not creating the jbrowse "bin" directory properly during deployment

nathandunn commented 9 years ago

not creating the jbrowse "bin" directory properly during deployment. Here is the setup.log:

cd src/main/webapp/jbrowse ./install_jbrowse.sh: line 25: cd: src/main/webapp/jbrowse: No such file or directory
chmod +x bin/cpanm chmod: bin/cpanm: No such file or directory
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON ./install_jbrowse.sh: line 27: bin/cpanm: No such file or directory
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON ./install_jbrowse.sh: line 28: bin/cpanm: No such file or directory
bin/cpanm -v --notest -l ../../../../extlib/ --installdeps . ./install_jbrowse.sh: line 29: bin/cpanm: No such file or directory
bin/cpanm -v --notest -l ../../../../extlib/ --installdeps . ./install_jbrowse.sh: line 30: bin/cpanm: No such file or directory
set -e
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON ./install_jbrowse.sh: line 32: bin/cpanm: No such file or directory

I'd run into this before, not sure what the fix was.

nathandunn commented 9 years ago

@cmdcolin Does this last patch fix this?

After an "apollo clean" I should be able to do "apollo run" or "apollo deploy" and it should install those directories. I'm not seeing it, but we may have misunderstood each other.

cmdcolin commented 9 years ago

What I saw was that the apollo script was trying to run install_jbrowse.sh before the jbrowse folder had been copied to the "src/main/webapp/jbrowse" folder, which is where install_jbrowse.sh assumes that jbrowse is, so it was giving the error "cd: src/main/webapp/jbrowse: No such file or directory" as in the original post

So I think that "apollo deploy" should properly run install_jbrowse.sh now after the patch (however, I still find this step a little confusing because I feel like jbrowse scripts should be installed before apollo deploy is run)

cmdcolin commented 9 years ago

Some other notes:

1) apparently the ant copy task isn't preserving the executable permissions on the jbrowse bin folder when it does the copy, and since the install_jbrowse.sh script is grabbing the bin folder after the ant task, this becomes a little problematic: http://stackoverflow.com/questions/14603625/how-to-preserve-exec-file-in-ant-copy-task

2) we are also copying the jbrowse .git subdirectory during apollo deploy, so the war file becomes a little oversized

nathandunn commented 9 years ago

Both good catches. My intuition is that you can probably just use the chmod task in ant. Barring that, just using rsync to do the copy (excluding .git) would also work.

Nathan

On Dec 1, 2014, at 10:37 AM, Colin Diesh notifications@github.com wrote:

Some other notes:

1) apparently the ant copy task isn't preserving the executable permissions on the jbrowse bin folder when it does the copy, and since the install_jbrowse.sh script is grabbing the bin folder after the ant task, this becomes a little problematic: http://stackoverflow.com/questions/14603625/how-to-preserve-exec-file-in-ant-copy-task http://stackoverflow.com/questions/14603625/how-to-preserve-exec-file-in-ant-copy-task 2) we are also copying the jbrowse .git subdirectory during apollo deploy, so the war file becomes a little oversized

— Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/97#issuecomment-65112259.

cmdcolin commented 9 years ago

I guess it is actually not copying the .git directory...I had other things inside my github clone that were inflating the filesize. The other issue is solved using chmod in the install_jbrowse.sh now

nathandunn commented 9 years ago

I don't think that it works still. Test case:
1 - ./apollo clean-all 2 - ./apollo deploy

nathandunn commented 9 years ago

ndunn:Apollo% ./apollo clean-all [INFO] Scanning for projects... [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building Apollo 1.0.2 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ apollo --- [INFO] Deleting /Users/ndunn/repositories/Apollo/target [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.275 s [INFO] Finished at: 2014-12-01T13:49:33-08:00 [INFO] Final Memory: 6M/245M [INFO] ------------------------------------------------------------------------ ndunn:Apollo% ./apollo deploy [INFO] Scanning for projects... [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building Apollo 1.0.2 [INFO] ------------------------------------------------------------------------ [WARNING] The POM for gbol:resources:jar:1.0 is missing, no dependency information available [INFO] [INFO] --- maven-antrun-plugin:1.7:run (default) @ apollo --- [WARNING] Parameter tasks is deprecated, use target instead [INFO] Executing tasks

main:

copy-web-apollo-config: [echo] copying config ... [copy] Warning: Could not find file /Users/ndunn/repositories/Apollo/hibernate.xml to copy. [copy] Warning: Could not find file /Users/ndunn/repositories/Apollo/log4j2.json to copy. [copy] Warning: Could not find file /Users/ndunn/repositories/Apollo/log4j2-test.json to copy.

