New wavelength changes #2163

qidane · 2014-03-12T23:12:42Z

No description provided.

sbesson · 2014-03-13T08:39:10Z

Added breaking and exclude labels. Note the --breaking strategy does not work for this PRs.

qidane · 2014-03-13T09:04:18Z

This PR will be in the breaking line but I wanted it excluded from that for the moment as @aleksandra-tarkowska has an incompatible breaking PR that needs to go in first.
#1742 - 11591 user ip

qidane · 2014-03-13T18:22:22Z

Totally untested, but at least it now compiles!

jburel · 2014-03-13T20:47:56Z

@qidane: if we renamed the method in the Pojos class(typo fix), we will have to mark them deprecated in the 5.0 line and add the new ones so we can remove them in 5.1

sbesson · 2014-03-13T21:01:34Z

@qidane: want to add a --depends-on comment to the PR and remove the hardcoded submodule bump to let Travis compile?

qidane · 2014-03-13T22:55:10Z

--depends-on ome/bioformats#881

sbesson · 2014-03-14T08:54:48Z

Restarted the Travis build (to account for the dependency comment). 👍
Once #1742 is in, we will need to merge origin/develop into this PR to get the latest upgrade script.

qidane · 2014-03-14T09:21:58Z

I need to rework the commits and group the changes in a more logical manner. I will do this as part of the rebase where I fix the Database version/patch and upgrade script.

qidane · 2014-03-14T12:54:47Z

Now builds, tests compile and run, not all unit tests pass.

We could run the ci builds while I look to see that the unit test problems are.

sbesson · 2014-03-14T19:07:46Z

👍 this went through the OMERO breaking pipeline. Note all integration tests did not fully pass, see http://ci.openmicroscopy.org/view/Breaking/job/OMERO-5.1-breaking-integration-java/5/.

sbesson · 2014-03-14T19:09:39Z

Also do we need an upgrade script from 5.1DEV__0 to 5.1DEV__1 ?

jburel · 2014-03-14T20:40:53Z

@sbesson: The original plan was not to have an upgrade script between 5.1DEV_x versions but one from 5.0.x to 5.1Dev

jburel · 2014-03-14T20:45:44Z

After discussion with @sbesson, it might difficult complicate with the actual set-up not to have an upgrade script.
so it is probably good to have one in place between 5.1DEV__(x-1) to 5.1DEV__x

joshmoore · 2014-03-15T06:37:26Z

I'd also agree that having the individual scripts keeps us honest and long-term makes our lives easier.

sbesson · 2014-03-17T15:41:53Z

http://ci.openmicroscopy.org/job/OMERO-5.1-breaking-upgrade/22/ is green with the last commit.

mtbc · 2014-03-17T16:03:38Z

components/blitz/src/ome/formats/model/ChannelProcessor.java

 		setChannelColor(channel, channelIndex,
-				ColorsFactory.determineColor(value));
+				ColorsFactory.determineColor(new java.lang.Double(valueFilter)));


You shouldn't need the java.lang. bit. Actually, valueFilter.doubleValue() would suffice. Same below.

mtbc · 2014-03-17T16:05:38Z

Still some copyrights to update, like ChannelProcessor.

mtbc · 2014-03-17T16:08:12Z

components/blitz/src/pojos/ChannelAcquisitionData.java

 		if (lightSettings == null) lightSettings = new LightSettingsI();
 		lightSettings.setAttenuation(omero.rtypes.rdouble(value));
 	}

 	/**
-	 * Returns the wavelength of the light source.
+	 * Sets the wavelength of the light source.


nice catch (-:

joshmoore · 2014-03-18T15:16:34Z

Travis is unhappy:

MetadataRetrieve

public PositiveFloat getChannelExcitationWavelength(int imageIndex,

^

return type PositiveFloat is not compatible with PositiveInteger

/home/travis/build/openmicroscopy/openmicroscopy/components/blitz/src/ome/services/blitz/impl/OmeroMetadata.java:697: error: getChannelEmissionWavelength(int,int) in OmeroMetadata cannot implement getChannelEmissionWavelength(int,int) in MetadataRetrieve

public PositiveFloat getChannelEmissionWavelength(int imageIndex,

sbesson · 2014-03-18T15:59:37Z

Restarted Travis build after @qidane pushed his bioformats changes.

qidane · 2014-03-19T15:12:38Z

Integration test failed due to timeout elsewhere in code.
http://ci.openmicroscopy.org/job/OMERO-5.1-breaking-integration-java/8/testngreports/?

Reruning test.

sbesson · 2014-03-20T11:08:07Z

Removing breaking label

sbesson · 2014-03-20T11:25:28Z

Saved and upgraded the merge DB

[hudson@ome-c6100-3 ~]$ pg_dump -U omero -Fc -f ~/OMERO-5.1-merge-deploy-20032013.db.dump OMERO-5.1-merge-deploy
[hudson@ome-c6100-3 ~]$ file ~/OMERO-5.1-merge-deploy-20032013.db.dump 
/home/hudson/OMERO-5.1-merge-deploy-20032013.db.dump: PostgreSQL custom database dump - v1.12-0
[hudson@ome-c6100-3 ~]$ psql -U omero OMERO-5.1-merge-deploy < /opt/hudson/workspace/OMERO-5.1-breaking-upgrade/VERSION/LAST_DEV/label/ome-c6100-3/OMERO.server/sql/psql/OMERO5.1DEV__1/OMERO5.1DEV__0.sql 
BEGIN
CREATE FUNCTION
 omero_assert_db_version 
-------------------------

(1 row)

DROP FUNCTION
INSERT 0 1
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
UPDATE 1
                                 status                                 
------------------------------------------------------------------------
                                                                       +
                                                                       +
                                                                       +
 YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.1DEV__1+
                                                                       +
                                                                       +

(1 row)

COMMIT
[hudson@ome-c6100-3 ~]$

sbesson · 2014-03-21T11:57:59Z

No blocker found at this point. Small fixes will be addressed in subsequent PRs. Merging.

