Use SLF4J for logging #155

sbliven · 2014-08-26T16:32:25Z

I believe we reached a consensus on the mailing list to use slf4j for logging, due to its easy interoperability with other logging frameworks.

The “beauty" of slf4j is that it provides a logging framework that doesn’t impose any downstream restrictions or requirements and will actually insulate users from logging dependencies that come from other third-party libraries that you may include. It allows the end user to include the logging framework of their choice, defaulting to a NOP version if none is specified.
-- Andy Law, biojava-dev list, May 25, 2014

Todo:

Create a usage policy & documentation (http://www.biojava.org/wiki/BioJava3_logging)
Add slf4j & an implementation to the pom file
Change any existing uses of java.util.logging to use slf4j (there shouldn't be ~~any~~ many of these)
Convert println/printStackTrace statements to logger calls

This would be a great project for someone trying to start contributing to BioJava.

heuermh · 2014-08-26T16:43:58Z

+1, and biojava-legacy too.

Just make sure that the only compile time dependency is on slf4j-api. There may be a test scoped dependency on say slf4j-simple for logging during unit tests.

- added runTime scope binding for log4j2 since it's the one logger framework that was used already elsewhere. We even had already some config files for it in the structure module - added the safe config to all poms of modules. Config files for log4j2 are only in the structure module. Other modules will have to add config files if needed - default level in config files set to: warn for run, info for test - moved logging in the PDB parser to slf4j

Introducing slf4j #155

…ctly

Test configuration uses INFO and production uses WARN

Convert core package to use slf4j #155

Convert aaproperties and alignment packages to slf4j #155

…ojava#155

Convert org.biojava3.genome to slf4j #155

- some improvement in exceptions and logging biojava#111 and biojava#155

Updated packages to use slf4j for logging #155

- also improvements for biojava#111 and biojava#155 - some more work to do to make sure AtomCache and the Readers don't double read the environment variables/system properties

- reduced the number of initialisations in AtomCache and readers - now all chem comp providers use PDB_CACHE_DIR - a few biojava#111 and biojava#155 fixes

- some improvements for biojava#111, biojava#155 and biojava#185

andreasprlic · 2014-10-08T22:21:14Z

can we close this?

josemduarte · 2014-10-09T08:13:50Z

Indeed there's been enormous progress in this. But I'd say that the structure package needs some more work, there's still quite a few hidden prints to stdout/stderr. Let's give it a bit more time.

Update org.biojava.bio.structure (main) package in biojava3-structure project to use slf4j #155

- also some improvement for biojava#191: now a TranslationException will be thrown when compound not known - a few improvements for other issues: biojava#111, biojava#155, biojava#185

sbliven · 2015-01-06T11:59:29Z

How about now, @josemduarte? Logging doesn't change the API, so it can easily go out in patch commits.

josemduarte · 2015-01-06T12:11:34Z

Yep let's close it, I think the logging coverage now is quite decent. Surely there must be some other places with missing logging but we can add more commits later

dmyersturnbull · 2015-01-20T23:12:35Z

Re-opening this for now so that I can reference it in commits.

…ied some code, made clone() call super.clone(), and switched from StringWriter and StringBuffer to the faster (asynchronous) StringBuilder.

…ied some code, made clone() call super.clone(), and switched from StringWriter and StringBuffer to the faster (asynchronous) StringBuilder. Small improvements to rcsb package and to Astral class.

sbliven · 2015-01-23T15:33:31Z

Can't you reference a closed issue? jose's commits seem to have been picked up after it closed.

dmyersturnbull · 2015-01-23T20:58:25Z

Yes, apparently I can! (I didn't know.)

sbliven added this to the BioJava 4.0.0 milestone Aug 26, 2014

sbliven added the enhancement label Aug 26, 2014

This was referenced Aug 27, 2014

mmcif warnings #154

Closed

Improving exception handling #111

Closed

josemduarte added a commit that referenced this issue Aug 28, 2014

Merge pull request #159 from josemduarte/master

d9974e7

Introducing slf4j #155

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 28, 2014

Some fixes for biojava#111 and biojava#155

abff5ed

josemduarte added a commit that referenced this issue Aug 28, 2014

Some fixes for #111 and #155

f5eae5c

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 29, 2014

Important fix for biojava#155, was not specifying runtime scope corre…

8e7c44f

…ctly

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 29, 2014

More on biojava#155 and biojava#111

794b3e1

sbliven added a commit to sbliven/biojava-sbliven that referenced this issue Aug 29, 2014

Changing logging configuration (biojava#155)

0827cdf

Test configuration uses INFO and production uses WARN

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 29, 2014

More biojava#111 and biojava#155

7059e1b

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 30, 2014

biojava#155 and some biojava#111

818972a

josemduarte added a commit to josemduarte/biojava that referenced this issue Aug 31, 2014

