solvebio 1.7.1 → 1.7.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 31db4c26b2c9b63dcbebbe8696a37b3e0946c831
+  data.tar.gz: 84b6c054b263fde61e0123c03eabbe9240cd4177
+SHA512:
+  metadata.gz: 6874a148c1e5a109981fdb3aa649437c58c8037232f3cbcdd25b9c31365290575c1a3f29ec6934710695aea5986f96ef419686b7eff07fad4cfcea153eb7a41d
+  data.tar.gz: 24f926d966b43b7ab239993169bfe35f87abfb1f0e0c9f3a4f93d91133e0a9b1647d31b253ecc18c8d645219ee1da631163dd6846a8142515704a6a1c2a8cd1c

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.1
+current_version = 1.7.2
 files = lib/solvebio/version.rb
 commit = True
 tag = False

data/Gemfile

@@ -3,7 +3,7 @@ source "https://rubygems.org"
 
 gem 'addressable'
 gem 'rest_client'
-gem 'netrc',  '~>0.7.7'  # rest_client needs netrc 0.7.7
+gem 'netrc', '~>0.7.7'  # rest_client needs netrc 0.7.7
 group :test do
     gem 'webmock'
 end

data/README.md

@@ -27,9 +27,7 @@ Installing from Git
 
 First, install dependencies:
 	
-    gem install rest_client
-    gem install addressable
-    gem install netrc
+    gem install rest_client addressable netrc
 
 Install from source:
 

data/Rakefile

@@ -25,7 +25,7 @@ end
 
 task :install => :gem do
   Dir.chdir(ROOT_DIR) do
-    sh %{gem install --both pkg/#{gemspec.file_name}}
+    sh %{gem install --dev --both pkg/#{gemspec.file_name}}
   end
 end
 

data/installer

@@ -43,20 +43,36 @@ function ctrl_c() {
 
 echo "    Installing SolveBio for Ruby..."
 echo
-echo "    IMPORTANT: Your computer's password may be required. It will NOT be sent to SolveBio."
 
 # Setup the log
 LOG=/tmp/solvebio-ruby.log
 echo "SolveBio Ruby Guided Installer log" > $LOG
 echo `date` >> $LOG
 
-# Are we installing or upgrading?
-if [ $(gem list | grep solvebio -c) -ne 0 ]; then
-    sudo gem update solvebio 2>&1 >> $LOG
-else
-    sudo gem install -q solvebio 2>&1 >> $LOG
+RUBY=`which ruby`
+
+if [ "$RUBY" == "" ]; then
+    echo "    Ruby is not installed. Please install Ruby before installing SolveBio for Ruby."
+    fail_exit
+fi
+
+GEM=`which gem`
+
+if [ "$RUBY" == "" ]; then
+    echo "    Ruby is not installed. Please install Ruby before installing SolveBio for Ruby."
+    fail_exit
+fi
+
+# TODO: check ruby and gem versions
+GEM_OWNER=`ls -l $GEM | awk '{ print $3 }'`
+
+if [ "$GEM_OWNER" == "root" ]; then
+    GEM="sudo ${GEM}"
+    echo "    IMPORTANT: Your computer's password may be required. It will NOT be sent to SolveBio."
 fi
 
+$GEM install solvebio 2>&1 >> $LOG
+
 if [ $? -eq 0 ]; then
     VERSION=`ruby -e "require 'solvebio'; print SolveBio::VERSION"`
     echo
@@ -68,6 +84,15 @@ if [ $? -eq 0 ]; then
     echo
     echo "    ##############################################"
     echo
+
+    # Detect old credentials in ~/.netrc (they will interfere with Ruby's Rest Client)
+    NETRC_WARN=`grep -c "solvebio" ~/.netrc`
+    if [ "$NETRC_WARN" -gt "0" ]; then
+        echo
+        echo "Warning: SolveBio credentials were found in ~/.netrc"
+        echo "Please delete the lines in ~/.netrc with SolveBio credentials."
+        echo
+    fi
 else
     fail_exit
 fi

data/lib/solvebio/cli/irbrc.rb

@@ -12,21 +12,14 @@ IRB.conf[:PROMPT][:SIMPLE] = {
 require 'solvebio'
 require 'solvebio/cli'
 