copy.apollo.plugin.webapp:

git.revision:

install-release-version: [echo] IS RELEASE 1.0.2 [copy] Copying 1 file to /Users/ndunn/repositories/Apollo/src/main/webapp

install-no-release-version:

install-version:

setup-jbrowse:

git.clone: [exec] Submodule 'src/FileSaver' (git://github.com/dkasenberg/FileSaver.js.git) registered for path 'src/FileSaver' [exec] Submodule 'src/dbind' (git://github.com/rbuels/dbind.git) registered for path 'src/dbind' [exec] Submodule 'src/dgrid' (git://github.com/SitePen/dgrid.git) registered for path 'src/dgrid' [exec] Submodule 'src/dijit' (https://github.com/dojo/dijit.git) registered for path 'src/dijit' [exec] Submodule 'src/dojo' (https://github.com/dojo/dojo.git) registered for path 'src/dojo' [exec] Submodule 'src/dojox' (https://github.com/dojo/dojox.git) registered for path 'src/dojox' [exec] Submodule 'src/jDataView' (git://github.com/rbuels/jDataView.git) registered for path 'src/jDataView' [exec] Submodule 'src/json-schema' (git://github.com/kriszyp/json-schema.git) registered for path 'src/json-schema' [exec] Submodule 'src/jszlib' (git://github.com/rbuels/jszlib.git) registered for path 'src/jszlib' [exec] Submodule 'src/lazyload' (git://github.com/rbuels/lazyload.git) registered for path 'src/lazyload' [exec] Submodule 'src/put-selector' (git://github.com/kriszyp/put-selector.git) registered for path 'src/put-selector' [exec] Submodule 'src/util' (https://github.com/dojo/util.git) registered for path 'src/util' [exec] Submodule 'src/xstyle' (git://github.com/kriszyp/xstyle.git) registered for path 'src/xstyle' [exec] Submodule path 'src/FileSaver': checked out '4f79d8e66662b63df4928bfce769cdafae846600' [exec] Submodule path 'src/dbind': checked out '2b70834f3b88227274f158358a9c6f0cd09070ac' [exec] Submodule path 'src/dgrid': checked out '77901232965572a7e955ee17168751be9e19fb1d' [exec] Submodule path 'src/dijit': checked out '623c3737f5115807a1b1296c0aead855091d31dc' [exec] Submodule path 'src/dojo': checked out 'e92c9e4fa5e3e78253dfcc7e1b9b4621f04b180b' [exec] Submodule path 'src/dojox': checked out 'e99b2428d87f15d03e6a8ba1f78d15486be75fa2' [exec] Submodule path 'src/jDataView': checked out 'db0893d468ba034fadbbb5700d4ed79ab0dc236e' [exec] Submodule path 'src/json-schema': checked out 'f56cecb21b176755ad91f58c1ccfa55e5fb93186' [exec] Submodule path 'src/jszlib': checked out '18cd14e592652c10f7b494b1e29f891b0a5590a4' [exec] Submodule path 'src/lazyload': checked out 'd428749c5400213340d65d6156f43224ee477586' [exec] Submodule path 'src/put-selector': checked out 'f64ede2230f913c0ca224dce03106c1edc0ec542' [exec] Submodule path 'src/util': checked out '1448ca077eb7c702da4d7130541e74267f5c4daa' [exec] Submodule path 'src/xstyle': checked out '5c457b479db2cfd05d8a16a2f092ff82c4a7add6'

copy.apollo.plugin.jbrowse: [echo] copying plugin to jbrowse git ... [copy] Copying 212 files to /Users/ndunn/repositories/Apollo/jbrowse-download/plugins/WebApollo [echo] Will be setting up jbrowse [copy] Copying 10485 files to /Users/ndunn/repositories/Apollo/src/main/webapp/jbrowse [copy] Copied 1737 empty directories to 1 empty directory under /Users/ndunn/repositories/Apollo/src/main/webapp/jbrowse

install.jbrowse.perl: [exec] Installing Perl prerequisites ... [exec] failed. See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

copy-resources: [INFO] Executed tasks [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ apollo --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 567 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ apollo --- [INFO] Compiling 434 source files to /Users/ndunn/repositories/Apollo/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ apollo --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 15 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ apollo --- [INFO] Compiling 25 source files to /Users/ndunn/repositories/Apollo/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ apollo --- [INFO] Surefire report directory: /Users/ndunn/repositories/Apollo/target/surefire-reports

