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jburel commented 4 years ago

do not register the id cc @joshmoore @dominikl

To test this PR

Download the imagej zip from the daily build
place the jar in the plugins directory of Fiji
Go to the jars directory of Fiji, in the bioformats folder, remove formats-api-xx.jar
Start Fiji and Go to Edit>Options>Misc...
In the dialog that pops up, select Debug mode and Click OK
Open an image in OMERO

Check that there is no line like

OmeroReader.initFile(omero:server=workshop.openmicroscopy.org
user=xxx
port=4064
pass=xxx
groupID=5
iid=49206)

see https://github.com/ome/omero-insight/issues/136 for background

mtbc commented 4 years ago

the imagej zip from the daily build

Which build? I'm not finding this.

jburel commented 4 years ago

https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-insight-build/

mtbc commented 4 years ago

Open an image in OMERO

Is this with Bio-Formats Remote Importer or somesuch?

Update: That offers a http:// dialog which seems odd so maybe not for connecting to OMERO.

jburel commented 4 years ago

No Start the OMERO ImageJ plugin i.e. connect to OMERO and open a small image (so it does not take too long) by double-clicking on the image

mtbc commented 4 years ago

Oh, doh, I just put the above zip in there, didn't unpack it, and in the libs/ subdir I had BF (which CI doesn't hide in a zip) so that's why I still saw some OME thing! Doing better now ...

mtbc commented 4 years ago

I am getting,

out> OmeroReader.initFile()
out> loci.ome.io.OmeroReader.initFile(omero:server=localhost
user=user-2
port=4064
pass=xxx
groupID=3
iid=3)

Does that mean this PR is good but a companion is needed?

jburel commented 4 years ago

It looks that it is not included in the artifacts. I will check what is going on

dominikl commented 4 years ago

Still get the password printout with clean fiji and the plugin from https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-insight-build/438/ . Unfortunately can't build it locally.

dominikl commented 4 years ago

Now sometimes it's hidden, sometimes it's not. Here's the debug output (replaced my password with xxx where it was actually printed):

...
err >[WARN] UPGRADE AVAILABLE:Please upgrade to 5.6.1. See http://downloads.openmicroscopy.org/latest/omero for the latest version.

Server version: 5.6.1
Client version: Unknown
os_version: 10.13.6
java_version: 1.8.0_202
os_arch: x86_64
os_name: Mac OS X

Created new AdminFacility
Logged onto OMERO at: demo.openmicroscopy.org
User Name: dlindner -- Password: ************

UI for displaying ROIS annotations not implemented yet!
Created new BrowseFacility
Cannot listen to the Quit action of the menu.
setKeyUp: -1
runPlugIn: loci.plugins.LociImporter
runUserPlugIn: loci.plugins.LociImporter, arg=
Bio-Formats: parse core options
Bio-Formats: display option dialogs
Bio-Formats: loci.plugins.in.UpgradeDialog: prompt
Bio-Formats: loci.plugins.in.LocationDialog: skip
Bio-Formats: loci.plugins.in.IdDialog: skip
Bio-Formats: loci.plugins.in.MainDialog: prompt
GenericDialog font: false null
Created new ROIFacility
Created new DataManagerFacility
out> OmeroReader initializing omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=xxx
groupID=263
iid=119997

out> loci.ome.io.OmeroReader.initFile(omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=****
groupID=263
iid=119997
)

out> Parsing credentials

out> Logging in

out> Populating metadata

Bio-Formats: loci.plugins.in.FilePatternDialog: skip
out> OmeroReader initializing omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=xxx
groupID=263
iid=119997

out> loci.ome.io.OmeroReader.initFile(omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=****
groupID=263
iid=119997
)

out> Parsing credentials

out> Logging in

out> Populating metadata

out> OmeroReader initializing omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=xxx
groupID=263
iid=119997

out> loci.ome.io.OmeroReader.initFile(omero:server=demo.openmicroscopy.org
user=dlindner
port=4064
pass=****
groupID=263
iid=119997
)

out> Parsing credentials

out> Logging in

out> Populating metadata

Bio-Formats: loci.plugins.in.SeriesDialog: skip
Bio-Formats: loci.plugins.in.SwapDialog: skip
Bio-Formats: loci.plugins.in.RangeDialog: prompt
GenericDialog font: false null
Bio-Formats: loci.plugins.in.CropDialog: skip
Bio-Formats: loci.plugins.in.ColorDialog: skip
Bio-Formats: loci.plugins.in.MemoryDialog: skip
Bio-Formats: display metadata
Bio-Formats: read pixel data
stack.viewers: 1
CompositeImage: img["cats.jpg" (-2), 8-bit, 1280x720x3x1x1] 3 3
stack.viewers: 2
stack.viewers: 1
stack.viewers: 1
stack.viewers: 1
Bio-Formats: display pixels
Undo.reset: 0 null
ImageWindow.xbase: 694 java.awt.Point[x=694,y=323]
cats.jpg - C=0: trimProcessor
Undo.reset: 0 null
cats.jpg - C=1: trimProcessor
Undo.reset: 0 null
Bio-Formats: display ROIs
Bio-Formats: finish
windowActivated: cats.jpg - C=0
setMenuBar: 778ms (2)
cats.jpg - C=2--OMERO ID:119997: trimProcessor
Undo.reset: 0 null
windowActivated: cats.jpg - C=1
setMenuBar: 330ms (3)
cats.jpg - C=0: trimProcessor
Undo.reset: 0 null
windowActivated: cats.jpg - C=2--OMERO ID:119997
setMenuBar: 698ms (4)
cats.jpg - C=1: trimProcessor
Undo.reset: 0 null
focusGained: img["cats.jpg - C=2--OMERO ID:119997" (-6), 8-bit, 1280x720x1x1x1]

I used https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-insight-build/441/ and https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/418/jdk=JDK8,label=testintegration/artifact/bio-formats-build/bioformats/components/bio-formats-plugins/target/ just in case Fiji picks up the other bioformats jar in its plugins directory.

jburel commented 4 years ago

Did you remove the BF format-api.jar as indicated?

dominikl commented 4 years ago

👍 After replacing all bioformats jars (also in Fiji's jar directory) it works now, all passwords replaced with **** !

ome / omero-blitz

info in log #93