miga-base 0.2.5.0 → 0.2.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 367ffd0c85c1ad5bdbc44f4c88677fac5268c2e2
-  data.tar.gz: eb107b14279ea252e4287d40efa73a562d890451
+  metadata.gz: 6e4ee273a974861fa4772912cc4699b266c52a4e
+  data.tar.gz: 71ba801f05ae2823eb8225241abb43568dc1c72c
 SHA512:
-  metadata.gz: 7a2bf0f148315cd6cc0fd57e5ff48a6f88cb5be7ebcaeea4e3b6a0b820cc71fca1165f98287fcd94ffd5b330e3e352281c9d517d66b2df3219a4af067854c0e4
-  data.tar.gz: c8d884b0c56d075179c38470e4d0a34316ad14706c9a88ac171fc0230811e863090ce3a7ab0330c5c871d6754f15c01cae6b177cb6cf68b13153c3979934ff2a
+  metadata.gz: c2cfbbd2b11e449dfc58be1c76a566352117d34e4e69e40459578270389e1d49e974eb655c9e265e0ed780ef3d668ff68abffc315f350d2769a6df8242fdeab9
+  data.tar.gz: 65ba7369fa9159d852fb3afe9f74ca5f1c71b4fc05c15bfa7ddb9e38d9db1ce95e3b3551fbe823684ee269d3fb696608026512218526f03a8f7227de665c12e9

data/lib/miga/dataset.rb

@@ -188,10 +188,10 @@ class MiGA::Dataset < MiGA::MiGA
   # or nil.
   def add_result(result_type, save=true)
     return nil if @@RESULT_DIRS[result_type].nil?
-    base = project.path + "/data/" + @@RESULT_DIRS[result_type] +
-      "/" + name
+    base = File.expand_path("data/#{@@RESULT_DIRS[result_type]}/#{name}",
+              project.path)
     r_pre = MiGA::Result.load("#{base}.json")
-    return r_pre unless r_pre.nil? or save
+    return r_pre if (r_pre.nil? and not save) or not r_pre.nil?
     return nil unless result_files_exist?(base, ".done")
     r = self.send("add_result_#{result_type}", base)
     r.save unless r.nil?

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.2, 5, 0]
+  VERSION = [0.2, 5, 1]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2017, 3, 29)
+  VERSION_DATE = Date.new(2017, 3, 31)
   
   ##
   # Reference of MiGA.

metadata

@@ -1,103 +1,103 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.2.5.0
+  version: 0.2.5.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-03-29 00:00:00.000000000 Z
+date: 2017-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.7'
 - !ruby/object:Gem::Dependency
   name: daemons
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.2'
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.2.4
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.8'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '11'
 - !ruby/object:Gem::Dependency
   name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3'
 description: Microbial Genomes Atlas
@@ -108,31 +108,6 @@ extensions: []
 extra_rdoc_files:
 - README.md
 files:
-- Gemfile
-- LICENSE
-- README.md
-- Rakefile
-- actions/add_result.rb
-- actions/add_taxonomy.rb
-- actions/create_dataset.rb
-- actions/create_project.rb
-- actions/daemon.rb
-- actions/date.rb
-- actions/download_dataset.rb
-- actions/find_datasets.rb
-- actions/import_datasets.rb
-- actions/index_taxonomy.rb
-- actions/list_datasets.rb
-- actions/list_files.rb
-- actions/plugins.rb
-- actions/project_info.rb
-- actions/result_stats.rb
-- actions/tax_distributions.rb
-- actions/unlink_dataset.rb
-- bin/miga
-- lib/miga.rb
-- lib/miga/_data/aai-intax.tsv.gz
-- lib/miga/_data/aai-novel.tsv.gz
 - lib/miga/common.rb
 - lib/miga/daemon.rb
 - lib/miga/dataset.rb
@@ -146,6 +121,18 @@ files:
 - lib/miga/tax_index.rb
 - lib/miga/taxonomy.rb
 - lib/miga/version.rb
+- lib/miga.rb
+- test/common_test.rb
+- test/daemon_test.rb
+- test/dataset_test.rb
+- test/metadata_test.rb
+- test/project_test.rb
+- test/remote_dataset_test.rb
+- test/tax_index_test.rb
+- test/taxonomy_test.rb
+- test/test_helper.rb
+- lib/miga/_data/aai-intax.tsv.gz
+- lib/miga/_data/aai-novel.tsv.gz
 - scripts/_distances_functions.bash
 - scripts/_distances_noref_nomulti.bash
 - scripts/_distances_ref_nomulti.bash
@@ -168,15 +155,6 @@ files:
 - scripts/subclades.bash
 - scripts/trimmed_fasta.bash
 - scripts/trimmed_reads.bash
-- test/common_test.rb
-- test/daemon_test.rb
-- test/dataset_test.rb
-- test/metadata_test.rb
-- test/project_test.rb
-- test/remote_dataset_test.rb
-- test/tax_index_test.rb
-- test/taxonomy_test.rb
-- test/test_helper.rb
 - utils/adapters.fa
 - utils/mytaxa_scan.R
 - utils/mytaxa_scan.rb
@@ -185,6 +163,28 @@ files:
 - utils/subclades-compile.rb
 - utils/subclades-nj.R
 - utils/subclades.R
+- bin/miga
+- actions/add_result.rb
+- actions/add_taxonomy.rb
+- actions/create_dataset.rb
+- actions/create_project.rb
+- actions/daemon.rb
+- actions/date.rb
+- actions/download_dataset.rb
+- actions/find_datasets.rb
+- actions/import_datasets.rb
+- actions/index_taxonomy.rb
+- actions/list_datasets.rb
+- actions/list_files.rb
+- actions/plugins.rb
+- actions/project_info.rb
+- actions/result_stats.rb
+- actions/tax_distributions.rb
+- actions/unlink_dataset.rb
+- Gemfile
+- Rakefile
+- README.md
+- LICENSE
 homepage: http://enve-omics.ce.gatech.edu/miga
 licenses:
 - Artistic-2.0
@@ -193,25 +193,25 @@ post_install_message:
 rdoc_options:
 - lib
 - README.md
-- "--main"
+- --main
 - README.md
-- "--title"
+- --title
 - MiGA
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '1.9'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.8
+rubygems_version: 2.0.14
 signing_key: 
 specification_version: 4
 summary: MiGA