solvebio 1.7.0 → 1.7.1

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.0
+current_version = 1.7.1
 files = lib/solvebio/version.rb
 commit = True
 tag = False

data/installer

@@ -22,7 +22,10 @@ function fail_exit() {
     echo "    #####################################"
     echo
     echo "    Failed to install SolveBio."
-    echo "    Contact us at support@solvebio.com"
+    echo "    Contact us at support@solvebio.com for help."
+    echo
+    echo "    In your email, please copy/paste the output of:"
+    echo "        cat ${LOG}"
     echo
     echo "    #####################################"
     echo
@@ -42,18 +45,24 @@ 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 -q solvebio 2>&1 > /dev/null
+    sudo gem update solvebio 2>&1 >> $LOG
 else
-    sudo gem install -q solvebio 2>&1 > /dev/null
+    sudo gem install -q solvebio 2>&1 >> $LOG
 fi
 
 if [ $? -eq 0 ]; then
+    VERSION=`ruby -e "require 'solvebio'; print SolveBio::VERSION"`
     echo
     echo "    ##############################################"
     echo
-    echo "    Success! SolveBio for Ruby is now installed."
+    echo "    Success! SolveBio for Ruby ${VERSION} is now installed."
     echo
     echo "    Please run 'solvebio.rb login' to finish the setup."
     echo

data/lib/solvebio/api_operations.rb

@@ -3,7 +3,7 @@ module SolveBio
         module Create
             module ClassMethods
                 def create(params={})
-                    response = Client.request('post', url, {:payload => params} )
+                    response = Client.post(url, params)
                     Util.to_solve_object(response)
                 end
             end
@@ -55,10 +55,7 @@ module SolveBio
 
                 path = Dir.tmpdir unless path
                 filename = File.join(path, filename)
-                response = nil
-
-                response = Client.get(download_url, :raw => true,
-                                                :default_headers => false)
+                response = Client.get(download_url, :raw => true, :auth => false, :default_headers => false)
 
                 File.open(filename, 'wb') do |fh|
                     fh.write(response.body)

data/lib/solvebio/cli/auth.rb

@@ -14,7 +14,7 @@ module SolveBio
             def ask_for_credentials()
                 print_message('Enter your SolveBio credentials')
                 email = Readline.readline('Email: ', true)
-                puts 'Password (typing will be hidden): '
+                print 'Password (typing will be hidden): '
                 password = STDIN.noecho(&:gets).chomp
                 puts
                 return email, password
@@ -29,7 +29,7 @@ module SolveBio
                     :ruby_implementation   => RbConfig::CONFIG['RUBY_SO_NAME'],
                     :architecture          => RbConfig::CONFIG['arch'],
                 }
-                Client.request('post', '/v1/reports/install', {:payload => data}) rescue nil
+                Client.post('/v1/reports/install', data) rescue nil
             end
 
             def login
@@ -46,7 +46,7 @@ module SolveBio
                 }
 
                 begin
-                    response = Client.post('/v1/auth/token', {:payload => data})
+                    response = Client.post('/v1/auth/token', data)
                 rescue SolveBio::SolveError => e
                     puts "Login failed: #{e.to_s}"
                     return false

data/lib/solvebio/client.rb

@@ -1,7 +1,7 @@
 module SolveBio
     class Client
-        attr_reader :headers, :api_host
-        attr_accessor :api_key
+        attr_reader :headers
+        attr_accessor :api_host, :api_key
 
         # Add our own kind of Authorization tokens. This has to be
         # done this way, late, because the rest-client gem looks for
@@ -13,8 +13,8 @@ module SolveBio
         end
 
         def initialize(api_key=nil, api_host=nil)
-            @api_key = api_key || SolveBio.api_key
-            @api_host = api_host || SolveBio.api_host
+            @api_key = api_key
+            @api_host = api_host
 
             # Mirroring comments from:
             # http://ruby-doc.org/stdlib-2.1.2/libdoc/net/http/rdoc/Net/HTTP.html
@@ -32,7 +32,9 @@ module SolveBio
 
         DEFAULT_REQUEST_OPTS = {
             :raw             => false,
-            :default_headers => true
+            :default_headers => true,
+            :auth            => true,
+            :json            => true
         }
 
         # Issues an HTTP GET across the wire via the Ruby 'rest-client'
@@ -44,14 +46,14 @@ module SolveBio
         # Issues an HTTP POST across the wire via the Ruby 'rest-client'
         # library. See *request* for information on opts.
         def post(url, data, opts={})
-            opts[:payload] =
-                if opts.member?(:no_json)
-                    data
-                else
-                    data.to_json
-                end
+            opts[:payload] = data
             request('post', url, opts)
         end
+        
+        def put(url, data, opts={})
+            opts[:payload] = data
+            request('put', url, opts)
+        end
 
         # Issues an HTTP Request across the wire via the Ruby 'rest-client'
         # library.
@@ -59,7 +61,8 @@ module SolveBio
             opts = DEFAULT_REQUEST_OPTS.merge(opts)
 
             # Expand URL with API host if none was given
-            api_host = @api_host or SolveBio.api_host
+            api_host = @api_host || SolveBio.api_host
+            api_key = opts[:auth] ? (@api_key || SolveBio.api_key) : nil
 
             if not api_host
                 raise SolveError.new('No SolveBio API host is set')
@@ -68,12 +71,12 @@ module SolveBio
             end
 
             # Handle some default options and add authorization header
-            if opts[:default_headers] and @api_key
-                headers = @headers.merge(opts[:headers]||{})
-                authorization = "Token #{@api_key}"
-            else
-                headers = nil
-                authorization = nil
+            headers = opts[:default_headers] ? @headers.merge(opts[:headers] || {}) : nil
+            authorization = api_key ? "Token #{api_key}" : nil
+
+            # By default, encode payload as JSON
+            if ['post', 'put', 'patch'].include?(method.downcase) and opts[:json]
+                opts[:payload] = opts[:payload].to_json
             end
 
             SolveBio::logger.debug('API %s Request: %s' % [method.upcase, url])
@@ -141,6 +144,10 @@ module SolveBio
         def self.post(url, data, opts={})
             client.post(url, data, opts)
         end
+        
+        def self.put(url, data, opts={})
+            client.put(url, data, opts)
+        end
 
         def self.request(method, url, opts={})
             client.request(method, url, opts)

data/lib/solvebio/sample.rb

@@ -35,7 +35,7 @@ module SolveBio
                 :genome_build  => genome_build,
                 :vcf_file => File.open(vcf_file, 'rb')
             }
-            response = Client.post(url, data, :no_json => true)
+            response = Client.post(url, data, :json => false)
             Util.to_solve_object(response)
         end
 

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.0'
+    VERSION = '1.7.1'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.0
+  version: 1.7.1
   prerelease: 
 platform: ruby
 authors: