rbbt-util 5.5.16 → 5.5.17

checksums.yaml

@@ -1,7 +1,15 @@
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data/lib/rbbt/workflow.rb

@@ -119,7 +119,7 @@ module Workflow
     Log.info{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
     require_local_workflow(Misc.snake_case(wf_name)) or 
-    (Workflow.autoinstall and `rbbt install workflow #{Misc.snake_case(wf_name)}` and require_local_workflow(Misc.snake_case(wf_name))) or
+    (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)}` and require_local_workflow(Misc.snake_case(wf_name))) or
     raise("Workflow not found or could not be loaded: #{ wf_name }")
   end
 

data/share/rbbt_commands/app/install

@@ -0,0 +1,27 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+require 'rbbt-util'
+require 'rbbt/workflow'
+
+app = ARGV[0]
+repo = ARGV[1]
+
+raise "No app specified" if app.nil?
+
+app_dir = Rbbt.etc.app_dir.exists? ? Rbbt.etc.app_dir.read.strip : Rbbt.apps
+
+FileUtils.mkdir_p app_dir unless File.exists? app_dir
+
+Misc.in_dir(app_dir) do
+  if File.exists? app
+    `(cd #{ app }; git pull)`
+  else
+    if repo.nil?
+      repo_base_url = Rbbt.etc.app_repo.exists? ? Rbbt.etc.app_repo.read.strip : 'https://github.com/Rbbt-Apps/'
+      repo = File.join(repo_base_url, app + '.git')
+    end
+    Log.warn "Cloning #{ repo }"
+    `git clone "#{repo}"`
+  end
+end

data/share/rbbt_commands/file_server/add

@@ -0,0 +1,12 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+
+resource, url = ARGV
+
+config_file = Rbbt.etc.file_servers
+
+file_servers = config_file.exists? ? config_file.yaml : {}
+file_servers[resource] = url
+Open.write(config_file.find(:user), file_servers.to_yaml)
+

data/share/rbbt_commands/file_server/list

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+
+config_file = Rbbt.etc.file_servers
+raise "No file servers defined in #{Rbbt.etc.file_servers}" unless Rbbt.etc.file_servers.exists?
+config_file.yaml.sort_by{|k,v| k}.each do |resource, server|
+  puts [resource, server] * "\t"
+end
+

data/share/rbbt_commands/file_server/remove

@@ -0,0 +1,12 @@
+#!/usr/bin/env ruby
+
+require 'rbbt'
+
+resource = ARGV.first
+
+config_file = Rbbt.etc.file_servers
+
+file_servers = config_file.exists? ? config_file.yaml : {}
+file_servers.delete resource
+Open.write(config_file.find(:user), file_servers.to_yaml)
+

data/share/rbbt_commands/workflow/remote/add

@@ -2,7 +2,7 @@
 
 require 'rbbt'
 
-url, workflow = ARGV
+workflow, url = ARGV
 url = File.join(url, workflow) unless url =~ /\/#{workflow}$/
 config_file = Rbbt.etc.remote_workflows
 remote_workflows = config_file.exists? ? config_file.yaml : {}

metadata

@@ -1,55 +1,55 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.16
+  version: 5.5.17
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-05 00:00:00.000000000 Z
+date: 2013-11-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: lockfile
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
@@ -84,6 +84,16 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - LICENSE
+- README.rdoc
+- bin/rbbt
+- bin/rbbt_Rutil.rb
+- bin/rbbt_dangling_locks.rb
+- bin/rbbt_exec.rb
+- bin/rbbt_monitor.rb
+- bin/rbbt_query.rb
+- bin/run_workflow.rb
+- bin/tchash.rb
+- bin/tsv.rb
 - etc/app.d/base.rb
 - etc/app.d/entities.rb
 - etc/app.d/finder.rb
@@ -146,21 +156,24 @@ files:
 - share/Rlib/util.R
 - share/config.ru
 - share/install/software/lib/install_helpers
+- share/rbbt_commands/app/install
 - share/rbbt_commands/app/start
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list
 - share/rbbt_commands/conf/web_user/remove
-- share/rbbt_commands/install/workflow
+- share/rbbt_commands/file_server/add
+- share/rbbt_commands/file_server/list
+- share/rbbt_commands/file_server/remove
 - share/rbbt_commands/study/task
 - share/rbbt_commands/tsv/attach
 - share/rbbt_commands/tsv/change_id
 - share/rbbt_commands/tsv/info
+- share/rbbt_commands/workflow/install
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
-- README.rdoc
 - test/rbbt/association/test_index.rb
 - test/rbbt/resource/test_path.rb
 - test/rbbt/test_annotations.rb
@@ -179,6 +192,7 @@ files:
 - test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_util.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_cmd.rb
 - test/rbbt/util/test_colorize.rb
@@ -186,7 +200,6 @@ files:
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_R.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_tmpfile.rb
@@ -195,15 +208,6 @@ files:
 - test/rbbt/workflow/test_task.rb
 - test/test_helper.rb
 - test/test_rbbt.rb
-- bin/tsv.rb
-- bin/tchash.rb
-- bin/run_workflow.rb
-- bin/rbbt_query.rb
-- bin/rbbt_exec.rb
-- bin/rbbt_Rutil.rb
-- bin/rbbt_monitor.rb
-- bin/rbbt
-- bin/rbbt_dangling_locks.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
 metadata: {}
@@ -213,52 +217,52 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/association/test_index.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/test_soap.rb
 - test/rbbt/resource/test_path.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_resource.rb
 - test/rbbt/test_annotations.rb
-- test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_colorize.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/workflow/test_soap.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/test_task.rb
-- test/test_helper.rb
 - test/test_rbbt.rb
+- test/test_helper.rb