specify_cli 0.0.5

data/spec/spec_helper.rb

@@ -0,0 +1,116 @@
+# frozen_string_literal: true
+
+require 'pry'
+
+require_relative 'helpers'
+require_relative '../lib/specify'
+
+SPSPEC = Specify::Database.new('SPSPEC',
+                               user: 'specmaster',
+                               password: 'masterpass')
+DB = SPSPEC.connect
+
+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require spec_helper` which will cause
+# this file to always be loaded, without a need to explicitly require it in any
+# files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, consider making
+# a separate helper file that requires the additional dependencies and performs
+# the additional setup, and require it from the spec files that actually need
+# it.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on
+    # a real object. This is generally recommended, and will default to
+    # `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+  # This option will default to `:apply_to_host_groups` in RSpec 4 (and will
+  # have no way to turn it off -- the option exists only for backwards
+  # compatibility in RSpec 3). It causes shared context metadata to be
+  # inherited by the metadata hash of host groups and examples, rather than
+  # triggering implicit auto-inclusion in groups with matching metadata.
+  config.shared_context_metadata_behavior = :apply_to_host_groups
+
+  # This allows you to limit a spec run to individual examples or groups
+  # you care about by tagging them with `:focus` metadata. When nothing
+  # is tagged with `:focus`, all examples get run. RSpec also provides
+  # aliases for `it`, `describe`, and `context` that include `:focus`
+  # metadata: `fit`, `fdescribe` and `fcontext`, respectively.
+  config.filter_run_when_matching :focus
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = "spec/examples.txt"
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
+  #   - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
+  config.disable_monkey_patching!
+
+  # This setting enables warnings. It's recommended, but in some cases may
+  # be too noisy due to issues in dependencies.
+  config.warnings = true
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = "doc"
+  end
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+
+  config.include Helpers
+
+  config.warnings = false
+
+  config.around do |example|
+    DB.transaction(rollback: :always, auto_savepoint: true) { example.run }
+  end
+end

data/spec/support/db.yml

@@ -0,0 +1,12 @@
+---
+:dir_names:
+  sp_resource: localhost
+:hosts:
+  localhost:
+    :port: 3306
+    :databases:
+      SPSPEC:
+        :db_user:
+          :name: specmaster
+          :password: masterpass
+        :sp_user: specuser

data/spec/support/stub.yaml

@@ -0,0 +1,17 @@
+---
+:stub_generator:
+  :host: localhost
+  :database: SPSPEC
+  :collection: Test Collection
+  :config: spec/support/db.yml
+dataset_name: 'stubs with default locality'
+accession: 2018-AA-001
+cataloger: specmanager
+collecting_data:
+  Country: United States
+default_locality_name: default stub locality US
+determination:
+  Family: Asaphidae
+preparation:
+  :type: Specimen
+  :count: 1

data/spec/support/stub_locality.yaml

@@ -0,0 +1,19 @@
+---
+:stub_generator:
+  :host: localhost
+  :database: SPSPEC
+  :collection: Test Collection
+  :config: spec/support/db.yml
+dataset_name: 'stubs with locality'
+accession: 2018-AA-001
+cataloger: specmanager
+collecting_data:
+  Country: United States
+  State: Kansas
+  County: Douglas County
+  :locality: Downtown Lawrence
+determination:
+  Family: Asaphidae
+preparation:
+  :type: Specimen
+  :count: 1

