Contents
22. General Release
Purpose of the test is to make sure the particular application on the release day is built correctly, starts, connects and opens an image as expected (when applicable).
Click onto the application you are assigned to test in the Contents above
22.1. OMERO.clients
Download and open the application and login as any user
(all platforms) Check other Ice versions of OMERO.insight*.zip files on artifacts page.
(all platforms) Check one of the OMERO.importer*.zip files on artifacts page
(Windows only) Check that there is no “exe4j” popup prior to Insight splashscreen.
(all platforms) Check that the application starts and you can log in.
(all platforms, Insight only) Check that you can expand a dataset and open an image with multi-z (Choose one of the
.dv
images in datasets named likearchived dv
ornon-archived dv
- present in almost every user/group.)(all platforms, Insight only) Check that you can click onto the Projection tab in the opened image.
(all platforms) Check that you can execute any script.
(all platforms) Check that you can delete the image.
22.2. IJ/Fiji Plugin
22.3. OMERO.server
Download the appropriate OMERO.server*.zip and unzip the downloaded file.
Configure the server.
Start the server and the web server.
Check that the server starts as expected.
Download and open OMERO.insight and go to the appropriate port address in your web browser to login to OMERO.web.
Login in OMERO.insight and OMERO.web connecting to the server you just started.
Check that the clients connect to the server and login is successful.
Check that DropBox imports a file successfully
Check that you can execute (any) script using (any) client
22.4. OMERO.matlab toolbox
Install Matlab (development).
In order to be able to execute the testing commands in Matlab, perform the necessary steps in the workflow described in Matlab docs using the build indicated in the Standup Notes. Then, execute in Matlab (
hostname
,username
,password
andimageID
needs to be substituted by valid values):client = loadOmero(hostname); % to use a different port than the default one. % client = loadOmero(hostname, port); session = client.createSession(username, password); image = getImages(session, imageID); plane = getPlane(session, image, 0, 0, 0); datasets = getDatasets(session); figure; imshow(plane, []); client.closeSession();
After you have executed the above commands,
Check that all 7 commands executed without errors.
Check that after
figure; imshow(plane, []);
the image is displayed in Matlab.
Go to Matlab docs and find the paragraph
Create a Dataset...
underWriting
section. Follow the commands to create a Dataset and link it to a Project.Check that a Dataset was created.
Go to Matlab docs and find the paragraph
Creating ROI
underROIs
section. Follow the commands to create a ROI and link it to an Image.Check that a ROI was created.
Go to Matlab docs and find the section
Deleting data
. Follow the commands to Delete an Image, a Dataset and a Project.Check that the I/D/P was deleted.
22.5. OMERO Virtual Appliance
This section is only valid for testing versions prior to 5.2.2.
Follow the Virtual Appliance docs to get the Virtual Appliance started - skip the steps as appropriate in case you have already installed Virtual Box.
Start OMERO.insight and OMERO.web as described in the docs and try to login.
Check that Insight and Web start okay and you can login successfully.
Check that you can import and then open a small image (any small image will do).
22.6. Bio-Formats MATLAB/Octave
Warning
Milestone or SNAPSHOT versions cannot be tested using the version of GNU Octave installed by the Ubuntu 16.04 package manager (4.0.x) as only versions of the format x.y.z are accepted by the implementation (https://wiki.octave.org/OEP:pkg#version_definition).
System installation
Install MATLAB or GNU Octave on your operating system using the appropriate downloads or package manager.
Install the Bio-Formats MATLAB toolbox or the Bio-Formats Octave package.
Download one of our sample images. Alternatively, use any small image on your local disk or on squig.
Follow the instructions here up to and including the section
Displaying images
.Check that the image opens as expected.
Set the root logger to DEBUG level:
loci.common.DebugTools.setRootLevel('DEBUG');
Reopen the image using the same commands as previously.
Check that the amount of logging increases in the MATLAB command prompt.
Docker (GNU Octave only)
Clone https://github.com/openmicroscopy/bio-formats-octave-docker, update the
VERSION
argument and build the Docker image:$ docker build -t bio-formats-octave .
