etna 0.1.27 → 0.1.32

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Files changed (29) hide show
  1. checksums.yaml +4 -4
  2. data/etna.completion +137 -55
  3. data/lib/etna.rb +1 -0
  4. data/lib/etna/application.rb +4 -0
  5. data/lib/etna/client.rb +30 -2
  6. data/lib/etna/clients/magma/formatting.rb +2 -1
  7. data/lib/etna/clients/magma/formatting/models_odm_xml.rb +293 -0
  8. data/lib/etna/clients/magma/models.rb +13 -1
  9. data/lib/etna/clients/magma/workflows/create_project_workflow.rb +1 -1
  10. data/lib/etna/clients/magma/workflows/crud_workflow.rb +19 -2
  11. data/lib/etna/clients/magma/workflows/materialize_magma_record_files_workflow.rb +46 -30
  12. data/lib/etna/clients/magma/workflows/model_synchronization_workflow.rb +1 -1
  13. data/lib/etna/clients/magma/workflows/update_attributes_from_csv_workflow.rb +19 -6
  14. data/lib/etna/clients/magma/workflows/walk_model_tree_workflow.rb +33 -6
  15. data/lib/etna/clients/metis/client.rb +6 -1
  16. data/lib/etna/clients/metis/models.rb +15 -0
  17. data/lib/etna/clients/metis/workflows/metis_download_workflow.rb +15 -11
  18. data/lib/etna/clients/metis/workflows/metis_upload_workflow.rb +83 -13
  19. data/lib/etna/clients/metis/workflows/sync_metis_data_workflow.rb +43 -79
  20. data/lib/etna/command.rb +10 -0
  21. data/lib/etna/cwl.rb +701 -0
  22. data/lib/etna/directed_graph.rb +50 -0
  23. data/lib/etna/filesystem.rb +145 -15
  24. data/lib/etna/generate_autocompletion_script.rb +11 -6
  25. data/lib/etna/hmac.rb +2 -2
  26. data/lib/etna/route.rb +44 -4
  27. data/lib/etna/spec/auth.rb +6 -6
  28. data/lib/etna/user.rb +15 -11
  29. metadata +33 -3
data/lib/etna/user.rb CHANGED
@@ -7,14 +7,14 @@ module Etna
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  }
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  def initialize params, token=nil
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- @first, @last, @email, @encoded_permissions, encoded_flags = params.values_at(:first, :last, :email, :perm, :flags)
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+ @name, @email, @encoded_permissions, encoded_flags = params.values_at(:name, :email, :perm, :flags)
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  @flags = encoded_flags&.split(/;/) || []
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  @token = token unless !token
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  raise ArgumentError, "No email given!" unless @email
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  end
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- attr_reader :first, :last, :email, :token
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+ attr_reader :name, :email, :token
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  def permissions
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  @permissions ||= @encoded_permissions.split(/\;/).map do |roles|
@@ -36,10 +36,6 @@ module Etna
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  @flags.include?(flag)
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  end
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- def name
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- "#{first} #{last}"
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- end
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-
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  def projects
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  permissions.keys
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  end
@@ -50,7 +46,7 @@ module Etna
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  viewer: /[Vv]/,
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  restricted: /[AEV]/,
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  }
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- def has_roles(project, *roles)
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+ def has_any_role?(project, *roles)
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  perm = permissions[project.to_s]
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  return false unless perm
@@ -59,15 +55,23 @@ module Etna
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  end
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  def is_superuser? project=nil
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- has_roles(:administration, :admin)
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+ has_any_role?(:administration, :admin)
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+ end
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+
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+ def is_supereditor? project=nil
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+ has_any_role?(:administration, :admin, :editor)
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+ end
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+
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+ def is_superviewer? project=nil
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+ has_any_role?(:administration, :admin, :editor, :viewer)
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  end
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  def can_edit? project
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- is_superuser? || has_roles(project, :admin, :editor)
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+ is_supereditor? || has_any_role?(project, :admin, :editor)
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  end
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  def can_view? project
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- is_superuser? || has_roles(project, :admin, :editor, :viewer)
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+ is_superviewer? || has_any_role?(project, :admin, :editor, :viewer)
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  end
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  # superusers - administrators of the Administration group - cannot
@@ -79,7 +83,7 @@ module Etna
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  end
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  def is_admin? project
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- is_superuser? || has_roles(project, :admin)
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+ is_superuser? || has_any_role?(project, :admin)
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  end
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  def active? project=nil
metadata CHANGED
@@ -1,14 +1,14 @@
1
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  --- !ruby/object:Gem::Specification
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  name: etna
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  version: !ruby/object:Gem::Version
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- version: 0.1.27
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+ version: 0.1.32
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  platform: ruby
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  authors:
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  - Saurabh Asthana
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2021-01-14 00:00:00.000000000 Z
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+ date: 2021-04-05 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rack
@@ -39,7 +39,7 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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- name: net-http-persistent
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+ name: nokogiri
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ">="
@@ -80,6 +80,34 @@ dependencies:
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  - - ">="
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  - !ruby/object:Gem::Version
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  version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: concurrent-ruby
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: concurrent-ruby-ext
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  description: See summary
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  email: Saurabh.Asthana@ucsf.edu
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  executables:
@@ -107,6 +135,7 @@ files:
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135
  - lib/etna/clients/magma/client.rb
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136
  - lib/etna/clients/magma/formatting.rb
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137
  - lib/etna/clients/magma/formatting/models_csv.rb
138
+ - lib/etna/clients/magma/formatting/models_odm_xml.rb
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139
  - lib/etna/clients/magma/models.rb
111
140
  - lib/etna/clients/magma/workflows.rb
112
141
  - lib/etna/clients/magma/workflows/add_project_models_workflow.rb
@@ -139,6 +168,7 @@ files:
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  - lib/etna/controller.rb
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  - lib/etna/cross_origin.rb
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  - lib/etna/csvs.rb
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+ - lib/etna/cwl.rb
142
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  - lib/etna/describe_routes.rb
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  - lib/etna/directed_graph.rb
144
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  - lib/etna/environment_scoped.rb