lagotto-rb 0.2.0

checksums.yaml

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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
+rvm:
+  - 2.1.7
+  - 2.2.3

data/CHANGELOG.md

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+## 0.2.0 (2016-01-08)
+
++ First version 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:
+    lagotto-rb (0.1.3.9000)
+      faraday (~> 0.9.1)
+      faraday_middleware (~> 0.10.0)
+      launchy (~> 2.4, >= 2.4.2)
+      multi_json (~> 1.0)
+      thor (~> 0.18)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.3.8)
+    codecov (0.1.1)
+      json
+      simplecov
+      url
+    docile (1.1.5)
+    faraday (0.9.2)
+      multipart-post (>= 1.2, < 3)
+    faraday_middleware (0.10.0)
+      faraday (>= 0.7.4, < 0.10)
+    json (1.8.3)
+    launchy (2.4.3)
+      addressable (~> 2.3)
+    multi_json (1.11.2)
+    multipart-post (2.0.0)
+    power_assert (0.2.4)
+    rake (0.9.6)
+    simplecov (0.10.0)
+      docile (~> 1.1.0)
+      json (~> 1.8)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    test-unit (3.1.3)
+      power_assert
+    thor (0.19.1)
+    url (0.3.2)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.6)
+  codecov (~> 0.1)
+  lagotto-rb!
+  rake (~> 0)
+  simplecov (~> 0.10)
+  test-unit (~> 3.1)
+
+BUNDLED WITH
+   1.10.6

data/LICENSE

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+Copyright (C) 2016 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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+lagotto-rb
+==========
+
+[![Build Status](https://api.travis-ci.org/lagotto/lagotto-rb.png)](https://travis-ci.org/lagotto/lagotto-rb)
+[![gem version](https://img.shields.io/gem/v/lagotto-rb.svg)](https://rubygems.org/gems/lagotto-rb)
+[![codecov.io](http://codecov.io/github/lagotto/lagotto-rb/coverage.svg?branch=master)](http://codecov.io/github/lagotto/lagotto-rb?branch=master)
+
+A Ruby client for the Lagotto application for article level metrics data
+
+__This is alpha software, so expect changes__
+
+Other Lagotto clients:
+
+* R - [alm](https://github.com/ropensci/alm)
+* Python - [pyalm](https://github.com/lagotto/pyalm)
+
+## Changes
+
+For changes see the [Changelog][changelog]
+
+## API
+
+Methods in relation to [Lagotto API][lapi] routes
+
+* `/works` - `Lagotto.works()`
+* `/works_sources` - `Lagotto.works_sources()`
+* `/events` - `Lagotto.events()`
+* `/publishers` - `Lagotto.publishers()`
+* `/groups` - `Lagotto.groups()`
+* `/references` - `Lagotto.references()`
+* `/work_types` - `Lagotto.work_types()`
+* `/docs` - `Lagotto.docs()`
+* `/relation_types` - `Lagotto.relation_types()`
+* `/sources` - `Lagotto.sources()`
+* `/recommendations` - `Lagotto.recommendations()`
+* `/status` - `Lagotto.status()`
+
+## Install
+
+### Release version
+
+```
+gem install lagotto-rb
+```
+
+### Development version
+
+Install dependencies
+
+```
+git clone git@github.com:sckott/serrano.git
+cd serrano
+rake install
+```
+
+### In Ruby repl
+
+Get altmetrics by DOI
+
+```ruby
+Lagotto.works(ids: 'http://doi.org/10.15468/DL.SQNY5P', instance: "crossref")
+```
+
+Search for altmetrics by source
+
+```ruby
+Lagotto.works(source: 'twitter', instance: "crossref")
+```
+
+Make a `/works` route request by source
+
+```ruby
+Lagotto.works_sources(source: 'twitter', per_page: 2)
+```
+
+Make a `/events` route request
+
+```ruby
+Lagotto.events(ids: '10.1371/journal.pone.0029797', instance: "crossref")
+```
+
+Make a `/publishers` route request
+
+```ruby
+Lagotto.publishers(id: 340)
+```
+
+Make a `/groups` route request
+
+```ruby
+Lagotto.groups()
+```
+
+Make a `/references` route request
+
+```ruby
+Lagotto.references(per_page: 5, instance: 'crossref')
+```
+
+### On the CLI
+
+```
+~$ lagotto
+Commands:
+  lagotto help [COMMAND]  # Describe available commands or one specific command
+  lagotto version         # Get lagotto-rb version
+  lagotto works [ids]     # Get works by ids
+```
+
+```
+# A single id
+~$ lagotto works http://doi.org/10.1371/journal.pone.0025110
+
+DOI: 10.1371/journal.pone.0033693
+type: journal-article
+title: Methylphenidate Exposure Induces Dopamine Neuron Loss and Activation of Microglia in the Basal Ganglia of Mice
+
+# JSON output
+~$ lagotto works --limit=2 --json
+
+{"meta":{"status":"ok","message-type":"work-list", ...
+
+# JSON output, parse with jq
+~$ lagotto works --limit=2 --json | jq .works[].DOI
+
+"10.1371/journal.pgen.1005692"
+"10.1371/journal.pgen.1005425"
+```
+
+## 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
+
+[lapi]: http://alm.plos.org/docs/api
+[changelog]: https://github.com/lagotto/lagotto-rb/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
+end
+
+desc "Run tests"
+task :default => :test
+
+desc "Build lagotto-rb docs"
+task :docs do
+	system "yardoc"
+end
+
+desc "bundle install"
+task :b do
+  system "bundle install"
+end
+
+desc "clean out builds"
+task :clean do
+  system "ls | grep [0-9].gem | xargs rm"
+end
+
+desc "Build lagotto-rb"
+task :build do
+	system "gem build lagotto-rb.gemspec"
+end
+
+desc "Install lagotto-rb"
+task :install => :build do
+	system "gem install lagotto-rb-#{Lagotto::VERSION}.gem"
+end
+
+desc "Release to Rubygems"
+task :release => :build do
+  system "gem push lagotto-rb-#{Lagotto::VERSION}.gem"
+end