data/spec/support/viewsets/paleo.views.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<viewset name="Paleo Views" i18nresname="views" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<!-- dude, it would be so awesome if that worked!! -->
+	<views>
+		<view name="CollectionObject" class="edu.ku.brc.specify.datamodel.CollectionObject" busrules="edu.ku.brc.specify.datamodel.busrules.CollectionObjectBusRules" isinternal="false" resourcelabels="false">
+			<desc><![CDATA[The Collection Object form.]]></desc>
+			<altviews>
+				<altview name="Collection Object View" viewdef="Collection Object" mode="view"/>
+				<altview name="Collection Object Edit" viewdef="Collection Object" mode="edit" default="true"/>
+			</altviews>
+		</view>
+	</views>
+
+	<viewdefs>
+		<viewdef type="form" name="Collection Object" class="edu.ku.brc.specify.datamodel.CollectionObject" gettable="edu.ku.brc.af.ui.forms.DataGetterForObj" settable="edu.ku.brc.af.ui.forms.DataSetterForObj">
+			<desc><![CDATA[The Collection Object form.]]></desc>
+			<enableRules/>
+			<columnDef>100px,2px,195px,5px,96px,2px,210px,5px,94px,2px,116px,15px,p:g</columnDef>
+			<columnDef os="lnx">115px,2px,195px,5px,125px,2px,210px,5px,125px,2px,131px,15px,p:g</columnDef>
+			<columnDef os="mac">130px,2px,215px,5px,128px,2px,260px,5px,138px,2px,145px,15px,p:g</columnDef>
+			<columnDef os="exp">p,2px,min(p;250px),5px:g,p,2px,p:g,5px:g,p,2px,p:g(2),p,p:g</columnDef>
+			<rowDef auto="true" cell="p" sep="2px"/>
+			<rows>
+				<row>
+					<cell type="label" label="Viewset for Collection, uploaded from sp_view_loader" colspan="13" initialize="align=center"/>
+				</row>
+			</rows>
+		</viewdef>
+	</viewdefs>
+</viewset>

data/spec/support/viewsets/paleo.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<viewset name="Paleo Views" i18nresname="views" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<!-- dude, it would be so awesome if that worked!! -->
+	<views>
+		<view name="CollectionObject" class="edu.ku.brc.specify.datamodel.CollectionObject" busrules="edu.ku.brc.specify.datamodel.busrules.CollectionObjectBusRules" isinternal="false" resourcelabels="false">
+			<desc><![CDATA[The Collection Object form.]]></desc>
+			<altviews>
+				<altview name="Collection Object View" viewdef="Collection Object" mode="view"/>
+				<altview name="Collection Object Edit" viewdef="Collection Object" mode="edit" default="true"/>
+			</altviews>
+		</view>
+	</views>
+
+	<viewdefs>
+		<viewdef type="form" name="Collection Object" class="edu.ku.brc.specify.datamodel.CollectionObject" gettable="edu.ku.brc.af.ui.forms.DataGetterForObj" settable="edu.ku.brc.af.ui.forms.DataSetterForObj">
+			<desc><![CDATA[The Collection Object form.]]></desc>
+			<enableRules/>
+			<columnDef>100px,2px,195px,5px,96px,2px,210px,5px,94px,2px,116px,15px,p:g</columnDef>
+			<columnDef os="lnx">115px,2px,195px,5px,125px,2px,210px,5px,125px,2px,131px,15px,p:g</columnDef>
+			<columnDef os="mac">130px,2px,215px,5px,128px,2px,260px,5px,138px,2px,145px,15px,p:g</columnDef>
+			<columnDef os="exp">p,2px,min(p;250px),5px:g,p,2px,p:g,5px:g,p,2px,p:g(2),p,p:g</columnDef>
+			<rowDef auto="true" cell="p" sep="2px"/>
+			<rows>
+				<row>
+					<cell type="label" label="Viewset for Collection, uploaded from sp_view_loader" colspan="13" initialize="align=center"/>
+				</row>
+			</rows>
+		</viewdef>
+	</viewdefs>
+</viewset>

