I am trying to run the ruby plugin foo.rb as given on this link-http://logstash.net/docs/1.3.3/extending/example-add-a-new-filter .
As specified there I have created the ruby file inside /logstash-1.5.0.beta1/lib/logstash/filters/foo.rb
The command for running the conf file is given as-
% logstash --pluginpath . -f example.conf
What exactly should I write in the place of 'pluginpath'?
On specifying the path of foo.rb it is giving me the following errors-
Clamp::UsageError: Unrecognised option '--lib/logstash/filters/foo.rb'
signal_usage_error at /home/administrator/Softwares/logstash-1.5.0.beta1/vendor/bundle/jruby/1.9/gems/clamp-0.6.3/lib/clamp/command.rb:103
find_option at /home/administrator/Softwares/logstash-1.5.0.beta1/vendor/bundle/jruby/1.9/gems/clamp-0.6.3/lib/clamp/option/parsing.rb:62
parse_options at /home/administrator/Softwares/logstash-1.5.0.beta1/vendor/bundle/jruby/1.9/gems/clamp-0.6.3/lib/clamp/option/parsing.rb:28
parse at /home/administrator/Softwares/logstash-1.5.0.beta1/vendor/bundle/jruby/1.9/gems/clamp-0.6.3/lib/clamp/command.rb:52
run at /home/administrator/Softwares/logstash-1.5.0.beta1/lib/logstash/runner.rb:155
call at org/jruby/RubyProc.java:271
run at /home/administrator/Softwares/logstash-1.5.0.beta1/lib/logstash/runner.rb:171
call at org/jruby/RubyProc.java:271
initialize at /home/administrator/Softwares/logstash-1.5.0.beta1/vendor/bundle/jruby/1.9/gems/stud-0.0.18/lib/stud/task.rb:12
What should I do? Thanks in advance! :)
Related
My goal is to use bcftools to check that the reference alleles in my dataset (vcf file) match with a reference genome (fasta file) using the fixref plugin.
Working on command line, I first set the following environment:
export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
The following code is recommended for test datasets with mismatches:
bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m top
When I run this code using my own files (please note that my data is .vcf, not .bcf) I get the following error:
[main] Unrecognized command
If I simply enter:
bcftools
I get a list of the only 5 commands (view, index, cat, ld, ldpair) that I can use. So although I've set the environment, does it somehow need to be activated? Do I need to run my command through a bash script?
bcftools
was pointing to a deprecated version of bcftools (0.1.19) in ../bin/, while
BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
was pointing to the plugins for bcftools version 1.10.2 outside /bin/
Replacing ../bin/bcftools (0.1.19 with 1.10.2) was the fix.
I get the below error when I use pyspark via Zeppelin.
The python & spark interpreters work and all environment variables are set correctly.
print os.environ['PYTHONPATH']
/x01/spark_u/spark/python:/x01/spark_u/spark/python/lib/py4j-0.10.4-src.zip:/x01/spark_u/spark/python:/x01/spark_u/spark/python/lib/py4j-0.10.4-src.zip:/x01/spark_u/spark/python/lib/py4j-0.10.4-src.zip:/x01/spark_u/spark/python/lib/pyspark.zip:/x01/spark_u/spark/python:/x01/spark_u/spark/python/pyspark:/x01/spark_u/zeppelin/interpreter/python/py4j-0.9.2/src:/x01/spark_u/zeppelin/interpreter/lib/python
zepplin-env.sh is set with the below vars
export PYSPARK_PYTHON=/usr/local/bin/python2
export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/py4j-0.10.4-src.zip:${PYTHONPATH}
export SPARK_YARN_USER_ENV="PYTHONPATH=${PYTHONPATH}"
See the below log file
INFO [2017-11-01 12:30:42,972] ({pool-2-thread-4}
RemoteInterpreter.java[init]:221) - Create remote interpreter
org.apache.zeppelin.spark.PySparkInterpreter
org.apache.zeppelin.interpreter.InterpreterException:
paragraph_1509038605940_-1717438251's Interpreter pyspark not
found
Thank you in advance
I found a workaround for the above issue.The interpreter not found issue does not happen when I create note inside a directory.The issue only happens when I use notes at toplevel.Addionally I foud out that this issue does not happen in 0.7.2 version
Ex :
enter image description here
I followed this quickstart:
https://docs.prediction.io/templates/classification/quickstart/
and this document for evaluation metrics
https://docs.prediction.io/evaluation/paramtuning/
Everything seems ok until the step build and run evaluation metrics
pio eval org.template.classification.AccuracyEvaluation \
org.template.classification.EngineParamsList
I am getting the exception:
Exception in thread "main" scala.reflect.internal.MissingRequirementError: object org.template.classification.AccuracyEvaluation not found.