-have_completion = nil
 begin
-    require 'bond' and require 'bond/completion'
-    have_completion = 'bond'
+    require 'bond'
+    Bond.start
 rescue LoadError
     begin
-        have_completion = require 'irb/completion'
+        require 'irb/completion'
     rescue LoadError
-        have_completion = false
-    end
-end
-
-unless have_completion
-    if have_completion != 'bond'
-        puts "Please install the 'bond' getm for better autocompletion"
+        puts "To enable tab-completion, please install the 'bond' gem (gem install bond)."
     end
 end
 

data/lib/solvebio/filter.rb

@@ -144,9 +144,11 @@ module SolveBio
                         begin
                             value = Float(value)
                         rescue
-                            raise(TypeError,
-                                  "Invalid field value #{value} for #{key}; " +
-                                  "Should be a number")
+                            if /\d{4}-\d{2}-\d{2}/ !~ value
+                                raise(TypeError,
+                                      "Invalid field value #{value} for #{key}; " +
+                                      "Should be a number or a date in the format 'YYYY-MM-DD'.")
+                            end
                         end
                         tuple = [key, value]
                     when 'range'
@@ -230,10 +232,8 @@ module SolveBio
                         else
                             rv << {key => process_filters(val)}
                         end
-                    elsif f.kind_of?(Array)
-                        rv << f
                     else
-                        raise TypeError, "Invalid filter class #{f.class}"
+                        rv << f
                     end
                 end
             end
@@ -300,9 +300,9 @@ module SolveBio
             end
 
             if chromosome.nil?
-                f &= SolveBio::Filter.new({"chromosome" => nil})
+                f &= SolveBio::Filter.new({"#{FIELD_CHR}" => nil})
             else
-                f &= SolveBio::Filter.new({"chromosome" => chromosome.sub('chr', '')})
+                f &= SolveBio::Filter.new({"#{FIELD_CHR}" => chromosome.sub('chr', '')})
             end
 
             @filters = f.filters

data/lib/solvebio/query.rb

@@ -151,6 +151,9 @@ module SolveBio
             result = Tabulate.tabulate(buffer[0], ['Fields', 'Data'], ['right', 'left'], true)
             return "\n#{result}\n\n... #{(size - 1).pretty_int} more results."
         end
+        # Force inspect to always call to_s.
+        # This happens automatically in Ruby < 2.0.0
+        alias_method(:inspect, :to_s)
 
         # Convert SolveBio::QueryPaging object to a Hash type
         def to_h

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.1'
+    VERSION = '1.7.2'
 end

data/solvebio.gemspec

@@ -52,13 +52,12 @@ EOD
   ## List your runtime dependencies here. Runtime dependencies are those
   ## that are needed for an end user to actually USE your code.
 
-  s.add_dependency('netrc',   '>=0.7.7')      # handling .netrc
-  s.add_dependency('rest_client', '>=1.8.1')  # better URI handler
-  s.add_dependency('addressable', '>=2.3.6')  # better URI parsing
+  s.add_dependency('netrc', '~> 0.7')
+  s.add_dependency('rest_client', '~> 1.8', '>= 1.8.1')
+  s.add_dependency('addressable', '~> 2.3', '>= 2.3.6')
 
   ## List your development dependencies here. Development dependencies are
   ## those that are only needed during development
-  # s.add_development_dependency('DEVDEPNAME', [">= 1.1.0", "< 2.0.0"])
   s.add_development_dependency('rake')
   s.add_development_dependency('rdoc')
   s.add_development_dependency('webmock')

