openbel-api 1.0.1-java → 1.0.2-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -3,6 +3,19 @@ All notable changes to openbel-api will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [1.0.1][1.0.1] - 2016-06-08
+### Added
+- Renaming APIs and code on [new terminology][new terminology].
+
+- BEL specification version can be set in configuration file which controls the BEL version used as input/output. Affected APIs:
+
+  - */api/datasets*
+  - */api/expressions*
+  - */api/nanopubs*
+
+- Support storage of BEL 2.0 nanopubs.
+- Added */api/expressions/validation* API that returns syntax and signature validations for a BEL expression.
+
 ## [1.0.0][1.0.0] - TBD
 ### Added
 - Support JWT authentication via *token* query parameter ([PR #108][108]).
@@ -74,6 +87,7 @@ Datasets are stored with a URI computed from the scheme and host that is serving
   - Retrieve equivalent namespace values from the individual.
   - Retrieve orthologous namespace values from the individual.
 
+[1.0.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.1
 [1.0.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.2...1.0.0
 [0.6.2]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.1...0.6.2
 [0.6.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.0...0.6.1
@@ -91,3 +105,5 @@ Datasets are stored with a URI computed from the scheme and host that is serving
 [102]:                         https://github.com/OpenBEL/openbel-api/issues/102
 [105]:                         https://github.com/OpenBEL/openbel-api/issues/105
 [108]:                         https://github.com/OpenBEL/openbel-api/issues/108
+[new terminology]:             https://github.com/OpenBEL/openbel-api#vocabulary
+

data/README.md

@@ -223,6 +223,40 @@ server {
 
 API documentation with *Try it* functionality is available here [OpenBEL API documentation][OpenBEL API documentation].  You can download the [RAML 0.8][RAML] or Swagger specification files, try it on the webpage or generate curl, httpie, and various language templates for using the API.
 
+## Development
+
+### branches
+
+- master branch
+  - Contains stable code. Releases are created from this branch using a tag (e.g. `MAJOR.MINOR.PATCH`).
+
+- next branch
+  - Contains unstable code. Commits should be merged into master after it stabilizes.
+
+### releases
+
+Releases of *openbel-api* should follow these steps:
+
+1. Update the version in the `VERSION` file.
+
+2. Add changes for this version to the `CHANGELOG` file. This file is modelled after http://keepachangelog.com/.
+
+3. Push the changes for `VERSION` and `CHANGELOG` on the master branch.
+
+4. Ensure the *master* branch has all of the required changes.
+
+5. Create a git tag, named after the version, on the *master* branch. Push this tag to GitHub.
+
+6. Create the Ruby and Java RubyGem for *openbel-api*.
+
+  `gem build .gemspec`
+
+7. Create a release on GitHub for this version and attach the gem file.
+
+8. Push gems to RubyGems.
+
+  `gem push openbel-api-VERSION-java.gem`
+
 -----
 
 Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] community.

data/VERSION

@@ -1 +1 @@
-1.0.1
+1.0.2

data/app/openbel/api/routes/datasets.rb

@@ -71,6 +71,19 @@ module OpenBEL
 
         def check_dataset(io, type)
           begin
+
+            # See https://github.com/OpenBEL/openbel-api/issues/120
+            BEL.nanopub(io, type, :language => @bel_version).each do |nanopub|
+              BEL.object_convert(String, nanopub.to_h) { |str|
+                unless str.valid_encoding?
+                  msg = 'Invalid encoding. UTF-8 is required.'
+                  response = render_json({:status => 415, :msg => msg})
+                  halt(415, { 'Content-Type' => 'application/json' }, response)
+                end
+              }
+            end
+            io.rewind
+
             nanopub         = BEL.nanopub(io, type).each.first
 
             unless nanopub

data/lib/openbel/api/nanopub/mongo.rb

@@ -97,9 +97,7 @@ module OpenBEL
         references = @collection.aggregate(
           [
             {
-              :$project => {
-                "references.namespaces" => 1
-              }
+              :$project => {"references.namespaces" => 1}
             },
             {
               :$unwind => "$references.namespaces"
@@ -107,22 +105,30 @@ module OpenBEL
             {
               :$project => {
                 keyword: "$references.namespaces.keyword",
-                uri: "$references.namespaces.uri"
+                type:    "$references.namespaces.type",
+                domain:  "$references.namespaces.domain"
               }
             },
             {
               :$group => {
-                _id: "$keyword", uri: {
-                  :$addToSet => "$uri"
+                _id: "$keyword",
+                type: {
+                  :$addToSet => "$type"
+                },
+                domain: {
+                  :$addToSet => "$domain"
                 }
               }
             },
             {
-              :$unwind => "$uri"
+              :$unwind => "$type"
+            },
+            {
+              :$unwind => "$domain"
             },
             {
               :$project => {
-                keyword: "$_id", uri: "$uri", _id: 0
+                keyword: "$_id", type: "$type", domain: "$domain", _id: 0
               }
             }
           ],
@@ -135,10 +141,19 @@ module OpenBEL
         union = []
         remap = {}
         references.each do |obj|
-          obj = obj.to_h
-          obj[:keyword] = obj.delete("keyword")
-          obj[:uri]     = obj.delete("uri")
-          union, new_remap = BEL::Nanopub.union_namespace_references(union, [obj], 'incr')
+          keyword = obj['keyword']
+          type = obj['type']
+          domain = obj['domain']
+          uri = url = nil
+          if type == :url
+              url = domain
+          elsif type == :uri
+              uri = domain
+          end
+          args = [keyword, uri, url]
+          namespace = BELParser::Expression::Model::Namespace.new(*args)
+          union, new_remap =
+            BEL::Nanopub.union_namespace_references(union, [namespace], 'incr')
           remap.merge!(new_remap)
         end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.2
 platform: java
 authors:
 - Anthony Bargnesi