sequencescape-client-api 0.3.10 → 0.4.0.pre.rc1
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- checksums.yaml +4 -4
- data/.rubocop.yml +44 -0
- data/.rubocop_todo.yml +338 -0
- data/.ruby-version +1 -0
- data/Gemfile +1 -1
- data/README.markdown +13 -0
- data/lib/sequencescape-api.rb +1 -1
- data/lib/sequencescape-api/actions.rb +9 -8
- data/lib/sequencescape-api/associations.rb +8 -6
- data/lib/sequencescape-api/associations/base.rb +1 -1
- data/lib/sequencescape-api/associations/base/instance_methods.rb +10 -8
- data/lib/sequencescape-api/associations/belongs_to.rb +4 -4
- data/lib/sequencescape-api/associations/has_many.rb +14 -13
- data/lib/sequencescape-api/associations/has_many/json.rb +1 -1
- data/lib/sequencescape-api/associations/has_many/validation.rb +1 -1
- data/lib/sequencescape-api/composition.rb +11 -7
- data/lib/sequencescape-api/connection_factory.rb +6 -5
- data/lib/sequencescape-api/connection_factory/actions.rb +17 -12
- data/lib/sequencescape-api/core.rb +12 -7
- data/lib/sequencescape-api/core_ext/array.rb +1 -1
- data/lib/sequencescape-api/core_ext/hash.rb +3 -3
- data/lib/sequencescape-api/errors.rb +2 -2
- data/lib/sequencescape-api/finder_methods.rb +16 -11
- data/lib/sequencescape-api/rails.rb +8 -7
- data/lib/sequencescape-api/resource/active_model.rb +1 -1
- data/lib/sequencescape-api/resource/attribute_groups.rb +11 -7
- data/lib/sequencescape-api/resource/attributes.rb +8 -8
- data/lib/sequencescape-api/resource/instance_methods.rb +17 -9
- data/lib/sequencescape-api/resource/json.rb +18 -15
- data/lib/sequencescape-api/resource/modifications.rb +20 -11
- data/lib/sequencescape-api/resource_model_proxy.rb +7 -5
- data/lib/sequencescape-api/version.rb +1 -1
- data/lib/sequencescape.rb +1 -2
- data/lib/sequencescape/bait_library.rb +1 -1
- data/lib/sequencescape/bait_library_layout.rb +2 -2
- data/lib/sequencescape/barcoded_asset.rb +1 -1
- data/lib/sequencescape/batch.rb +6 -6
- data/lib/sequencescape/behaviour/qced.rb +3 -4
- data/lib/sequencescape/behaviour/receptacle.rb +3 -3
- data/lib/sequencescape/behaviour/state_driven.rb +4 -4
- data/lib/sequencescape/bulk_transfer.rb +1 -1
- data/lib/sequencescape/comment.rb +0 -2
- data/lib/sequencescape/extraction_attribute.rb +1 -1
- data/lib/sequencescape/library_event.rb +1 -1
- data/lib/sequencescape/library_tube.rb +1 -1
- data/lib/sequencescape/lot.rb +0 -1
- data/lib/sequencescape/lot_type.rb +1 -2
- data/lib/sequencescape/order_template.rb +1 -2
- data/lib/sequencescape/pipeline.rb +1 -1
- data/lib/sequencescape/plate.rb +19 -15
- data/lib/sequencescape/plate/pooling.rb +9 -3
- data/lib/sequencescape/plate/well_structure.rb +6 -6
- data/lib/sequencescape/plate_conversion.rb +3 -3
- data/lib/sequencescape/plate_creation.rb +3 -3
- data/lib/sequencescape/plate_purpose.rb +3 -3
- data/lib/sequencescape/plate_template.rb +0 -2
- data/lib/sequencescape/pooled_plate_creation.rb +3 -3
- data/lib/sequencescape/project.rb +2 -1
- data/lib/sequencescape/qc_decision.rb +0 -1
- data/lib/sequencescape/qc_file.rb +0 -3
- data/lib/sequencescape/qcable.rb +0 -3
- data/lib/sequencescape/qcable_creator.rb +0 -3
- data/lib/sequencescape/request.rb +3 -3
- data/lib/sequencescape/search.rb +10 -8
- data/lib/sequencescape/specific_tube_creation.rb +2 -2
- data/lib/sequencescape/stamp.rb +0 -1
- data/lib/sequencescape/state_change.rb +2 -2
- data/lib/sequencescape/study.rb +1 -1
- data/lib/sequencescape/submission.rb +1 -2
- data/lib/sequencescape/tag2_layout.rb +3 -3
- data/lib/sequencescape/tag2_layout_template.rb +2 -2
- data/lib/sequencescape/tag_group.rb +0 -1
- data/lib/sequencescape/tag_layout.rb +3 -3
- data/lib/sequencescape/tag_layout_template.rb +4 -4
- data/lib/sequencescape/transfer.rb +2 -2
- data/lib/sequencescape/transfer_request.rb +4 -5
- data/lib/sequencescape/transfer_template.rb +2 -2
- data/lib/sequencescape/tube.rb +3 -3
- data/lib/sequencescape/tube_creation.rb +3 -3
- data/lib/sequencescape/tube_from_tube_creation.rb +3 -3
- data/lib/sequencescape/tube_purpose.rb +3 -3
- data/lib/sequencescape/user.rb +2 -2
- data/lib/sequencescape/volume_update.rb +1 -1
- data/lib/sequencescape/well.rb +0 -2
- data/lib/sequencescape/work_completion.rb +1 -1
- data/sequencescape-api.gemspec +18 -17
- data/spec/sequencescape-api/associations_spec.rb +4 -2
- data/spec/sequencescape-api/finding_methods_spec.rb +3 -1
- data/spec/sequencescape-api/modifications_spec.rb +17 -16
- data/spec/sequencescape-api/root_spec.rb +11 -6
- data/spec/spec_helper.rb +3 -1
- data/spec/support/contract_helper.rb +18 -10
- data/spec/support/namespaces.rb +9 -9
- data/spec/support/shared_examples.rb +2 -0
- metadata +53 -35
- data/.rvmrc +0 -52
data/.rvmrc
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#!/usr/bin/env bash
