specify_cli 0.0.5

checksums.yaml

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data/.gitignore

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+.DS_Store
+tags
+/pkg
+/html

data/.rspec

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+--require spec_helper

data/Gemfile

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+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
+
+# testing
+gem 'pry'
+gem 'rspec'
+gem 'rubocop-rspec'
+gem 'pry-byebug'
+
+# documentation
+gem 'gem-man'
+gem 'ronn'
+
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    specify_cli (0.0.5)
+      gli (= 2.17.2)
+      mysql2 (= 0.5.2)
+      sequel (= 5.11.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    aruba (0.14.6)
+      childprocess (>= 0.6.3, < 0.10.0)
+      contracts (~> 0.9)
+      cucumber (>= 1.3.19)
+      ffi (~> 1.9.10)
+      rspec-expectations (>= 2.99)
+      thor (~> 0.19)
+    ast (2.4.0)
+    backports (3.11.4)
+    builder (3.2.3)
+    byebug (10.0.2)
+    childprocess (0.9.0)
+      ffi (~> 1.0, >= 1.0.11)
+    coderay (1.1.2)
+    contracts (0.16.0)
+    cucumber (3.1.2)
+      builder (>= 2.1.2)
+      cucumber-core (~> 3.2.0)
+      cucumber-expressions (~> 6.0.1)
+      cucumber-wire (~> 0.0.1)
+      diff-lcs (~> 1.3)
+      gherkin (~> 5.1.0)
+      multi_json (>= 1.7.5, < 2.0)
+      multi_test (>= 0.1.2)
+    cucumber-core (3.2.0)
+      backports (>= 3.8.0)
+      cucumber-tag_expressions (~> 1.1.0)
+      gherkin (>= 5.0.0)
+    cucumber-expressions (6.0.1)
+    cucumber-tag_expressions (1.1.1)
+    cucumber-wire (0.0.1)
+    diff-lcs (1.3)
+    ffi (1.9.25)
+    gem-man (0.3.0)
+    gherkin (5.1.0)
+    gli (2.17.2)
+    hpricot (0.8.6)
+    jaro_winkler (1.5.1)
+    method_source (0.9.0)
+    multi_json (1.13.1)
+    multi_test (0.1.2)
+    mustache (1.0.5)
+    mysql2 (0.5.2)
+    parallel (1.12.1)
+    parser (2.5.1.2)
+      ast (~> 2.4.0)
+    powerpack (0.1.2)
+    pry (0.11.3)
+      coderay (~> 1.1.0)
+      method_source (~> 0.9.0)
+    pry-byebug (3.6.0)
+      byebug (~> 10.0)
+      pry (~> 0.10)
+    rainbow (3.0.0)
+    rake (12.3.1)
+    rdiscount (2.2.0.1)
+    rdoc (6.0.4)
+    ronn (0.7.3)
+      hpricot (>= 0.8.2)
+      mustache (>= 0.7.0)
+      rdiscount (>= 1.5.8)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.1)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
+    rubocop (0.58.2)
+      jaro_winkler (~> 1.5.1)
+      parallel (~> 1.10)
+      parser (>= 2.5, != 2.5.1.1)
+      powerpack (~> 0.1)
+      rainbow (>= 2.2.2, < 4.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (~> 1.0, >= 1.0.1)
+    rubocop-rspec (1.29.0)
+      rubocop (>= 0.58.0)
+    ruby-progressbar (1.10.0)
+    sequel (5.11.0)
+    thor (0.20.0)
+    unicode-display_width (1.4.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  aruba
+  gem-man
+  pry
+  pry-byebug
+  rake
+  rdoc
+  ronn
+  rspec
+  rubocop-rspec
+  specify_cli!
+
+BUNDLED WITH
+   1.16.3

data/LICENSE.txt

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+MIT License
+
+Copyright (c) 2018 Martin Stein
+
+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.rdoc

