bio-publisci 0.0.8 → 0.1.0

metadata

@@ -1,100 +1,214 @@
 --- !ruby/object:Gem::Specification
 name: bio-publisci
 version: !ruby/object:Gem::Version
-  version: 0.0.8
-  prerelease: 
+  version: 0.1.0
 platform: ruby
 authors:
 - Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-21 00:00:00.000000000 Z
+date: 2013-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf-4store
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdf-turtle
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdf-rdfxml
+  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: json-ld
+  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: rserve-client
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: sparql
   requirement: !ruby/object:Gem::Requirement
-    none: false
     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: slop
+  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: sinatra
+  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: sinatra-contrib
+  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: sinatra-linkeddata
+  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: sinatra-cross_origin
+  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: rack-flash3
+  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: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -102,7 +216,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -110,7 +223,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -118,7 +230,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -126,23 +237,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: cucumber
   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: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -150,7 +258,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -158,39 +265,34 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.21
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.0.21
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -198,7 +300,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -206,40 +307,37 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: spoon
   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: spira
   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: ! 'A toolkit for publishing scientific results and datasets using RDF,
+description: 'A toolkit for publishing scientific results and datasets using RDF,
   OWL, and related technologies '
 email: wstrinz@gmail.com
 executables:
 - bio-publisci
+- bio-publisci-server
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
@@ -255,6 +353,7 @@ files:
 - README.rdoc
 - Rakefile
 - bin/bio-publisci
+- bin/bio-publisci-server
 - examples/bio-band_integration.rb
 - examples/no_magic.prov
 - examples/no_magic.rb
@@ -320,11 +419,14 @@ files:
 - lib/bio-publisci/mixins/vocabulary.rb
 - lib/bio-publisci/output.rb
 - lib/bio-publisci/parser.rb
+- lib/bio-publisci/post_processor.rb
 - lib/bio-publisci/query/query_helper.rb
 - lib/bio-publisci/r_client.rb
 - lib/bio-publisci/readers/arff.rb
+- lib/bio-publisci/readers/base.rb
 - lib/bio-publisci/readers/csv.rb
 - lib/bio-publisci/readers/dataframe.rb
+- lib/bio-publisci/readers/maf.rb
 - lib/bio-publisci/readers/r_cross.rb
 - lib/bio-publisci/readers/r_matrix.rb
 - lib/bio-publisci/store.rb
@@ -332,6 +434,7 @@ files:
 - lib/bio-publisci/writers/base.rb
 - lib/bio-publisci/writers/csv.rb
 - lib/bio-publisci/writers/dataframe.rb
+- lib/bio-publisci/writers/json.rb
 - lib/r2rdf.rb
 - lib/template_bak.rb
 - lib/template_bak/publisci.rb
@@ -354,23 +457,72 @@ files:
 - lib/vocabs/wot.rb
 - lib/vocabs/xhtml.rb
 - lib/vocabs/xsd.rb
+- resources/maf_example.maf
+- resources/maf_rdf.ttl
+- resources/primer.ttl
 - resources/queries/code_resources.rq
 - resources/queries/codes.rq
 - resources/queries/dataset.rq
 - resources/queries/dimension_ranges.rq
 - resources/queries/dimensions.rq
+- resources/queries/gene.rq
+- resources/queries/hugo_to_ensembl.rq
+- resources/queries/maf_column.rq
 - resources/queries/measures.rq
 - resources/queries/observation_labels.rq
 - resources/queries/observations.rq
+- resources/queries/patient.rq
+- resources/queries/patient_list.rq
+- resources/queries/patients_with_mutation.rq
 - resources/queries/properties.rq
 - resources/queries/test.rq
 - resources/weather.numeric.arff
+- scripts/get_gene_lengths.rb
 - scripts/islet_mlratio.rb
 - scripts/scan_islet.rb
 - scripts/update_reference.rb
+- server/helpers.rb
+- server/public/src-min-noconflict/LICENSE
+- server/public/src-min-noconflict/ace.js
+- server/public/src-min-noconflict/ext-chromevox.js
+- server/public/src-min-noconflict/ext-elastic_tabstops_lite.js
+- server/public/src-min-noconflict/ext-emmet.js
+- server/public/src-min-noconflict/ext-keybinding_menu.js
+- server/public/src-min-noconflict/ext-language_tools.js
+- server/public/src-min-noconflict/ext-modelist.js
+- server/public/src-min-noconflict/ext-old_ie.js
+- server/public/src-min-noconflict/ext-searchbox.js
+- server/public/src-min-noconflict/ext-settings_menu.js
+- server/public/src-min-noconflict/ext-spellcheck.js
+- server/public/src-min-noconflict/ext-split.js
+- server/public/src-min-noconflict/ext-static_highlight.js
+- server/public/src-min-noconflict/ext-statusbar.js
+- server/public/src-min-noconflict/ext-textarea.js
+- server/public/src-min-noconflict/ext-themelist.js
+- server/public/src-min-noconflict/ext-whitespace.js
+- server/public/src-min-noconflict/keybinding-emacs.js
+- server/public/src-min-noconflict/keybinding-vim.js
+- server/public/src-min-noconflict/mode-ruby.js
+- server/public/src-min-noconflict/snippets/ruby.js
+- server/public/src-min-noconflict/theme-twilight.js
+- server/public/src-min-noconflict/worker-coffee.js
+- server/public/src-min-noconflict/worker-css.js
+- server/public/src-min-noconflict/worker-javascript.js
+- server/public/src-min-noconflict/worker-json.js
+- server/public/src-min-noconflict/worker-lua.js
+- server/public/src-min-noconflict/worker-php.js
+- server/public/src-min-noconflict/worker-xquery.js
+- server/routes.rb
+- server/views/dsl.haml
+- server/views/dump.haml
+- server/views/import.haml
+- server/views/new_repository.haml
+- server/views/query.haml
+- server/views/repository.haml
 - spec/ORM/data_cube_orm_spec.rb
 - spec/ORM/prov_model_spec.rb
 - spec/analyzer_spec.rb
+- spec/bnode_spec.rb
 - spec/csv/bacon.csv
 - spec/csv/moar_bacon.csv
 - spec/data_cube_spec.rb
@@ -378,8 +530,11 @@ files:
 - spec/dsl_spec.rb
 - spec/generators/csv_spec.rb
 - spec/generators/dataframe_spec.rb
+- spec/generators/maf_spec.rb
 - spec/generators/r_cross_spec.rb
 - spec/generators/r_matrix_spec.rb
+- spec/length_lookup_spec.rb
+- spec/maf_query_spec.rb
 - spec/metadata/metadata_dsl_spec.rb
 - spec/prov/activity_spec.rb
 - spec/prov/agent_spec.rb
@@ -410,29 +565,25 @@ files:
 homepage: http://github.com/wstrinz/bioruby-publisci
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -2716100516942950987
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Publish scientific results to the semantic web
 test_files: []