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero render info Image:4007801 --style json
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Using session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
{"channels": {"1": {"end": 1093.0, "min": 0.0, "color": "00FF00", "max": 65535.0, "label": "H2B-eGFP", "start": 0.0, "active": true}, "2": {"end": 439.0, "min": 0.0, "color": "FF0000", "max": 65535.0, "label": "myr-tdTomato", "start": 0.0, "active": true}}, "greyscale": false, "version": 2, "z": 495, "t": 266}
As opposed to
(omeropy) sbesson@ls30630:~ $ ~/Downloads/OMERO.py-5.4.7-ice36-b93/bin/omero render info Image:4007801 --style yaml > /tmp/out.yml
ERROR:omero.gateway:No Pillow installed, line plots and split channel will fail!
Using session for public@idr.openmicroscopy.org:4064. Idle timeout: 10 min. Current group: Public
(omeropy) sbesson@ls30630:~ $ ~/venvs/flake8/bin/yamllint /tmp/out.yml
/tmp/out.yml
1:1 warning missing document start "---" (document-start)
2:81 error line too long (88 > 80 characters) (line-length)
3:5 error wrong indentation: expected 6 but found 4 (indentation)
4:81 error line too long (81 > 80 characters) (line-length)
5:5 error wrong indentation: expected 6 but found 4 (indentation)
7:1 error too many blank lines (1 > 0) (empty-lines)
(omeropy) sbesson@ls30630:~ $ cat /tmp/out.yml
channels:
0: {active: true, color: 00FF00, end: 1093.0, label: H2B-eGFP, max: 65535.0, min: 0.0,
start: 0.0}
1: {active: true, color: FF0000, end: 439.0, label: myr-tdTomato, max: 65535.0,
min: 0.0, start: 0.0}
greyscale: false
with the current version.
I have extensions to the info --style
integration tests to compare the output but I propose to merge this and open as a follow-up PR before cutting a patch release unless you would rather combine the code and the tests here.
Now released as https://pypi.org/project/omero-cli-render/ |
Fixes #19
Makes the 'info' command output yamllint compatible.
Test:
./omero render info --style yaml Image:123 > test.yml
Then
yamllint test.yml
shouldn't report any errors/warnings.