More logging biojava#155

c3aea0c

josemduarte added a commit to josemduarte/biojava that referenced this issue Sep 17, 2014

Better logging and remove some warnings, biojava#155

fedb4a7

josemduarte added a commit that referenced this issue Sep 17, 2014

Merge pull request #166 from benjamintboyle/master

bf15113

Convert core package to use slf4j #155

josemduarte added a commit that referenced this issue Sep 18, 2014

Merge pull request #170 from benjamintboyle/master

5a8e196

Convert aaproperties and alignment packages to slf4j #155

josemduarte added a commit to josemduarte/biojava that referenced this issue Sep 18, 2014

Adding missing log4j2.xml files and unifying config across modules bi…

809e9c8

…ojava#155

josemduarte added a commit that referenced this issue Sep 19, 2014

Merge pull request #171 from benjamintboyle/master

2f6cad5

Convert org.biojava3.genome to slf4j #155

josemduarte added a commit to josemduarte/biojava that referenced this issue Sep 20, 2014

Full fix for biojava#148, all tests pass

6613e03

- some improvement in exceptions and logging biojava#111 and biojava#155

josemduarte added a commit to josemduarte/biojava that referenced this issue Sep 20, 2014

Full fix for biojava#148, all tests pass

6b50276

- some improvement in exceptions and logging biojava#111 and biojava#155

josemduarte added a commit to josemduarte/biojava that referenced this issue Sep 20, 2014

More biojava#111 and biojava#155

65bdcd2

dmyersturnbull mentioned this issue Sep 20, 2014

Improve Biojava exception handling #176

Closed

benjamintboyle mentioned this issue Sep 21, 2014

Updated packages to use slf4j for logging #155 #177

Merged

andreasprlic added a commit that referenced this issue Sep 22, 2014

Merge pull request #177 from benjamintboyle/master

621ecf8

Updated packages to use slf4j for logging #155

josemduarte added a commit to josemduarte/biojava that referenced this issue Oct 1, 2014

More fixes for PDB_DIR reading, plus some biojava#111 and biojava#155

17e641c

josemduarte added a commit to josemduarte/biojava that referenced this issue Oct 6, 2014

Now handling obsolete paths too biojava#181

d9dbca4

- some improvements for biojava#111, biojava#155 and biojava#185

benjamintboyle mentioned this issue Oct 10, 2014

Update org.biojava.bio.structure (main) package in biojava3-structure project to use slf4j #155 #192

Merged

andreasprlic added a commit that referenced this issue Oct 11, 2014

Merge pull request #192 from benjamintboyle/master

a0bad76

Update org.biojava.bio.structure (main) package in biojava3-structure project to use slf4j #155

josemduarte added a commit that referenced this issue Nov 21, 2014

Removing warnings, some #111 and #155

e8234f3

josemduarte added a commit to josemduarte/biojava that referenced this issue Nov 25, 2014

Added some methods. Fixed some biojava#111 and biojava#155

d7cada6

josemduarte added a commit to josemduarte/biojava that referenced this issue Nov 27, 2014

Converting java.logging to slf4j in structure gui, biojava#155

2fbb172

josemduarte added a commit to josemduarte/biojava that referenced this issue Dec 9, 2014

Better logging in sifts biojava#155

3a077b1

josemduarte closed this as completed Jan 6, 2015

josemduarte added a commit to josemduarte/biojava that referenced this issue Jan 6, 2015

More logging fixes biojava#155

0e3838e

josemduarte added a commit to josemduarte/biojava that referenced this issue Jan 6, 2015

More logging fixes biojava#155

de5422a

dmyersturnbull reopened this Jan 20, 2015

dmyersturnbull closed this as completed Jan 23, 2015

josemduarte added a commit that referenced this issue Feb 20, 2015

Some better logging, #155

6e2b8ed

josemduarte mentioned this issue May 16, 2016

Cleanup issues #484

Closed

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Use SLF4J for logging #155

Use SLF4J for logging #155

sbliven commented Aug 26, 2014

heuermh commented Aug 26, 2014

andreasprlic commented Oct 8, 2014

josemduarte commented Oct 9, 2014

sbliven commented Jan 6, 2015

josemduarte commented Jan 6, 2015

dmyersturnbull commented Jan 20, 2015

sbliven commented Jan 23, 2015

dmyersturnbull commented Jan 23, 2015

Use SLF4J for logging #155

Use SLF4J for logging #155

Comments

sbliven commented Aug 26, 2014

heuermh commented Aug 26, 2014

andreasprlic commented Oct 8, 2014

josemduarte commented Oct 9, 2014

sbliven commented Jan 6, 2015

josemduarte commented Jan 6, 2015

dmyersturnbull commented Jan 20, 2015

sbliven commented Jan 23, 2015

dmyersturnbull commented Jan 23, 2015