Download one of our sample images. Alternatively, use any small image on your local disk or on squig.
Run the
travis_test.m
on the image e.g.:$ docker run -ti -v /data/:/data/ bio-formats-octave travis_test.m /data/tubhiswt-2D/tubhiswt_C0.ome.tif
Check that the image opens as expected.
Check that the amount of logging increases in the second execution.
22.7. Bio-Formats: ImageJ/Fiji testing
ImageJ
Use ImageJ for this section, not Fiji.
Remove any previous
bioformats_package.jar
orloci_tools.jar
files from your ImageJ Plugins folder. Put the freshly downloadedbioformats_package.jar
into the Plugins folder of ImageJ and start ImageJ.Check that there is a
LOCI
menu item under thePlugins
menu and when you select it, the submenu asks you to useBio-Formats
menu.Check that there is a
Bio-Formats
menu item under thePlugins
menu.
Select
Plugins
>Bio-Formats
>Bio-Formats Importer
and import a small image (any small image will do).Check that the image imports successfully.
Leave the imported image open in ImageJ and Select
Plugins
>Bio-Formats
>Bio-Formats Exporter
and export this image.Check that the image exports successfully.
Select
Plugins
>Bio-Formats
>Bio-Formats Remote Importer
and paste the URLhttps://downloads.openmicroscopy.org/images/DV/U2OS/U2OS_Eg5_PH3_001_R3D.dv
into the first dialog that pops up.Check that the image imports successfully.
Select
Help
>About Plugins
>Bio-Formats Plugins...
Check that the URLs shown in the popup link to existing and sensible pages.
Check that the release version and date are correct.
Fiji
This testing assumes the release artifacts have been deployed to the Bio-Formats update site.
Use Fiji for this section, not ImageJ.
Activate the Bio-Formats update site
in addition to the Java-8 update site.In the ImageJ Updater Window ensure that the
plugins/bio-formats_plugins.jar
file and jars in thejars/bio-formats
folder are listed for update.Check check that the
Update Site
for each is listed as theBio-Formats
update site.Check the
Status/Action
field for each should be set toInstall it
orUpdate it
.Check click on
Advanced Mode
, then select each file and ensure the date and version in theDetails
panel is correct.
Select
Help
>About Plugins
>Bio-Formats Plugins...
Check that the URLs shown in the popup link to existing and sensible pages.
Check that the release version and date are correct.
In the ImageJ Updater Window select
Apply Changes
to run the update and restart FIJISelect
Plugins
>Bio-Formats
>Bio-Formats Importer
and import a small image (any small image will do).Check that the image imports successfully.
Leave the imported image open in ImageJ and select
Plugins
>Bio-Formats
>Bio-Formats Exporter
and export this image.Check that the image exports successfully.
Select
Plugins
>Bio-Formats
>Bio-Formats Remote Importer
and paste the URLhttps://downloads.openmicroscopy.org/images/DV/U2OS/U2OS_Eg5_PH3_001_R3D.dv
into the first dialog that pops upCheck that the image imports successfully.
22.8. Bio-Formats command-line tools
Download and unzip the bftools.zip.
Move into this folder.
Execute the
bfconvert
command on the cmd line, for example:$ touch test.fake $ ./bfconvert test.fake test.ome.tiff
Check that a new image with the name you chose and the chosen extension (for example
.ome.tiff
) was created.
Execute the
showinf
command on the cmd line, using the.ome.tiff
image created in previous step$ ./showinf -version
Check that the correct version, revision and build date are returned after the first command.
$ ./showinf <image_path>
Check that the image in the <image_path> in the second command opens.
$ ./showinf -omexml <image_path>
Check that the image in the <image_path> in the second command opens, the OME-XML is validated and displayed
22.9. Downloads page
Go to the downloads page and
Check the general layout (no gross misformattings or similar)
Check that clicking on all links in the text everywhere (e.g. like to the docs in the first paragraph, in the explanatory texts under the download blocks) will bring you to the advertised place.
NO NEED to download the clients or servers
Check that you can download the
Source code
,OMERO API documentation
,OMERO Java Downloads
,OMERO Python Downloads
Check
Source code links