phenoscaperb 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 7cdb4d2944c4a7754d8d8024b8528fd9c0470f75
+  data.tar.gz: 2b1cd5af6ef8938a9e60d8068f19f70a36efaf2c
+SHA512:
+  metadata.gz: c368c6a26ac0c956b00dcf34c94fffffb3c73bad358e291a7916b828bdd5e93966cc4e016549effc1c69fb752212cde056b6edd1dc479a49cd54dfb0776982f0
+  data.tar.gz: b13308c4e5a589b19559ac15f44ea191f7b008b0c7f4fbe99149ff7152a0e08a946ab662792405d51d5dd8561ccfc97e34d6524f333c59ba8f4fd711c33c48b7

data/.gitignore

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+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalisation:
+/.bundle/
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+#Gemfile.lock
+.ruby-version
+.ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+cache/
+
+lib/serrano/response.rb

data/.travis.yml

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+language: ruby
+cache: bundler
+rvm:
+  - 2.1.8
+  - 2.2.4
+  - 2.4.2
+script:
+  bundle exec rake test TESTOPTS="-v"

data/CHANGELOG.md

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+## 0.1.0 (2017-12-19)
+
+* First release to rubygems

data/CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant
+(http:contributor-covenant.org), version 1.0.0, available at
+http://contributor-covenant.org/version/1/0/0/

data/Gemfile

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+source 'https://rubygems.org'
+
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    phenoscaperb (0.1.0)
+      faraday (~> 0.12.0.1)
+      faraday_middleware (~> 0.11.0.1)
+      multi_json (~> 1.12, >= 1.12.1)
+      nokogiri (~> 1.8, >= 1.8.1)
+      thor (~> 0.20.0)
+      xml-to-hash (~> 1.0, >= 1.0.3)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.5.0)
+      public_suffix (~> 2.0, >= 2.0.2)
+    codecov (0.1.10)
+      json
+      simplecov
+      url
+    crack (0.4.3)
+      safe_yaml (~> 1.0.0)
+    docile (1.1.5)
+    faraday (0.12.0.1)
+      multipart-post (>= 1.2, < 3)
+    faraday_middleware (0.11.0.1)
+      faraday (>= 0.7.4, < 1.0)
+    hashdiff (0.3.2)
+    json (2.0.3)
+    mini_portile2 (2.3.0)
+    multi_json (1.12.2)
+    multipart-post (2.0.0)
+    nokogiri (1.8.1)
+      mini_portile2 (~> 2.3.0)
+    power_assert (0.3.1)
+    public_suffix (2.0.5)
+    rake (12.0.0)
+    safe_yaml (1.0.4)
+    simplecov (0.14.1)
+      docile (~> 1.1.0)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    test-unit (3.2.1)
+      power_assert
+    thor (0.20.0)
+    url (0.3.2)
+    vcr (3.0.3)
+    webmock (2.3.2)
+      addressable (>= 2.3.6)
+      crack (>= 0.3.2)
+      hashdiff
+    xml-to-hash (1.0.3)
+      nokogiri (~> 1, >= 1.6)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.14, >= 1.14.6)
+  codecov (~> 0.1.10)
+  json (~> 2.0, >= 2.0.3)
+  phenoscaperb!
+  rake (~> 12.0, >= 12.0.0)
+  simplecov (~> 0.14.1)
+  test-unit (~> 3.2, >= 3.2.1)
+  vcr (~> 3.0, >= 3.0.3)
+  webmock (~> 2.3, >= 2.3.2)
+
+BUNDLED WITH
+   1.16.0

