solvebio 1.7.2 → 1.7.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 84b6c054b263fde61e0123c03eabbe9240cd4177
+  metadata.gz: fe11b480aa4ded4563e8615f5aff700e65d79d28
+  data.tar.gz: 951035287b583008e5351229aa3c46f7ab3e4d7d
 SHA512:
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+  data.tar.gz: 4f56c1719d719818b2cecbe90923832edf0831eb9bfb9acbcaf61289553b2b91e910d8cea2640b191ba93531d96e39ece7c64cf02a96e470473fae0a5652929b

data/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.2
+current_version = 1.7.3
 files = lib/solvebio/version.rb
 commit = True
 tag = False

data/.travis.yml

@@ -1,4 +1,5 @@
 language: ruby
+sudo: false
 before_script:
 - gem install netrc --version=0.7.7
 - gem install rest_client addressable webmock

data/Rakefile

@@ -25,7 +25,8 @@ end
 
 task :install => :gem do
   Dir.chdir(ROOT_DIR) do
-    sh %{gem install --dev --both pkg/#{gemspec.file_name}}
+    sh %{gem install --both pkg/#{gemspec.file_name}}
+    # sh %{gem install --dev --both pkg/#{gemspec.file_name}}
   end
 end
 

data/lib/solvebio/api_operations.rb

@@ -108,23 +108,6 @@ module SolveBio
             def self.included base
                 base.extend ClassMethods
             end
-
-            def to_s
-                if self.class.constants.member?(:TAB_FIELDS)
-                    items = self.class.const_get(:TAB_FIELDS).map{
-                        |name| [name, self[name]]
-                    }
-                else
-                    items = self
-                end
-                return Tabulate.tabulate(items, ['Fields', 'Data'],
-                                                   ['right', 'left'], true)
-            end
-
-            def size
-                self[:total]
-            end
-            alias :total :size
         end
         
         module Search

data/lib/solvebio/cli/tutorial.md

@@ -0,0 +1,124 @@
+
+     ____        _           ____  _
+    / ___|  ___ | |_   _____| __ )(_) ___
+    \___ \ / _ \| \ \ / / _ \  _ \| |/ _ \
+     ___) | (_) | |\ V /  __/ |_) | | (_) |
+    |____/ \___/|_| \_/ \___|____/|_|\___/
+                                For Ruby
+
+
+# Welcome to the SolveBio Ruby Tutorial!
+
+First, open the SolveBio Ruby shell by typing "solvebio.rb".
+
+The SolveBio Ruby Shell is based on IRB. When you log in, it will automatically pick up your API key.
+
+View this tutorial online: https://www.solvebio.com/docs/ruby-tutorial
+
+
+## Navigate the Library
+
+List all available depositories:
+
+    Depository.all
+
+
+Depositories are versioned containers of datasets. There are many versions of each depository, and each version may have one or more datasets.
+
+To list all datasets from all depositories:
+
+    Dataset.all
+
+
+Pass "latest=true" to get all the latest versions of each dataset:
+
+    Dataset.all(:latest => true)
+
+
+To retrieve a dataset by its full name ("ClinVar/3.0.0-2014-12-05/Variants"):
+
+    Dataset.retrieve('ClinVar/3.0.0-2014-12-05/Variants')
+
+By leaving out the version (for example: "ClinVar/Variants"), you get a quick shortcut to the latest version of any dataset.
+**Be careful here: you should always specify an exact version in your production code**.
+
+
+## Query a Dataset
+
+Every dataset in SolveBio can be queried the same way. You can build queries manually in the Ruby shell, or use our visual Workbench (https://www.solvebio.com/workbench).
+
+In this example, we will query the latest Variants dataset from ClinVar.
+
+    dataset = Dataset.retrieve('ClinVar/Variants')
+    dataset.query
+
+
+The "query()" function returns a Ruby enumerable so you can loop through all the results easily.
+
+To examine a single result more closely, you may treat the query response as a list of dictionaries:
+
+    dataset.query[0]
+
+
+You can also slice the result set like any other Ruby array:
+
+    dataset.query[0..100]
+
+
+## Filter a Dataset
+
+To narrow down your query, you can filter on any field. For example, to get all variants in ClinVar that are Pathogenic, you would filter on the `clinical_significance` field for "Pathogenic":
+
+    dataset.query.filter(:clinical_significance => 'Pathogenic')
+
+
+By default, adding more filters will result in a boolean AND query (all filters must match):
+
+    dataset.query.filter(:clinical_significance => 'Pathogenic', :review_status => 'single')
+
+
+Use the "Filter" class to do more advanced filtering. For example, combine a few filters using boolean OR:
+
+    filters = Filter(:clinical_significance => 'Pathogenic') | Filter(:clinical_significance => 'Benign')
+    dataset.query.filter(filters)
+
+
+## Genomic Datasets
+
+Some SolveBio datasets allow querying by genome build. We call these "genomic datasets". To find out if a dataset is genomic, and what genome builds are supported:
+
+    dataset.is_genomic
+    > true
+    dataset.genome_builds
+    > ['GRCh38', 'GRCh37']
+
+
+By default, build 'GRCh37' will be selected if it is available. If not, the most recent build will be selected by default. To manually select a genome build when querying, specify the build as a query parameter:
+
+    dataset.query(:genome_build => 'GRCh38')
+
+
+On genomic datasets, you may query by position (single nucleotide) or by range:
+
+    dataset.query(:genome_build => 'GRCh37').position('chr1', 976629)
+    > ...
+    dataset.query(:genome_build => 'GRCh37').range('chr1', 976629, 1000000)
+    > ...
+
+
+Position and range queries return all results that overlap with the specified coordinate(s).
+Add the parameter `exact=true` to request exact matches.
+
+
+    dataset.query(:genome_build => 'GRCh37').position('chr1', 883516, exact=true)
+    > ...
+    dataset.query(:genome_build => 'GRCh37').range('chr9', 136289550, 136289579, exact=true)
+    > ...
+
+
+## Next Steps
+
+To learn more about a dataset and its fields, use `dataset.help()`.
+For more information on queries and filters, see the API reference: https://www.solvebio.com/docs/api?ruby
+
+