data/test/solvebio/test_filter.rb

@@ -49,7 +49,7 @@ module SolveBio
 
         def test_genomic_filter
             assert_equal(
-                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 13], ["genomic_coordinates.stop", 32200000], ["chromosome", "hg38"]]}]>',
+                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 13], ["genomic_coordinates.stop", 32200000], ["genomic_coordinates.chromosome", "hg38"]]}]>',
                          SolveBio::GenomicFilter.
                          new("hg38", "13", 32200000, 32500000).inspect)
         end
@@ -65,21 +65,21 @@ module SolveBio
         def test_genomic_single_position
             f = SolveBio::GenomicFilter.new('chr1', 100)
             assert_equal(
-                '<GenomicFilter [{:and=>[["genomic_coordinates.start__gte", 100.0], ["genomic_coordinates.start__lte", 100.0], ["chromosome", "1"]]}]>',
+                '<GenomicFilter [{:and=>[["genomic_coordinates.start__gte", 100.0], ["genomic_coordinates.start__lte", 100.0], ["genomic_coordinates.chromosome", "1"]]}]>',
                 f.inspect)
 
             f = SolveBio::GenomicFilter.new('chr1', 100, 100, true)
             assert_equal(
-                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 100], ["genomic_coordinates.stop", 100], ["chromosome", "1"]]}]>',
+                '<GenomicFilter [{:and=>[["genomic_coordinates.start", 100], ["genomic_coordinates.stop", 100], ["genomic_coordinates.chromosome", "1"]]}]>',
                 f.inspect)
         end
 
         def test_range
             f = SolveBio::GenomicFilter.new('chr1', 100, 200)
-            assert_equal('<GenomicFilter [{:and=>[{:or=>[{:and=>[["genomic_coordinates.start__gte", 200.0], ["genomic_coordinates.start__lte", 100.0]]}, ["genomic_coordinates.start__range", [100, 201]], ["genomic_coordinates.stop__range", [100, 201]]]}, ["chromosome", "1"]]}]>',
+            assert_equal('<GenomicFilter [{:and=>[{:or=>[{:and=>[["genomic_coordinates.start__gte", 200.0], ["genomic_coordinates.start__lte", 100.0]]}, ["genomic_coordinates.start__range", [100, 201]], ["genomic_coordinates.stop__range", [100, 201]]]}, ["genomic_coordinates.chromosome", "1"]]}]>',
                          f.inspect)
             f = SolveBio::GenomicFilter.new('chr1', 100, 200, true)
-            assert_equal('<GenomicFilter [{:and=>[["genomic_coordinates.start", 100], ["genomic_coordinates.stop", 200], ["chromosome", "1"]]}]>',
+            assert_equal('<GenomicFilter [{:and=>[["genomic_coordinates.start", 100], ["genomic_coordinates.stop", 200], ["genomic_coordinates.chromosome", "1"]]}]>',
                          f.inspect)
         end
     end

metadata

@@ -1,125 +1,118 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.1
-  prerelease: 
+  version: 1.7.2
 platform: ruby
 authors:
 - SolveBio
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-14 00:00:00.000000000 Z
+date: 2014-12-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.7.7
+        version: '0.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.7.7
+        version: '0.7'
 - !ruby/object:Gem::Dependency
   name: rest_client
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.1
 - !ruby/object:Gem::Dependency
   name: addressable
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.3.6
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.3'
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.3.6
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: webmock
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio you
-  can
-
+description: |
+  SolveBio is a platform for biomedical datasets. With SolveBio you can
   forget about parsing complex flat files and sifting through cryptic
-
   datasets. Just use the Ruby Client and API to explore massive
-
   datasets and automate just about any bioinformatics workflow.
 
-
   See https://www.solvebio.com/ for more information.
-
-'
 email: contact@solvebio.com
 executables:
 - solvebio.rb
@@ -127,9 +120,9 @@ extensions: []
 extra_rdoc_files:
 - LICENSE
 files:
-- .bumpversion.cfg
-- .gitignore
-- .travis.yml
+- ".bumpversion.cfg"
+- ".gitignore"
+- ".travis.yml"
 - Gemfile
 - Gemspec
 - LICENSE
@@ -194,26 +187,25 @@ files:
 homepage: https://www.solvebio.com
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options:
-- --charset=UTF-8
+- "--charset=UTF-8"
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.0
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.4.5
 signing_key: 
 specification_version: 2
 summary: Ruby bindings for the SolveBio API