data/spec/user_type_spec.rb

@@ -0,0 +1,79 @@
+# frozen_string_literal: true
+
+# Tests for the
+module Specify
+  RSpec.describe UserType do
+    let :collection do
+      Model::Collection.first CollectionName: 'Test Collection'
+    end
+
+    let(:user_type) { described_class.new('guest') }
+
+    it { expect(user_type).to respond_to :save }
+
+    it { expect(user_type).to respond_to :view_set_dir= }
+
+    describe '#add_app_resource_dir(values)' do
+      let(:agent) { Model::Agent.first Email: 'john.doe@example.com' }
+      let :values do
+        {
+      	  DisciplineType: 'spec type',
+      	  UserType: user_type.name,
+      	  IsPersonal: false,
+      	  collection: collection,
+      	  discipline: collection.discipline,
+        }
+      end
+
+      subject do
+        user_type.add_app_resource_dir(values.merge(created_by: agent,
+                                                    user: agent.user))
+      end
+
+      it do
+      	is_expected.to be_a(Model::AppResourceDir)
+      	  .and have_attributes DisciplineType: 'spec type',
+      	                       UserType: 'guest',
+      	                       IsPersonal: false,
+      	                       collection: collection,
+      	                       discipline: collection.discipline
+      end
+    end
+
+    describe '#valid?' do
+      context 'when the user type name is valid' do
+      	subject { user_type.valid? }
+
+      	it { is_expected.to be_truthy }
+      end
+
+      context 'when the user type name is invalid' do
+        subject { described_class.new('root').valid? }
+
+        it { is_expected.to be_falsey }
+      end
+    end
+
+    describe '#view_set_dir(collection)' do
+      subject { user_type.view_set_dir(collection) }
+
+      it do
+        is_expected
+          .to have_attributes DisciplineType: 'Invertebrate Paleontology',
+                              IsPersonal: false,
+                              UserType: 'guest',
+                              collection: collection,
+                              discipline: collection.discipline
+      end
+    end
+
+    describe '#view_set(collection)' do
+      subject { user_type.view_set(collection) }
+
+      it 'returns the ViewSetObject for the given collection' do
+        is_expected
+          .to have_attributes Name: 'Paleo Views'
+      end
+    end
+  end
+end

data/specify_cli.gemspec

@@ -0,0 +1,27 @@
+require File.join([File.dirname(__FILE__),'lib','specify','version.rb'])
+
+spec = Gem::Specification.new do |s|
+  s.name = 'specify_cli'
+  s.version = Specify::VERSION
+  s.author = 'Martin Stein'
+  s.licenses = ['MIT']
+  s.email = 'loveablelobster@fastmail.fm'
+  s.homepage = 'https://github.com/loveablelobster/specify_cli'
+  s.platform = Gem::Platform::RUBY
+  s.summary = Specify::SUMMARY
+  s.description = Specify::DESCRIPTION
+  s.files = `git ls-files`.split("
+")
+  s.require_paths << 'lib'
+  s.has_rdoc = true
+  s.extra_rdoc_files = ['README.rdoc','specify_cli.rdoc']
+  s.rdoc_options << '--title' << 'specify_cli' << '--main' << 'README.rdoc' << '-ri'
+  s.bindir = 'bin'
+  s.executables << 'specify_cli'
+  s.add_development_dependency('rake')
+  s.add_development_dependency('rdoc')
+  s.add_development_dependency('aruba')
+  s.add_runtime_dependency('gli','2.17.2')
+  s.add_runtime_dependency('mysql2','0.5.2')
+  s.add_runtime_dependency('sequel','5.11.0')
+end