at scala.reflect.internal.MissingRequirementError$.signal(MissingRequirementError.scala:16)
at scala.reflect.internal.MissingRequirementError$.notFound(MissingRequirementError.scala:17)
at scala.reflect.internal.Mirrors$RootsBase.ensureModuleSymbol(Mirrors.scala:126)
at scala.reflect.internal.Mirrors$RootsBase.staticModule(Mirrors.scala:161)
at scala.reflect.internal.Mirrors$RootsBase.staticModule(Mirrors.scala:21)
at io.prediction.workflow.WorkflowUtils$.getEvaluation(WorkflowUtils.scala:103)
at io.prediction.workflow.CreateWorkflow$$anonfun$19.apply(CreateWorkflow.scala:146)
at io.prediction.workflow.CreateWorkflow$$anonfun$19.apply(CreateWorkflow.scala:144)
Could anyone help me with this?
Thank you very much.
Had the exact same problem. Fixed it by doing the following:
For each .scala file in engine_dir/src/main/scala/org/template/engine_name/ you need to change the first line from...
package <SomeTemplateName>
To the following (replacing engine_name with the name of the folder in the path mentioned above):
package org.template.<engine_name>
Then, in engine.json you need to change the following line...
"engineFactory": "<template name>.<template engine>",
To the following (once again replacing engine_name with the name of the folder in the path mentioned above):
"engineFactory": "org.template.<engine name>.<template engine>",
Now re-run...
pio build
pio train
pio deploy
Then you should be able to run the model evaluation without errors.
Simply run it like this
$ pio eval org.example.classification.AccuracyEvaluation \
org.example.classification.EngineParamsList
You dont have to change anything. The class package from the sample was org.example.classification not org.template.classification
So every example I've looked up indicates this is how one is supposed to do it but I think I may have found a bug unless there's another way to do this.
I'm using upload! to upload assets to a remote list of servers. The task looks like this:
desc "Upload grunt compiled css/js."
task :upload_assets do
on roles(:all) do
%w{/htdocs/css /htdocs/js}.each do |asset|
upload! "#{fetch(:local_path) + asset}", "#{release_path.to_s + '/' + asset}", recursive: true
end
end
end
If local_path is defined as an absolute path such as:
set :local_path:, '/home/dcmbrown/projects/ABC'
This works fine. However if I do the following:
set :local_path:, '~/projects/ABC'
I end up getting the error:
The deploy has failed with an error: Exception while executing on ec2-54-23-88-125.us-west-2.compute.amazon.com: No such file or directory - ~/projects/ABC/htdocs/css
It's not a ' vs " issue as I've tried both (and I didn't think capistrano paid attention to that anyway).
Is this a bug? Is there a work around? Am I just doing it wrong?
I ended up discovering the best way to do this is to actually use path expansion! (headsmack)
irb> File.expand_path('~dcmbrown/projects/ABC')
=> "/home/dcmbrown/projects/ABC"
Of course what I'd like is to do automatic path expansion but you can't have everything. I think I was mostly dumbstruck that it didn't automatically; so much so I spent a couple of hours trying to figure out why it didn't work and ended up wasting time asking here. :(
I don't think the error is coming from the remote server, it just looks like it since it's running that upload command in the context of a deploy.
I just created a single cap task to just do an upload using the "~" character and it also fails with
cap aborted!
SSHKit::Runner::ExecuteError: Exception while executing as deploy#XXX: No such file or directory # rb_file_s_stat - ~/Projects/testapp/public/404.html
It appears to be a Ruby issue not Capistrano as this also fails in a Ruby console
~/Projects/testapp $ irb
2.2.2 :003 > File.stat('~/Projects/testapp/public/404.html')
Errno::ENOENT: No such file or directory # rb_file_s_stat - ~/Projects/testapp/public/404.html
from (irb):3:in `stat'
from (irb):3
from /Users/supairish/.rvm/rubies/ruby-2.2.2/bin/irb:11:in `<main>'
I am trying to load a graph in fuseki. The server is working as it should.
But when I try s-put inside the fuseki folder it tells me s-put is not found?!
hdeus$ ls
DEPENDENCIES config.ttl s-delete
Data fuseki s-get
LICENSE fuseki-server s-head
NOTICE fuseki-server.bat s-post
ReleaseNotes.txt fuseki-server.jar s-put
config-examples.ttl fuseki_config.ttl s-query
config-inf-tdb.ttl log4j.properties s-update
config-tdb.ttl pages s-update-form
hdeus$ sudo ./s-put http://localhost:3030/ds/data default Data/books.ttl
sudo: ./s-put: command not found
Any idea what the problem might be? I tried copy/paste s-put from the ls output but stil nothing... I am working in mac os X
Is the file executable? If you unpacked from the zip file, you need to set the s-* executable. Also, you need ruby installed.