etna 0.1.14 → 0.1.20

data/lib/etna/multipart_serializable_nested_hash.rb

@@ -0,0 +1,50 @@
+module Etna
+  module MultipartSerializableNestedHash
+    def self.included(cls)
+      cls.instance_eval do
+        def self.encode_multipart_pairs(value, base_key, is_root, &block)
+          if value.is_a? Hash
+            value.each do |k, v|
+              encode_multipart_pairs(v, is_root ? k : "#{base_key}[#{k}]", false, &block)
+            end
+          elsif value.is_a? Array
+            value.each_with_index do |v, i|
+              # This is necessary to ensure that arrays of hashes that have hetergenous keys still get parsed correctly
+              # Since the only way to indicate a new entry in the array of hashes is by re-using a key that existed in
+              # the previous hash.
+              if v.is_a? Hash
+                encode_multipart_pairs(i, "#{base_key}[][_idx]", false, &block)
+              end
+
+              encode_multipart_pairs(v, "#{base_key}[]", false, &block)
+            end
+          else
+            raise "base_key cannot be empty for a scalar value!" if base_key.length == 0
+
+            if value.respond_to?(:read)
+              yield [base_key, UploadIO.new(value, 'application/octet-stream'), {filename: 'blob'}]
+            else
+              yield [base_key, value.to_s]
+            end
+          end
+        end
+
+
+        def self.encode_multipart_content(value, base_key = '', is_root = true)
+          result = []
+          self.encode_multipart_pairs(value, base_key, is_root) { |pair| result << pair }
+          result
+        end
+      end
+    end
+
+    def encode_multipart_content(base_key = '')
+      value = self
+      if value.respond_to? :as_json
+        value = value.as_json
+      end
+
+      self.class.encode_multipart_content(value, base_key)
+    end
+  end
+end

data/lib/etna/route.rb

@@ -118,7 +118,7 @@ module Etna
 
     def hmac_authorized?(request)
       # either there is no hmac requirement, or we have a valid hmac
-      !@auth[:hmac] || request.env['etna.hmac'].valid?
+      !@auth[:hmac] || request.env['etna.hmac']&.valid?
     end
 
     def route_name(options)

data/lib/etna/server.rb

@@ -66,6 +66,9 @@ module Etna
       end
 
       [404, {}, ["There is no such path '#{request.path}'"]]
+    rescue => e
+      application.logger.log_error(e)
+      raise
     end
 