data/LICENSE

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+Copyright (C) 2017 Scott Chamberlain
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+phenoscaperb
+============
+
+[![gem version](https://img.shields.io/gem/v/phenoscaperb.svg)](https://rubygems.org/gems/phenoscaperb)
+[![Build Status](https://travis-ci.org/phenoscape/phenoscaperb.svg?branch=master)](https://travis-ci.org/phenoscape/phenoscaperb)
+[![codecov.io](http://codecov.io/github/phenoscape/phenoscaperb/coverage.svg?branch=master)](http://codecov.io/github/phenoscape/phenoscaperb?branch=master)
+
+`phenoscaperb` is a low level client for the [Phenoscape API][phenoscapeapi]
+
+[Phenoscape][] is a datastore of computable phenotypes for studies of evolution and genetics.
+
+## Changes
+
+For changes see the [Changelog][changelog]
+
+## API
+
+Taxa
+
+* `/taxon` - `Phenoscape::Taxon.taxon`
+* `/taxon/with_rank` - `Phenoscape::Taxon.taxon_with_rank`
+* `/taxon/with_phenotype` - `Phenoscape::Taxon.with_phenotype`
+* `/taxon/annotations` - `Phenoscape::Taxon.annotations`
+
+Genes
+
+* `/gene` - `Phenoscape::Gene.gene`
+* `/gene/search` - `Phenoscape::Gene.search`
+* `/gene/affecting_entity_phenotype` - `Phenoscape::Gene.affecting_entity_phenotype`
+
+Terms
+
+* `/term` - `Phenoscape::Terms.term`
+* `/term/search` - `Phenoscape::Terms.search`
+* `/term/search_classes` - `Phenoscape::Terms.search_classes`
+* `/term/label` - `Phenoscape::Terms.label`
+* `/term/labels` - `Phenoscape::Terms.labels`
+* `/term/classification` - `Phenoscape::Terms.classification`
+* `/term/all_ancestors` - `Phenoscape::Terms.all_ancestors`
+* `/term/all_descendants` - `Phenoscape::Terms.all_descendants`
+* `/term/least_common_subsumers` - `Phenoscape::Terms.least_common_subsumers`
+
+Ontotrace
+
+* `/ontotrace` - `Phenoscape::Ontotrace.ontotrace`
+
+Studies
+
+* `/studies/query` - `Phenoscape::Studies.query`
+* `/studies/taxa` - `Phenoscape::Studies.taxa`
+* `/studies/phenotypes` - `Phenoscape::Studies.phenotypes`
+* `/studies/matrix` - `Phenoscape::Studies.matrix`
+
+## Install
+
+### Development version
+
+```
+git clone git@github.com:phenoscape/phenoscaperb.git
+cd phenoscaperb
+rake install
+```
+
+### Release version
+
+```
+gem install phenoscaperb
+```
+
+## Setup
+
+This is most likely not needed ...
+
+You can swap out the base URL by passing named options in a block to `Phenoscape.configuration`.
+
+This will also be the way to set up other user options, if any are needed down the road (though `base_url` is the only one right now).
+
+```ruby
+Phenoscape.configuration do |config|
+  config.base_url = "the new url"
+end
+```
+
+## in Ruby
+
+A few examples
+
+`Phenoscape::Taxa.taxon`
+
+```ruby
+require 'phenoscaperb'
+tax = Phenoscape::Taxa
+tax.taxon(iri: "http://purl.obolibrary.org/obo/VTO_0067193")
+#> => {"rank"=>{"@id"=>"http://purl.obolibrary.org/obo/TAXRANK_0000006", "label"=>"species"},
+#>  "label"=>"Apterichtus equatorialis",
+#>  "extinct"=>false,
+#>  "common_name"=>"Finless eel",
+#>  "@id"=>"http://purl.obolibrary.org/obo/VTO_0067193"}
+```
+
+`Phenoscape::Genes.gene`
+
+```ruby
+require 'phenoscaperb'
+ge = Phenoscape::Genes
+ge.gene(iri: "http://www.informatics.jax.org/marker/MGI:104842")
+#> => {"@id"=>"http://www.informatics.jax.org/marker/MGI:104842", "label"=>"Coil", "taxon"=>{"@id"=>"http://purl.obolibrary.org/obo/NCBITaxon_10090", "label"=>"Mus musculus"}}
+```
+
+`Phenoscape::Ontotrace.ontotrace`
+
+```ruby
+require 'phenoscaperb'
+onto = Phenoscape::Ontotrace
+onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>", ret: "text")
+#> => <?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n<nexml xmlns=\"http://www.nexml.org/2009\" xmlns:dc=\"http://purl.org/dc/terms/\" xmlns:dwc=\"http://rs.tdwg.org/dwc/terms/\" xmlns:obo=\"http://purl.obolibrary.org/obo/\" xmlns:ps=\"http://vocab.phenoscape.org/\" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" version=\"0.9\" xsi:schemaLocation=\"http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd http://www.bioontologies.org/obd/schema/pheno http://purl.org/phenoscape/phenoxml.xsd\">\r\n  <meta xsi:type=\"LiteralMeta\" property=\"dc:creator\" />\r\n  <meta xsi:type=\"LiteralMeta\" property=\"dc:description\">Generated from the Phenoscape Knowledgebase on 2017-12-19 by Ontotrace query:\r\n* taxa: &lt;http://purl.obolibrary.org/obo/VTO_0058051&gt;\r\n* entities: &lt;http://purl.obolibrary.org/obo/BFO_0000050&gt;</meta>\r\n  <otus id=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\" />\r\n  <characters id=\"c49fb5508-08a8-4252-93eb-50ac042eca46\" xsi:type=\"StandardCells\" otus=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\">\r\n    <format />\r\n    <matrix />\r\n  </characters>\r\n  <trees id=\"t416da46f-0871-4c9a-ae39-43edbe473b6d\" otus=\"t4813128d-4f2b-417f-bf5a-d568dd584a64\" />\r\n</nexml>\r\n
+```
+
+## cli
+
+cli options thus far
+
+* `ph version`
+* `ph taxon`
+* `ph term`
+
+For the `jq` command line tool see <https://stedolan.github.io/jq/>
+
+```
+ph taxon http://purl.obolibrary.org/obo/VTO_0067193 | jq .
+```
+
+```
+{
+  "rank": {
+    "@id": "http://purl.obolibrary.org/obo/TAXRANK_0000006",
+    "label": "species"
+  },
+  "label": "Apterichtus equatorialis",
+  "extinct": false,
+  "common_name": "Finless eel",
+  "@id": "http://purl.obolibrary.org/obo/VTO_0067193"
+}
+```
+
+## Meta
+
+* Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+* License: MIT
+
+[Phenoscape]: http://kb.phenoscape.org
+[phenoscapeapi]: http://kb.phenoscape.org/apidocs/#/
+[changelog]: https://github.com/sckott/phenoscaperb/blob/master/CHANGELOG.md