data/lib/solvebio/cli/tutorial.rb

@@ -2,11 +2,34 @@ module SolveBio
     module CLI
         module Tutorial
             def tutorial
-                puts <<-TUTORIAL
-    # Tutorial coming soon!
-    TUTORIAL
+                tutorial_file = File.join(File.dirname(__FILE__), "tutorial.md")
+                less = which('less') 
+                if less
+                    exec less + ' ' + tutorial_file
+                else
+                    puts File.read(tutorial_file)
+                    puts
+                    puts "#######################################################################"
+                    puts
+                    puts "Warning: 'less' command not found in $PATH."
+                    puts "Read the tutorial online at https://www.solvebio.com/docs/ruby-tutorial"
+                    puts
+                    puts "#######################################################################"
+                    puts
+                end
             end
             module_function :tutorial
+
+            def which(cmd)
+                exts = ENV['PATHEXT'] ? ENV['PATHEXT'].split(';') : ['']
+                ENV['PATH'].split(File::PATH_SEPARATOR).each do |path|
+                    exts.each { |ext|
+                        exe = File.join(path, "#{cmd}#{ext}")
+                        return exe if File.executable?(exe) && !File.directory?(exe)
+                    }
+                end
+                return nil
+            end
         end
     end
 end

data/lib/solvebio/client.rb

@@ -74,6 +74,11 @@ module SolveBio
             headers = opts[:default_headers] ? @headers.merge(opts[:headers] || {}) : nil
             authorization = api_key ? "Token #{api_key}" : nil
 
+            # In Rest-Client, GET params are parsed from headers[:params]
+            if opts[:params]
+                headers.merge!({:params => opts[:params]})
+            end
+
             # By default, encode payload as JSON
             if ['post', 'put', 'patch'].include?(method.downcase) and opts[:json]
                 opts[:payload] = opts[:payload].to_json

data/lib/solvebio/dataset.rb

@@ -6,6 +6,9 @@ module SolveBio
         include SolveBio::APIOperations::Delete
         include SolveBio::APIOperations::Help
 