T E S T S

Running org.bbop.apollo.it.AnnotationEditorServiceTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 sec Running org.bbop.apollo.it.AnnotationEditorServiceWithPersistentStorageTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.bbop.apollo.unit.AnnotationEditorTest ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console. Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.081 sec Running org.bbop.apollo.unit.AnnotationSessionTest Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec Running org.bbop.apollo.unit.BlastAlignmentTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.bbop.apollo.unit.BlatCommandLineTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.bbop.apollo.unit.FeatureLazyResiduesTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.001 sec Running org.bbop.apollo.unit.FormatUtilTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.bbop.apollo.unit.JEDatabaseTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.bbop.apollo.unit.JSONUtilTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.gmod.gbol.hibernate.AbstractGBOLHibernateTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.gmod.gbol.hibernate.BioObjectHandlerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.gmod.gbol.hibernate.FlybaseConfigurationTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.gmod.gbol.hibernate.FlybaseGenotypeTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.gmod.gbol.hibernate.HibernateHandlerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec Running org.gmod.gbol.unit.BioFeatureTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec Running org.gmod.gbol.unit.BioObjectConfigurationTest No CVTerms for class: foo Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec Running org.gmod.gbol.unit.FileHandlerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.gmod.gbol.unit.GFF3HandlerTest 13:51:57.538 [main] ERROR - Can't handle directive 'gff-version 3' yet. 13:51:57.539 [main] ERROR - Can't handle directive 'sequence-region 2LHet 1 190000' yet. Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 sec Running org.gmod.gbol.unit.SequenceUtilTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec

Results :

Tests run: 55, Failures: 0, Errors: 0, Skipped: 11

[INFO] [INFO] --- maven-war-plugin:2.3:war (default-war) @ apollo --- [INFO] Packaging webapp [INFO] Assembling webapp [apollo] in [/Users/ndunn/repositories/Apollo/target/apollo-1.0.2] [INFO] Processing war project [INFO] Copying webapp resources [/Users/ndunn/repositories/Apollo/src/main/webapp] [INFO] Webapp assembled in [4214 msecs] [INFO] Building war: /Users/ndunn/repositories/Apollo/target/apollo-1.0.2.war [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:28 min [INFO] Finished at: 2014-12-01T13:52:08-08:00 [INFO] Final Memory: 26M/302M [INFO] ------------------------------------------------------------------------ ndunn:Apollo%

nathandunn commented 9 years ago

setup.log file from above output.

cd src/main/webapp/jbrowse
chmod +x bin/cpanm
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON /Users/ndunn/.cpanm/build.log: No such file or directory at /loader/0x7fa12181b108/App/cpanminus/script.pm line 224.
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON /Users/ndunn/.cpanm/build.log: No such file or directory at /loader/0x7fb10201cb08/App/cpanminus/script.pm line 224.
bin/cpanm -v --notest -l ../../../../extlib/ --installdeps . /Users/ndunn/.cpanm/build.log: No such file or directory at /loader/0x7fce350048c0/App/cpanminus/script.pm line 224.
bin/cpanm -v --notest -l ../../../../extlib/ --installdeps . /Users/ndunn/.cpanm/build.log: No such file or directory at /loader/0x7fa25301b0c0/App/cpanminus/script.pm line 224.
set -e
bin/cpanm -v --notest -l ../../../../extlib DBI DBD::Pg Crypt::PBKDF2 LWP::UserAgent JSON /Users/ndunn/.cpanm/build.log: No such file or directory at /loader/0x7ff69b81a108/App/cpanminus/script.pm line 224.

nathandunn commented 9 years ago

@cmdcolin I needed to blow out my ~/.cpanm directory . .. works now . . thanks!

GMOD / Apollo

not creating the jbrowse "bin" directory properly during deployment #97

T E S T S