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/test-*.rb']
+  t.verbose = true
+  t.warning = false
+end
+
+desc "Run tests"
+task :default => :test
+
+desc "Build phenoscaperb docs"
+task :docs do
+	system "yardoc"
+end
+
+desc "bundle install"
+task :bundle do
+  system "bundle install"
+end
+
+desc "clean out builds"
+task :clean do
+  system "ls | grep [0-9].gem | xargs rm"
+end
+
+desc "Build phenoscaperb"
+task :build do
+	system "gem build phenoscaperb.gemspec"
+end
+
+desc "Install phenoscaperb"
+task :install => [:bundle, :build] do
+	system "gem install phenoscaperb-#{Phenoscape::VERSION}.gem"
+end
+
+desc "Release to Rubygems"
+task :release => :build do
+  system "gem push phenoscaperb-#{Phenoscape::VERSION}.gem"
+end

data/bin/ph

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+#!/usr/bin/env ruby
+
+require "thor"
+require "phenoscaperb"
+require "multi_json"
+
+class Sr < Thor
+  include Thor::Actions
+  # class_option :json, :type => :boolean, :default => false
+
+  desc "taxon [IRI]", "Get taxon by taxon IRI"
+  long_desc <<-LONGDESC
+    `ph taxon` accepts an IRI to search for taxa
+
+    \x5$ ph taxon http://purl.obolibrary.org/obo/VTO_0067193
+
+    {"rank":{"@id":"http://purl.obolibrary.org/obo/TAXRANK_0000006","label":"species"},"label":"Apterichtus equatorialis","extinct":false,"common_name":"Finless eel","@id":"http://purl.obolibrary.org/obo/VTO_0067193"}
+  LONGDESC
+  option :iri, :type => :string
+  def taxon(iri=nil)
+    tax = Phenoscape::Taxa
+    puts MultiJson.encode(tax.taxon(iri: iri))
+  end
+
+  desc "term [IRI]", "Info for a term"
+  long_desc <<-LONGDESC    
+    `ph term` accepts a term IRI
+
+    \x5$ ph term http://purl.obolibrary.org/obo/UBERON_0011618
+
+    {"@id":"http://purl.obolibrary.org/obo/UBERON_0011618","label":"basihyal bone","definition":"Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch.","relationships":[{"property":{"@id":"http://purl.obolibrary.org/obo/RO_0002202","label":"develops from"},"value":{"@id":"http://purl.obolibrary.org/obo/UBERON_0011615","label":"basihyal cartilage"}}]}
+  LONGDESC
+  option :iri, :type => :string
+  def term(iri=nil)
+    tm = Phenoscape::Terms
+    puts MultiJson.encode(tm.term(iri: iri))
+  end
+
+  desc "version", "Get phenoscaperb version"
+  def version
+    puts Phenoscape::VERSION
+  end
+
+end
+
+Sr.start(ARGV)

data/lib/phenoscaperb.rb

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+require "phenoscaperb/version"
+require "phenoscaperb/request"
+require "phenoscaperb/Taxa"
+require "phenoscaperb/Ontotrace"
+require "phenoscaperb/Terms"
+require "phenoscaperb/Genes"
+require "phenoscaperb/Studies"
+
+# @!macro phenoscape_params
+#   @param verbose [Boolean] Print request headers to stdout. Default: false
+
+# @!macro phenoscape_options
+#   @param options [Hash] Hash of options for configuring the request, passed on to Faraday.new
+#     - timeout [Fixnum] open/read timeout Integer in seconds
+#     - open_timeout [Fixnum] read timeout Integer in seconds
+#     - proxy [Hash] hash of proxy options
+#       - uri [String] Proxy Server URI
+#       - user [String] Proxy server username
+#       - password [String] Proxy server password
+#     - params_encoder [Hash] not sure what this is
+#     - bind [Hash] A hash with host and port values
+#     - boundary [String] of the boundary value
+#     - oauth [Hash] A hash with OAuth details
+
+##
+# Phenoscape - The top level module for using methods to access the Phenoscape API
+
+module Phenoscape
+  extend Configuration
+
+  define_setting :base_url, "http://kb.phenoscape.org/api"
+
+end