data/specify_cli.rdoc

@@ -0,0 +1 @@
+= specify_cli - A command line interface for _Specify_

metadata

@@ -0,0 +1,246 @@
+--- !ruby/object:Gem::Specification
+name: specify_cli
+version: !ruby/object:Gem::Version
+  version: 0.0.5
+platform: ruby
+authors:
+- Martin Stein
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2018-08-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: gli
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.17.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.17.2
+- !ruby/object:Gem::Dependency
+  name: mysql2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.2
+- !ruby/object:Gem::Dependency
+  name: sequel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 5.11.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 5.11.0
+description: |
+  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
+email: loveablelobster@fastmail.fm
+executables:
+- specify_cli
+extensions: []
+extra_rdoc_files:
+- README.rdoc
+- specify_cli.rdoc
+files:
+- ".gitignore"
+- ".rspec"
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- bin/specify_cli
+- lib/specify.rb
+- lib/specify/branch_parser.rb
+- lib/specify/cli.rb
+- lib/specify/cli/database_setup.rb
+- lib/specify/cli/stubs.rb
+- lib/specify/cli/viewset.rb
+- lib/specify/configuration.rb
+- lib/specify/configuration/config.rb
+- lib/specify/configuration/db_config.rb
+- lib/specify/configuration/host_config.rb
+- lib/specify/database.rb
+- lib/specify/models.rb
+- lib/specify/models/accession.rb
+- lib/specify/models/agent.rb
+- lib/specify/models/app_resource_data.rb
+- lib/specify/models/app_resource_dir.rb
+- lib/specify/models/auto_numbering_scheme.rb
+- lib/specify/models/collecting_event.rb
+- lib/specify/models/collection.rb
+- lib/specify/models/collection_object.rb
+- lib/specify/models/createable.rb
+- lib/specify/models/determination.rb
+- lib/specify/models/discipline.rb
+- lib/specify/models/division.rb
+- lib/specify/models/geography.rb
+- lib/specify/models/geography/administrative_division.rb
+- lib/specify/models/geography/geographic_name.rb
+- lib/specify/models/geography/geography.rb
+- lib/specify/models/institution.rb
+- lib/specify/models/locality.rb
+- lib/specify/models/preparation.rb
+- lib/specify/models/preparation_type.rb
+- lib/specify/models/record_set.rb
+- lib/specify/models/record_set_item.rb
+- lib/specify/models/taxonomy.rb
+- lib/specify/models/taxonomy/common_name.rb
+- lib/specify/models/taxonomy/rank.rb
+- lib/specify/models/taxonomy/taxon.rb
+- lib/specify/models/taxonomy/taxonomy.rb
+- lib/specify/models/tree_queryable.rb
+- lib/specify/models/updateable.rb
+- lib/specify/models/user.rb
+- lib/specify/models/view_set_object.rb
+- lib/specify/number_format.rb
+- lib/specify/services.rb
+- lib/specify/services/service.rb
+- lib/specify/services/stub_generator.rb
+- lib/specify/services/view_loader.rb
+- lib/specify/session.rb
+- lib/specify/user_type.rb
+- lib/specify/version.rb
+- man/specify_cli-database.1
+- man/specify_cli-database.1.html
+- man/specify_cli-database.1.ronn
+- man/specify_cli-repository.1
+- man/specify_cli-repository.1.html
+- man/specify_cli-repository.1.ronn
+- man/specify_cli-stubs.1
+- man/specify_cli-stubs.1.html
+- man/specify_cli-stubs.1.ronn
+- man/specify_cli-viewset.1
+- man/specify_cli-viewset.1.html
+- man/specify_cli-viewset.1.ronn
+- man/specify_cli.1
+- man/specify_cli.1.html
+- man/specify_cli.1.ronn
+- spec/branch_parser_spec.rb
+- spec/cli/stubs_spec.rb
+- spec/configuration/config_spec.rb
+- spec/configuration/db_config_spec.rb
+- spec/configuration/host_config_spec.rb
+- spec/database_spec.rb
+- spec/examples.txt
+- spec/helpers.rb
+- spec/models/app_resource_data_spec.rb
+- spec/models/app_resource_dir_spec.rb
+- spec/models/auto_numbering_scheme_spec.rb
+- spec/models/collection_object_spec.rb
+- spec/models/collection_spec.rb
+- spec/models/discipline_spec.rb
+- spec/models/record_set_spec.rb
+- spec/models/user_spec.rb
+- spec/models/view_set_object_spec.rb
+- spec/number_format_spec.rb
+- spec/services/stub_generator_spec.rb
+- spec/services/view_loader_spec.rb
+- spec/session_spec.rb
+- spec/spec_helper.rb
+- spec/support/db.yml
+- spec/support/stub.yaml
+- spec/support/stub_locality.yaml
+- spec/support/viewsets/paleo.views.xml
+- spec/support/viewsets/paleo.xml
+- spec/user_type_spec.rb
+- specify_cli.gemspec
+- specify_cli.rdoc
+homepage: https://github.com/loveablelobster/specify_cli
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options:
+- "--title"
+- specify_cli
+- "--main"
+- README.rdoc
+- "-ri"
+require_paths:
+- lib
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.7.6
+signing_key: 
+specification_version: 4
+summary: A command line interface for Specify
+test_files: []