     def initialize

data/lib/etna/spec/vcr.rb

@@ -0,0 +1,99 @@
+require 'webmock/rspec'
+require 'vcr'
+require 'openssl'
+require 'digest/sha2'
+require 'base64'
+
+def setup_base_vcr(spec_helper_dir)
+  VCR.configure do |c|
+    c.hook_into :webmock
+    c.cassette_serializers
+    c.cassette_library_dir = ::File.join(spec_helper_dir, 'fixtures', 'cassettes')
+    c.allow_http_connections_when_no_cassette = true
+
+    c.register_request_matcher :try_body do |request_1, request_2|
+      if request_1.headers['Content-Type'].first =~ /application\/json/
+        if request_2.headers['Content-Type'].first =~ /application\/json/
+          request_1_json = begin
+            JSON.parse(request_1.body) rescue 'not-json'
+          end
+          request_2_json = begin
+            JSON.parse(request_2.body) rescue 'not-json'
+          end
+
+          request_1_json == request_2_json
+        else
+          false
+        end
+      else
+        request_1.body == request_2.body
+      end
+    end
+
+    c.default_cassette_options = {
+        serialize_with: :compressed,
+        record: if ENV['IS_CI'] == '1'
+          :none
+        else
+          ENV['RERECORD'] ? :all : :once
+        end,
+        match_requests_on: [:method, :uri, :try_body]
+    }
+
+    # Filter the authorization headers of any request by replacing any occurrence of that request's
+    # Authorization value with <AUTHORIZATION>
+    c.filter_sensitive_data('<AUTHORIZATION>') do |interaction|
+      interaction.request.headers['Authorization'].first
+    end
+
+    c.before_record do |interaction|
+      key = prepare_vcr_secret
+
+      if interaction.response.body && !interaction.response.body.empty?
+        cipher = OpenSSL::Cipher.new("AES-256-CBC")
+        iv = cipher.random_iv
+
+        cipher.encrypt
+        cipher.key = key
+        cipher.iv = iv
+
+        encrypted = cipher.update(interaction.response.body)
+        encrypted << cipher.final
+
+        interaction.response.body = [iv, encrypted].pack('mm')
+      end
+    end
+
+    c.before_playback do |interaction|
+      key = prepare_vcr_secret
+
+      if interaction.response.body && !interaction.response.body.empty?
+        iv, encrypted = interaction.response.body.unpack('mm')
+
+        cipher = OpenSSL::Cipher.new("AES-256-CBC")
+        cipher.decrypt
+        cipher.key = key
+        cipher.iv = iv
+
+        plain = cipher.update(encrypted)
+        plain << cipher.final
+
+        interaction.response.body = plain
+      end
+    end
+  end
+end
+
+def prepare_vcr_secret
+  secret = ENV["CI_SECRET"]
+
+  if (secret.nil? || secret.empty?) && ENV['IS_CI'] != '1'
+    current_example = RSpec.current_example
+    RSpec::Core::Pending.mark_pending! current_example, 'CI_SECRET must be set to run this test'
+    raise "CI_SECRET must be set to run this test"
+  end
+
+  digest = Digest::SHA256.new
+  digest.update(secret)
+  digest.digest
+end

data/lib/etna/templates/attribute_actions_template.json

@@ -0,0 +1,43 @@
+// Make sure to remove all comments before using -- JSON doesn't allow comments!
+[
+  // Attribute actions can be "add_attribute", "update_attribute", "rename_attribute", or "add_link".
+  // These are all executed at the same time -- so you can't "update" an attribute that you "add"
+  //    in the same file -- everything must already exist on the server."
+  {
+    "action_name": "add_attribute",
+    "model_name": "assay_name", // Each action must include a model_name that it applies to.
+    "attribute_type": "string", // When adding, you must include attribute_type, attribute_name, desc, and display_name.
+    "attribute_name": "notes",
+    "display_name": "Notes",
+    "desc": "for notes that you have."
+  },
+  {
+    "action_name": "update_attribute",
+    "model_name": "document",
+    "attribute_name": "version", // When updating, you must include model_name and attribute_name, but any additional values are optional.
+    "read_only": true
+  },
+  {
+    "action_name": "rename_attribute",
+    "model_name": "assay_name",
+    "attribute_name": "vendor",
+    "new_attribute_name": "e_vendor" // When renaming an attribute, you need to include a "new_attribute_name" value.
+  },
+  {
+    // Links require two hashes inside of a "links" attribute.
+    "action_name": "add_link",
+    "links": [
+      {
+        "model_name": "assay_name",
+        "attribute_name": "document",
+        "attribute_type": "link" // One link must be of type "link". This has a one-to-one relationship with the other model.
+        // In this case, each assay_name has one document record, but document records can point to zero-or-more assay_name records.
+      },
+      {
+        "model_name": "document",
+        "attribute_name": "assay_name",
+        "attribute_type": "collection" // The other link must be of type "collection". This is a one-to-many relationship with the other model.
+      }
+    ]
+  }
+]

data/lib/etna/test_auth.rb

@@ -43,7 +43,9 @@ module Etna
     end
 
     def approve_hmac(request)
-      hmac_signature = etna_param(request, :signature) || 'invalid'
+      hmac_signature = etna_param(request, :signature)
+
+      return false unless hmac_signature
 
       headers = (etna_param(request, :headers)&.split(/,/) || []).map do |header|
         [ header.to_sym, etna_param(request, header) ]

data/lib/etna/user.rb

@@ -7,7 +7,9 @@ module Etna
     }
 
     def initialize params, token=nil
-      @first, @last, @email, @encoded_permissions = params.values_at(:first, :last, :email, :perm)
+      @first, @last, @email, @encoded_permissions, encoded_flags = params.values_at(:first, :last, :email, :perm, :flags)
+
+      @flags = encoded_flags&.split(/;/) || []
       @token = token unless !token
       raise ArgumentError, "No email given!" unless @email
     end
@@ -30,6 +32,10 @@ module Etna
       end.inject([],:+).to_h
     end
 