+        LIST_FIELDS = [%w(full_name title description),
+                       %w(Name Title Description)]
+
         def depository
             return Depository.retrieve(self.depository)
         end

data/lib/solvebio/depository.rb

@@ -11,8 +11,11 @@ module SolveBio
         include SolveBio::APIOperations::Update
         include SolveBio::APIOperations::Help
 
+        @@permanent_attributes = Set.new([:id, :latest_version])
+
         # Fields that get shown by tabulate
-        TAB_FIELDS = %w(description full_name latest_version name title url)
+        LIST_FIELDS = [%w(full_name title description),
+                       %w(Name Title Description)]
 
         def versions(name=nil, params={})
             # construct the depo version full name
@@ -34,5 +37,9 @@ module SolveBio
             results
         end
 
+        def latest_version
+            return versions(self[:latest_version].split('/')[-1])
+        end
+
     end
 end

data/lib/solvebio/depository_version.rb

@@ -6,8 +6,8 @@ module SolveBio
         include SolveBio::APIOperations::Help
 
         # Fields that get shown by tabulate
-        TAB_FIELDS = %w(datasets_url depository description full_name
-                       latest url)
+        LIST_FIELDS = [%w(full_name title description),
+                       %w(Name Title Description)]
 
         def datasets_url(name=nil)
             name ||= self['name']

data/lib/solvebio/list_object.rb

@@ -1,6 +1,5 @@
 module SolveBio
     class ListObject < SolveObject
-
         def [](k)
             case k
             when String, Symbol
@@ -45,10 +44,26 @@ module SolveBio
             self.to_a[i]
         end
 
+        def size
+            self[:total]
+        end
+        alias :total :size
+
         def to_a
             return Util.to_solve_object(self.data)
         end
 
+        def to_s
+            if self.data[0] and self.data[0].class.constants.member?(:LIST_FIELDS)
+                # Tabulate the result list
+                fields, headers = self.data[0].class::LIST_FIELDS
+                items = self.data.map { |item| fields.map{ |field| item[field] } }
+                return "\n" + Tabulate.tabulate(items, headers)
+            end
+            super
+        end
+        alias :inspect :to_s
+
         def each(*pass)
             return self unless block_given?
             i = 0

data/lib/solvebio/query.rb

@@ -41,16 +41,15 @@ module SolveBio
             @filters      = params[:filters].kind_of?(SolveBio::Filter) ? params[:filters].filters : (params[:filters] || [])
 
             @response     = nil
-            # Limit defines the total number of results that will be returned
+            # limit defines the total number of results that will be returned
             # from a query involving 1 or more pagination requests.
             @limit        = params[:limit] || INT_MAX
-            # Page limit and page offset are the low level API limit and offset params.
-            # page_offset may be changed periodically during sequential pagination requests.
+            # page_size/page_offset are the low level API limit and offset params.
             @page_size   = params[:page_size] || DEFAULT_PAGE_SIZE
-            # Page offset can only be set by execute()
+            # page_offset can only be set by execute()
             # It always contains the current absolute offset contained in the buffer.
             @page_offset  = nil
-            # @slice is set to tell the Query object that is being sliced and "def each" should not
+            # slice is set to tell the Query object that is being sliced and "def each" should not
             # reset the page_offset to 0 before iterating.
             @slice        = nil
 

data/lib/solvebio/tabulate.rb

@@ -3,6 +3,11 @@ module SolveBio
         TYPES = {NilClass => 0, Fixnum => 1, Float => 2, String => 4}
 
         INVISIBILE_CODES = %r{\\x1b\[\d*m}  # ANSI color codes
+        
+        def self.tty_cols
+            cols = (ENV['COLUMNS'].to_i || 80 rescue 80)
+            return cols > 0 ? cols : 80
+        end
 
         Line = Struct.new(:start, :hline, :sep, :last)
 
@@ -288,23 +293,21 @@ module SolveBio
             return rows, headers
         end
 