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+= specify_cli - A command line interface for _Specify_
+
+Author:: Martin Stein
+Copyright:: Copyright (c) 2018 by Martin Stein
+License:: Distributes under the MIT License, see LICENSE.txt in the source
+          distribution
+
+specify_cli is a tool that allows certain tasks in a Specify database
+(http://www.sustain.specifysoftware.org) to be carried out from the command
+line.
+Currently supported tasks:
+- upload of views to the database
+- generation of stub records
+
+== Install
+
+Install:
+
+Build with
+
+    rake package
+
+Then install the gem.
+
+== Use
+
+For more help:
+
+    specify_cli --help
+    gem man specify_cli
+
+== For developers
+
+Install bundler:
+
+    gem install bundler
+    
+Install development dependencies
+
+    bundle install
+
+:include:specify_cli.rdoc
+

data/Rakefile

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+require 'rake/clean'
+require 'rubygems'
+require 'rubygems/package_task'
+require 'rdoc/task'
+Rake::RDocTask.new do |rd|
+  rd.main = "README.rdoc"
+  rd.rdoc_files.include("README.rdoc","lib/**/*.rb","bin/**/*")
+  rd.title = 'Your application title'
+end
+
+spec = eval(File.read('specify_cli.gemspec'))
+
+Gem::PackageTask.new(spec) do |pkg|
+end
+task :default => :package