+    def has_flag?(flag)
+      @flags.include?(flag)
+    end
+
     def name
       "#{first} #{last}"
     end
@@ -75,5 +81,9 @@ module Etna
     def is_admin? project
       is_superuser? || has_roles(project, :admin)
     end
+
+    def active? project=nil
+      permissions.keys.length > 0
+    end
   end
 end

data/lib/helpers.rb

@@ -0,0 +1,90 @@
+require_relative './etna/clients'
+require_relative './etna/environment_scoped'
+
+module WithEtnaClients
+  def environment
+    EtnaApp.instance.environment
+  end
+
+  def token(ignore_environment: false)
+    unless ignore_environment
+      if environment == :many
+        raise "You have multiple environments configured, please specify your environment by adding --environment <staging|production|development>"
+      elsif environment == :none
+        raise "You do not have a successfully configured environment, please run #{program_name} config set https://polyphemus.ucsf.edu"
+      end
+    end
+
+    env_token = ENV['TOKEN']
+    if !env_token
+      puts "No environment variable TOKEN is set.  You should set your token with `export TOKEN=<your.janus.token>` before running."
+      redirect = EtnaApp.instance.config(:auth_redirect)
+
+      if redirect.nil? && EtnaApp.instance.environment == :production
+        redirect = 'https://janus.ucsf.edu/'
+      end
+
+      unless redirect.nil?
+        puts "Open your browser to #{redirect} to complete login and copy your token."
+      end
+
+      exit
+    end
+
+    env_token
+  end
+
+  def magma_client
+    @magma_client ||= Etna::Clients::Magma.new(
+        token: token,
+        ignore_ssl: EtnaApp.instance.config(:ignore_ssl),
+        # Persistent connections cause problem with magma restarts, until we can fix that we should force them
+        # to close + reopen each request.
+        persistent: false,
+        **EtnaApp.instance.config(:magma, environment) || {})
+  end
+
+  def metis_client
+    @metis_client ||= Etna::Clients::Metis.new(
+        token: token,
+        ignore_ssl: EtnaApp.instance.config(:ignore_ssl),
+        **EtnaApp.instance.config(:metis, environment) || {})
+  end
+
+  def janus_client
+    @janus_client ||= Etna::Clients::Janus.new(
+        token: token,
+        ignore_ssl: EtnaApp.instance.config(:ignore_ssl),
+        **EtnaApp.instance.config(:janus, environment) || {})
+  end
+
+  def polyphemus_client
+    @polyphemus_client ||= Etna::Clients::Polyphemus.new(
+        token: token,
+        ignore_ssl: EtnaApp.instance.config(:ignore_ssl),
+        **EtnaApp.instance.config(:polyphemus, environment) || {})
+  end
+end
+
+module WithLogger
+  def logger
+    EtnaApp.instance.logger
+  end
+end
+
+module StrongConfirmation
+  def confirm
+    puts "Confirm Y/n:"
+    input = STDIN.gets.chomp
+    if input.downcase != "y"
+      puts "Bailing..."
+      return false
+    end
+
+    true
+  end
+end
+
+WithEtnaClientsByEnvironment = EnvironmentScoped.new do
+  include WithEtnaClients
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: etna
 version: !ruby/object:Gem::Version
-  version: 0.1.14
+  version: 0.1.20
 platform: ruby
 authors:
 - Saurabh Asthana
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-08-03 00:00:00.000000000 Z