-        TTY_COLS = ENV['COLUMNS'].to_i || 80 rescue 80
         # Return a string which represents a row of data cells.
         def build_row(cells, padding, first, sep, last)
-
             pad = ' ' * padding
             padded_cells = cells.map{|cell| pad + cell + pad }
             rendered_cells = (first + padded_cells.join(sep) + last).rstrip
 
             # Enforce that we don't wrap lines by setting a max
             # limit on row width which is equal to TTY_COLS (see printing)
-            if rendered_cells.size > TTY_COLS
+            if rendered_cells.size > Tabulate.tty_cols
                 if not cells[-1].end_with?(' ') and not cells[-1].end_with?('-')
                     terminating_str = ' ... '
                 else
                     terminating_str = ''
                 end
-                prefix = rendered_cells[0..TTY_COLS - terminating_str.size - 2]
+                prefix = rendered_cells[0..Tabulate.tty_cols - terminating_str.size - 2]
                 rendered_cells = "%s%s%s" % [prefix, terminating_str, last]
             end
 
@@ -395,6 +398,7 @@ module SolveBio
                     end
                 end
             end
+
             return lines.join("\n")
         end
 
@@ -426,8 +430,11 @@ module SolveBio
             end
 
             # format rows and columns, convert numeric values to strings
-            cols = list_of_lists[0].zip(*list_of_lists[1..-1]) if
-                list_of_lists.size > 1
+            if list_of_lists.size == 1
+                cols = [[list_of_lists[0][0]], [list_of_lists[0][1]]]
+            else
+                cols = list_of_lists[0].zip(*list_of_lists[1..-1])
+            end
 
             coltypes = cols.map{|c| column_type(c)}
 
@@ -459,7 +466,7 @@ module SolveBio
             else
                 # align headers and add headers
                 minwidths =
-                    minwidths.zip(cols).map{|minw, c| [minw, c[0].send(width_fn)].max}
+                    minwidths.zip(cols).map{|minw, c| [minw, c ? c[0].send(width_fn) : 0].max}
                 headers   =
                     headers.zip(aligns, minwidths).map{|h, a, minw| align_header(h, a, minw)}
             end
@@ -471,9 +478,10 @@ module SolveBio
             # make sure values don't have newlines or tabs in them
             rows.each do |r|
                 r.each_with_index do |c, i|
-                    r[i] = c.gsub("\n", '').gsub("\t", '')
+                    r[i] = c.gsub("\n", '').gsub("\t", '').gsub("\r", '')
                 end
             end
+
             return format_table(tablefmt, headers, rows, minwidths, aligns)
         end
     end

data/lib/solvebio/version.rb

@@ -1,3 +1,3 @@
 module SolveBio
-    VERSION = '1.7.2'
+    VERSION = '1.7.3'
 end

data/test/solvebio/test_query_tabulate.rb

@@ -16,7 +16,7 @@ module SolveBio
         def test_query_tabulate
             old_verbose = $VERBOSE
             $VERBOSE=nil
-            SolveBio::Tabulate.const_set(:TTY_COLS, 66)
+            ENV['COLUMNS'] = "66"
             $VERBOSE=old_verbose
             dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
             results = dataset.query().filter(:hgnc_id => 2396)

data/test/solvebio/test_tabulate.rb

@@ -61,7 +61,7 @@ module SolveBio
         def test_tabulate
             old_verbose = $VERBOSE
             $VERBOSE=nil
-            SolveBio::Tabulate.const_set(:TTY_COLS, 80)
+            ENV['COLUMNS'] = "80"
             $VERBOSE=old_verbose
             tsv = simple_separated_format("\t")
             expected = <<-EOS

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: solvebio
 version: !ruby/object:Gem::Version
-  version: 1.7.2
+  version: 1.7.3
 platform: ruby
 authors:
 - SolveBio
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-15 00:00:00.000000000 Z
+date: 2014-12-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: netrc
@@ -140,6 +140,7 @@ files:
 - lib/solvebio/cli/credentials.rb
 - lib/solvebio/cli/irb.rb
 - lib/solvebio/cli/irbrc.rb
+- lib/solvebio/cli/tutorial.md
 - lib/solvebio/cli/tutorial.rb
 - lib/solvebio/client.rb
 - lib/solvebio/dataset.rb