data/bin/specify_cli

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require 'gli'
+require 'specify'
+
+include GLI::App
+
+program_desc Specify::DESCRIPTION
+
+version Specify::VERSION
+
+subcommand_option_handling :normal
+arguments :strict
+
+sessions = []
+script_dir = Dir.pwd
+
+desc 'Connect to host.'
+arg_name '[name]'
+default_value 'localhost'
+flag %i[H host]
+
+desc 'Port number to use for connection.'
+arg_name '[number]'
+default_value '3306'
+flag %i[p port]
+
+desc 'MySQL/MariaDB user for login.'
+arg_name '[name]'
+flag %i[u user]
+
+desc 'Password to use when connecting to server. Omit for password prompt.'
+arg_name '[name]'
+flag %i[P password]
+
+desc 'Database to use.'
+arg_name '[name]'
+flag %i[D database]
+
+desc 'Specify User used for the session.'
+arg_name '[name]'
+flag %i[U specify_user]
+
+desc 'YAML File with settings for database connections and directory mappings.'
+arg_name '[path]'
+default_value File.expand_path('~/.specify_dbs.rc.yaml')
+flag %i[c db_config]
+
+desc 'Add a database configuration.'
+long_desc <<~HEREDOC
+  Add information to work with a Specify database. Use the global option -H to
+  provide the host.
+HEREDOC
+arg_name '[database]'
+command [:database, :d] do |c|
+  c.action do |global_options, options, args|
+    host = global_options[:host]
+    database = args.shift
+
+    file = File.expand_path(global_options[:db_config])
+
+    Specify::CLI.db_config! file, global_options
+
+    db_config = Specify::Configuration::DBConfig.new host, database, file
+
+    if db_config.known?
+      STDERR.puts "#{database} on #{host} is already configured"
+      exit 0
+    else
+      unless db_config.host?
+        exit 1 unless Specify::CLI.configure_host(db_config)
+      end
+      Specify::CLI.configure_database db_config
+    end
+  end
+end
+
+desc 'Map a git repository to a host for automatic target resolution.'
+long_desc <<~HEREDOC
+  Maps the path of a directory containing a Git repository with Specify resource
+  files to a hostname.
+HEREDOC
+arg_name '[repository_name]'
+command [:repository, :r] do |c|
+  c.desc 'Map the current directory/repository to the host'
+  c.switch %i[c current]
+
+  c.action do |global_options, options, args|
+    host = global_options[:host]
+    dir = options[:current] ? Dir.pwd : File.expand_path(args.shift)
+
+    file = File.expand_path(global_options[:db_config])
+
+    Specify::CLI.db_config! file, global_options
+
+    host_config = Specify::Configuration::HostConfig.new file
+
+    unless host_config.directory? dir
+      host_config.map_directory dir, host
+      host_config.save
+    end
+  end
+end
+
+desc 'Create stub records'
+long_desc <<~HEREDOC
+  The stubs command creates n stub records (where n is the number passed as the
+  [count] argument) in the collection passed as the [collection] argument.
+  Provide host, database, and connection information using global options.
+HEREDOC
+arg_name '[collection] [count]'
+command [:stubs, :s] do |c|
+  c.desc 'Load stub record information from a YAML file.'
+  c.arg_name '[yaml_file]'
+  c.flag %i[f file]
+
+  c.desc 'Specify user appearing as cataloger and owner of the record set.'
+  c.arg_name '[name]'
+  c.flag %i[c cataloger]
+
+  c.desc 'Name of the datas set (record set) generated.'
+  c.arg_name '[name]'
+  c.flag %i[d dataset]
+
+  c.desc 'Accession number for the accession to which the stub records belong.'
+  c.arg_name '[accession_number]'
+  c.flag %i[a accession]
+
+  c.desc 'Geographic and locality information for the stub records.'
+  c.arg_name '[geography]'
+  c.flag %i[g geography]
+
+  c.desc 'Default locality name if geographic information has no locality.'
+  c.arg_name '[name]'
+  c.flag %i[l locality]
+
+  c.desc 'Taxon to which stub records are determined.'
+  c.arg_name 'taxon'
+  c.flag %i[t taxon]
+
+  c.desc 'Preparation type for the stub records, if they have preparations.'
+  c.arg_name '[name]'
+  c.flag %i[p preptype]
+
+  c.desc 'Number of preparation items (requires --preptype to be set).'
+  c.arg_name '[number]'
+  c.flag %i[n prepcount]
+
+  c.action do |global_options, options, args|
+    count = args.pop.to_i
+    params = if options[:file]
+               file = File.expand_path(options[:file])
+               Psych.load_file(file)
+             else
+               Specify::CLI.wrap_args(global_options, args, options.compact)
+             end
+
+    stub_generator = Specify::Service::StubGenerator.unwrap params
+
+    sessions << stub_generator.session
+
+    Specify::CLI.make_stubs stub_generator, count
+  end
+end
+
+desc 'Upload a view to the database.'
+long_desc <<~HEREDOC
+  Uploads a view definition file (.views.xml) to the database. Viewsets can be
+  uploaded to either of the following levels: discipline, collection, user type,
+  user.
+HEREDOC
+arg_name '[collection] [file]'
+command [:viewset, :vs] do |c|
+  c.desc 'Use current branch to resolve target.'
+  c.switch :b
+
+  c.desc 'Resolve target from branch name.'
+  c.arg_name '[name]'
+  c.flag %i[B branch]
+
+  c.desc 'Upload to collection level.'
+  c.switch :c
+
+  c.desc 'Upload to discipline level.'
+  c.switch :d
+
+  c.desc 'Upload to specific user type [name] in the collection.'
+  c.arg_name '[name]'
+  c.flag %i[t user_type]
+
+  c.desc 'Upload to specify user [name] in the collection.'
+  c.arg_name '[name]'
+  c.flag %i[u user]
+
+  c.action do |global_options, options, args|
+    file = File.expand_path(args.pop)
+    collection = args.shift
+    config = global_options[:db_config]
+    params = { host: global_options[:host],
+               database: global_options[:database],
+               collection: collection,
+               specify_user: global_options[:specify_user],
+               config: config }
+
+    view_loader = if options[:b] || options[:B]
+                    path = File.dirname(File.expand_path(file))
+                    Dir.chdir path unless script_dir == path
+                    Specify::Service::ViewLoader.from_branch path: path,
+                                                             name: options[:B],
+                                                             config: config
+                  else
+                    raise 'collection required' unless collection
+                    params[:level] = Specify::CLI.level options
+                    Specify::Service::ViewLoader.new params
+                  end
+    sessions << view_loader.session
+    view_loader.import file
+  end
+end
+
+pre do |global, command, options, args|
+  # Pre logic here
+  # Return true to proceed; false to abort and not call the
+  # chosen command
+  # Use skips_pre before a command to skip this block
+  # on that command only
+  true
+end
+
+post do |global, command, options, args|
+  # Post logic here
+  # Use skips_post before a command to skip this
+  # block on that command only
+  sessions.each(&:close)
+  Dir.chdir script_dir unless script_dir == Dir.pwd
+end
+
+on_error do |exception|
+  # Error logic here
+  # return false to skip default error handling
+
+  sessions.each(&:close)
+  Dir.chdir script_dir unless script_dir == Dir.pwd
+  true
+end
+
+exit run(ARGV)