+date: 2020-12-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rack
@@ -66,37 +66,102 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rollbar
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: See summary
 email: Saurabh.Asthana@ucsf.edu
-executables: []
-extensions: []
+executables:
+- etna
+extensions:
+- ext/completions/extconf.rb
 extra_rdoc_files: []
 files:
+- bin/etna
+- etna.completion
+- etna_app.completion
+- ext/completions/extconf.rb
+- lib/commands.rb
 - lib/etna.rb
 - lib/etna/application.rb
 - lib/etna/auth.rb
 - lib/etna/client.rb
+- lib/etna/clients.rb
+- lib/etna/clients/enum.rb
+- lib/etna/clients/janus.rb
+- lib/etna/clients/janus/client.rb
+- lib/etna/clients/janus/models.rb
+- lib/etna/clients/magma.rb
+- lib/etna/clients/magma/client.rb
+- lib/etna/clients/magma/formatting.rb
+- lib/etna/clients/magma/formatting/models_csv.rb
+- lib/etna/clients/magma/models.rb
+- lib/etna/clients/magma/workflows.rb
+- lib/etna/clients/magma/workflows/add_project_models_workflow.rb
+- lib/etna/clients/magma/workflows/attribute_actions_from_json_workflow.rb
+- lib/etna/clients/magma/workflows/create_project_workflow.rb
+- lib/etna/clients/magma/workflows/crud_workflow.rb
+- lib/etna/clients/magma/workflows/ensure_containing_record_workflow.rb
+- lib/etna/clients/magma/workflows/file_attributes_blank_workflow.rb
+- lib/etna/clients/magma/workflows/file_linking_workflow.rb
+- lib/etna/clients/magma/workflows/json_converters.rb
+- lib/etna/clients/magma/workflows/json_validators.rb
+- lib/etna/clients/magma/workflows/model_synchronization_workflow.rb
+- lib/etna/clients/magma/workflows/record_synchronization_workflow.rb
+- lib/etna/clients/magma/workflows/update_attributes_from_csv_workflow.rb
+- lib/etna/clients/metis.rb
+- lib/etna/clients/metis/client.rb
+- lib/etna/clients/metis/models.rb
+- lib/etna/clients/metis/workflows.rb
+- lib/etna/clients/metis/workflows/metis_download_workflow.rb
+- lib/etna/clients/metis/workflows/metis_upload_workflow.rb
+- lib/etna/clients/polyphemus.rb
+- lib/etna/clients/polyphemus/client.rb
+- lib/etna/clients/polyphemus/models.rb
+- lib/etna/clients/polyphemus/workflows.rb
+- lib/etna/clients/polyphemus/workflows/set_configuration_workflow.rb
 - lib/etna/command.rb
 - lib/etna/controller.rb
 - lib/etna/cross_origin.rb
+- lib/etna/csvs.rb
 - lib/etna/describe_routes.rb
+- lib/etna/directed_graph.rb
+- lib/etna/environment_scoped.rb
 - lib/etna/errors.rb
 - lib/etna/ext.rb
+- lib/etna/generate_autocompletion_script.rb
 - lib/etna/hmac.rb
+- lib/etna/json_serializable_struct.rb
 - lib/etna/logger.rb
+- lib/etna/multipart_serializable_nested_hash.rb
 - lib/etna/parse_body.rb
 - lib/etna/route.rb
 - lib/etna/server.rb
 - lib/etna/sign_service.rb
 - lib/etna/spec.rb
 - lib/etna/spec/auth.rb
+- lib/etna/spec/vcr.rb
 - lib/etna/symbolize_params.rb
+- lib/etna/templates/attribute_actions_template.json
 - lib/etna/test_auth.rb
 - lib/etna/user.rb
+- lib/helpers.rb
 homepage: http://github.com/mountetna/etna
 licenses: []
 metadata: {}
-post_install_message: 
+post_install_message: "\n\n\e[1;31mAdd 'source ~/etna.completion' to your .bashrc
+  to get etna command line completions!\e[0m\n\n"
 rdoc_options: []
 require_paths:
 - lib