New wavelength changes

sbesson · 2014-03-21T12:01:41Z

Upgraded the latest DB trout

[hudson@ome-c6100-3 ~]$ pg_dump -U omero -Fc -f ~/OMERO-5.1-latest-deploy-21032014.db.dump OMERO-5.1-latest-deploy
[hudson@ome-c6100-3 ~]$ file ~/OMERO-5.1-latest-deploy-21032014.db.dump 
/home/hudson/OMERO-5.1-latest-deploy-21032014.db.dump: PostgreSQL custom database dump - v1.12-0
[hudson@ome-c6100-3 ~]$ psql -U omero OMERO-5.1-latest-deploy < /opt/hudson/workspace/OMERO-5.1-breaking-upgrade/VERSION/LAST_DEV/label/ome-c6100-3/OMERO.server/sql/psql/OMERO5.1DEV__1/OMERO5.1DEV__0.sql
BEGIN
CREATE FUNCTION
 omero_assert_db_version 
-------------------------

(1 row)

DROP FUNCTION
INSERT 0 1
ALTER TABLE
ALTER TABLE
ALTER TABLE
ALTER TABLE
UPDATE 1
                                 status                                 
------------------------------------------------------------------------
                                                                       +
                                                                       +
                                                                       +
 YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.1DEV__1+
                                                                       +
                                                                       +

(1 row)

COMMIT
[hudson@ome-c6100-3 ~]$

qidane · 2014-03-25T09:12:26Z

--no-rebase

sbesson added breaking labels Mar 13, 2014

mtbc mentioned this pull request Mar 14, 2014

fix #11877: move import logs to upload jobs instead of annotations #2055

Merged

sbesson removed the exclude label Mar 14, 2014

jburel and others added 13 commits March 14, 2014 10:37

Replace int by float for emission wavelength.

571966b

Replace int by float in excitation wavelength.

ab68d54

Replace int by float for laser.

ee4e54d

Update copyright.

cef76e3

Handle wavelength as float instead of int.

2e3c46f

Replace int by float in lightsource settings.

a5b9ce5

Updating db and model

62b8a00

Update pojos for PositiveFloat wavelength

1ee3a3d

Update Metadata store and implementation

cda5278

Update Color processing and Rendering

f9a259b

Update clients

af2c785

Update the unit tests

c5b322c

Update the OmeroJava tests

acd7161

Adding 1DEV_0 to 1DEV_1 upgrade script

54a3055

mtbc reviewed Mar 17, 2014
View reviewed changes

Removing unneeded java.lang. from Float & Double

21dc9ac

Updating validateLightSourceSettings for double

60cbba2

sbesson added develop and removed breaking labels Mar 20, 2014

qidane added 2 commits March 20, 2014 16:36

Correcting Double to Float conversion

e9dfc76

Rework logic and float/double conversion

1073755

sbesson added a commit that referenced this pull request Mar 21, 2014

Merge pull request #2163 from qidane/new-wavelength

1ac4751

New wavelength changes

sbesson merged commit 1ac4751 into ome:develop Mar 21, 2014

qidane deleted the new-wavelength branch March 21, 2014 12:15

sbesson mentioned this pull request Mar 21, 2014

Update develop submodules #2178

Merged

sbesson added this to the 5.1.0-m1 milestone Oct 14, 2014

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New wavelength changes #2163

New wavelength changes #2163

qidane commented Mar 12, 2014

sbesson commented Mar 13, 2014

qidane commented Mar 13, 2014

qidane commented Mar 13, 2014

jburel commented Mar 13, 2014

sbesson commented Mar 13, 2014

qidane commented Mar 13, 2014

sbesson commented Mar 14, 2014

qidane commented Mar 14, 2014

qidane commented Mar 14, 2014

sbesson commented Mar 14, 2014

sbesson commented Mar 14, 2014

jburel commented Mar 14, 2014

jburel commented Mar 14, 2014

joshmoore commented Mar 15, 2014

sbesson commented Mar 17, 2014

mtbc Mar 17, 2014

mtbc commented Mar 17, 2014

mtbc Mar 17, 2014

joshmoore commented Mar 18, 2014

sbesson commented Mar 18, 2014

qidane commented Mar 19, 2014

sbesson commented Mar 20, 2014

sbesson commented Mar 20, 2014

sbesson commented Mar 21, 2014

sbesson commented Mar 21, 2014

qidane commented Mar 25, 2014

New wavelength changes #2163

New wavelength changes #2163

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qidane commented Mar 12, 2014

sbesson commented Mar 13, 2014

qidane commented Mar 13, 2014

qidane commented Mar 13, 2014

jburel commented Mar 13, 2014

sbesson commented Mar 13, 2014

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