Logback conversion

[joshmoore]

This PR moves any explicit use of log4j to logback. No log4j.properties or similar should remain in the repository, and it should in fact be possible to remove the log4j jars.

A next step will be to remove all hard-coded dependencies on any slf4j binding, perhaps by providing our own which delegates.

Testing instructions will be forthcoming. Certainly all of the merge/test jobs (openbytes, performance, full-repo, test_images_good) need to continue to work as expected.

[joshmoore]

@sbesson : are you ok to test out the state of matlab logging with a merge build including joshmoore#2 ?

[joshmoore]

Here seems to be the state of this PR as far as I can tell (with @melissalinkert's PR merged):

IJ2+bioformats_package.jar+no logging jars

sh run in ImageJ prints SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". on the console 🆗

IJ2+bioformats_package.jar+logback jars

Works as expected. Edit>Options>Debug clearly shows BF logging 👍

IJ2+bioformats_package.jar+log4j jars

Nothing on the console: 👍
Edit>Options>Debug shows err >log4j:WARN No appenders could be found for logger (ome.scifio.common.ReflectedUniverse). 👍 This is probably better than the no logging jars scenario.

---

Next step is to examine the CI fixes.

[joshmoore]

Status update:

• I'm in the process of looking at bftools.zip as well. There we have the issue that an SLF4J should almost certainly be provided.
• Log4j will need to be re-added for MATLAB. Commit forthcoming.

[joshmoore]

With the last change, the following seems to work:

bioformats/artifacts$ CLASSPATH=loci_tools.jar jython -c 'import ome.scifio.common.DebugTools as DT; DT.enableLogging("DEBUG"); import org.slf4j.LoggerFactory as LF; LF.getLogger("foo").info("bar"); print LF.getLogger("foo").__class__'
bar
<type 'org.slf4j.impl.Log4jLoggerAdapter'>

bioformats/artifacts$ CLASSPATH=bioformats_package.jar jython -c 'import ome.scifio.common.DebugTools as DT; DT.enableLogging("DEBUG"); import org.slf4j.LoggerFactory as LF; LF.getLogger("foo").info("bar"); print LF.getLogger("foo").__class__'
bar
<type 'ch.qos.logback.classic.Logger'>

However, I'm not sure which logback.xml file is getting used (if any).

[joshmoore]

With the last commit (4579666), the above Jython tests also work with the mvn jars:

export WHICH=loci_tools
export CLASSPATH=$HOME/.m2/repository/ome/$WHICH/5.0.0-SNAPSHOT/$WHICH-5.0.0-SNAPSHOT.jar

[sbesson]

Using Bio-Formats 4.4.10

>> [~, version] = bfCheckJavaPath()

version =

4.4.10

>> loci.common.DebugTools.enableLogging('DEBUG');
>> r=bfGetReader('~/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv');
loci.formats.in.DeltavisionReader.initFile(/Users/sebastien/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv)
Reading header
Populating core metadata
Reading extended header
Populating original metadata
Populating OME metadata
Reading header
Populating original metadata
Populating OME metadata
Expected positive value for PhysicalSizeZ; got 0.0

Using the bfmatlab.zip artifact of http://ci.openmicroscopy.org/view/Failing/job/BIOFORMATS-5.0-merge-daily/712/

>> [~, version] = bfCheckJavaPath()

version =

5.0.0-DEV

>> loci.common.DebugTools.enableLogging('DEBUG');
>> r=bfGetReader('~/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv');
DeltavisionReader initializing /Users/sebastien/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv
DeltavisionReader initializing /Users/sebastien/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv
loci.formats.in.DeltavisionReader.initFile(/Users/sebastien/Desktop/SoftwareDay-Data/09072011_WTMEFs_ca_001.dv)
Reading header
Populating core metadata
Reading extended header
Populating original metadata
Populating OME metadata
Reading header
Populating original metadata
Populating OME metadata
Expected positive value for PhysicalSizeZ; got 0.0

I guess that's a 👍 from the MATLAB side

[melissalinkert]

bftools changes seem fine on Windows and Linux.

[ximenesuk]

Adding debug="true" to the logback.xml file under the bftools I get the following when running one of the tools:

jrs-macbookpro-25031:tools cblackburn$ ./bfconvert ~/Work/Images/dv/SMN10ul03_R3D_D3D.dv smn.tiff
14:01:59,747 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
14:01:59,747 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
14:01:59,747 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/Users/cblackburn/Work/repos/ome/components/bioformats/tools/logback.xml]
14:01:59,916 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
14:01:59,919 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stdout]
14:01:59,944 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
14:01:59,988 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
14:01:59,988 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stdout] to Logger[ROOT]
14:01:59,989 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
14:01:59,991 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@41aac3f8 - Registering current configuration as safe fallback point
...

which looks good to me.

[joshmoore]

Great, thanks, @ximenesuk. Merging to open another PR.

[pwalczysko]

I do not have the error output in the logging window when having just "loci_tools.jar" in the plugins folder. cf section "Bio-formats only" of https://docs.google.com/document/d/1O5xQqhFpWi1zlMwgDn75qvtYwCXmTCLToIs8M5fYQVA/edit#

[joshmoore]

--rebased-to #910