data/bin/lagotto

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+#!/usr/bin/env ruby
+
+require "thor"
+require "lagotto-rb"
+require "multi_json"
+
+class Lg < Thor
+  include Thor::Actions
+  # class_option :json, :type => :boolean, :default => false
+
+  desc "works [ids]", "Get works by ids"
+  long_desc <<-LONGDESC
+    `lagotto works` accepts one or more ids to search for works
+
+    Toggle `json` to get simplified (summary) or complete output (JSON)
+
+    # A single id
+    \x5$ lagotto works http://doi.org/10.1371/journal.pone.0025110
+
+    DOI: 10.1371/journal.pone.0033693
+    \x5type: journal-article
+    \x5title: Methylphenidate Exposure Induces Dopamine Neuron Loss and Activation of Microglia in the Basal Ganglia of Mice
+
+    # No ids
+    \x5$ lagotto works --limit=2
+
+    DOI: 10.1371/journal.pone.0146052
+    \x5id: http://doi.org/10.1371/journal.pone.0146052
+    \x5title: What Do We Learn from Spheroid Culture Systems? Insights from Tumorspheres Derived from Primary Colon Cancer Tissue
+
+    DOI: 10.1371/journal.pone.0145401
+    \x5id: http://doi.org/10.1371/journal.pone.0145401
+    \x5title: Social Factors Influencing Child Health in Ghana
+
+    # JSON output
+    \x5$ lagotto works --limit=2 --json
+
+    {"meta":{"status":"ok","message-type":"work-list", ...
+
+    # JSON output, parse with jq
+    \x5$ lagotto works --limit=2 --json | jq .works[].DOI
+
+    "10.1371/journal.pgen.1005692"
+    \x5"10.1371/journal.pgen.1005425"
+  LONGDESC
+  option :limit, :type => :numeric, :default => 50
+  option :json, :type => :boolean, :default => false
+  def works(ids = nil)
+    puts ids
+    out = Lagotto.works(ids: ids, per_page: options[:limit])
+    if !options[:json]
+      if ids.nil?
+        out = out['works'].collect { |x| x.select { |k,v| k[/DOI|id|^title$/] } }
+      else
+        out = [out['works'][0].select { |k,v| k[/DOI|id|^title$/] }]
+      end
+      out.each do |x|
+        puts 'DOI: ' + x['DOI'].to_s
+        puts 'id: ' + x['id']
+        puts 'title: ' + x['title']
+        puts
+      end
+    else
+      puts MultiJson.encode(out)
+    end
+  end
+
+  desc "version", "Get lagotto-rb version"
+  def version
+    puts Lagotto::VERSION
+  end
+
+  private
+
+  def print_works(data)
+    if data.is_a? Array
+      data = data[0]['message']['items']
+    else
+      data = data.collect { |x| x['message'].select { |k,v| k[/DOI|type|title/] } }
+    end
+    data.each do |x|
+      puts 'DOI: ' + x['DOI']
+      puts 'type: ' + x['type']
+      puts 'title: ' + x['title'][0]
+      puts
+    end
+  end
+
+end
+
+Lg.start(ARGV)

data/examples/alerts.rb

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+require 'alm'
+
+# Get alerts data from a Lagotto instance
+Lagotto.alerts(user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+Lagotto.alerts(user: ENV["CROSSREF_ALERTS_USER"], pwd: ENV["CROSSREF_ALERTS_PWD"], instance: "crossref")
+Lagotto.alerts(user: ENV["PKP_ALERTS_USER"], pwd: ENV["PKP_ALERTS_PWD"], instance: "pkp")
+
+# Query for alerts
+Lagotto.alerts(q: 'timed', user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+
+# Filter to those unresolved
+Lagotto.alerts(unresolved: true, user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+
+# Filter by alert class name
+Lagotto.alerts(class_name: 'EventCountIncreasingTooFastError', user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+
+# Get alerts by DOI
+Lagotto.alerts(ids: "10.1371/journal.pone.0029797", user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+
+# Paging
+Lagotto.alerts(per_page: 2, user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+Lagotto.alerts(per_page: 2, page: 2, user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])
+
+# Filter by alert level (of severity)
+Lagotto.alerts(level: "error", user: ENV["PLOS_ALERTS_USER"], pwd: ENV["PLOS_ALERTS_PWD"])