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# This is an RVM Project .rvmrc file, used to automatically load the ruby
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# development environment upon cd'ing into the directory
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# First we specify our desired <ruby>[@<gemset>], the @gemset name is optional,
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# Only full ruby name is supported here, for short names use:
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# echo "rvm use 1.9.3" > .rvmrc
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environment_id="ruby-2.3.7@sequencescape-api"
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# Uncomment the following lines if you want to verify rvm version per project
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# rvmrc_rvm_version="1.15.3 (master)" # 1.10.1 seams as a safe start
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# eval "$(echo ${rvm_version}.${rvmrc_rvm_version} | awk -F. '{print "[[ "$1*65536+$2*256+$3" -ge "$4*65536+$5*256+$6" ]]"}' )" || {
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# echo "This .rvmrc file requires at least RVM ${rvmrc_rvm_version}, aborting loading."
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# return 1
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# }
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# First we attempt to load the desired environment directly from the environment
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# file. This is very fast and efficient compared to running through the entire
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# CLI and selector. If you want feedback on which environment was used then
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# insert the word 'use' after --create as this triggers verbose mode.
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if [[ -d "${rvm_path:-$HOME/.rvm}/environments"
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&& -s "${rvm_path:-$HOME/.rvm}/environments/$environment_id" ]]
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then
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\. "${rvm_path:-$HOME/.rvm}/environments/$environment_id"
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[[ -s "${rvm_path:-$HOME/.rvm}/hooks/after_use" ]] &&
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\. "${rvm_path:-$HOME/.rvm}/hooks/after_use" || true
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if [[ $- == *i* ]] # check for interactive shells
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then echo "Using: $(tput setaf 2)$GEM_HOME$(tput sgr0)" # show the user the ruby and gemset they are using in green
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else echo "Using: $GEM_HOME" # don't use colors in non-interactive shells
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fi
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else
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# If the environment file has not yet been created, use the RVM CLI to select.
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rvm --create use "$environment_id" || {
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echo "Failed to create RVM environment '${environment_id}'."
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return 1
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}
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fi
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# If you use bundler, this might be useful to you:
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# if [[ -s Gemfile ]] && {
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# ! builtin command -v bundle >/dev/null ||
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# builtin command -v bundle | GREP_OPTIONS= \grep $rvm_path/bin/bundle >/dev/null
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# }
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# then
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# printf "%b" "The rubygem 'bundler' is not installed. Installing it now.\n"
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# gem install bundler
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# fi
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# if [[ -s Gemfile ]] && builtin command -v bundle >/dev/null
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# then
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# bundle install | GREP_OPTIONS= \grep -vE '^Using|Your bundle is complete'
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# fi
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